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deadly77
04-08-2019, 05:08 PM
It was the first I1 SNP to be discovered. The first paper distinguishing I1, if I'm not mistaken, was published in 2004. That was one year after the first human genome sequence was completed, at the cost of 3 billion dollars. You couldn't just find SNPs willy-nilly back then. So much has changed so fast!

Ah yes - perhaps I misunderstood what MWauthy was asking - I thought it was why the Szeged researchers picked M253 for this Conqueror paper, but I see what Megalophias means - why I-M253 as the haplogroup name rather than I-S107 or I-L80 for example. And yes, I think you're correct - M253 from Peter Underhill's group at Stanford.

Indeed, a lot has changed fast - you can go and look at the archived ISOGG trees from the early years to see how sparse the phylogenetic Y tree was prior to NGS. Mind you, direct to consumer Y-DNA testing back in the early days started out with 12 STRs. Different times...

deadly77
04-08-2019, 05:21 PM
To answer the question about low coverage it can be because of poor quality in the sample due to degradation from time and environment or the casting of a wide net, or maybe both.

I think that specifically in the case of K2/26 and SzO/540 it's more down to how the researchers designed the enrichment assay rather than degradation. Although with such a incomplete dataset, it's not easy to tell. I guess you might get some idea by looking at the excel file in the supporting information - SzO/540 looks like it has 9 SNPs missing from the 168 they aimed for, K2/26 looks like it has 56 missing from their list (I may have miscounted a little).

oz
04-08-2019, 07:59 PM
They should give those I1 samples to the Polish folks that worked on the Wielbark samples maybe they'd do a better job. We might wait forever for the bam files to be released but hey at least they assigned the I1 subclades better.

deadly77
04-08-2019, 10:36 PM
They should give those I1 samples to the Polish folks that worked on the Wielbark samples maybe they'd do a better job. We might wait forever for the bam files to be released but hey at least they assigned the I1 subclades better.

Do you mean this one? https://www.academia.edu/33791135/2017_Zenczak_.....Piontek_..._Y-chromosome_haplogroup_assignment_through_next_gene ration_sequencing_of_enriched_ancient_DNA_librarie s

I haven't found anything more detailed than this document at Academia which is an abstract from a poster. I'm not aware of any actual paper, preprint or supporting information. There are some raw data files at ENA which look like they are associated with this study, but only FASTQ files - no BAM files - and I haven't figured out a way to reliably convert FASTQ files to BAM files on a Windows machine (which is what I have available).

The abstract describes a "custom-design approach for target enrichment of over 5K Y-chromosome SNPs" - the approach in principle is not dissimilar to what the folks in the Hungarian Conquerer paper are using - of course 5K is better than 168, but I'd expect the samples listed in this poster abstract to have a lot of gaps too. I guess it depends how good they are at guessing which regions to enrich. But we really need to see data to evaluate that. The best coverage has come from samples that have WGS.

From the poster abstract, they say 8 I1 samples, 3 of which are I-L1237 and one of which is I-Z59. I'm not sure if there's deeper analysis or if that's as good as it gets. If anyone knows, I'd like to know. And L1237 was observed in the Hungarian Conquerer samples - so if either K2/26 or SzO/540 were positive for L1237, it would have been seen.

oz
04-09-2019, 12:27 AM
Is there still a possibility that either of the Avar, Magyar could've been the brother branch of L1237, the S10360 or Y3968? Yfull and ftdna label the same markers differently I guess which just probably adds more confusion.

Or that they could've been Z63 at all...

deadly77
04-09-2019, 07:56 AM
Is there still a possibility that either of the Avar, Magyar could've been the brother branch of L1237, the S10360 or Y3968? Yfull and ftdna label the same markers differently I guess which just probably adds more confusion.

Or that they could've been Z63 at all...

Yes, there is a possibility that these samples could be positive for S10360, Y3968 or even Z63 as we don't have a confirmed negative call for these SNPs. However, the absence of a negative doesn't mean that the SNP where the position is not read is positive. There would be just as much of a case for saying these samples were Z58+ or on one of the branches that are negative for DF29. There's no data to confirm or disprove these SNPs.

Perhaps some visuals would help to explain what I'm seeing in IGV when I look at the BAM files.

Here's M253 (has reading, derived or positive): 29730

Here's L1237 (has reading, ancestral or negative): 29731

Now, here's S10360 (no reading, no data, can't tell if negative or positive): 29732

Here's Y3968 (no reading, no data, can't tell if negative or positive):29733

And here's Z63 (no reading, no data, can't tell if negative or positive):29734

deadly77
04-09-2019, 08:10 AM
If I go back to the position for M253 and zoom out, you can see the derived or positive read for M253 in the middle and it's flanked by a fair amount of shaded grey, which represents positions on the Y chromosome that are have a reading close to ChrY(hg19):15022707, but either side of that there's regions where there is no reading (white space).

29736

Most of the BAM files for K2/26 and SzO/540 look like this - get readings where they have targeted one of the 168 SNPs with their enrichment assay, white space almost everywhere else. WGS has a more even coverage across the Y chromosome. For example, here's what it looks like if I add SZ45 (WGS I-Y14999 sample from Szolad in the Lombard cemetery paper) below the two conqueror samples - lot less white spaces: 29739

Even more apparent when I zoom out further: 29740

oz
04-09-2019, 09:32 AM
Gotcha, and thanks a lot for having the patience to explain the process... although I didn't ask for a lot of detail. I just wanted to clarify what's going on with those samples, if they're leaning towards any sort of subclade under M253. So basically they could be anything.
Oh well, hopefully more Dna studies near my neck of the woods from post AD era will come up in the future that might find more I1 and Z63.

deadly77
04-13-2019, 02:47 PM
I was having a chat with forum member Celt_?? and he asked me if I knew of any Google Maps with the locations ancient Hg I locations. He shared a link to one that Rocca had prepared for ancient R1b-U152. It looked like a pretty nice way to summarize the data, so I thought I'd have a go at putting one together for the ancient I1 samples that we've discussed in this thread.

Try this out and see if the link works: https://www.google.com/maps/d/viewer?mid=1znTXv7qpl4_2T4u9068jOaLzpsjNf62F&ll=55.53882686743272%2C-26.647114350000038&z=3

If you click on one of the pins on the map or the name in the left-hand menu, should pop up with more information. I've put together a brief summary of the context, selected Y-DNA SNP calls, reference to the relevant publication and if appropriate a link to the YFull tree for four of the sampls.

Please let me know if you find mistakes, information that is missing, etc. There's also a few options for colour coding, icons, etc. that I haven't incorporated yet. I included the pre I1 samples - I'll probably colour code them different. Not sure if it's better to colour code by different subclades or time period. I'm thinking the latter may be a better option given that some of them the subclade assignment is limited by the design of the sequencing or the quality of the ancient sample, but I'm open to suggestions.

JMcB
04-13-2019, 03:01 PM
I was having a chat with forum member Celt_?? and he asked me if I knew of any Google Maps with the locations ancient Hg I locations. He shared a link to one that Rocca had prepared for ancient R1b-U152. It looked like a pretty nice way to summarize the data, so I thought I'd have a go at putting one together for the ancient I1 samples that we've discussed in this thread.

Try this out and see if the link works: https://www.google.com/maps/d/viewer?mid=1znTXv7qpl4_2T4u9068jOaLzpsjNf62F&ll=55.53882686743272%2C-26.647114350000038&z=3

If you click on one of the pins on the map or the name in the left-hand menu, should pop up with more information. I've put together a brief summary of the context, selected Y-DNA SNP calls, reference to the relevant publication and if appropriate a link to the YFull tree for four of the sampls.

Please let me know if you find mistakes, information that is missing, etc. There's also a few options for colour coding, icons, etc. that I haven't incorporated yet. I included the pre I1 samples - I'll probably colour code them different. Not sure if it's better to colour code by different subclades or time period. I'm thinking the latter may be a better option given that some of them the subclade assignment is limited by the design of the sequencing or the quality of the ancient sample, but I'm open to suggestions.

Very nice, indeed! Thank you for your efforts! Personally, I would color code them as you’re suggesting.

Edit: Just so you know, there a small typo in the CL63 I-Y2245 information, where Italy is spelled Italu. This is great reading and nicely organized, with links to all of the papers. Well done!

deadly77
04-13-2019, 03:31 PM
Very nice, indeed! Thank you for your efforts! Personally, I would color code them as you’re suggesting.

Edit: Just so you know, there a small typo in the CL63 I-Y2245 information, where Italy is spelled Italu. This is great reading and nicely organized, with links to all of the papers. Well done!

Thanks - that's an easy one to correct :)

Adrian Stevenson
04-14-2019, 07:03 AM
Well done! A nice piece of work.

I will enjoy reading it in full.

Cheers, Ade.

deadly77
04-15-2019, 10:11 PM
There was a paper on "Ancient genomes indicate population replacement in Early Neolithic Britain" that was published today https://www.nature.com/articles/s41559-019-0871-9 - the article itself is not open access although as always there is a lot of stuff in the supplementary material including Y-DNA haplogroup assignments. There is also the preprint on biorxiv here https://www.biorxiv.org/content/10.1101/267443v1

The samples in the supplementary material are overwhelmingly I2a2 - not unexpected for Mesolithic and Neolithic Britain. They do mention that one of the samples, the fantastically named "TottyPot_1" near Cheddar, Somerset was assigned to haplogroup I and they note that it has a derived allele for Z2842, one of the >300 SNPs that defines the I1 haplogroup. However, they also note that TottyPot_1 carries 2 ancestral alleles at other I1 defining SNPs, so this wouldn't be I1 (at least the way I define I1). BAM file is very small (13MB).

oz
04-15-2019, 11:32 PM
Lol.... Totty_pot I can't read that without chuckling.
Is it anything like that BAL051 sample?

deadly77
04-16-2019, 08:22 AM
Lol.... Totty_pot I can't read that without chuckling.
Is it anything like that BAL051 sample?

Yes - that rather tickled me as well. There's even a beer named after the site https://www.cheddarales.co.uk/totty-pot-dark-porter/a/6/ from Cheddar Ales which have the tang line "simply gorgeous" - a fantastic pun on the Cheddar Gorge https://en.wikipedia.org/wiki/Cheddar_Gorge - although it's an extremely cheesy pun (I'll stop there...)

Anything like BAL051? Yeah, in that it's got a mixture of derived and ancestral SNPs so isn't after the TMRCA of modern I1. But in a different location and a very different time period - TottyPot_1" C14, cal. 95% 2831-2461 cal. BCE (4008±39 BP, OxA-16460) - much later than BAL051.

I guess it's going to depend on how many ancestral and derived I1 SNPs in TottyPot_1 and how many are read. If there's a lot of ancestral and Z2842 is the only derived one, it may be just a false positive. Either way, TottyPot_1 is likely to be a dead lineage with no Y-DNA descendants today.

oz
04-16-2019, 04:54 PM
Bummer for Totty_pot. Maybe he didn't want to have kids though, didn't care for that.

deadly77
04-16-2019, 11:03 PM
Bummer for Totty_pot. Maybe he didn't want to have kids though, didn't care for that.

Hah - I think I have found out one reason why - the archaeological site description wasn't covered in the paper published this week as the site description and sample was previously published in the Olade 2018 paper and in the supporting info here https://media.nature.com/original/nature-assets/nature/journal/v555/n7695/extref/nature25738-s2.pdf they have a description of the TottyPot site and samples on page 111. The Olade paper seems to reference a different (older) individual from as TP1 compared to what this week's paper refers to as TottyPot_1, although cross referencing the Harvard ID and radiocarbon lab ID: "A left femur from a 10-year-old child (TP 2004.9/257) dated to the Late Neolithic was analyzed with aDNA: I5374/TP 2004.9/257: 2830–2461 calBCE (4008±39 BP, OxA-16460)"

So unless things were a bit different in the late Neolithic, I don't think any 10 year olds are fathering children.

Although Y-DNA lines can become extinct for other reasons than not having any children - having only daughters or his sons (or other descendants further down the line) not having sons to carry on the Y line. Must have happened a lot of times close to the I1 Y-line because of the bottleneck.

oz
04-17-2019, 12:54 AM
Yeah I just made a silly joke. To get serious let's recap for a moment. I mean stop and think how hard life back then must have been and how different it was. No supermarkets, no medicine, no hospitals, no technology other than stone, fire and wood. Put the people today to live in those conditions and maybe at best 1 out of a 100 would survive and even smaller number than that father sons who will continue to father more sons. Just the sheer statistics of all this it's hard to even wrap your mind around it.
I think when looking at these haplogroups and stuff, it's nothing but sheer luck and founder effects no matter how much some try to romanticize their haplogroup or whatever, it's silly and those people don't have a good grasp on reality. I know I made a comment once about how an I* guy was really determined to survive and become the I1 guy after more than 300 mutations and who knows how many generations, again let not anyone be confused by my sarcasm.

spruithean
04-17-2019, 03:26 PM
For a minute there I thought we were going to have an ancient I1 in Britain well before R1b. It looks like there were a lot of pre-I1 lines that died out, with the DF29 et. al. becoming the most successful.

I'm curious about the Hungarian Conqueror I1 who appears to be East Asian-European mix, the conquerors would be Magyar correct?

deadly77
04-28-2019, 11:23 PM
I went through TottyPot_1 BAM file - no call for pretty much all of the I1 SNPs - only one SNP had any read - Z2806/CTS6765 1T (ancestral). I looked for the Z2842 that the authors mentioned in the supplementary material, but to my view that one is a no call. Perhaps the SNP calling tool they are using is giving out some false reports or the wrong ID I5374 for the BAM file. Oh well, I guess we can put this in the ignore pile.

Looking through over 300 SNPs is a bit of a pain, but thankfully the IGV allows you to load several BAM files at the same time, so I used this to review some of the lower coverage samples to see what could be found among the big block of I1 SNPs, mostly to check that they are I1. All of these discussed at various points in the thread above and on the Google Map. Below is more housekeeping rather than anything new.

For the two samples from the Hungarian Conquerer preprint, K2/26 had reads for M253 1T, L80 2G, L840 4G and SzO/540 had M253 14T, L80 19G, M258 8C/1T, L840 14G, F3033 2A. Z2790 1A and that is all. Everything else was a no call.

US14 has derived reads for 29 of the >300 SNPs that define the I1 haplogroup: Z2751, L118, CTS10338, Z2846, CTS3268, Z2698/FGC2435, CTS11036/Z2863, CTS2970, Z2917, FGC2440, F3033, Z2805, S109, CTS7751, CTS10, L75, Z2852, L124, CTS4037, Z2864, FGC2441, Y1952, Z2776, CTS5134, CTS2044, Y1859, Z2832, Z2815, Z2687. All of the SNPs listed are one-read derived SNPs, but they're phylogenetically consistent with each other. This gives a bit more confidence in the I1 assignment to go along with the one-read positive for DF29 (but no call for all phyloequivalent SNPs).

STR241 was one of the three from the Medieval Bavarian paper - the other two had some positive reads for I-DF29 or phyloequivalent SNPs, but STR241 was no call for all of the I-DF29 branch SNPs, but has quite a few derived reads in the big I1 block - L840 56G, Z2880 1A, Z2778 1C, P40 7T, PAGE123 1A, Z2846 1G, Z2811 1C, CTS1755/Z2750 1T, CTS6076 1G, L125 46C 1T, CTS5705 1C, CTS8716 1T.

As well as the I-DF29 branch SNPs, the Anglo-Saxon NO3423 had quite a lot of derived reads in the I1 big block: Z2789 2T, Z2880 1A, Z2841 2C, Z2756 1T, Z2802 2T, Z2679 1G, Z2785 1C, Z2729 3T, Z2751 2A, Z2883 1T, Y1962 C Insertion, Y1868 1A, Z2798 2T, Z2779 1C ,Y1958 T insertion, Z2823 1T, Z2747 1G, Z2733 2T, CTS3268 1A, Z2711/FGC2439 1A, CTS11042 1C, FGC33327 1A, Z2725 1T, Z2866 1G, P203 1A, Z2730 1G, Z2848 2T, CTS2644 1A, V5203 2A, CTS11534 2G, Z2917 2T, Y1951 A insertion, Y1863 1G, CTS313/Z2681 1C, CTS2732 1A, Z2865 1G, CTS9749 1G, L125 1C, L81 1C, CTS10613 2C, CTS898 2C, Z2887 1T, CTS1748 2G, Z2862 1C, CTS8716 1T, Z2839 1T, Z2836 2G, CTS6006 2A, Z2678 2T, Z2790 2A, Z2878 1G, Z2708 1A, Z2874 2C, Z2772 1C, CTS5891 2G, Z2860 1A, Y1886 1C, Z2736 1T, L124 1C, CTS4295 2T, CTS4037 1A, Z2864 3G, Z2784 1T, Z2787 1A, L764 1T, CTS209 1G, FGC2441 1G, CTS10140 1A, CTS8597 6T, S22865 2A, Z2740 1A, Y1929 3C, FGC2431 2C, Z2806/CTS6765 2C, Z2828 2G, CTS1965 1T, CTS11675 1T, CTS4387 1T, Z2689 2C, Z2815 2T, Z2687 1G, Z2690 1C, CTS12609 1G, Z2851 2G

As I said, not a lot new - confirms the Hungarian Conquerer samples are so low coverage only basic haplogroup can likely be determined, US14 and STR241 are more solidly I1, but still don't know anything more definitive than that.

janan
04-28-2019, 11:26 PM
Some posts in this thread have touched upon the reason there are so few findings of ancient I1 in Scandinavia, the area where I1 now dominates, with more than 50 percent of males carrying the haplogroup in some parts of Sweden. The soil in Fennoscandia might be a reason. If you were a stone age man and didn’t want geneticians to fiddle with your dna a few thousand years after your death, Sweden would have been a good place to get buried in. Look at the following map:

https://images.app.goo.gl/P6iG2CSqVoX92bJEA

The blue patches are areas with sedimentary bedrock. The soil in these areas are calcareous and thus preserves bones well. The rest has acid soil which eat bones. Consequently, most (all?) ancient humans with readable dna have been found in these areas. Gotland: Stora Förvar, Ajvide, Stora Bjärs, Ire. Patch west of lake Vättern: Gökhem. Patch east of lake Vättern: Motala. Patch in southmost province of Scania: Abbekås, Ängamöllan, and others.

Moreover, these parts belong to the most fertile in Sweden. So they have continually been inhabitated and cultivated and many graves must have been plowed away.

The rest of the country was obviously packed with now dissolved I1 individuals, since the ice age. Or not.

JonikW
04-29-2019, 10:09 AM
Some posts in this thread have touched upon the reason there are so few findings of ancient I1 in Scandinavia, the area where I1 now dominates, with more than 50 percent of males carrying the haplogroup in some parts of Sweden. The soil in Fennoscandia might be a reason. If you were a stone age man and didn’t want geneticians to fiddle with your dna a few thousand years after your death, Sweden would have been a good place to get buried in. Look at the following map:

https://images.app.goo.gl/P6iG2CSqVoX92bJEA

The blue patches are areas with sedimentary bedrock. The soil in these areas are calcareous and thus preserves bones well. The rest has acid soil which eat bones. Consequently, most (all?) ancient humans with readable dna have been found in these areas. Gotland: Stora Förvar, Ajvide, Stora Bjärs, Ire. Patch west of lake Vättern: Gökhem. Patch east of lake Vättern: Motala. Patch in southmost province of Scania: Abbekås, Ängamöllan, and others.

Moreover, these parts belong to the most fertile in Sweden. So they have continually been inhabitated and cultivated and many graves must have been plowed away.

The rest of the country was obviously packed with now dissolved I1 individuals, since the ice age. Or not.

Very informative, thanks. Does anyone have a map of Iron Age inhumation burials in Scandinavia? It would be good to know what is potentially available. The only map I can immediately find is excusively of richly furnished burials, in one of Malcolm Todd's books. The biggest concentration of those is in the blue zone of Denmark, in Fyn. One hurdle for any site might be an understandable reluctance to excavate. For example, the burials at Borre in Norway start in the Migration Period but I remember reading in the museum there that they want to leave things undisturbed for more technologically advanced generations.

spruithean
04-29-2019, 11:49 AM
I'd be interested in seeing these sorts of maps, though I'm not sure where to look.

Janan raises some good points, obviously pH levels of various soils are going to have some influence on the preservation of DNA and even skeletal remains. Another thing obviously is the practice of cremation, which seems to have been quite common in early Germanic areas.

JonikW, you mention locations that have yet to be excavated do to the wish of not disturbing the site and waiting for better technology, this seems like a good idea in all honesty.

I think the ancient I1 we have so far is fairly telling in regards to which groups of people brought it around the world, that was sort of obvious without ancient samples :lol:

janan
05-10-2019, 12:57 PM
Got curious about the potential for new DNA findings. I've asked around and although osteologists likely have a pretty good grip, there doesn't seem to be a compilation of inhumation finds with good potential for DNA analyses.

The Swedish national heritage board has a web site which allows you to browse finds. I've made searches in the most interesting provinces of Sweden (the soil...) for reports about graves characterized as "fornminne" (~ "ancient heritage") or "undersökt och borttagen" (~ "examined and removed"), with the report including the word "skelett". This gives:

Skåne: 120
Östergötland: 24
Västergötland: 48
Gotland: 74
Öland: 43

Many reports cover several graves. On the other hand, some of them are not interesting - the bones are mostly decomposed, the skeleton is not human, the find is not ancient, etc. You would have to read each report to get closer to the right figure. But still, I believe there are quite a few skeletons with potential out there. It's more about time, resources, and refinement of techniques. But it's really frustrating just sitting and waiting for the results to come out :frusty:

Here's the link to the web site:
http://www.fmis.raa.se/cocoon/fornsok

JonikW
05-10-2019, 02:17 PM
Got curious about the potential for new DNA findings. I've asked around and although osteologists likely have a pretty good grip, there doesn't seem to be a compilation of inhumation finds with good potential for DNA analyses.

The Swedish national heritage board has a web site which allows you to browse finds. I've made searches in the most interesting provinces of Sweden (the soil...) for reports about graves characterized as "fornminne" (~ "ancient heritage") or "undersökt och borttagen" (~ "examined and removed"), with the report including the word "skelett". This gives:

Skåne: 120
Östergötland: 24
Västergötland: 48
Gotland: 74
Öland: 43

Many reports cover several graves. On the other hand, some of them are not interesting - the bones are mostly decomposed, the skeleton is not human, the find is not ancient, etc. You would have to read each report to get closer to the right figure. But still, I believe there are quite a few skeletons with potential out there. It's more about time, resources, and refinement of techniques. But it's really frustrating just sitting and waiting for the results to come out :frusty:

Here's the link to the web site:
http://www.fmis.raa.se/cocoon/fornsok

Nice work, and thanks janan. It's good we've now got some idea of what might be available for testing from Sweden, with all the usual caveats of course.

spruithean
05-15-2019, 10:03 PM
Here from another thread, looks like we have another ancient I1, this time out of Finland.


I uploaded Huseby Klev sample ble008 to Gedmatch. Processing was done with two programs:

BA7487306 pileupCaller
BF1047725 extract23 with a modified SNP filter

I noticed the sample had Y-DNA and MorleyDNA predicted it to be I1 I1-L759 (I1-CTS10140, I1-CTS10338) and yhaplo's result was I-CTS88 I-M170 I

At most it seems to be I-M253 and no further SNPs.

I can't find much on this yet, but from first glance, Huseby Klev is 10,000 years old.... it's more likely I-M170 then.

deadly77
05-16-2019, 07:34 AM
Here from another thread, looks like we have another ancient I1, this time out of Finland.



At most it seems to be I-M253 and no further SNPs.

I can't find much on this yet, but from first glance, Huseby Klev is 10,000 years old.... it's more likely I-M170 then.

I looked at the paper - it's open access here https://www.nature.com/articles/s42003-019-0399-1

According to Table 1, Ble008 is listed as sex XX, not XY.

spruithean
05-16-2019, 12:30 PM
I looked at the paper - it's open access here https://www.nature.com/articles/s42003-019-0399-1

According to Table 1, Ble008 is listed as sex XX, not XY.

Interesting. It may be an error or a mistake when the ID was posted in the other thread. Either way, I am not too confident it would even be I1 at 10,000 YBP.

Shaikorth
05-16-2019, 12:50 PM
Interesting. It may be an error or a mistake when the ID was posted in the other thread. Either way, I am not too confident it would even be I1 at 10,000 YBP.

If it's just I1 with missing defining SNP's of modern I1 MRCA and doesn't belong to any modern clades it is possible. I1-I2 separated way back.

spruithean
05-16-2019, 01:29 PM
If it's just I1 with missing defining SNP's of modern I1 MRCA and doesn't belong to any modern clades it is possible. I1-I2 separated way back.

Perhaps pre-I1 or pre-pre-I1 :lol:

deadly77
05-16-2019, 04:53 PM
Or it could be nothing because there is no real Y-DNA in this sample. If you look at Table 1 in the paper, Ble008 has the most coverage out of all the samples, more than three times the coverage of Ble007, but Ble007 has 2.65 times more Yseq than Ble008. Also, comparing the ratios of Yseq to Xseq across the samples, the ratio of Y:X for Ble004 and Ble008 is pretty low compared to Ble007.

I've loaded up the BAM files of all three samples from this paper into IGV and checking them for I1 SNPs. A third of the way through and there is zero evidence for Y-DNA haplogroup I1 in any of these three samples. So far, Ble 007 has a lot more calls in Y chromsome than Ble008 or Ble004. All of the positions where there is a read are ancestral for I1 so far.

I also took a look into the X chromosome of Ble008's BAM file - a lot of positions were visually heterozygous which to me indicates that there are two X chromosomes.

I'd say Ble008 and Ble004 are female and the Y-DNA calls are probably homologous with X chromosome or autosomes. Ble007 is male but not haplogroup I1 (or even pre-I1 so far).

spruithean
05-16-2019, 05:04 PM
I figured as much, the study even mentions possibilities of contamination and the items they are testing are extremely old.

spruithean
05-17-2019, 02:35 PM
I was having a chat with forum member Celt_?? and he asked me if I knew of any Google Maps with the locations ancient Hg I locations. He shared a link to one that Rocca had prepared for ancient R1b-U152. It looked like a pretty nice way to summarize the data, so I thought I'd have a go at putting one together for the ancient I1 samples that we've discussed in this thread.

Try this out and see if the link works: https://www.google.com/maps/d/viewer?mid=1znTXv7qpl4_2T4u9068jOaLzpsjNf62F&ll=55.53882686743272%2C-26.647114350000038&z=3

If you click on one of the pins on the map or the name in the left-hand menu, should pop up with more information. I've put together a brief summary of the context, selected Y-DNA SNP calls, reference to the relevant publication and if appropriate a link to the YFull tree for four of the sampls.

Please let me know if you find mistakes, information that is missing, etc. There's also a few options for colour coding, icons, etc. that I haven't incorporated yet. I included the pre I1 samples - I'll probably colour code them different. Not sure if it's better to colour code by different subclades or time period. I'm thinking the latter may be a better option given that some of them the subclade assignment is limited by the design of the sequencing or the quality of the ancient sample, but I'm open to suggestions.


I'm seeing this map just now :lol: , how behind am I...

Very nice work! I also like the skull and crossbones for lineages we are sure died out and the question marks for the presumably pre-I1 lineages. I've been pondering the exact path that the (pre-I1?) I1 haplogroup took in Europe, obviously they've found various pre-I1 lineages from Scandinavia, Iberia and Hungary so that's a large spread. How exactly did I1 end up in northern Europe? Did it come up through a mixing of Linear Pottery Culture with what was to become Funnelbeaker and then from there at some point it was firmly rooted in Scandinavia? Or are the pre-I1's found in Central Europe and Iberia both extinct branches and some lineage of pre-I1 eventually produced I1-M253 in Scandinavia?

I guess for now it's just hypotheticals and a lot of head scratching. For now I suppose I1 folk should be pleased with what has been found so far, at least there is a decent amount of I1-M253 in Migration Period and the Medieval era!

deadly77
05-18-2019, 04:26 PM
I'm seeing this map just now :lol: , how behind am I...

Very nice work! I also like the skull and crossbones for lineages we are sure died out and the question marks for the presumably pre-I1 lineages. I've been pondering the exact path that the (pre-I1?) I1 haplogroup took in Europe, obviously they've found various pre-I1 lineages from Scandinavia, Iberia and Hungary so that's a large spread. How exactly did I1 end up in northern Europe? Did it come up through a mixing of Linear Pottery Culture with what was to become Funnelbeaker and then from there at some point it was firmly rooted in Scandinavia? Or are the pre-I1's found in Central Europe and Iberia both extinct branches and some lineage of pre-I1 eventually produced I1-M253 in Scandinavia?

I guess for now it's just hypotheticals and a lot of head scratching. For now I suppose I1 folk should be pleased with what has been found so far, at least there is a decent amount of I1-M253 in Migration Period and the Medieval era!

Cheers - the map is definitely a work in progress. I was trying to keep organized with an excel spreadsheet, but it was getting a bit messy. Celt?? shared a link to Rocca's ancient R1b-U152 map which is a really nice piece of work and I thought this might be a better way to organize the I1 samples that we know about and get them into some kind of format before the hoped for avalanche of ancient I1 samples to be sequenced in the future (hoping here, rather than believing, but oh well...) One thing I like is being able to look at the map data as a whole and then click on individual samples and get a lot more detail just on that sample. I found the spreadsheet was a bit difficult to isolate the data of one sample without being a little overwhelmed.

I went for the skull and crossbones for the ancient samples that were before the estimated TMRCA of modern I1 and had confirmed ancestral reads among the I1 SNPs, and I went for question marks with the ones which don't have ancestral I1 SNPs but have less than 15% of the relevant I1 SNPs with derived read. Things may change if we get more definition or branching between the break off from I and the TMRCA of I1. Not everyone agrees with me - I had some negative feedback regarding this map in a Facebook group. But I made the map for my own records and organization. If other folks find it useful, great. Regardless, I'm not the police of who is I1 and who is not I1.

As to whether the pre-I1 samples contributed as ancestor to the I1 TMRCA line or not, I think it's too difficult to say. The large number of no calls among the I1 SNPs for these samples adds a lot of uncertainty. I think we'd have a better idea if we had a greater percentage of those SNPs called and we had more examples in total. That way we'd have a greater consistency over the order of the mutations and that may allow us to define some samples as extinct lineages. My hunch is that BAL051, BAB5, SF11 are not direct ancestors of I1 TMRCA, but right now, not enough data to say for sure.

But yeah, I think that the pre-I1 lineages were more geographically spread than just Scandinavia. I think there will be more found in other locations around Europe. I think it's possible that there were more than one mini-bottleneck that didn't make it to the I1 TMRCA. My own feeling is that during the migration of R1b into and through Europe, the Y lineage that became I1 became incorporated among those people and his Y descendants "hitched a ride" with that group, despite much more diverse earlier origins that aren't with that group. I'd say that's why the population expansion from the TMRCA (which doesn't neccesarily need to be in Scandinavia) into diverse descendant subclades occurs around the same time. I think thats also why we don't find I1 ancient samples in isolation in the majority of the locations that we have data for - almost always found with R-U106 in particular. But again, the small number of ancient I1 samples means that it's difficult to draw any meaningful conclusions with confidence. Again, not enough data. We have what we have for now, hopefully we have more samples with better sequencing in the future.

spruithean
05-18-2019, 11:18 PM
Cheers - the map is definitely a work in progress. I was trying to keep organized with an excel spreadsheet, but it was getting a bit messy. Celt?? shared a link to Rocca's ancient R1b-U152 map which is a really nice piece of work and I thought this might be a better way to organize the I1 samples that we know about and get them into some kind of format before the hoped for avalanche of ancient I1 samples to be sequenced in the future (hoping here, rather than believing, but oh well...) One thing I like is being able to look at the map data as a whole and then click on individual samples and get a lot more detail just on that sample. I found the spreadsheet was a bit difficult to isolate the data of one sample without being a little overwhelmed.

I certainly agree that it makes it much easier to get a visual representation of the distribution of the ancient samples so far. Charts with data are good when just pure data is needed, but some of us like that visual for sure. It definitely looks like if we get more and more samples it will be easier to track via the map.


I went for the skull and crossbones for the ancient samples that were before the estimated TMRCA of modern I1 and had confirmed ancestral reads among the I1 SNPs, and I went for question marks with the ones which don't have ancestral I1 SNPs but have less than 15% of the relevant I1 SNPs with derived read. Things may change if we get more definition or branching between the break off from I and the TMRCA of I1. Not everyone agrees with me - I had some negative feedback regarding this map in a Facebook group. But I made the map for my own records and organization. If other folks find it useful, great. Regardless, I'm not the police of who is I1 and who is not I1.

Ah, ok I see. I certainly agree with the choice to define the pre-TMRCA ancient I1 as pre-I1 or label them with question marks or skulls. I1 by definition to me is the haplogroup with 309 defining mutations and a rather young TMRCA, so everything prior to that can't literally be I1.


As to whether the pre-I1 samples contributed as ancestor to the I1 TMRCA line or not, I think it's too difficult to say. The large number of no calls among the I1 SNPs for these samples adds a lot of uncertainty. I think we'd have a better idea if we had a greater percentage of those SNPs called and we had more examples in total. That way we'd have a greater consistency over the order of the mutations and that may allow us to define some samples as extinct lineages. My hunch is that BAL051, BAB5, SF11 are not direct ancestors of I1 TMRCA, but right now, not enough data to say for sure.

I don't think we may ever be sure whether those lineages are ancestral to modern I1, we don't even have any idea what the chronological order is for the SNPs that are phyloequivalent for M253. I'm also not sure we'll ever know considering soil in Scandinavia can be rather destructive to genetic material (same goes for parts of Britain, notably the new Saxon Tomb). I have seen the current I1 origin theory via Eupedia and some various comments on Eurogenes and elsewhere that it is believed I1 or pre-I1 was present in Mesolithic Central Europeans with the LBK culture which eventually led into the Funnelbeakers and Corded Ware and the eventual rise of Nordic Bronze Age and Germanic cultural development. However, I don't think we have enough to make assumptions yet.


But yeah, I think that the pre-I1 lineages were more geographically spread than just Scandinavia. I think there will be more found in other locations around Europe. I think it's possible that there were more than one mini-bottleneck that didn't make it to the I1 TMRCA. My own feeling is that during the migration of R1b into and through Europe, the Y lineage that became I1 became incorporated among those people and his Y descendants "hitched a ride" with that group, despite much more diverse earlier origins that aren't with that group. I'd say that's why the population expansion from the TMRCA (which doesn't neccesarily need to be in Scandinavia) into diverse descendant subclades occurs around the same time. I think thats also why we don't find I1 ancient samples in isolation in the majority of the locations that we have data for - almost always found with R-U106 in particular. But again, the small number of ancient I1 samples means that it's difficult to draw any meaningful conclusions with confidence. Again, not enough data. We have what we have for now, hopefully we have more samples with better sequencing in the future.

That is actually quite reasonable and it would explain some of the diversity, distribution and the non-isolated finds. A hitched ride with the R1b folk would make sense indeed!

Admittedly I'm pretty chuffed to share a paternal lineage to some degree with some of those recent aDNA finds (Avar-era Hungarian, Conqueror-era Hungarian, Longobards, Icelanders, Baiuvarii, etc). It's definitely not something I'd anticipated back in the early genetic genealogy days, that's for sure.

Paul333
05-18-2019, 11:37 PM
Or it could be nothing because there is no real Y-DNA in this sample. If you look at Table 1 in the paper, Ble008 has the most coverage out of all the samples, more than three times the coverage of Ble007, but Ble007 has 2.65 times more Yseq than Ble008. Also, comparing the ratios of Yseq to Xseq across the samples, the ratio of Y:X for Ble004 and Ble008 is pretty low compared to Ble007.

I've loaded up the BAM files of all three samples from this paper into IGV and checking them for I1 SNPs. A third of the way through and there is zero evidence for Y-DNA haplogroup I1 in any of these three samples. So far, Ble 007 has a lot more calls in Y chromsome than Ble008 or Ble004. All of the positions where there is a read are ancestral for I1 so far.

I also took a look into the X chromosome of Ble008's BAM file - a lot of positions were visually heterozygous which to me indicates that there are two X chromosomes.

I'd say Ble008 and Ble004 are female and the Y-DNA calls are probably homologous with X chromosome or autosomes. Ble007 is male but not haplogroup I1 (or even pre-I1 so far).

Regarding No3423 I-DF29. The Anglo Saxon cemetery at Norton North East England was not christian. It was dated from at least the mid sixth century, and was pagan, with associated grave goods.

spruithean
05-19-2019, 12:27 AM
Regarding No3423 I-DF29. The Anglo Saxon cemetery at Norton North East England was not christian. It was dated from at least the mid sixth century, and was pagan, with associated grave goods.

Was it really a pagan burial? Should we really consider it an Anglo-Saxon then? Would it possibly be a Viking burial then?

Here is part of the supplementary data for the burial:


1.3 Norton on Tees
Two Anglo-Saxon cemeteries were excavated in the village of Norton, Teesside, north east England. They
were located 200m apart and one of these, Norton East Mill, dated to the pagan Anglo*Saxon period
(550*-650AD), while the adjacent cemetery, Norton Bishopsmill, dates to 650*-910AD and was Christian.
The pagan cemetery contained 120 burials, many of which were furnished with grave goods, while the
Christian burial ground contained the unfurnished burials of 100 skeletons. Analysis of the skeletal
remains has revealed differences in the age and sex distributions as well as the pathology at the two sites
47,48

I seem to remember NO3423 being from Bishopsmill.

JonikW
05-19-2019, 12:44 AM
Was it really a pagan burial? Should we really consider it an Anglo-Saxon then? Would it possibly be a Viking burial then?

Here is part of the supplementary data for the burial:



I seem to remember NO3423 being from Bishopsmill.

I agree. I'm sure he was from the Christian period from what we read at the time.

JMcB
05-19-2019, 03:36 AM
Regarding No3423 I-DF29. The Anglo Saxon cemetery at Norton North East England was not christian. It was dated from at least the mid sixth century, and was pagan, with associated grave goods.



I seem to remember NO3423 being from Bishopsmill.



I agree. I'm sure he was from the Christian period from what we read at the time.


Norton Bishopsmill, dates to 650–910 AD and was a Christian Anglo-Saxon cemetery excavated in the village of Norton, Teesside, northeast England 14. We sampled 3 individuals from burials of 100 skeletons and selected the best preserved, NO3423, for the present study (Supplementary Notes 1 and 2 and Supplementary Fig. 1).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735653/pdf/ncomms10326.pdf

deadly77
05-19-2019, 07:52 AM
Regarding No3423 I-DF29. The Anglo Saxon cemetery at Norton North East England was not christian. It was dated from at least the mid sixth century, and was pagan, with associated grave goods.

From the supplementary information file (page 30): 1.3 Norton on Tees - Two AngloSaxon cemeteries were excavated in the village of Norton, Teesside, north east England. They were located 200m apart and one of these, Norton East Mill, dated to the pagan AngloSaxon period (550650AD), while the adjacent cemetery, Norton Bishopsmill, dates to 650910AD and was Christian. The pagan cemetery contained 120 burials, many of which were furnished with grave goods, while the Christian burial ground contained the unfurnished burials of 100 skeletons. Analysis of the skeletal remains has revealed differences in the age and sex distributions as well as the pathology at the two sites 47,48. https://www.nature.com/articles/ncomms10326#supplementary-information

From the manuscript of the paper (last sentence of Results - Archaeological samples, just before section on Sequencing results and sample contamination): Norton Bishopsmill, dates to 650–910 AD and was a Christian Anglo-Saxon cemetery excavated in the village of Norton, Teesside, northeast England14. We sampled 3 individuals from burials of 100 skeletons and selected the best preserved, NO3423, for the present study (Supplementary Notes 1 and 2 and Supplementary Fig. 1). https://www.nature.com/articles/ncomms10326

deadly77
05-19-2019, 07:56 AM
From the supplementary information file (page 30): 1.3 Norton on Tees - Two AngloSaxon cemeteries were excavated in the village of Norton, Teesside, north east England. They were located 200m apart and one of these, Norton East Mill, dated to the pagan AngloSaxon period (550650AD), while the adjacent cemetery, Norton Bishopsmill, dates to 650910AD and was Christian. The pagan cemetery contained 120 burials, many of which were furnished with grave goods, while the Christian burial ground contained the unfurnished burials of 100 skeletons. Analysis of the skeletal remains has revealed differences in the age and sex distributions as well as the pathology at the two sites 47,48. https://www.nature.com/articles/ncomms10326#supplementary-information

From the manuscript of the paper (last sentence of Results - Archaeological samples, just before section on Sequencing results and sample contamination): Norton Bishopsmill, dates to 650–910 AD and was a Christian Anglo-Saxon cemetery excavated in the village of Norton, Teesside, northeast England14. We sampled 3 individuals from burials of 100 skeletons and selected the best preserved, NO3423, for the present study (Supplementary Notes 1 and 2 and Supplementary Fig. 1). https://www.nature.com/articles/ncomms10326

Ah - I see that Spruithean, JonikW and JMcB already had covered that. Cheers folks.

deadly77
05-19-2019, 08:21 AM
I certainly agree that it makes it much easier to get a visual representation of the distribution of the ancient samples so far. Charts with data are good when just pure data is needed, but some of us like that visual for sure. It definitely looks like if we get more and more samples it will be easier to track via the map.



Ah, ok I see. I certainly agree with the choice to define the pre-TMRCA ancient I1 as pre-I1 or label them with question marks or skulls. I1 by definition to me is the haplogroup with 309 defining mutations and a rather young TMRCA, so everything prior to that can't literally be I1.



I don't think we may ever be sure whether those lineages are ancestral to modern I1, we don't even have any idea what the chronological order is for the SNPs that are phyloequivalent for M253. I'm also not sure we'll ever know considering soil in Scandinavia can be rather destructive to genetic material (same goes for parts of Britain, notably the new Saxon Tomb). I have seen the current I1 origin theory via Eupedia and some various comments on Eurogenes and elsewhere that it is believed I1 or pre-I1 was present in Mesolithic Central Europeans with the LBK culture which eventually led into the Funnelbeakers and Corded Ware and the eventual rise of Nordic Bronze Age and Germanic cultural development. However, I don't think we have enough to make assumptions yet.



That is actually quite reasonable and it would explain some of the diversity, distribution and the non-isolated finds. A hitched ride with the R1b folk would make sense indeed!

Admittedly I'm pretty chuffed to share a paternal lineage to some degree with some of those recent aDNA finds (Avar-era Hungarian, Conqueror-era Hungarian, Longobards, Icelanders, Baiuvarii, etc). It's definitely not something I'd anticipated back in the early genetic genealogy days, that's for sure.

The "hitched ride" theory I first heard while listening to The Insight podcast. It's a great regular podcast by Spencer Wells and Razib Khan of Insitome, often with guests and a variety of subjects related to genomics. This particular episode here: https://insitome.libsyn.com/y-chromosomal-stars specifically discussing I1 (albeit briefly) from 36.30min when Razib Khan brings it up. The more i've thought about it, it makes a lot of sense. Survived by assimilation and benefitted from being part of a succesful group of largely R1b.

Yes, I'm also pretty chuffed with what we have so far. Although I'm greedy for more :)

deadly77
05-19-2019, 09:52 AM
I received an email from Hunter Provyn - he's the developer of the Phylogeographer/Mygrations webiste - he says he's keen to add more ancient DNA references to his portal ad he's been collaborating with Carlos Quiles of Indo-European.eu who has sent him 1600 dated, geolocated ancient Y-DNA samples he has been collecting. I looked through the spreadsheet and unfortunately there's several errors that we've discussed previously on this thread, including from taking misreported publication data at face value (eg. SVK-A1 I-Z131, CL63 I1-Z79, etc.) and misassignments due applying shorthand SNPs to the wrong version of the ISOGG tree in the ancient Iceland paper (eg. SSJ-A2 and HSJ-A1 listed as I-A8182 and SBT-A1 listed as I-S26062), SF11 being I1, etc. I've replied with a list of corrections and added samples that aren't in his spreadsheet.

It does however list three I1 samples that were not on my radar. Two of these were from the Sigtuna paper (Krzewinska 2018) where we've already discussed 84005 (I-CTS2208, I-Z74 in the paper) - the spreadsheet lists urm035 as I1 and DF29 (paper says haplogroup BDCDEF) and urm045 as I1 and Z60, Z61 (paper says haplogroup not determined) and lists Sylvester as responsible (who also lists 84005 as I-CTS2208 in the spreadsheet). I've got the BAM files and I'll take a look and see if I can verify this.

There was also an additional I1 in the spreasheet with sample AE 1154, referenicing Bavaria, Rott2018 and Altenerding-Klettham cemetery. I figured this would be from the same paper AED 249, STR 486, STR 241. However, I can't find any sample AE 1154 in the paper.

JonikW
05-19-2019, 10:09 AM
The "hitched ride" theory I first heard while listening to The Insight podcast. It's a great regular podcast by Spencer Wells and Razib Khan of Insitome, often with guests and a variety of subjects related to genomics. This particular episode here: https://insitome.libsyn.com/y-chromosomal-stars specifically discussing I1 (albeit briefly) from 36.30min when Razib Khan brings it up. The more i've thought about it, it makes a lot of sense. Survived by assimilation and benefitted from being part of a succesful group of largely R1b.

Yes, I'm also pretty chuffed with what we have so far. Although I'm greedy for more :)

It's worth trying to pinpoint the potential location of the massive Stone Age bottleneck that led to the explosion of modern I1 and how this ties in with the expansion of R1a and R1b folk and eventual formation of a Germanic culture. The Battle Axe/Single Grave/Corded Ware Culture’s entry into Scandinavia and blending with the people that were already there seems a good place to start and the dates look right.
Perhaps the indigenous I1 were seen by the incomers as holding some knowledge, skill, power or authority that was worth incorporating.
This passage in an early chapter of “The Spoils of Victory” published by the national museum in Copenhagen is interesting. It shows clues in the artefact assemblages that could illustrate the bottleneck and subsequent events. The text below was written by Kaul Flemming: “Throughout the Neolithic period one notes a number of important changes, some of which took place during the Middle Neolithic Funnel Beaker Culture. At an early stage of this culture the number of bog finds of earthenware vessels drops radically, so that around 3000 BC the custom of placing them in bogs has by and large stopped. Around the same time the number of Funnel Beaker Culture battle-axes in the bogs also declines, as do the large depositions of amber. By contrast the deposition of flint axes in bogs continues, now in the form of among other things thick-butted and thin-bladed axes. Another find category shows the same picture - the sacrificial layers in front of the megalithic tomb facades. Here too the number of deposited earthenware vessels declines drastically at the same time, but axes, now even in increasing numbers, continue to be deposited throughout the remainder of the Funnel Beaker Culture.
During the transition to the Single Grave Culture (the period is also called MN b) several cultural changes took place, for instance other burial types and other pottery forms came into use. But as far as the depositions in the bogs are concerned, the Danish area in general seems to display a certain continuity; for the changes in the deposition customs had already taken place during the period of the Middle Neolithic Funnel Beaker Culture (also called MN A), and the general features that are found in depositions at the end of Funnel Beaker Culture seem to continue into the Single Grave Culture.”
So there may be mixed evidence of disruption and continuity, just as occurred in Britain during what we now know were periods of population replacement. Most archaeologists had simply missed the implications

spruithean
05-19-2019, 11:50 AM
The "hitched ride" theory I first heard while listening to The Insight podcast. It's a great regular podcast by Spencer Wells and Razib Khan of Insitome, often with guests and a variety of subjects related to genomics. This particular episode here: https://insitome.libsyn.com/y-chromosomal-stars specifically discussing I1 (albeit briefly) from 36.30min when Razib Khan brings it up. The more i've thought about it, it makes a lot of sense. Survived by assimilation and benefitted from being part of a succesful group of largely R1b.

Yes, I'm also pretty chuffed with what we have so far. Although I'm greedy for more :)

Thanks for sharing that link, I'll give it a listen, any discussion mentioning I1, even if briefly, is probably important. I don't see very much discussion of I1 on most of the big blogs such as Eurogenes or Quiles Indo-European blog.


I received an email from Hunter Provyn - he's the developer of the Phylogeographer/Mygrations webiste - he says he's keen to add more ancient DNA references to his portal ad he's been collaborating with Carlos Quiles of Indo-European.eu who has sent him 1600 dated, geolocated ancient Y-DNA samples he has been collecting. I looked through the spreadsheet and unfortunately there's several errors that we've discussed previously on this thread, including from taking misreported publication data at face value (eg. SVK-A1 I-Z131, CL63 I1-Z79, etc.) and misassignments due applying shorthand SNPs to the wrong version of the ISOGG tree in the ancient Iceland paper (eg. SSJ-A2 and HSJ-A1 listed as I-A8182 and SBT-A1 listed as I-S26062), SF11 being I1, etc. I've replied with a list of corrections and added samples that aren't in his spreadsheet.

Don't tell anyone at Eurogenes about this collaboration! I know there is some rivalry between the two camps in terms of what ancient people brought R1a or R1b and spoke this or that language :lol:

I hope that Mr. Provyn is willing to go through with corrections of the aDNA samples that you've examined. It is certainly a bit strange that these papers used old forms of ISOGG when most of us have moved on and refer to haplogroups with the main root and terminal SNP method.



It does however list three I1 samples that were not on my radar. Two of these were from the Sigtuna paper (Krzewinska 2018) where we've already discussed 84005 (I-CTS2208, I-Z74 in the paper) - the spreadsheet lists urm035 as I1 and DF29 (paper says haplogroup BDCDEF) and urm045 as I1 and Z60, Z61 (paper says haplogroup not determined) and lists Sylvester as responsible (who also lists 84005 as I-CTS2208 in the spreadsheet). I've got the BAM files and I'll take a look and see if I can verify this.

There was also an additional I1 in the spreasheet with sample AE 1154, referenicing Bavaria, Rott2018 and Altenerding-Klettham cemetery. I figured this would be from the same paper AED 249, STR 486, STR 241. However, I can't find any sample AE 1154 in the paper.

I'm not familiar with URM035 and URM045, however if there were errors and broad haplogroup designations in the paper such as "BCDEF" that seems a bit suspect and warrants deeper investigation, interesting that it is designated I-Z60/Z61 in the spreadsheet. That could be very interesting if confirmed. I think most ancient I1 we'll find will be Migration Period and within the Medieval period (and of course the higher middle ages up to colonial eras). Obvious places to look are already being looked at as of late.

I suspect that AE 1154 may be a error, I've not seen that sample anywhere in that paper and I've scoured it a few times. However perhaps it is referencing something else that may flown under the radar that was picked up recently. Perhaps time will tell.

Paul333
05-19-2019, 01:22 PM
Was it really a pagan burial? Should we really consider it an Anglo-Saxon then? Would it possibly be a Viking burial then?

Here is part of the supplementary data for the burial:



I seem to remember NO3423 being from Bishopsmill.

Appologies, you are correct. The earlier Norton pagan cemetery, was discovered by children playing in the bankside, of Mill Lane, in 1982, and excavated, between 1983-1985. The later nearby Bishopsmill,'christian cemetery', was found during later building work.

I confused the two separate cemeterys as one, despite owning the 1992,Sherlock & Welch research Report 82, regarding the first of these, the Mill Lane cemetery.

JonikW
05-19-2019, 08:51 PM
I wonder whether deadly77 and other well versed experts on ancient I1 see any implications for us here. Very interesting.

Edit: it kind of goes with what I posted earlier today on Scandinavia but I don't know what to make of any of it. I'm sure someone sees the bigger picture. I guess a small population of I1 got involved early on with the invaders, got lucky and expanded quite rapidly.

http://eurogenes.blogspot.com/2019/05/who-were-people-of-nordic-bronze-age.html?m=1

spruithean
05-19-2019, 09:01 PM
I wonder whether deadly77 and other well versed experts on ancient I1 see any implications for us here. Very interesting.

Edit: it kind of goes with what I posted earlier today on Scandinavia but I don't know what to make of any of it. I'm sure someone sees the bigger picture.

http://eurogenes.blogspot.com/2019/05/who-were-people-of-nordic-bronze-age.html?m=1

I had been hoping some comments about I1 would appear in that thread. A commenter under the name "Angantyr" claims that Nordic_LN II RISE179 is I1. That sample is on deadly's ancient I1 map as a pre-I1. Which I believe is appropriate as it is a low coverage sample and it was no call for ">99%" of the defining I1 SNPs.

I think we can't be too lenient (but can't be too strict either) on what we define as I1. We already know I1 has a young TMRCA so true I1 will be in that timeframe.

EDIT: keep your eye on this Eurogenes post, the comments are getting quite interesting!

deadly77
05-20-2019, 07:52 AM
It's worth trying to pinpoint the potential location of the massive Stone Age bottleneck that led to the explosion of modern I1 and how this ties in with the expansion of R1a and R1b folk and eventual formation of a Germanic culture. The Battle Axe/Single Grave/Corded Ware Culture’s entry into Scandinavia and blending with the people that were already there seems a good place to start and the dates look right.
Perhaps the indigenous I1 were seen by the incomers as holding some knowledge, skill, power or authority that was worth incorporating.
This passage in an early chapter of “The Spoils of Victory” published by the national museum in Copenhagen is interesting. It shows clues in the artefact assemblages that could illustrate the bottleneck and subsequent events. The text below was written by Kaul Flemming: “Throughout the Neolithic period one notes a number of important changes, some of which took place during the Middle Neolithic Funnel Beaker Culture. At an early stage of this culture the number of bog finds of earthenware vessels drops radically, so that around 3000 BC the custom of placing them in bogs has by and large stopped. Around the same time the number of Funnel Beaker Culture battle-axes in the bogs also declines, as do the large depositions of amber. By contrast the deposition of flint axes in bogs continues, now in the form of among other things thick-butted and thin-bladed axes. Another find category shows the same picture - the sacrificial layers in front of the megalithic tomb facades. Here too the number of deposited earthenware vessels declines drastically at the same time, but axes, now even in increasing numbers, continue to be deposited throughout the remainder of the Funnel Beaker Culture.
During the transition to the Single Grave Culture (the period is also called MN b) several cultural changes took place, for instance other burial types and other pottery forms came into use. But as far as the depositions in the bogs are concerned, the Danish area in general seems to display a certain continuity; for the changes in the deposition customs had already taken place during the period of the Middle Neolithic Funnel Beaker Culture (also called MN A), and the general features that are found in depositions at the end of Funnel Beaker Culture seem to continue into the Single Grave Culture.”
So there may be mixed evidence of disruption and continuity, just as occurred in Britain during what we now know were periods of population replacement. Most archaeologists had simply missed the implications

Interesting - I think there's definitely something in that worth thinking about. It might be difficult to verify from DNA of any ancient remains that are found, given that I1 was likely down to a single lineage (or at least a very small groups of lineages among a population). Talk about a needle in a haystack. Within a few generations, the I1 individual would not have been overtly outwardly distinguishable from the R1b group that they became assimilated into. Perhaps "hiding in plain sight" is a better analogy than hitching a ride.

deadly77
05-20-2019, 08:28 AM
Thanks for sharing that link, I'll give it a listen, any discussion mentioning I1, even if briefly, is probably important. I don't see very much discussion of I1 on most of the big blogs such as Eurogenes or Quiles Indo-European blog.



Don't tell anyone at Eurogenes about this collaboration! I know there is some rivalry between the two camps in terms of what ancient people brought R1a or R1b and spoke this or that language :lol:

I hope that Mr. Provyn is willing to go through with corrections of the aDNA samples that you've examined. It is certainly a bit strange that these papers used old forms of ISOGG when most of us have moved on and refer to haplogroups with the main root and terminal SNP method.




I'm not familiar with URM035 and URM045, however if there were errors and broad haplogroup designations in the paper such as "BCDEF" that seems a bit suspect and warrants deeper investigation, interesting that it is designated I-Z60/Z61 in the spreadsheet. That could be very interesting if confirmed. I think most ancient I1 we'll find will be Migration Period and within the Medieval period (and of course the higher middle ages up to colonial eras). Obvious places to look are already being looked at as of late.

I suspect that AE 1154 may be a error, I've not seen that sample anywhere in that paper and I've scoured it a few times. However perhaps it is referencing something else that may flown under the radar that was picked up recently. Perhaps time will tell.

I've found the Insitome podcast really interesting as a series - they also cover a lot of different areas in other blog posts. Really worth listening to.

Yes, Hunter says thanks and he will update the spreadsheet with corrections. I've discussed a few things with him before and I think he's keen to have accuracy. He's put a short video on YouTube discussing the collaboration on these ancient samples with Carlos Quiles and Vadim Urasin from YFull here https://www.youtube.com/watch?v=zjQa4VI43fA&feature=youtu.be&fbclid=IwAR131HPF6SAVvKEGNYlniplnGmFr7vGewQJMUjfJL YGfUNCMshz5F5PNTeU his main goal appears to be getting the data into a format that's compatible with his Phylogeographer tool.

I think the longhand nomenclature for persists due to familiarity of those who have likely used that nomenclature for years. As a relative latecomer, I often have to look those up and translate the alphabet soup. I much prefer I-L338 rather than I1a2a1a1a1a1 (as defined by 2019 ISOGG tree). The longhand nomenclature also changes from year to year on the ISOGG tree, which is where I think Carlos Quiles is making mistakes in I1 subclades in his spreadsheet regarding the ancient Iceland genomes. The supplementary information in that Science 2018 paper defines that the authors are using the 2016 version of the ISOGG tree - as long as you follow that, there's no conflict - SSJ-A2 is I1a1b3 which is I-Z74, HSJ-A1 is I1a1b3b which is I-L813, SBT-A1 is I1a2a1a2 which is I-F2642. All fine. Problem comes when Carlos Quiles takes the longhand data of these samples and then looks at a later version of the ISOGG tree and incorrectly interprets SSJ-A2 and HSJ-A1 as I-A8182 and SBT-A1 as I-S26062. It's another arguement for moving on from this obsolete nomenclature to avoid the confusion.

I haven't done full analysis of urm035 and urm 045 yet, but the assignments are matching up with the BAM files - urm035 has derived calls for DF29 and Z2892/CTS9848 but an ancestral call for Z2893 among the I-DF29 branch. Also one read ancestral for Z59 and Z140 so far. urm045 has derived calls for Z2893 and Z2892/CTS9848 among the I-DF29 branch and derived for S439/Z61. All these are one read SNPs so not solid yet and I'll dig a bit deeper and see if there's a bit more evidence. Probably not reported in paper as any indentifying Y-SNPs were below threshold for reporting or they weren't looking in the right places. They did get 84005 as I1a1b3/I-Z74 in the paper though.

Yeah, I havent found AE 1154 either - in the paper or at ENA (where the other three I1 from that paper are). It could be a mis-transcription of AED249 that we already know about.

deadly77
05-20-2019, 08:32 AM
Thanks for sharing that link, I'll give it a listen, any discussion mentioning I1, even if briefly, is probably important. I don't see very much discussion of I1 on most of the big blogs such as Eurogenes or Quiles Indo-European blog.



Don't tell anyone at Eurogenes about this collaboration! I know there is some rivalry between the two camps in terms of what ancient people brought R1a or R1b and spoke this or that language :lol:

I hope that Mr. Provyn is willing to go through with corrections of the aDNA samples that you've examined. It is certainly a bit strange that these papers used old forms of ISOGG when most of us have moved on and refer to haplogroups with the main root and terminal SNP method.




I'm not familiar with URM035 and URM045, however if there were errors and broad haplogroup designations in the paper such as "BCDEF" that seems a bit suspect and warrants deeper investigation, interesting that it is designated I-Z60/Z61 in the spreadsheet. That could be very interesting if confirmed. I think most ancient I1 we'll find will be Migration Period and within the Medieval period (and of course the higher middle ages up to colonial eras). Obvious places to look are already being looked at as of late.

I suspect that AE 1154 may be a error, I've not seen that sample anywhere in that paper and I've scoured it a few times. However perhaps it is referencing something else that may flown under the radar that was picked up recently. Perhaps time will tell.

I've found the Insitome podcast really interesting as a series - they also cover a lot of different areas in other blog posts. Really worth listening to.

Yes, Hunter says thanks and he will update the spreadsheet with corrections. I've discussed a few things with him before and I think he's keen to have accuracy. He's put a short video on YouTube discussing the collaboration on these ancient samples with Carlos Quiles and Vadim Urasin from YFull here https://www.youtube.com/watch?v=zjQa4VI43fA&feature=youtu.be&fbclid=IwAR131HPF6SAVvKEGNYlniplnGmFr7vGewQJMUjfJL YGfUNCMshz5F5PNTeU his main goal appears to be getting the data into a format that's compatible with his Phylogeographer tool.

I think the longhand nomenclature for persists due to familiarity of those who have likely used that nomenclature for years. As a relative latecomer, I often have to look those up and translate the alphabet soup. I much prefer I-L338 rather than I1a2a1a1a1a1 (as defined by 2019 ISOGG tree). The longhand nomenclature also changes from year to year on the ISOGG tree, which is where I think Carlos Quiles is making mistakes in I1 subclades in his spreadsheet regarding the ancient Iceland genomes. The supplementary information in that Science 2018 paper defines that the authors are using the 2016 version of the ISOGG tree - as long as you follow that, there's no conflict - SSJ-A2 is I1a1b3 which is I-Z74, HSJ-A1 is I1a1b3b which is I-L813, SBT-A1 is I1a2a1a2 which is I-F2642. All fine. Problem comes when Carlos Quiles takes the longhand data of these samples and then looks at a later version of the ISOGG tree and incorrectly interprets SSJ-A2 and HSJ-A1 as I-A8182 and SBT-A1 as I-S26062. It's another arguement for moving on from this obsolete nomenclature to avoid the confusion.

I haven't done full analysis of urm035 and urm 045 yet, but the assignments are matching up with the BAM files - urm035 has derived calls for DF29 and Z2892/CTS9848 but an ancestral call for Z2893 among the I-DF29 branch. Also one read ancestral for Z59 and Z140 so far. urm045 has derived calls for Z2893 and Z2892/CTS9848 among the I-DF29 branch and derived for S439/Z61. All these are one read SNPs so not solid yet and I'll dig a bit deeper and see if there's a bit more evidence. Probably not reported in paper as any indentifying Y-SNPs were below threshold for reporting or they weren't looking in the right places. They did get 84005 as I1a1b3/I-Z74 in the paper though.

Yeah, I havent found AE 1154 either - in the paper or at ENA (where the other three I1 from that paper are). It could be a mis-transcription of AED249 that we already know about.

oz
05-20-2019, 09:04 AM
I'm a little confused with the "hitched a ride" from the invaders, a ride to where exactly? Europe? Scandinavia? How does that make any sense if I1 is most likely native to Northern Europe? Hitched a ride to the steppe women? Disneyland? I don't understand what those words are supposed to convey, it needs to be clarified.
What seems fairly evident so far is that I1 probably started to spread throughout Europe from Northern Europe only about 2000 years ago with ancient Germanic peoples and at that point BB and Corded Ware were already ancient history.

JonikW
05-20-2019, 09:47 AM
Thanks again for your wonderful work deadly77. I see now this comment from David in his Nordic thread:

"The high frequencies of U106 and I1 in Scandinavia are best explained by extreme local founder effects during the Bronze Age.

Not migrations of U106 and I1 rich populations into Scandinavia from, say, the Carpathian Basin.

It's unlikely that anyone will find the relevant, ancestral I1 in the ancient DNA before the founder effect. That is, dating to the TRB, Battle Axe or BB periods."

deadly77
05-20-2019, 10:22 AM
I had been hoping some comments about I1 would appear in that thread. A commenter under the name "Angantyr" claims that Nordic_LN II RISE179 is I1. That sample is on deadly's ancient I1 map as a pre-I1. Which I believe is appropriate as it is a low coverage sample and it was no call for ">99%" of the defining I1 SNPs.

I think we can't be too lenient (but can't be too strict either) on what we define as I1. We already know I1 has a young TMRCA so true I1 will be in that timeframe.

EDIT: keep your eye on this Eurogenes post, the comments are getting quite interesting!

That's exactly why I've gone for pre-I1 rather than I1. RISE179 has derived calls for only two of the 312 SNPs that define the I1 haplogroup. Put it another way, I's say that I'd assign 2/312=0.64% confidence that RISE179 was an individual that had derived mutations for all of the I1 SNPs. Some of those no calls could be ancestral, or they could all be derived to make RISE179. I just think there's too much uncertainty to say I1 for sure. And both of the derived calls are one read SNPs which can be false positive. SVK-A1 from the ancient Iceland paper has a one-read derived call for Z131+, but that doesn't make SVK-A1 part of I-Z131 branch, especially when further digging shows a lot more cooroborating evidence that he's actually I-FGC21682.

I feel that RISE179 shouldn't be ignored and is of interest (which is why that sample is on the map), but given the low quality and coverage in the BAM file I wouldn't consider is as exhibit A or a star piece of evidence to make any points regarding I1 haplogroup.

You also make a good point about not being too lenient or too strict on what defines I1. Definitelty agree that we shouldn't ring fence ourselves too heavily on what we don't know, and revise criteria as definition as we go on. As an example, check out the ISOGG Y tree for haplogroup I in 2009 which is only 10 years ago - so much unknown compared to today: https://isogg.org/tree/2009/ISOGG_HapgrpI09.html

deadly77
05-20-2019, 11:51 AM
I wonder whether deadly77 and other well versed experts on ancient I1 see any implications for us here. Very interesting.

Edit: it kind of goes with what I posted earlier today on Scandinavia but I don't know what to make of any of it. I'm sure someone sees the bigger picture. I guess a small population of I1 got involved early on with the invaders, got lucky and expanded quite rapidly.

http://eurogenes.blogspot.com/2019/05/who-were-people-of-nordic-bronze-age.html?m=1

Cheers, but I'd say that what I bring to the table is understanding how to read the raw data and fit that into a Y-DNA phylogenetic tree. I'd say I'm much less well read on the populations, tribal groups and migrations of those time periods. I feel that a lot of you guys have a better handle on some of those aspects than I do. Most of my interest in history before getting interested in DNA is from later time periods, but have found a lot of this rather fascinating and learning a lot as I go along and keen to learn more.

I haven't got too involved in the population genetics discussions using primarily autosomal DNA as my learning curve and familiarity with autosomal DNA hasn't got to the same point as where I am with Y-DNA. I read some of the discussions and I think I understand the outputs and graphs, although I'm not as clear on how the data is put together and how things work "under the hood" in the same way that I approach Y-DNA. More to learn, but I feel that there's a lot of hand-waving and bias in some of those discussions - and I mean generally rather than specifically referring to the linked post - and that is also the case for some of the Y-DNA discussions as well. Probably my background as a scientist (although not in genetics or biology) that makes me a bit wary of taking too much at face value.

deadly77
05-20-2019, 12:10 PM
Thanks again for your wonderful work deadly77. I see now this comment from David in his Nordic thread:

"The high frequencies of U106 and I1 in Scandinavia are best explained by extreme local founder effects during the Bronze Age.

Not migrations of U106 and I1 rich populations into Scandinavia from, say, the Carpathian Basin.

It's unlikely that anyone will find the relevant, ancestral I1 in the ancient DNA before the founder effect. That is, dating to the TRB, Battle Axe or BB periods."

Yeah, I'd agree with that. Not impossible, but I agree it would be unlikely - but sometimes you can find needles in haystacks. But not always.

Also agree with the founder effect point. This paper by Batini et al in Nature Communications 2015 compares this (article is open access) https://www.nature.com/articles/ncomms8152 using SNP data and we can see it in the STR convergence of our match lists - or as Robin Spencer more appropriately calls it a lack of STR divergence from a recent founder on his Tracking Back Website: http://scaledinnovation.com/gg/gg.html?rr=convergence

spruithean
05-20-2019, 12:24 PM
I've found the Insitome podcast really interesting as a series - they also cover a lot of different areas in other blog posts. Really worth listening to.

Yes, Hunter says thanks and he will update the spreadsheet with corrections. I've discussed a few things with him before and I think he's keen to have accuracy. He's put a short video on YouTube discussing the collaboration on these ancient samples with Carlos Quiles and Vadim Urasin from YFull here https://www.youtube.com/watch?v=zjQa4VI43fA&feature=youtu.be&fbclid=IwAR131HPF6SAVvKEGNYlniplnGmFr7vGewQJMUjfJL YGfUNCMshz5F5PNTeU his main goal appears to be getting the data into a format that's compatible with his Phylogeographer tool.

I think the longhand nomenclature for persists due to familiarity of those who have likely used that nomenclature for years. As a relative latecomer, I often have to look those up and translate the alphabet soup. I much prefer I-L338 rather than I1a2a1a1a1a1 (as defined by 2019 ISOGG tree). The longhand nomenclature also changes from year to year on the ISOGG tree, which is where I think Carlos Quiles is making mistakes in I1 subclades in his spreadsheet regarding the ancient Iceland genomes. The supplementary information in that Science 2018 paper defines that the authors are using the 2016 version of the ISOGG tree - as long as you follow that, there's no conflict - SSJ-A2 is I1a1b3 which is I-Z74, HSJ-A1 is I1a1b3b which is I-L813, SBT-A1 is I1a2a1a2 which is I-F2642. All fine. Problem comes when Carlos Quiles takes the longhand data of these samples and then looks at a later version of the ISOGG tree and incorrectly interprets SSJ-A2 and HSJ-A1 as I-A8182 and SBT-A1 as I-S26062. It's another arguement for moving on from this obsolete nomenclature to avoid the confusion.

I haven't done full analysis of urm035 and urm 045 yet, but the assignments are matching up with the BAM files - urm035 has derived calls for DF29 and Z2892/CTS9848 but an ancestral call for Z2893 among the I-DF29 branch. Also one read ancestral for Z59 and Z140 so far. urm045 has derived calls for Z2893 and Z2892/CTS9848 among the I-DF29 branch and derived for S439/Z61. All these are one read SNPs so not solid yet and I'll dig a bit deeper and see if there's a bit more evidence. Probably not reported in paper as any indentifying Y-SNPs were below threshold for reporting or they weren't looking in the right places. They did get 84005 as I1a1b3/I-Z74 in the paper though.

Yeah, I havent found AE 1154 either - in the paper or at ENA (where the other three I1 from that paper are). It could be a mis-transcription of AED249 that we already know about.

That's pretty frustrating that Mr. Quiles would do it that way but I suppose he's not alone, and it's pretty disappointing that the teams working on these ancient DNA works would be so neglectful of the fact that the ISOGG nomenclature and alphabet soup change every year, the only thing that doesn't change is the shorthand nomenclature. I-L338 is always I-L338, this way confusion is very low. I can't even look at older mentions (or newer mentions) of R1b and R1a clades if they don't have their terminal SNP mentioned. The size of some of those alphabet soups for R1 clades is ridiculous :lol:

Keep us posted on those urm guys, they could get really interesting and even a tentative placement as simply I-DF29 for both is a hell of lot better than "ND" and "BCDEF". I was reading (yet again) the Sigtuna paper yesterday, quite an interesting read in terms of where some of these people likely came from in relation to Sigtuna.

Thanks again for all the work you do on these BAM files, it's definitely not something I'm able to do, or probably capable of :lol:

So Hunter refers to YFulls data? I had wondered as there is another phylogeography tracker that seems based off of FTDNA's data, which the creator of that site has begun posting here. http://scaledinnovation.com/gg/snpTracker.html , For my SNP, Hunter's tracker and the above tracker are a fair bit different in terms of dating and I suppose naming. YFull still has A14097 lumped in with A14094 (my fault really as I've been tardy with anything related to sending off data to them), while the other has A14097 above A14094/M4050. Not too big of a deal though.

I had suspected that AE sample to be a typo. Seemed to similar in the beginning to AED.


I'm a little confused with the "hitched a ride" from the invaders, a ride to where exactly? Europe? Scandinavia? How does that make any sense if I1 is most likely native to Northern Europe? Hitched a ride to the steppe women? Disneyland? I don't understand what those words are supposed to convey, it needs to be clarified.
What seems fairly evident so far is that I1 probably started to spread throughout Europe from Northern Europe only about 2000 years ago with ancient Germanic peoples and at that point BB and Corded Ware were already ancient history.

I think Razib Khan was simply saying that I1 carriers hitched a ride with these R1b rich groups wherever it may have been and "prospered" off the fortune of these R1b clans. This could have happened anywhere, and given the proliferation of I1 probably occured in the Bronze Age it could have happened in Northern Europe? I didn't quite get the impression that he was implying (totally) I1 literally hitched a migratory ride somewhere with the R1b folks, more that it was just benefit by association. Perhaps a bit parasitic...

I wish we had more definitive answers, I1 is a missing link in a lot of the ancient DNA...


Thanks again for your wonderful work deadly77. I see now this comment from David in his Nordic thread:

"The high frequencies of U106 and I1 in Scandinavia are best explained by extreme local founder effects during the Bronze Age.

Not migrations of U106 and I1 rich populations into Scandinavia from, say, the Carpathian Basin.

It's unlikely that anyone will find the relevant, ancestral I1 in the ancient DNA before the founder effect. That is, dating to the TRB, Battle Axe or BB periods."

Exactly this, which sort of fits with the definition, (stay with me here my brain is not cooperating today), I1's TMRCA is sometime in the Bronze Age if the YFull and other TMRCA estimates are correct, that places it sometime in 27th-25th century BC if not earlier or later (some context, the Instructions of Shuruppak were likely written sometime in the space of 2600 to 2500 BCE). So I1 came out of hiding at some point around this time, yet we've found potential I1 samples pre-dating this by a long time as BAB5 is dated to around 5600-4900 BCE, and BAL051 is dated even earlier than that. However their SNP calls are rather underwhelming for being definitive for being I1-M253. This is why deadly and several others have begun to label these samples as pre-I1 (including the Nordic LN and BA guys), but we already know that I1's split from I2 is likely quite some time before I1 really started expanding, so it's not necessarily a surprise that we find pre-I1 or quasi-I1 lineages in strange places.


That's exactly why I've gone for pre-I1 rather than I1. RISE179 has derived calls for only two of the 312 SNPs that define the I1 haplogroup. Put it another way, I's say that I'd assign 2/312=0.64% confidence that RISE179 was an individual that had derived mutations for all of the I1 SNPs. Some of those no calls could be ancestral, or they could all be derived to make RISE179. I just think there's too much uncertainty to say I1 for sure. And both of the derived calls are one read SNPs which can be false positive. SVK-A1 from the ancient Iceland paper has a one-read derived call for Z131+, but that doesn't make SVK-A1 part of I-Z131 branch, especially when further digging shows a lot more cooroborating evidence that he's actually I-FGC21682.

I feel that RISE179 shouldn't be ignored and is of interest (which is why that sample is on the map), but given the low quality and coverage in the BAM file I wouldn't consider is as exhibit A or a star piece of evidence to make any points regarding I1 haplogroup.

You also make a good point about not being too lenient or too strict on what defines I1. Definitelty agree that we shouldn't ring fence ourselves too heavily on what we don't know, and revise criteria as definition as we go on. As an example, check out the ISOGG Y tree for haplogroup I in 2009 which is only 10 years ago - so much unknown compared to today: https://isogg.org/tree/2009/ISOGG_HapgrpI09.html

I definitely agree that we should stick with caution with how these old samples are labeled indeed. I'm definitely not saying we should ignore the pre-I1 samples, those are likely important, even if they might be extinct lineages, they at least give us a picture of how dispersed I1 related lineages could have been. We know YFull still estimates the formation of I1 to be 27,500 years ago in regards to when it split from I2.

Ah, the old ISOGG 2009 tree, I think that was when FTDNA had finally determined that my bunch weren't just I-M170 and that we were in the I-M253 haplogroup.

spruithean
05-20-2019, 05:53 PM
Cheers, but I'd say that what I bring to the table is understanding how to read the raw data and fit that into a Y-DNA phylogenetic tree. I'd say I'm much less well read on the populations, tribal groups and migrations of those time periods. I feel that a lot of you guys have a better handle on some of those aspects than I do. Most of my interest in history before getting interested in DNA is from later time periods, but have found a lot of this rather fascinating and learning a lot as I go along and keen to learn more.

I haven't got too involved in the population genetics discussions using primarily autosomal DNA as my learning curve and familiarity with autosomal DNA hasn't got to the same point as where I am with Y-DNA. I read some of the discussions and I think I understand the outputs and graphs, although I'm not as clear on how the data is put together and how things work "under the hood" in the same way that I approach Y-DNA. More to learn, but I feel that there's a lot of hand-waving and bias in some of those discussions - and I mean generally rather than specifically referring to the linked post - and that is also the case for some of the Y-DNA discussions as well. Probably my background as a scientist (although not in genetics or biology) that makes me a bit wary of taking too much at face value.

I'd say the Bronze Age or so is a bit early to be thinking of specific Germanic tribes, as they are relatively late compared to the Gallic tribes, Thracians, Illyrians, and Scytho-Sarmatian groups we hear about earlier in records.

I'm with you on the autosomal DNA, while it is fascinating and it can be entertaining to see where one plots in the grand scheme of things or where "fit" in relation to various ancient populations it can seem like some people have a bit of bias towards what they want their generated results to "say". I'm also not sure I'm skilled enough to design ways to calculate my own potential best fits with these new calculators like G25 or nMonte.

Though I do find the autosomal calculations quite interesting in relation to ancient populations like Goths, Gepids, Scythians, Celts, Bronze Age peoples, etc.


Yeah, I'd agree with that. Not impossible, but I agree it would be unlikely - but sometimes you can find needles in haystacks. But not always.

Also agree with the founder effect point. This paper by Batini et al in Nature Communications 2015 compares this (article is open access) https://www.nature.com/articles/ncomms8152 using SNP data and we can see it in the STR convergence of our match lists - or as Robin Spencer more appropriately calls it a lack of STR divergence from a recent founder on his Tracking Back Website: http://scaledinnovation.com/gg/gg.html?rr=convergence

Thanks for linking that study, I had seen some of the images of it, but I guess it slipped my mind to actually go looking for it :lol:, I've seen my own cases of convergence in my end of the F2642 tree. A few years ago I had a match to some Danish families with a similar surname to my own and in all honesty the surnames were essentially identical, just in different languages and I initially wondered if it was a legitimate match, however Big Y has shown that they are on a totally separate branch of F2642 (and they are more closely related to SBT-A1 than me). This is also seen closer to my part of the F2642 tree, especially between JMcB and myself. My family's haplotype is a reasonable match to several of JMcB's group however Big Y again showed that we are basically on sibling branches of the F2642 tree. I think if it wasn't for NGS I'd probably still be pursuing false leads.

spruithean
05-23-2019, 05:55 PM
Just to share some Polish ancient I1...

This was originally posted by Tomenable on another forum


All of these samples are from 7 locations:

Late Iron Age (dates) samples:

KO = Kowalewko (100-300 AD)
MZ = Maslomecz (200-400 AD)

Early Medieval (dates) samples:

NA = Niemcza (900-1000 AD)
SI = Sowinki (1000-1100 AD)
LO = Legowo (1000-1200 AD)
GO = Gniezno (1000-1200 AD)
ME = Markowice (1000-1200 AD)



I'm not sure which samples are I1, but two, KO_55 and ME_7 are certainly I1:

KO_55, Kowalewko (100-300 AD), I1a3a1a1-Y6626
KO_45, Kowalewko (100-300 AD), I2a2a1b2a-L801
KO_22, Kowalewko (100-300 AD), G2a2b-L30
KO_57, Kowalewko (100-300 AD), G2a2b-L30

ME_7, Markowice (1000-1200 AD), I1a2a2a5-Y5384
NA_13, Niemcza, (900-1000 AD), I2a1b2-L621
NA_18, Niemcza, (900-1000 AD), J2a1a-L26

Other confirmed males (but no Y-DNA assignment) include:

Ancient group (3): KO_18, KO_36, KO_8
Medieval (7): NA_29, NA_2, NA_3, ME_4, LO_5, SI_10, SI_11

In total there must be 9 samples of I1, because ME_7 is not included here:

https://www.academia.edu/33791135/20..._DNA_libraries

Only samples from Kowalewko, Maslomecz, Legowo and Niemcza are here.

So I1a2a2a5-Y5384 from Early Medieval Markowice is our 9th sample of I1

Credit goes to Tomenable.

Perhaps some of these could go to the ancient I1 map at some point, perhaps if they are fully vetted, or tentatively added for now? I should add that the Kowalewko samples have been attributed to the Wielbark culture (AFAIK) which is where the early Goths, Gepids and Rugii were believed to have originated before migrating onward to the Chernyakhov cultural sphere.

JonikW
05-23-2019, 07:54 PM
Just to share some Polish ancient I1...

This was originally posted by Tomenable on another forum



Credit goes to Tomenable.

Perhaps some of these could go to the ancient I1 map at some point, perhaps if they are fully vetted, or tentatively added for now? I should add that the Kowalewko samples have been attributed to the Wielbark culture (AFAIK) which is where the early Goths, Gepids and Rugii were believed to have originated before migrating onward to the Chernyakhov cultural sphere.

So the Wielbark one is L338 unless I'm missing something. I hope we can reach a little further downstream on that. Interesting.

spruithean
05-23-2019, 08:00 PM
Y6626 is part of L1237, which is downstream of Z63, which is normally dubbed the "Eastern Germanic" branch. Not L338 it seems.

https://www.yfull.com/tree/I-L1237/, one of Collegno Longobards is I-Y2245, which is just upstream of L1237.

JonikW
05-23-2019, 08:12 PM
Y6626 is part of L1237, which is downstream of Z63, which is normally dubbed the "Eastern Germanic" branch. Not L338 it seems.

https://www.yfull.com/tree/I-L1237/, one of Collegno Longobards is I-Y2245, which is just upstream of L1237.

Thanks spruithean, knew I could rely on you. :)

deadly77
05-23-2019, 11:26 PM
Just to share some Polish ancient I1...

This was originally posted by Tomenable on another forum



Credit goes to Tomenable.

Perhaps some of these could go to the ancient I1 map at some point, perhaps if they are fully vetted, or tentatively added for now? I should add that the Kowalewko samples have been attributed to the Wielbark culture (AFAIK) which is where the early Goths, Gepids and Rugii were believed to have originated before migrating onward to the Chernyakhov cultural sphere.

Yes, these two have been on radar for a while - they've been on this forum since post #3. They keep getting brought up every so often but I've yet to find any real data on these samples.

I mentioned the issues that I have had trying to get reliable data to analyze or any more information aside from a poster on academia earlier on on this thread here https://anthrogenica.com/showthread.php?13783-Ancient-I-M253-samples-list&p=537149&viewfull=1#post537149 and https://anthrogenica.com/showthread.php?13783-Ancient-I-M253-samples-list&p=559825&viewfull=1#post559825

Unless something changes in terms of available data that I'm able to analyze or more information, there's nothing I can do to verify the SNP calls in those samples (or any of the other unnamed I1). So far, no paper published or update to data at ENA that I'm aware of.

I have tried take BAM files of other samples from this thread that I can run succesfully with IGV and run those through Felix Immanuel's BAM analysis kit, which seemed to be how folks were analyzing these samples in another thread on AG (after converting from FASTQ using one of Felix's other tools). Felix's BAM analysis kit hasn't been updated in a long time (2015?) and seems to really struggle with samples that have a lot of gaps in coverage. I often get very different results to when I do a manual review of the BAM. The Felix BAM analysis kit misses out a lot of SNPs and reports some that aren't there when looking at the BAM file via IGV. I don't really trust this tool for ancient sample analysis.

I'm going to hold off adding these to my map until the authors publish a paper that has more detail than a poster abstract or I can find a BAM file that can be read and verified in IGV. I'm happy to do the analysis, but from my perspective, there is nothing currently that can be reliably analyzed. If you're able to find anything, let me know.

spruithean
05-23-2019, 11:39 PM
Understandable, and this has been my concern as well in regard to which samples can be mapped. I'm surprised that we still haven't heard much about these Polish results since the small bits of info were first released, it's disappointing, but I bet eventually something will finally be released.

deadly77
05-24-2019, 08:28 AM
Understandable, and this has been my concern as well in regard to which samples can be mapped. I'm surprised that we still haven't heard much about these Polish results since the small bits of info were first released, it's disappointing, but I bet eventually something will finally be released.

Yeah, I tried looking in the "Early Medieval aDNA from Poland Coming Soon" thread on Anthrogenica but over 244 pages comprising 2443 posts, it's difficult to find any reference to actual data buried amongst the conjecture and bickering. Perhaps you could try asking Tomenable in the other forum .

deadly77
05-24-2019, 09:04 AM
Yeah, I tried looking in the "Early Medieval aDNA from Poland Coming Soon" thread on Anthrogenica but over 244 pages comprising 2443 posts, it's difficult to find any reference to actual data buried amongst the conjecture and bickering. Perhaps you could try asking Tomenable in the other forum .

And the haplogroup and subclade assignments for these two samples may very well be correct. But after seeing so many misassignments in publications and secondary analysis of I1 samples - for example: SVK-A1 listed as I1b in the Ebenesersdóttir et al. paper; CL63 listed as I1-Z79 in the Amorim et al paper and numerous holes in the supplementary information regarding calls on that sample and SZ45; Carlos Quiles misassigning HSJ-A1 and SSJ-A2 to I-A8182, SBT-A1 to I-S26062 and repeating the incorrect assignment in the paper of SVK-A1 as I1b, etc.; it's important to check against the raw data for I1 ancient DNA (and indeed all haplogroups).

deadly77
05-24-2019, 09:46 AM
That's pretty frustrating that Mr. Quiles would do it that way but I suppose he's not alone, and it's pretty disappointing that the teams working on these ancient DNA works would be so neglectful of the fact that the ISOGG nomenclature and alphabet soup change every year, the only thing that doesn't change is the shorthand nomenclature. I-L338 is always I-L338, this way confusion is very low. I can't even look at older mentions (or newer mentions) of R1b and R1a clades if they don't have their terminal SNP mentioned. The size of some of those alphabet soups for R1 clades is ridiculous :lol:

Keep us posted on those urm guys, they could get really interesting and even a tentative placement as simply I-DF29 for both is a hell of lot better than "ND" and "BCDEF". I was reading (yet again) the Sigtuna paper yesterday, quite an interesting read in terms of where some of these people likely came from in relation to Sigtuna.

Thanks again for all the work you do on these BAM files, it's definitely not something I'm able to do, or probably capable of :lol:

So Hunter refers to YFulls data? I had wondered as there is another phylogeography tracker that seems based off of FTDNA's data, which the creator of that site has begun posting here. http://scaledinnovation.com/gg/snpTracker.html , For my SNP, Hunter's tracker and the above tracker are a fair bit different in terms of dating and I suppose naming. YFull still has A14097 lumped in with A14094 (my fault really as I've been tardy with anything related to sending off data to them), while the other has A14097 above A14094/M4050. Not too big of a deal though.

I had suspected that AE sample to be a typo. Seemed to similar in the beginning to AED.



I think Razib Khan was simply saying that I1 carriers hitched a ride with these R1b rich groups wherever it may have been and "prospered" off the fortune of these R1b clans. This could have happened anywhere, and given the proliferation of I1 probably occured in the Bronze Age it could have happened in Northern Europe? I didn't quite get the impression that he was implying (totally) I1 literally hitched a migratory ride somewhere with the R1b folks, more that it was just benefit by association. Perhaps a bit parasitic...

I wish we had more definitive answers, I1 is a missing link in a lot of the ancient DNA...



Exactly this, which sort of fits with the definition, (stay with me here my brain is not cooperating today), I1's TMRCA is sometime in the Bronze Age if the YFull and other TMRCA estimates are correct, that places it sometime in 27th-25th century BC if not earlier or later (some context, the Instructions of Shuruppak were likely written sometime in the space of 2600 to 2500 BCE). So I1 came out of hiding at some point around this time, yet we've found potential I1 samples pre-dating this by a long time as BAB5 is dated to around 5600-4900 BCE, and BAL051 is dated even earlier than that. However their SNP calls are rather underwhelming for being definitive for being I1-M253. This is why deadly and several others have begun to label these samples as pre-I1 (including the Nordic LN and BA guys), but we already know that I1's split from I2 is likely quite some time before I1 really started expanding, so it's not necessarily a surprise that we find pre-I1 or quasi-I1 lineages in strange places.



I definitely agree that we should stick with caution with how these old samples are labeled indeed. I'm definitely not saying we should ignore the pre-I1 samples, those are likely important, even if they might be extinct lineages, they at least give us a picture of how dispersed I1 related lineages could have been. We know YFull still estimates the formation of I1 to be 27,500 years ago in regards to when it split from I2.

Ah, the old ISOGG 2009 tree, I think that was when FTDNA had finally determined that my bunch weren't just I-M170 and that we were in the I-M253 haplogroup.

Yep, it's frustrating. But as I've said several times before, in most cases Y-DNA analysis isn't the focus of the manuscript - usually just an entry in a table and a couple of sentences in most. I think perhaps the rapid expansion of phylogenetic trees since the introduction of NGS means a lot of folks aren't sure where to look for a reference and fall back to a default which may no longer be applicable.

I'll get through the two Sigtuna samples - just not sure when. These two samples have a lot of no calls so far. I'll try and find as much corroborating information from the BAM files.

You may be surprised if you get round to checking out any BAM files - it's actually a lot easier than I initially expected. The way I'm viewing them is time consuming rather than difficult, but it gives me the best chance of making the right calls.

Hunter Provyn developed Phylogeographer first and yes it's based on the YFull tree rather than the FTDNA tree. I believe that the decision was most likely driven by the fact that at the time of development, the YFull tree was public and access to subclades, age estimates and geographical data was easier for Hunter's data mining programs, while at the time FTDNA's Y-DNA was not public. Since then, Robin Spencer launched SNP Tracker which uses the public FTDNA haplotree as data source for SNPs and subclades, while using the YFull age estimate for the corresponding subclade. There's advantages and disadvantages to both - FTDNA has the larger number of samples but only from it's own customers and also includes folks who have done single SNP tests and SNP packs which may not lead to the terminal SNP on that tree. All of YFull's samples are NGS and so go as far as the terminal can be determined, as well as including other non-FTDNA vendors and academic samples. Both Hunter and Robin are doing good work which is worth checking out.

Agree with the other points.

spruithean
05-24-2019, 01:31 PM
Yeah, I tried looking in the "Early Medieval aDNA from Poland Coming Soon" thread on Anthrogenica but over 244 pages comprising 2443 posts, it's difficult to find any reference to actual data buried amongst the conjecture and bickering. Perhaps you could try asking Tomenable in the other forum .

:lol: combine that with Anthrogenica's wait time between searches and you'll be hours looking for the right post!


And the haplogroup and subclade assignments for these two samples may very well be correct. But after seeing so many misassignments in publications and secondary analysis of I1 samples - for example: SVK-A1 listed as I1b in the Ebenesersdóttir et al. paper; CL63 listed as I1-Z79 in the Amorim et al paper and numerous holes in the supplementary information regarding calls on that sample and SZ45; Carlos Quiles misassigning HSJ-A1 and SSJ-A2 to I-A8182, SBT-A1 to I-S26062 and repeating the incorrect assignment in the paper of SVK-A1 as I1b, etc.; it's important to check against the raw data for I1 ancient DNA (and indeed all haplogroups).

I mean we're only as good as the data provided by the documents, unless things are double checked. However these corrections should be made at some point so as not to cause confusion down the road.


Yep, it's frustrating. But as I've said several times before, in most cases Y-DNA analysis isn't the focus of the manuscript - usually just an entry in a table and a couple of sentences in most. I think perhaps the rapid expansion of phylogenetic trees since the introduction of NGS means a lot of folks aren't sure where to look for a reference and fall back to a default which may no longer be applicable.

I'll get through the two Sigtuna samples - just not sure when. These two samples have a lot of no calls so far. I'll try and find as much corroborating information from the BAM files.

You may be surprised if you get round to checking out any BAM files - it's actually a lot easier than I initially expected. The way I'm viewing them is time consuming rather than difficult, but it gives me the best chance of making the right calls.

Hunter Provyn developed Phylogeographer first and yes it's based on the YFull tree rather than the FTDNA tree. I believe that the decision was most likely driven by the fact that at the time of development, the YFull tree was public and access to subclades, age estimates and geographical data was easier for Hunter's data mining programs, while at the time FTDNA's Y-DNA was not public. Since then, Robin Spencer launched SNP Tracker which uses the public FTDNA haplotree as data source for SNPs and subclades, while using the YFull age estimate for the corresponding subclade. There's advantages and disadvantages to both - FTDNA has the larger number of samples but only from it's own customers and also includes folks who have done single SNP tests and SNP packs which may not lead to the terminal SNP on that tree. All of YFull's samples are NGS and so go as far as the terminal can be determined, as well as including other non-FTDNA vendors and academic samples. Both Hunter and Robin are doing good work which is worth checking out.

Agree with the other points.

Not only are phylogenetic trees cumbersome now, ISOGG's formatting now has become immensely unruly. YFull certainly has the leg-up on the competition here with the sheer simplicity and the use of the HG-SNP nomenclature. I like the combination of using both websites, they compliment each other I feel, and as time goes on they will improve further with the growth of databases.

deadly77
05-26-2019, 08:17 AM
Not only are phylogenetic trees cumbersome now, ISOGG's formatting now has become immensely unruly. YFull certainly has the leg-up on the competition here with the sheer simplicity and the use of the HG-SNP nomenclature. I like the combination of using both websites, they compliment each other I feel, and as time goes on they will improve further with the growth of databases.[/QUOTE]

Yes, that is especially annoying. I don't actually use ISOGG's tree very much any more, and to be honest that is probably more of a reason than they aren't as up to date as YFull or FTDNA. I often load up the page, go and do something else and come back to it several minutes later. And even then I often give up. I find that FTDNA's website and interface is also very clunky and slow which is frustrating, especially trying to navigate the results pages of larger projects - moving to another page of the main I1 project often times out with the "Houston, we have a problem..." error. YFull sometimes slow with loading different branches of the YFull tree although definitely not as slow as FTDNA or ISOGG. Inside the homepage of an account, YFull pretty fast on most things - slowest seems to be while looking up SNPs, positions, STRs in the Groups view.

Rebekah Canada commented on the performance of the YFull website on her Haplogroup blog here: https://haplogroup.org/yfull-launches-new-mtdna-tree/ - she notes that the YFull website scores fairly poorly using Google's Lighthouse tool, but she also notes that despite this, on most computers it loads within a few seconds and also lists the pingdom results.

I wasn't familiar with Google Lighthouse test, but she discusses it here: https://haplogroup.org/genetic-genealogy-the-lighthouse/ - also serves as a good list of genetic genealogy blogs.

spruithean
05-27-2019, 01:55 PM
Never heard of Google Lighthouse. I'll take a look, also thanks for sharing a link to that blog, always interesting to read genetics oriented blogs and websites.

Good to know I'm not the only one struggling to get the I1 DNA Project to load, at least the subclade projects load relatively quickly right now. Hopefully those don't start being problematic.

janan
05-27-2019, 10:15 PM
Thanks again for your wonderful work deadly77. I see now this comment from David in his Nordic thread:

"The high frequencies of U106 and I1 in Scandinavia are best explained by extreme local founder effects during the Bronze Age.

Not migrations of U106 and I1 rich populations into Scandinavia from, say, the Carpathian Basin.

It's unlikely that anyone will find the relevant, ancestral I1 in the ancient DNA before the founder effect. That is, dating to the TRB, Battle Axe or BB periods."

I'm intrigued by this extreme founder effect that would have expanded I1 in Scandinavia. What do you think caused it? Plague, invasion, the emergence of a dominant social class? When should anything such have happened and how is it supported by genetic and archeological evidence? I have tried to formulate some ideas but find myself more confused the more I think about it.

spruithean
05-28-2019, 01:38 AM
I'm intrigued by this extreme founder effect that would have expanded I1 in Scandinavia. What do you think caused it? Plague, invasion, the emergence of a dominant social class? When should anything such have happened and how is it supported by genetic and archeological evidence? I have tried to formulate some ideas but find myself more confused the more I think about it.

I've wondered this too and I suspect it could be an environmental thing that kept I-M253 bottlenecked until it finally expanded, obviously plague or conflict could also be the cause if not happening in tandem with an environmental scenario. Scandinavia didn't exactly lend itself to agriculture and other means at that time. Mr. Khan and a few others think maybe I-M253 hitched a ride with R-U106 and benefitted by association. I don't take this to mean they literally migrated with them, I interpret it to mean that whatever advances came with the cultures that were high in U106 (and the "Germanic" branches of R1a) directly benefitted the populations with I-M253 lineages. Obviously one of M253's descendants was successful since the majority of I1 descendants are I-DF29 subclades. There was definitely a preoccupation with boats leading up to the pre-Roman Iron Age, which obviously remained a focal point for the coastal populations along the North Sea and the Baltic. So the sea was definitely an important resource in this time considering farming would have been more difficult than other places.

Judging by the ancient I1 map and other data, it seems like I1 really expanded and diversified in Northern Europe, whether it originated there I don't know. We can't totally rely on BAB5 from Hungary or BAL051 from Spain.

This isn't gospel by any means, just my own ramblings at the moment...:wacko:

Hopefully we get some more I1 aDNA from the Repton study and others!

deadly77
05-28-2019, 07:57 AM
Indeed, fully agree that we can't totally rely on BAB5 from Hungary or BAL051 from Spain, but by the same token can't totally rely on SF11 or the RISE samples either.

Regarding plague, this is an interesting paper titled "Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline" that was published last year in Cell: https://www.cell.com/action/showPdf?pii=S0092-8674%2818%2931464-8 - unfortunately, it's behind a paywall, but you can read the summary and the graphical abstract: 30648 and and article about the paper with quotes from one of the authors here: https://www.sciencedaily.com/releases/2018/12/181206120035.htm

Around 4900 years ago, a series of plagues hit Northern Europe, noted in the graphical abstract by skulls and dates. At that point we have the first large settlements becoming common in Europe with people, animals, and stored food close together, and, likely, very poor sanitation - breeding ground for plague and disease. Throw in active trade with horses and wheeled carts migrating along trade routes: just the thing to ignite and spread the plague.

janan
05-28-2019, 09:24 AM
I've wondered this too and I suspect it could be an environmental thing that kept I-M253 bottlenecked until it finally expanded, obviously plague or conflict could also be the cause if not happening in tandem with an environmental scenario. Scandinavia didn't exactly lend itself to agriculture and other means at that time. Mr. Khan and a few others think maybe I-M253 hitched a ride with R-U106 and benefitted by association. I don't take this to mean they literally migrated with them, I interpret it to mean that whatever advances came with the cultures that were high in U106 (and the "Germanic" branches of R1a) directly benefitted the populations with I-M253 lineages. Obviously one of M253's descendants was successful since the majority of I1 descendants are I-DF29 subclades. There was definitely a preoccupation with boats leading up to the pre-Roman Iron Age, which obviously remained a focal point for the coastal populations along the North Sea and the Baltic. So the sea was definitely an important resource in this time considering farming would have been more difficult than other places.

Judging by the ancient I1 map and other data, it seems like I1 really expanded and diversified in Northern Europe, whether it originated there I don't know. We can't totally rely on BAB5 from Hungary or BAL051 from Spain.

This isn't gospel by any means, just my own ramblings at the moment...:wacko:

Hopefully we get some more I1 aDNA from the Repton study and others!
I'll join your rambling :-)

"Environmental thing"? Are you thinking of climate change? Scandinavia up until and including the bronze age was as warm as northern France is today. You could grow grapes here then. Archeological evidence show the bronze age was a quite expansive time. Population growth, amassing riches, develping a specific culture. There was a climate change, but that was at the end of the bronze age when weather got colder and wetter. That might also be what helped end the bronze age, with its stratified society where an elite controlled resources and metal through long range trading networks. Iron were available everywhere (ores were picked up from the bottom of shallow lakes), so no need anymore for the elite's network of international business associates.

But that means the population bottle neck we're looking for happened in the break bronze/iron age. Why not.

spruithean
05-28-2019, 12:23 PM
deadly77, thanks for that link, that'll be a good read.

janan, :lol: I was most definitely confusing my time periods for the environment thing! Perhaps indeed it was a mixture of warfare and plague (see deadly's post). It is definitely bizarre in the case of I1, however I think things aren't very clear considering the oldest samples of I1 are found in the Migration Period leading up to the later Medieval eras. Everything older than that seems to be pre-I1 unless those samples are suddenly retested for more accuracy.

janan
05-28-2019, 02:36 PM
Indeed, fully agree that we can't totally rely on BAB5 from Hungary or BAL051 from Spain, but by the same token can't totally rely on SF11 or the RISE samples either.

Regarding plague, this is an interesting paper titled "Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline" that was published last year in Cell: https://www.cell.com/action/showPdf?pii=S0092-8674%2818%2931464-8 - unfortunately, it's behind a paywall, but you can read the summary and the graphical abstract: 30648 and and article about the paper with quotes from one of the authors here: https://www.sciencedaily.com/releases/2018/12/181206120035.htm

Around 4900 years ago, a series of plagues hit Northern Europe, noted in the graphical abstract by skulls and dates. At that point we have the first large settlements becoming common in Europe with people, animals, and stored food close together, and, likely, very poor sanitation - breeding ground for plague and disease. Throw in active trade with horses and wheeled carts migrating along trade routes: just the thing to ignite and spread the plague.

Ah yes the plague. The two individuals found to carry Yersinia pestis come from the Gökhem grave and belong to the funnel beaker culture, thus early European farmers. So these were killed off by the plague, and left the country open for the Yamna invasion who might have come to a largely abandonded country. If the farmers had been gone for say 100 years, there wouldn't have been much traces after them in the countryside. Also, pitted-ware culture expanded into earlier farmer's country at the same time.

On the other hand, there is a whole lot of EEF ancestry in present-day Swedes, around 20-30 %, which at least means that the farmers weren't eradicated. Same with SWG, still present in our DNA with 10-20 %. So there are no obvious evidence for a bottleneck or close-to-complete population replacement at these times, as there are e.g. in Great Britain where 90 % of the DNA was replaced when the Bell Beakers arrived.

There's just nothing clear with this case.

deadly77
05-28-2019, 04:56 PM
Ah yes the plague. The two individuals found to carry Yersinia pestis come from the Gökhem grave and belong to the funnel beaker culture, thus early European farmers. So these were killed off by the plague, and left the country open for the Yamna invasion who might have come to a largely abandonded country. If the farmers had been gone for say 100 years, there wouldn't have been much traces after them in the countryside. Also, pitted-ware culture expanded into earlier farmer's country at the same time.

On the other hand, there is a whole lot of EEF ancestry in present-day Swedes, around 20-30 %, which at least means that the farmers weren't eradicated. Same with SWG, still present in our DNA with 10-20 %. So there are no obvious evidence for a bottleneck or close-to-complete population replacement at these times, as there are e.g. in Great Britain where 90 % of the DNA was replaced when the Bell Beakers arrived.

There's just nothing clear with this case.

I wasn't implying that plague was the sole or primary reason for a Y-DNA bottleneck or founder event, my intention was that it was likely a contributing factor along with others that Spruithean suggested. But I though the premise of the paper was interesting given the quoted dates, although I haven't read the actual paper fully because it's not open access.

I also wasn't implying that there was a close-to-complete population replacement in the region at these times, more that the Y-DNA ancestry derives from a relatively recent founder effect. I think you're equating a Y-DNA bottleneck with a close-to-complete population eradication as the same thing, but for me there they aren't exactly the same. Apologies if I am misunderstanding your intention.

Statistically, throughout most of recorded history, only about 10% of all male lines have survived more than 30 generations (~1000 years). We don’t always need volcanoes or plagues or slaughtering clan lords to cause Y-DNA lineage extinctions. For almost all of history, and certainly prehistory, when population growth was very slow, simple chance - the throw of the dice on how many sons or daughters you have (or if any) - assures that most lineages will go extinct. A Y-DNA bottleneck isn't inexorably indicative of a total or close-to-complete population replacement. Of course thousands of other men survived at the time we are discussing and had descendants, but not neccesarily their strict patrilineage in the form of Y-DNA survived to these descendants (or without the same following massive expansion as the TMRCA of I1, R1a and R1b Y-DNA descendants in Europe). Ancestors outside of the Y-chromosome patrilineal line can contribute to the autosomal DNA makeup (to your point of percentage EEF or SWG (SHG?) ancestry of modern Swedes) but not be reflected in the Y-DNA haplogroup distribution of modern population. Likewise, the Y-DNA of ancient samples in Scandinavia prior to the founder effect - lots of samples of Y-DNA haplogroup I2 in Hum2, I0012, I0013, I0015, I0016, I0017, Steigen, SBj, Ansarve 8, Ansarve 14, Ansarve 17, Ansarve 16, etc. (which outstrip current known ancient samples of I1, R1a, R1b in this region prior to the founder effect) aren't well represented in the modern population (Y-DNA I2 appears to be less than 6% in Scandinavian countries).

Y-DNA bottleneck is from a single paternal line surviving and a founder effect after which we see all of the expansion of subclades from the SNP data of modern testers. This is also reflected in the STR variation signatures observed in modern I1 descendants as the relatively late TMRCA has the effect of resetting the odometer in terms of STR divergence from the modal or "convergence". R-U106 also observe these phenomena from a similarly recent TMRCA and expansion of SNP subclades that isn't observed in say, haplogroup E which has a point of diversity and TMRCA further back in time. We don't see bottlenecks of this nature in the same time period for mtDNA lineages - subclades of mtDNA branch off on a continuous basis expected from a simple model of steady birth/offspring/death so not close-to-complete population replacement at these times. Same with autosomal DNA ancestry. Y-DNA bottlenecks, founder events and expansions don't necessarily have to completely replace or eradicate the previous population.

deadly77
05-28-2019, 10:21 PM
Keep us posted on those urm guys, they could get really interesting and even a tentative placement as simply I-DF29 for both is a hell of lot better than "ND" and "BCDEF". I was reading (yet again) the Sigtuna paper yesterday, quite an interesting read in terms of where some of these people likely came from in relation to Sigtuna.



Just quickly on these ones - I was having another look at the Sigtuna paper, and the genome coverage for these two was really low - Table 1 has urm035 at genome coverage x0.26 and urm045 as x0.09 - that's the second worst male in the dataset. By comparison, the I1 sample 84005 was x1.03 and the only sample from this paper that's made it onto the YFull tree was 84001 which had genome coverage x3.7 on branch N-Y4339. My feeling is that the amount of info that we get from urm035 and urm045 may not be very much.

janan
05-29-2019, 09:32 AM
I'm just trying to get my head around this. I type faster than I think so please consider these posts of mine as "work in progress".


Y-DNA bottlenecks, founder events and expansions don't necessarily have to completely replace or eradicate the previous population.

Yes true. The SHG and EEF in us suggest no population replacement. And I also agree with:


We don't see bottlenecks of this nature in the same time period for mtDNA lineages

So why is there an "extreme founder effect" for a male lineage but not for female dittos? That some guy just got lucky might be true but should be a last resort as an explanation. So I think about male domination. Perhaps when the steppe herders arrived. The problem with that alternative is that I1 has not been found in any such related population so why would they be the source at all. An alternative is the formation and expansion of the Nordic bronze age. This is thought to be a time when an elite formed and enriched itself through control of trading networks. My guess is that this elite could be the founders that spread I1 through their domination of the society. If so, the origin of I1 might just as well be local.

Just rambling, of course.

spruithean
05-29-2019, 10:58 AM
Just quickly on these ones - I was having another look at the Sigtuna paper, and the genome coverage for these two was really low - Table 1 has urm035 at genome coverage x0.26 and urm045 as x0.09 - that's the second worst male in the dataset. By comparison, the I1 sample 84005 was x1.03 and the only sample from this paper that's made it onto the YFull tree was 84001 which had genome coverage x3.7 on branch N-Y4339. My feeling is that the amount of info that we get from urm035 and urm045 may not be very much.

Darn, that's too bad. Well at least we got some I1 from that Sigtuna paper, better than nothing. I'm sure we'll keep finding more I1 throughout the Migration Period and later eras, whether we'll find the puzzle piece I1 I'm not sure. I still think it is a bit misleading for a lot of these papers to a haplogroup call for sample "BCDEF", or some such.


I'm just trying to get my head around this. I type faster than I think so please consider these posts of mine as "work in progress".



Yes true. The SHG and EEF in us suggest no population replacement. And I also agree with:



So why is there an "extreme founder effect" for a male lineage but not for female dittos? That some guy just got lucky might be true but should be a last resort as an explanation. So I think about male domination. Perhaps when the steppe herders arrived. The problem with that alternative is that I1 has not been found in any such related population so why would they be the source at all. An alternative is the formation and expansion of the Nordic bronze age. This is thought to be a time when an elite formed and enriched itself through control of trading networks. My guess is that this elite could be the founders that spread I1 through their domination of the society. If so, the origin of I1 might just as well be local.

Just rambling, of course.

I'll ramble too...

That could be a possibility, I mean Allentoft et al (2015) did find "I1" and "I1a" in the Nordic Bronze Age, so perhaps there is something to that however Allentoft et al dubbed them I1/I1a, however here it has been decided that due to lower coverage, or few important SNPs tested, etc we call them pre-I1. However it wouldn't be a surprise if they were legitimate I1 lineages as they are dated to within that 4,600 YBP TMRCA timeframe. So perhaps you're on to something here, as you say an elite formed during the Nordic BA and perhaps in some part of Scandinavia the founder of modern I1 managed to take hold of that elite status in his area. I'm not sure we could say I1 arrived with Steppe descended cultures as no I1 has been found in the Yamnaya areas (those areas are fairly well tested at this point). I've thought on the off chance that the BAB5 in Hungary was a legitimate I1 that perhaps I1 was present in the LBK sphere (through absorption of hunter gatherers by the farmers) and some group of them ended up in Scandinavia and remained during the Funnelbeakers period and eventual rise of the the Corded Ware groups such as Single Grave or Battle-Axe cultures in Denmark and Norway/Sweden respectively, and perhaps it wasn't until the Bronze Age that I1 began to expand.

Perhaps one day they'll take another crack at some Nordic BA remains and grab a better sample.

I1 is really a sort of strange haplogroup in all seriousness, it's somewhat common or dominant in a certain range of Europe, yet it doesn't appear in aDNA as often as R1b, R1a, G, E, etc perhaps due to where these people lived and their funerary practices be that burying their dead in soil that doesn't preserve genetic material or cremating their dead.

deadly77
05-29-2019, 10:55 PM
I didn't realize that Allentoft actually mentioned I1 (or even I1a) at all for any of the samples - I couldn't find any reference to I1 or SNPs in either the manuscript, supplementary material or excel files. I had assumed that the labelling of these RISE samples (as well as SF11) as I1 came from the descriptions on the blog by Genetiker and then everyone quoted from there. I do see that there's a barplot which has the colours for I1, I1a on BaSca group in Extended Data Figure 6 near the end of the paper which I hadn't noticed before.

A couple of other sources have listed these samples: Jean Manco's ancient samples list in the Wayback Machine here https://web.archive.org/web/20170825051810/http://www.ancestraljourneys.org/copperbronzeagedna.shtml lists RISE179 and RISE175 from Allentoft 2015 as I rather than I1 for Y-DNA haplogroup on the Ancient European DNA of the Copper and Bronze Ages list, so I guess she didn't find it conclusive enough to call either of these samples as I1. Also, David Reich's lab at Harvard lists RISE175, RISE179, RISE210 and SF11 as I rather than I1 and doesn't list any haplogroup for RISE207 when I downloaded their dataset in April from here https://reich.hms.harvard.edu/downloadable-genotypes-present-day-and-ancient-dna-data-compiled-published-papers to it seemed that it wasn't definitive enough for them.

As I've said several times in the forum, I'm against assigning the RISE samples definitively as I1 based on the low number of derived reads, especially when the majority of the positions are only one-read. It's entirely possible that these could have been I1, but for me there's not enough data to be sure. Same with BAB5 - not enough data. SF11 and BAL051 are a bit easier to categorize due to to multiple ancestral reads. The Allentoft 2015 RISE samples and BAB5 could have ancestral reads as well or they could all be derived. My hunch is that these individuals aren't the ancestors of modern I1 population and were essentially extinct lineage offshoots. But there's not really enough evidence to assign definitively one way or another. I am aware of people who label some of these samples as I1 without understanding the subtleties and raw data. I think it's safer to categorize these samples separately. If there's reanalysis of some of these samples, or new samples come to light that make this a bit less muddy, it'll be worth revising. But on current evidence, it's not enough for me.

I'm still trying to get my head around where Allentoft et al got the I1a designation in Extended Data Figure 6 from. As far as I can tell, none of these samples have any reads (either ancestral or derived) for DF29 or phyloequivalent SNPs (which is how I would define I1a). Of course it's entirely possible that they're using an earlier version of the tree which defines I1a differently. I had a look at the ISOGG tree from 2015 and it looks that I1a is just defined by DF29 alone, although I1 above that is defined my much less SNPs than the current 312 on the YFull tree https://isogg.org/tree/2015/ISOGG_HapgrpI15.html - but may even be using an earlier reference than that - if you go back to 2006 I1 was then I1a and I2 was I1b https://isogg.org/tree/2006/ISOGG_HapgrpI06.html but can't really be that as Allentoft refers to I2. Perhaps I1a assignment comes from a further downstream SNP. I don't know. But analyzing the BAM file from scratch against the current YFull tree... yeah, not so much.

spruithean
05-30-2019, 12:00 AM
I didn't realize that Allentoft actually mentioned I1 (or even I1a) at all for any of the samples - I couldn't find any reference to I1 or SNPs in either the manuscript, supplementary material or excel files. I had assumed that the labelling of these RISE samples (as well as SF11) as I1 came from the descriptions on the blog by Genetiker and then everyone quoted from there. I do see that there's a barplot which has the colours for I1, I1a on BaSca group in Extended Data Figure 6 near the end of the paper which I hadn't noticed before.

A couple of other sources have listed these samples: Jean Manco's ancient samples list in the Wayback Machine here https://web.archive.org/web/20170825051810/http://www.ancestraljourneys.org/copperbronzeagedna.shtml lists RISE179 and RISE175 from Allentoft 2015 as I rather than I1 for Y-DNA haplogroup on the Ancient European DNA of the Copper and Bronze Ages list, so I guess she didn't find it conclusive enough to call either of these samples as I1. Also, David Reich's lab at Harvard lists RISE175, RISE179, RISE210 and SF11 as I rather than I1 and doesn't list any haplogroup for RISE207 when I downloaded their dataset in April from here https://reich.hms.harvard.edu/downloadable-genotypes-present-day-and-ancient-dna-data-compiled-published-papers to it seemed that it wasn't definitive enough for them.

As I've said several times in the forum, I'm against assigning the RISE samples definitively as I1 based on the low number of derived reads, especially when the majority of the positions are only one-read. It's entirely possible that these could have been I1, but for me there's not enough data to be sure. Same with BAB5 - not enough data. SF11 and BAL051 are a bit easier to categorize due to to multiple ancestral reads. The Allentoft 2015 RISE samples and BAB5 could have ancestral reads as well or they could all be derived. My hunch is that these individuals aren't the ancestors of modern I1 population and were essentially extinct lineage offshoots. But there's not really enough evidence to assign definitively one way or another. I am aware of people who label some of these samples as I1 without understanding the subtleties and raw data. I think it's safer to categorize these samples separately. If there's reanalysis of some of these samples, or new samples come to light that make this a bit less muddy, it'll be worth revising. But on current evidence, it's not enough for me.

I'm still trying to get my head around where Allentoft et al got the I1a designation in Extended Data Figure 6 from. As far as I can tell, none of these samples have any reads (either ancestral or derived) for DF29 or phyloequivalent SNPs (which is how I would define I1a). Of course it's entirely possible that they're using an earlier version of the tree which defines I1a differently. I had a look at the ISOGG tree from 2015 and it looks that I1a is just defined by DF29 alone, although I1 above that is defined my much less SNPs than the current 312 on the YFull tree https://isogg.org/tree/2015/ISOGG_HapgrpI15.html - but may even be using an earlier reference than that - if you go back to 2006 I1 was then I1a and I2 was I1b https://isogg.org/tree/2006/ISOGG_HapgrpI06.html but can't really be that as Allentoft refers to I2. Perhaps I1a assignment comes from a further downstream SNP. I don't know. But analyzing the BAM file from scratch against the current YFull tree... yeah, not so much.

I totally agree, I would rather define as accurately as possible based on the available evidence, assuming it is I1 or otherwise is "risky", a good example of bad calls going too far can be seen in a very recent pre-print from last year.

In regards to some of the calls I found this through a link while scrolling through one of their supplementary excel files,
https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

Genetiker lists them as I1-FGC2435/Z2698, I1-M450/S109, I1-Z2765/CTS3506, apparently these are phyloequivalents and part of the SNP pool of M253. I would definitely say these are pre-I1, until perhaps a later date when (and if) they are tested again.

I also found this link through the excel file: https://anthrogenica.com/showthread.php?4664-Request-Y-DNA-haplogroup-results-from-Allentoft-2015&p=89569&viewfull=1#post89569

I wonder how Genetiker managed to determine these results.

oz
05-30-2019, 12:05 AM
Yes the biggest mystery of I1-DF29 in particular, is did it originate/assimilate with the Corder Ware or Single Grave groups and "hitched a ride", or did it originate during Nordic BA, or was it hunter gatherers in isolation somewhere in Scandinavia before CW and the Neoliths etc, did it get there with the Funnelbeakers or some kind of Neoliths. That's the most interesting question or mystery at this point which will hopefully be resolved eventually. I'm kinda surprised someone from Scandinavia hasn't tried to tackle this subject yet and lead in the research. I1 makes up around 40% of their Y DNA and it's the most frequent HG in that region, and it probably originated in that region, and experienced some kind of founder effect. Shouldn't some Scandinavian genetics research team try and figure out when, where, how and why? Cultural politics obstructing the curiosity or what?

deadly77
05-30-2019, 07:53 AM
I totally agree, I would rather define as accurately as possible based on the available evidence, assuming it is I1 or otherwise is "risky", a good example of bad calls going too far can be seen in a very recent pre-print from last year.

In regards to some of the calls I found this through a link while scrolling through one of their supplementary excel files,
https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

Genetiker lists them as I1-FGC2435/Z2698, I1-M450/S109, I1-Z2765/CTS3506, apparently these are phyloequivalents and part of the SNP pool of M253. I would definitely say these are pre-I1, until perhaps a later date when (and if) they are tested again.

I also found this link through the excel file: https://anthrogenica.com/showthread.php?4664-Request-Y-DNA-haplogroup-results-from-Allentoft-2015&p=89569&viewfull=1#post89569

I wonder how Genetiker managed to determine these results.

Yes, that's the way I view it. I'd rather hedge on the side of conservative than "risky" - especially when it's quoted as being I1 as evidence for a theory.

Cheers for the links. I'd looked at Genetiker's blog quite some time ago but not recently. All the SNPs mentioned are ones I found while doing analysis of the BAM files and listed in the posts on this forum and the map. Genetiker doesn't list the quality of these calls (for example if they're one read). If you look at the comments thread, there's an exchange with Erik Holmund where Genetiker had originally assigned haplogroup I1a3a2 (which is considerably further along than I1) for RISE175 and RISE179 and Erik Holmund asks if he has identified the SNPs BY351 or BY352, by reference to the current ISOGG tree of 2015. Genetiker then changes RISE175 and RISE179 back to I1.

It seems to me that the way Genetiker views it is that if a sample is positive for any of the I1 SNPs, that sample is haplogroup I1, regardless of the quality of those calls (if they're one read or if they are in regions where the BAM file shows a lot of mutations in the same region), the quantity of derived calls on the I1 group of SNPs, and ignoring if there are disconfirming ancestral SNPs in the I1 block or derived calls for non-I1 haplogroups - as is the case for his analysis of SF11 which Genetiker labels "Stora Förvar 11 belonged to Y haplogroup I1~M253." here https://genetiker.wordpress.com/more-y-snp-calls-for-stora-forvar-11/

So, by that line of thinking, a single positive one read SNP in the I1 block qualifies a sample as I1. And that's the case for RISE207 which has a a derived single call for M450/S109 and no call for all other I1-defining SNPs. Which is why Genetiker has listed this sample as I1-M450/S109 in his list. It seems that the Allentoft et al researchers view this the same way and list RISE207 baSca I1 in that list from the forwarded Anthrogenica forum post of Bernard on that link you shared. And Haak et al. in the BAL051 also use that criteria for I1.

Conversely, Jean Manco's list, David Reich's dataset, GuÈ nther et al. don't go this far with labelling these samples as I1 and are a bit more conservative. I'm closer to that side of things than Genetiker/Allentoft et al/Haak et al. I guess it's a question of taxonomy and classification.

As for how Genetiker managed to determine these results, to me it seems that he downloads the BAM file and looks up the positions using a BAM viewer. I'm essentially doing the same thing, just with a bit more detail in regard to read quality calls, a more conservative haplogroup classification and without the overt supremacism.

spruithean
05-30-2019, 01:16 PM
I found this in a thread about Haplogroup N and the various associations of it: https://anthrogenica.com/showthread.php?17044-N-haplogroup-and-Siberian-admixture-linked-to-the-spread-of-Uralic-languages&p=567729&viewfull=1#post567729

Definitely seems like Allentoft et al's stuff has gotten around quite a bit with the perhaps confused haplogroup designations.

Shaikorth
05-30-2019, 02:42 PM
I1 is really a sort of strange haplogroup in all seriousness, it's somewhat common or dominant in a certain range of Europe, yet it doesn't appear in aDNA as often as R1b, R1a, G, E, etc perhaps due to where these people lived and their funerary practices be that burying their dead in soil that doesn't preserve genetic material or cremating their dead.

It's quite likely that lack of numbers is the main reason we see no Neolithic or Mesolithic I1 in ancient DNA record before the now visible star-like expansion. For all we know no more than ten men with ancestral I1 were simultaneously alive at any point between 15,000 bp and the metal ages.

xenus
05-30-2019, 09:49 PM
It's quite likely that lack of numbers is the main reason we see no Neolithic or Mesolithic I1 in ancient DNA record before the now visible star-like expansion. For all we know no more than ten men with ancestral I1 were simultaneously alive at any point between 15,000 bp and the metal ages.

I agree that the most reasonable cause is low numbers. We can however definitely say there were almost positively more than 10 living at any given time. There may have been bottlenecks down to a handful of men but the per generation male/female birth rate + survival to reproductive age would have wiped them out. It's got to be a combination of low numbers and, for instance, location. It's not out of the question that they were a localized minority HG among cultures we know of either.

Shaikorth
05-31-2019, 07:15 AM
I agree that the most reasonable cause is low numbers. We can however definitely say there were almost positively more than 10 living at any given time. There may have been bottlenecks down to a handful of men but the per generation male/female birth rate + survival to reproductive age would have wiped them out. It's got to be a combination of low numbers and, for instance, location. It's not out of the question that they were a localized minority HG among cultures we know of either.

I'm not saying this literally happened but statistically we don't need a population size greater than 1 at a certain point in post-Mesolithic past to explain the modern I1 frequencies. Many modern lineages could have been hanging by a thread for a long time before some fortunate event caused a star-like expansion.

janan
06-03-2019, 10:35 AM
I found this thread when searching for information about the origin of I1. At that time I knew about the Hungarian and Iberian finds (BAB5 and BAL0051) and also knew that there were a few finds from the Nordic bronze age. So there were at least a few traces of I1 to keep in mind when thinking about its origin. But now I have learned that all these finds are dubious. So now I know even less than I knew before I came here. :\ The mystery deepens.

spruithean
06-03-2019, 11:08 AM
It's not that they are necessarily dubious, it's more that approaching the samples with caution and being rather conservative with the haplogroup calls is the safest bet. BAL051, SF11, BAB5 and the Nordic Bronze Age samples are all important pieces to the history of I1 (for all we know those Nordic Bronze Age I1's may very well be actual legitimate I1, a few people seem to think so). With a MRCA of 4600 ybp the Bronze Age or Late Neolithic is when the haplogroup expanded, but before that there could have been several "I1-esque" lineages roaming about. YFull has a formed date of 27500 ybp, so that's an early split from I-M170, and a lot of time between then and when the first modern I1 lineage appeared.

Of course most of our ancient modern I1 is in the Migration/Medieval period, so that's at least something, but also kind of expected.

janan
06-03-2019, 06:09 PM
@spruithean

Maybe I used the wrong word. What you say is what I mean.

If the medieval period should be considered as the time of the great founder effect, then we have the black death. Current estimates point to loss of two thirds of the population in Sweden during the plague and the years following it.

Migration period did not affect the Nordics, AFAIK. Except Denmark, perhaps.

spruithean
06-14-2019, 08:38 PM
@spruithean

Maybe I used the wrong word. What you say is what I mean.

If the medieval period should be considered as the time of the great founder effect, then we have the black death. Current estimates point to loss of two thirds of the population in Sweden during the plague and the years following it.

Migration period did not affect the Nordics, AFAIK. Except Denmark, perhaps.

I don't think the TMRCA for I1 fits the Medieval period (4600 ybp according to YFull), more likely the Bronze Age (the common star-like growth seen in other haplogroups). I think the majority of our ancient samples will fall into the Medieval category (including Migration period), which so far seems to be the case. Hopefully we can finally get some I1 (not pre-I1) from the right timeframe. Obviously the older pre-I1 samples from the Paleolithic and Neolithic are still part of the same line that branched from I-M170 that gave us modern I1, so they can at least provide some information about this pre-I1 (quasi-I1?) group and the distribution in prehistoric Europe.

Perhaps, eventually if enough samples roll in, shifting the tree for I1 might result in pre-I1 being named I1 and current I1(M253) being named I1a, or something along those lines, which would then result in the nomenclature changing for I1b and I1c.

Something like this perhaps:

I-M170
- I1 (instead of pre-I1)
-- I1* (include the lineages of BAL051, SF11, BAB5, RISE175,179,207?)
-- I1a (current I1)
--- I1a1 (DF29, current I1a)
--- I1a2 (Z131, current I1b)
--- I1a3 (Z17925, current I1c)

Obviously we don't know the chronology of the 312 SNPs that define modern I1 and this tree above is purely hypothetical, so this is all subject to change.

deadly77
07-08-2019, 10:40 PM
Hi folks - I was out for a while as there were some issues with Anthrogenica forum blocking my IP address - all sorted out now thanks to admin DMXX.

I've had a bit more of a look at the two samples from the Sigtuna paper that may be I1 but weren't assigned any Y-DNA haplogroup in the paper. Gone through 100 of the I1 SNPs and urm035 is positive for 18 of those SNPs and urm045 is positive for 9 of those SNPs. All one read given the low depth coverage of theses samples. Both of these samples also have one ancestral read each. I don't think these ancestral reads are real - I think they are false negatives - perils of law read depth. But I'm happy to put these samples as I1 given the number of corrobotating positive reads for these SNPs - already outscoring the RISE samples from the Allentoft paper. I'll add them to the map once I've gone through those. I'll also have a look for subclades but I have a feeling I'll be lucky to find much more than we have at I-DF29 for urm035 and I-Z60 for urm045.

spruithean
07-09-2019, 03:30 AM
Hi folks - I was out for a while as there were some issues with Anthrogenica forum blocking my IP address - all sorted out now thanks to admin DMXX.

I've had a bit more of a look at the two samples from the Sigtuna paper that may be I1 but weren't assigned any Y-DNA haplogroup in the paper. Gone through 100 of the I1 SNPs and urm035 is positive for 18 of those SNPs and urm045 is positive for 9 of those SNPs. All one read given the low depth coverage of theses samples. Both of these samples also have one ancestral read each. I don't think these ancestral reads are real - I think they are false negatives - perils of law read depth. But I'm happy to put these samples as I1 given the number of corrobotating positive reads for these SNPs - already outscoring the RISE samples from the Allentoft paper. I'll add them to the map once I've gone through those. I'll also have a look for subclades but I have a feeling I'll be lucky to find much more than we have at I-DF29 for urm035 and I-Z60 for urm045.

Interesting that urm045 appears to be I-Z60, too bad about the low reads though, maybe at some point we'll hit a real treasure trove of ancient I1.

JonikW
07-09-2019, 02:51 PM
So it looks like the big Viking aDNA study we've been waiting for is wrapping up and should be published this year. Let's hope for plenty of I1.

https://lists.rootsweb.com/hyperkitty/list/y-dna-haplogroup-i.rootsweb.com/thread/35472249/

Bollox79
07-10-2019, 09:13 PM
So it looks like the big Viking aDNA study we've been waiting for is wrapping up and should be published this year. Let's hope for plenty of I1.

https://lists.rootsweb.com/hyperkitty/list/y-dna-haplogroup-i.rootsweb.com/thread/35472249/

Speaking of I1 and Vikings - any additional info on sample Pagan Migrant Icelander SSG-A3 (grave 4?) - Sílastaðir in Eyjafjarðarsýsla, North Iceland - as he is my maternal kinsman being T2b2b like I am - and I am pretty sure he is grave 4 with the male buried with the horse etc as grave 3 was the female (an earlier archaeological paper on that site listed grave 3 as a female with typical grave goods and grave 4 as a male with typical male grave goods/weapons and horse skeleton - I think they mixed them up in the paper as far as labeling)... they only have him listed as I1 in the paper for his Y-DNA group. I have an interest in him since he seems to be half Norse/half Gaelic in his autosomal ancestry and my MDKA on my maternal line was probably from around Limerick or SW Ireland or even SE where Vikings were active in this guy's period 10 - 11th cent... typology date being 850-1000 and a carbon date for SSG-A1 being 980-1020 AD. Figured this would be the place to ask my I1 cousin kinsmen (since you guys tend to tag along with U106 or the other way around hah!).

Cheers,
Charlie

deadly77
07-10-2019, 09:55 PM
Speaking of I1 and Vikings - any additional info on sample Pagan Migrant Icelander SSG-A3 (grave 4?) - Sílastaðir in Eyjafjarðarsýsla, North Iceland - as he is my maternal kinsman being T2b2b like I am - and I am pretty sure he is grave 4 with the male buried with the horse etc as grave 3 was the female (an earlier archaeological paper on that site listed grave 3 as a female with typical grave goods and grave 4 as a male with typical male grave goods/weapons and horse skeleton - I think they mixed them up in the paper as far as labeling)... they only have him listed as I1 in the paper for his Y-DNA group. I have an interest in him since he seems to be half Norse/half Gaelic in his autosomal ancestry and my MDKA on my maternal line was probably from around Limerick or SW Ireland or even SE where Vikings were active in this guy's period 10 - 11th cent... typology date being 850-1000 and a carbon date for SSG-A1 being 980-1020 AD. Figured this would be the place to ask my I1 cousin kinsmen (since you guys tend to tag along with U106 or the other way around hah!).

Cheers,
Charlie

Hi Charlie - I analyzed the BAM file for SSG-A3 a while ago when going through the I1 samples from the Ebenesersdóttir et al. Science 2018 paper. The coverage wasn't great, which lead to a lot of no calls and low read depth calls (all were only one or two reads). I tenatively put him at branch I-CTS6868. My SNPcalls from the BAM:

Derived SNPs: Z2892 1G, CTS6868 1C
Ancestral SNPs: L205 2A, Y44733 2C, Y196701G, Y13504 4T, Y18232 1T, Y36967 1C
No call SNPs; DF29, CTS9857, Z2891, Z2890, Z2893, Z2336, Y2592, Y2593, Z2337, S6346, L22, Y3549, Z2338, P109, Y3669, S7660, S11056, Y12927, Z74, Z75, CTS1793, L813, Z718, CTS9346, Z720, FGC9478, Y5153, Y5154, Y30806, Y36072, Y15505, Y18927, Y5476, Y7659, Y5483, Y23527, Y15038, Y19207, Y13038, Y13039, Y8943, Y17927, Y18234, Y18229, Y19728, Z58, Z59, Z60, Z140

I had in my notes that the paper described SSG-A2 and SSG-A3 as Pre-Christian migrants - said they had a lower 87Sr/86Sr isotope ratio than the Gaelic SSG-A4migrant, but the 87Sr/86Sr isotope ratio was considered too high for a childhood solely in Iceland. Notably, SSG-A3 is estimated to be an equal mix of Norse and Gaelic, indicating that some admixture occurred before arrival in Iceland, perhaps in Viking settlements in Scotland or Ireland.

I started keeping track of all of the ancient I1 samples (since there are not very many of them) in a Google Map which you can find here if you're interested in any of the other I1 samples: https://www.google.com/maps/d/viewer?mid=1znTXv7qpl4_2T4u9068jOaLzpsjNf62F&ll=55.538826867432704%2C-26.647114350000038&z=3

Bollox79
07-10-2019, 10:12 PM
Hi Charlie - I analyzed the BAM file for SSG-A3 a while ago when going through the I1 samples from the Ebenesersdóttir et al. Science 2018 paper. The coverage wasn't great, which lead to a lot of no calls and low read depth calls (all were only one or two reads). I tenatively put him at branch I-CTS6868. My SNPcalls from the BAM:

Derived SNPs: Z2892 1G, CTS6868 1C
Ancestral SNPs: L205 2A, Y44733 2C, Y196701G, Y13504 4T, Y18232 1T, Y36967 1C
No call SNPs; DF29, CTS9857, Z2891, Z2890, Z2893, Z2336, Y2592, Y2593, Z2337, S6346, L22, Y3549, Z2338, P109, Y3669, S7660, S11056, Y12927, Z74, Z75, CTS1793, L813, Z718, CTS9346, Z720, FGC9478, Y5153, Y5154, Y30806, Y36072, Y15505, Y18927, Y5476, Y7659, Y5483, Y23527, Y15038, Y19207, Y13038, Y13039, Y8943, Y17927, Y18234, Y18229, Y19728, Z58, Z59, Z60, Z140

I had in my notes that the paper described SSG-A2 and SSG-A3 as Pre-Christian migrants - said they had a lower 87Sr/86Sr isotope ratio than the Gaelic SSG-A4migrant, but the 87Sr/86Sr isotope ratio was considered too high for a childhood solely in Iceland. Notably, SSG-A3 is estimated to be an equal mix of Norse and Gaelic, indicating that some admixture occurred before arrival in Iceland, perhaps in Viking settlements in Scotland or Ireland.

I started keeping track of all of the ancient I1 samples (since there are not very many of them) in a Google Map which you can find here if you're interested in any of the other I1 samples: https://www.google.com/maps/d/viewer?mid=1znTXv7qpl4_2T4u9068jOaLzpsjNf62F&ll=55.538826867432704%2C-26.647114350000038&z=3

Cheers and thanks for the response Deadly77!!! Good to have someone tracking the I1 guys ;-)... and thanks for the info on my maternal kinsman ;-). I know there is a noticeable trend in the T2b2b group of MDKAs from either Ireland, Scotland and Isles and Scandinavia so sure looks "Vikingish"... I did a bit of an overview on my facebook page for friends and family members about him... and he had a type of Peterson sword - if that is anything to go by - was found in the Isle of Islay and also near Limerick where the Viking settlement was there - certainly it appears to be a connection between Ireland/Scotland i.e. the Western parts and also Viking activity perhaps - additionally there is an MDKA Doyle female in the T2b2b group and that is supposed to denote dark stranger etc - though I tend not to read TOO much into surnames...

Also can you give me an idea of the county of origins for kits positive for CTS6868? I know there is the I1 y-dna project, but you have to be a member to view results etc - trying to get an idea of the spread of CTS6868!

deadly77
07-10-2019, 10:40 PM
Cheers and thanks for the response Deadly77!!! Good to have someone tracking the I1 guys ;-)... and thanks for the info on my maternal kinsman ;-). I know there is a noticeable trend in the T2b2b group of MDKAs from either Ireland, Scotland and Isles and Scandinavia so sure looks "Vikingish"... I did a bit of an overview on my facebook page for friends and family members about him... and he had a type of Peterson sword - if that is anything to go by - was found in the Isle of Islay and also near Limerick where the Viking settlement was there - certainly it appears to be a connection between Ireland/Scotland i.e. the Western parts and also Viking activity perhaps - additionally there is an MDKA Doyle female in the T2b2b group and that is supposed to denote dark stranger etc - though I tend not to read TOO much into surnames...

Also can you give me an idea of the county of origins for kits positive for CTS6868? I know there is the I1 y-dna project, but you have to be a member to view results etc - trying to get an idea of the spread of CTS6868!

Actually, even being a member of the main I1 Y-DNA project at FTDNA is no guarantee of being able to view any of the results on the project pages. The DNA results pages load so slowly that they often time out with the "Houston, we have a problem message" and to be honest, it's got to the point where I haven't looked at them for months because the experience is rather frustrating. So you're not actually missing much. Quite a few of the subclades of I1 have their own projects which are a lot more manageable.

However, there are a couple of public data sources that you can check out without needing to be a member which should give you a good enough idea of the geographic spread of modern I-CTS6868. Try the I-CTS6868 tree at YFull here https://www.yfull.com/tree/I-CTS6868/ and the FTDNA public haplotree here https://www.familytreedna.com/public/y-dna-haplotree/I;name=I-CTS6868 - if you click on the three vertical dots on the right hand side of the page in line with I-CTS6868 it will bring up a pop up window for "Country Report" - click that and a different pop up will come up with statistics for countries.

As you can see, I-CTS6868 is a very large subclade of I1. Sorry but the low coverage of SSG-A3 didn't allow anything more defined than than in terms of downstream SNPs. As you can see from YFull tree and FTDNA public haplotree, it's largely focused on Northern Scandinavia (Finland, Sweden, Norway) with a smattering from the other countries where I1 normally found. But largely on the Northern end of the I1 distribution.

Bollox79
07-10-2019, 11:13 PM
Actually, even being a member of the main I1 Y-DNA project at FTDNA is no guarantee of being able to view any of the results on the project pages. The DNA results pages load so slowly that they often time out with the "Houston, we have a problem message" and to be honest, it's got to the point where I haven't looked at them for months because the experience is rather frustrating. So you're not actually missing much. Quite a few of the subclades of I1 have their own projects which are a lot more manageable.

However, there are a couple of public data sources that you can check out without needing to be a member which should give you a good enough idea of the geographic spread of modern I-CTS6868. Try the I-CTS6868 tree at YFull here https://www.yfull.com/tree/I-CTS6868/ and the FTDNA public haplotree here https://www.familytreedna.com/public/y-dna-haplotree/I;name=I-CTS6868 - if you click on the three vertical dots on the right hand side of the page in line with I-CTS6868 it will bring up a pop up window for "Country Report" - click that and a different pop up will come up with statistics for countries.

As you can see, I-CTS6868 is a very large subclade of I1. Sorry but the low coverage of SSG-A3 didn't allow anything more defined than than in terms of downstream SNPs. As you can see from YFull tree and FTDNA public haplotree, it's largely focused on Northern Scandinavia (Finland, Sweden, Norway) with a smattering from the other countries where I1 normally found. But largely on the Northern end of the I1 distribution.

Deadly thanks again! Ok so likely Northern in his Y-DNA which makes sense etc... I know what you mean with the "Houston, we have a problem" as I get that trying to view the U106 project of which I am a member - I can get around that by viewing it under colorized charts instead and just increasing the page size - maybe you can try that with the I1 project? Classic chart never seems to work - times out as you said... the Scando MKDAs for the T2b2b kits are from Norway and Sweden. I still need to get my full mtDNA done at FTDNA though... see exactly where I fall. I got the T2b2b result from when I first tested with National Genographic etc!

oz
07-10-2019, 11:19 PM
It definitely looks like the I-CTS6868 is very Finnish, interesting. I wonder when that founder effect happened, and if it's also the most common type of I1 in the Saami...

deadly77
07-11-2019, 01:53 PM
It definitely looks like the I-CTS6868 is very Finnish, interesting. I wonder when that founder effect happened, and if it's also the most common type of I1 in the Saami...

Well you can look at the TMRCA of I-CTS6868, YFull has it at 3900 ybp, 95% CI 4500-3300.

I've read on some other forums that Finland has a very high participation rate in Y-DNA testing, including in depth testing (Big Y, etc.) so that may inflate the figures somewhat, although undoubtably they have a big contribution. The Finland Project is the largest geographic project at FTDNA, with 16,262 members as of July 2 2019. The rest of the top 5 for comparison are Scotland 11,003; Ireland 9,102; France 9,003; Sweden 8,935; Cumberland Gap 7,863; Norway 7,600; Germany 7,438; British Isles by County 5,900; Arab Tribes 5,752. While there's undoutably a lot of Finland in I-CTS6868, the high participation may skew the data to look a bit higher than it really is across the entire subclade.

While there's a fair bit of Finland smattered across a variety of the I-CTS6868 subclades (and also through the rest of I1), it looks really very highly concentrated if you look at I-L258 and subclades below I-CTS6868: https://www.yfull.com/tree/I-L258/

I'm not aware of any ancient I1 Saami to date. There was this paper that came out last year on ancient Fennoscandian genomes https://www.nature.com/articles/s41467-018-07483-5?fbclid=IwAR3oF8n2KI4CDfPiXvzWQcPCKgCOheEF4Bw6Gv3 VrqjPnAGtnNUX6Og-RXE - there was no I1 among the ancients that they looked at in this paper: of the 14 samples, two were of such low coverage that they could not get much information from them, nine were females (and so don't have a Y-DNA haplogroup), and of the three males, two were N1c and one was I2. Although they do include a "high-coverage whole genome from a modern Saami individual" who is listed as I1a1b3a1, which would make him I-L258.

I think if this goes a bit too far off tangent into the modern distribution of haplogroups among the Saami of Finland, perhaps we should start a new thread focused on that and keep this thread for the ancients.

JonikW
07-17-2019, 08:01 PM
So the massive Viking paper is out and has loads of I1. We're going to be busy here, especially deadly77 I hope! :)

Edit: more than 70 I1 samples at a quick count.

rozenfeld
07-17-2019, 08:12 PM
So the massive Viking paper is out and has loads of I1. We're going to be busy here, especially deadly77 I hope! :)

Edit: more than 70 I1 samples at a quick count.

92, if I am counting correctly:


VK14 Russia_Ladoga_5680-12 Russia Ladoga Ladoga 10-12th centuries CE 0.162 Male I1 J1c1a
VK16 Russia_Ladoga_5680-2 Russia Ladoga Ladoga 1111+-27 0.228 Male I1 X2b4
VK20 Russia_Ladoga_5680-1 Russia Ladoga Ladoga 1062 ± 27 0.496 Male I1 H6c
VK23 Russia_Ladoga_5680-9 Russia Ladoga Ladoga 10-12th centuries CE 0.325 Male I1 U4a1a
VK29 Sweden_Skara 17 Sweden Skara Varnhem 10-12th centuries CE 3.208 Male I1 T2b3b
VK71 Denmark_Tollemosegard-BU Denmark Sealand Tollemosegård Late Germanic Iron Age/early Viking 0.174 Male I1 U5a1a
VK144 UK_Oxford_#8 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.159 Male I1 V1a1
VK148 UK_Oxford_#12 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.043 Male I1 H6a1a
VK149 UK_Oxford_#13 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.008 Male I1 H1a1
VK157 Poland_Bodzia B5 Poland Bodzia Bodzia 10-11th centuries CE 0.978 Male I1 H1c
VK163 UK_Oxford_#1 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.019 Male I1 U2e2a1a1
VK167 UK_Oxford_#5 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.902 Male I1 H4a1a4b
VK179 Greenland F2 Greenland Eastern Settlement Ø029a 10-12th centuries CE 1.84 Male I1 K1a3a
VK183 Greenland F6 Greenland Eastern Settlement Ø029a 10-12th centuries CE 0.535 Male I1 T2b21
VK186 Greenland KNK-[6] Greenland Eastern Settlement Ø64 Early Norse 0.813 Male I1 H1ao
VK248 Faroe_22 Faroes Faroes Church2 16-17th centuries CE 0.076 Male I1 H49a
VK316 Denmark_Hessum sk II Denmark Funen Hessum 9-11th centuries CE 1.458 Male I1 K1a4
VK343 Oland_1021 Sweden Oland Oland 9-11th centuries CE 1.259 Male I1 H3h
VK367 Denmark_Bogovej D Denmark Langeland Bogøvej 10th century CE 1.053 Male I1 J1b1a1
VK379 Oland_1077 Sweden Oland Oland 700 CE 0.07 Male I1 U3b1b
VK380 Oland_1078 Sweden Oland Oland 9-11th centuries CE 0.106 Male I1 H27
VK388 Norway_Nordland 253 Norway Nor_North Nordland 8-16th centuries CE 0.975 Male I1 J1c5
VK407 Sweden_Skara 274 Sweden Skara Varnhem 10-12th centuries CE 0.233 Male I1 H1c21
VK410 Russia_Ladoga_5680-15 Russia Ladoga Ladoga 1107+-27 0.129 Male I1 X2b+226
VK420 Norway_Hedmark 2813 Norway Nor_South Hedmark 8-11th centuries CE 1.534 Male I1 I4a
VK482 Estonia_Salme_II-P Estonia Saaremaa Salme 8th century CE 1.085 Male I1 H1a
VK519 Norway_Nordland 4691b Norway Nor_North Nordland 6-10th centuries CE 0.217 Male I1 HV0a1
VK539 Ukraine_Shestovitsa-8870-97 Ukraine Shestovitsa Shestovitsa 10-12th centuries CE 1.574 Male I1 V
VK554 Estonia_Salme_II-L Estonia Saaremaa Salme 8th century CE 0.933 Male I1 W6a
VK190 Greenland late-0996 Greenland Eastern Settlement Ø149 1360 CE 6.495 Male I1a K1a+195
VK223 Russia_Gnezdovo 75-140 Russia Gnezdovo Gnezdovo 10-11th centuries CE 0.35 Male I1a H13a1a1c
VK295 Denmark_Hessum sk 1 Denmark Funen Hessum 9-11th centuries CE 0.57 Male I1a T1a1
VK306 Sweden_Skara 33 Sweden Skara Varnhem 10-12th centuries CE 1.052 Male I1a H15a1
VK409 Russia_Ladoga_5680-14 Russia Ladoga Ladoga 10-12th centuries CE 0.168 Male I1a H3h
VK495 Estonia_Salme_II-C Estonia Saaremaa Salme 8th century CE 1.143 Male I1a H1b
VK506 Estonia_Salme_I-3 Estonia Saaremaa Salme 8th century CE 1.233 Male I1a J1c2
VK151 UK_Oxford_#15 UK Oxford St_John’s_College_Oxford 880-1000 CE 1.142 Male I1a1 T2b4+152
VK220 Russia_Ladoga_5680-11 Russia Ladoga Ladoga 10-12th centuries CE 1.815 Male I1a1 J2b1a
VK257 UK_Dorset-3723 UK Dorset Ridgeway_Hill_Mass_Grave_Dorset 10-11th centuries CE 1.017 Male I1a1 H5a1c1a
VK352 Oland_1012 Sweden Oland Oland 9-11th centuries CE 1.149 Male I1a1 H64
VK50 Gotland_Kopparsvik-53.64 Sweden Gotland Kopparsvik 900-1050 CE 6.231 Male I1a1a1a1a H1+16189
VK279 Denmark_Galgedil AXE Denmark Funen Galgedil 10th century CE 2.393 Male I1a1b I4a
VK320 Denmark_Bogovej Grav S Denmark Langeland Bogøvej 10th century CE 1.368 Male I1a1b U5a1a1
VK400 Sweden_Skara 236 Sweden Skara Varnhem 10-12th centuries CE 1.066 Male I1a1b H1+16239
VK404 Sweden_Skara 277 Sweden Skara Varnhem 10-12th centuries CE 1.425 Male I1a1b U4a2
VK473 Gotland_Kopparsvik-126 Sweden Gotland Kopparsvik 900-1050 CE 1.396 Male I1a1b N1a1a1a1
VK165 UK_Oxford_#3 UK Oxford St_John’s_College_Oxford 880-1000 CE 1.105 Male I1a1b1 U4b1b1
VK219 Russia_Ladoga_5680-10 Russia Ladoga Ladoga 992 ± 27 1.581 Male I1a1b1 T2b6a
VK221 Russia_Ladoga_5757-14 Russia Ladoga Ladoga 911+-27 1.953 Male I1a1b1 K1d
VK297 Denmark_Hundstrup Mose sk 2 Denmark Sealand Hundstrup_Mose 670-830 CE 0.667 Male I1a1b1 J1c2h
VK315 Denmark_Bakkendrup Grav 16 Denmark Sealand Bakkendrup 850-900 CE 0.584 Male I1a1b1 T1a1b
VK488 Estonia_Salme_II-H Estonia Saaremaa Salme 8th century CE 0.901 Male I1a1b1 H5c
VK507 Estonia_Salme_I-4 Estonia Saaremaa Salme 8th century CE 0.823 Male I1a1b1 HV6
VK509 Estonia_Salme_I-6 Estonia Saaremaa Salme 8th century CE 1.328 Male I1a1b1 H1n+146
VK510 Estonia_Salme_I-7 Estonia Saaremaa Salme 8th century CE 1.525 Male I1a1b1 H10e
VK549 Estonia_Salme_II-J Estonia Saaremaa Salme 8th century CE 1.676 Male I1a1b1 T2b5a
VK553 Estonia_Salme_II-M Estonia Saaremaa Salme 8th century CE 1.264 Male I1a1b1 K1c1h
VK70 Denmark_Tollemosegard-EW Denmark Sealand Tollemosegård Late Germanic Iron Age/early Viking 6.684 Male I1a1b1a1 H7d4
VK110 Iceland_115S Iceland Hofstadir Hofstadir 10-13th centuries CE 1.792 Male I1a1b1a1 H10+(16093)
VK176 UK_Oxford_#20 UK Oxford St_John’s_College_Oxford 880-1000 CE 2.415 Male I1a1b1a1 H10
VK281 Denmark_Barse Grav A Denmark Sealand Bårse 10th century CE 2.046 Male I1a1b1a1 T2
VK296 Denmark_Hundstrup Mose sk 1 Denmark Sealand Hundstrup_Mose 660-780 CE 0.458 Male I1a1b1a1 HV6
VK511 Estonia_Salme_II-X Estonia Saaremaa Salme 8th century CE 1.701 Male I1a1b1a1 T2a1a
VK291 Denmark_Bodkergarden Grav D, sk 1 Denmark Langeland Bødkergarden 9th century CE 1.113 Male I1a1b1a4a U5a1a2b
VK98 Iceland_083 Iceland Hofstadir Hofstadir 10-13th centuries CE 2.491 Male I1a1b1a4a2 T2b3b
VK382 Oland_1132 Sweden Oland Oland 700 CE 0.06 Male I1a1b1a4a2 H3g1
VK529 Norway_Nordland 642 Norway Nor_North Nordland 8-9th centuries CE 1.813 Male I1a1b1a4a2 H7
VK547 Norway_Nordland 4727 Norway Nor_North Nordland 8-11th centuries CE 4.732 Male I1a1b1a4a2 V
VK262 UK_Dorset-3739 UK Dorset Ridgeway_Hill_Mass_Grave_Dorset 10-11th centuries CE 1.22 Male I1a2a J1c4
VK301 Denmark_Ladby Grav 4 Denmark Funen Ladby 640-890 CE 0.731 Male I1a2a R0a2b
VK532 Kragehave Odetofter XL718 Denmark Sealand Kragehave Odetofter 100 CE 4.013 Male I1a2a U2e2a1a
VK337 Oland_1064 Sweden Oland Oland 858 ± 68 CE 2.042 Male I1a2a1a1a U5a1b3a
VK357 Oland_1097 Sweden Oland Oland 1053 ± 60 CE 1.387 Male I1a2a1a1a J2b1a
VK363 Denmark_Bogovej BT Denmark Langeland Bogøvej 10th century CE 1.337 Male I1a2a1a1a U4b1a1a1
VK327 Denmark_Ribe 6 Denmark Jutland Ribe 9-11th centuries CE 1.164 Male I1a2a1a1a1a H6a1a5
VK552 Estonia_Salme_II-K Estonia Saaremaa Salme 8th century CE 1.379 Male I1a2a1a1d H10e
VK146 UK_Oxford_#10 UK Oxford St_John’s_College_Oxford 880-1000 CE 1.182 Male I1a2a1a1d1a J1c3e1
VK483 Estonia_Salme_II-V Estonia Saaremaa Salme 8th century CE 1.78 Male I1a2a1a1d1a H16
VK485 Estonia_Salme_II-O Estonia Saaremaa Salme 8th century CE 0.709 Male I1a2a1a1d1a H16
VK492 Estonia_Salme_II-B Estonia Saaremaa Salme 8th century CE 1.015 Male I1a2a1a1d1a H1b5
VK515 Norway_Nordland 4512 Norway Nor_North Nordland 10th century CE 0.636 Male I1a2a1a1d1a H52
VK524 Norway_Nordland 3708 Norway Nor_North Nordland 10th century CE 1.606 Male I1a2a1a1d1a HV0a1
VK555 Estonia_Salme_II-I Estonia Saaremaa Salme 8th century CE 1.099 Male I1a2a1a1d1a U3b1b
VK490 Estonia_Salme_II-N Estonia Saaremaa Salme 8th century CE 0.946 Male I1a2a1a1d1a1a H16
VK491 Estonia_Salme_II-Õ Estonia Saaremaa Salme 8th century CE 1.433 Male I1a2a1a1d1a1a H6a1a
VK497 Estonia_Salme_II-Ö Estonia Saaremaa Salme 8th century CE 1.447 Male I1a2a1a1d1a1a H16
VK443 Oland_1101 Sweden Oland Oland 9-11th centuries CE 2.107 Male I1a2a1a1d2 U5b2b5
VK445 Denmark_Gl Lejre-A1896 Denmark Sealand Gl._Lejre 9-11th centuries CE 1.363 Male I1a2a2 U3b
VK446 Denmark_Galgedil LS Denmark Funen Galgedil 9-11th centuries CE 1.531 Male I1a2a2 U5a1a1+16362
VK496 Estonia_Salme_II-W Estonia Saaremaa Salme 8th century CE 1.978 Male I1a2a2a H1a
VK521 Sol941 Grav900 Brondsager Torsiinre Denmark Sealand Brondsager_Torsiinre 300 CE 4.538 Male I1a2a2a H16b
VK275 Denmark_Kaargarden 217 Denmark Langeland Kaagården 10th century CE 0.448 Male I1c H

oz
07-17-2019, 08:23 PM
I didn't bother with the counting but I didn't notice even one labeled as I1a3 lol.

spruithean
07-17-2019, 09:04 PM
Holy shit this is awesome! Like a treasure trove of Ancient I1! It's somewhat exciting!

JonikW
07-17-2019, 09:07 PM
"I1 is the most well represented haplogroup in our ancient dataset, and most regions contained individuals belonging to this lineage
289 (especially Estonia, Russia, Denmark and Greenland), with the exception of the Isle of Man, Ireland
290 and Italy, however these regions have comparatively small sample sizes which may not allow the
291 detection of this haplogroup. The ancient samples of the present-study are mainly distributed in two
292 main clades, I1a1b1-L22, which accounts for 71% of the I1 haplotypes in a Y-chromosome survey
of Finland184 293 , and I1a2a-S246. Of particular interest, the clade I1a2a1a1d1a-S247 is especially well
294 represented in Estonian samples, and is found mostly in present-day Finnish and Northern
295 Scandinavian groups.
296 While it likely that many I1 lineages dispersed into the British Isles from Scandinavia during the
297 Viking period, it is also probable that earlier Anglo-Saxon migrations also played a role, as suggested
by the East to West decreasing frequency cline of I lineages185 298 and the presence of the I1 lineage in
an individual from this period excavated in England186 299 )."

Edit: please excuse the footnote numbers...

spruithean
07-17-2019, 09:52 PM
I didn't bother with the counting but I didn't notice even one labeled as I1a3 lol.

Yeah, I noticed that. I noticed some I-Z140 (labelled I1a2a1a1a) from Sweden (800s) and Denmark (9th-11th). A lot of the Y-Hgs are just "I1" so perhaps analysis could reveal some Z63.


"I1 is the most well represented haplogroup in our ancient dataset, and most regions contained individuals belonging to this lineage
289 (especially Estonia, Russia, Denmark and Greenland), with the exception of the Isle of Man, Ireland
290 and Italy, however these regions have comparatively small sample sizes which may not allow the
291 detection of this haplogroup. The ancient samples of the present-study are mainly distributed in two
292 main clades, I1a1b1-L22, which accounts for 71% of the I1 haplotypes in a Y-chromosome survey
of Finland184 293 , and I1a2a-S246. Of particular interest, the clade I1a2a1a1d1a-S247 is especially well
294 represented in Estonian samples, and is found mostly in present-day Finnish and Northern
295 Scandinavian groups.
296 While it likely that many I1 lineages dispersed into the British Isles from Scandinavia during the
297 Viking period, it is also probable that earlier Anglo-Saxon migrations also played a role, as suggested
by the East to West decreasing frequency cline of I lineages185 298 and the presence of the I1 lineage in
an individual from this period excavated in England186 299 )."

Edit: please excuse the footnote numbers...


I was surprised by the amount of Z73 in Estonia, really quite interesting.

JMcB
07-17-2019, 09:54 PM
Quickly scanning through their supplementals and found this:

Pretty much as expected, I would think.

31842

A lot of interesting reading to do and it’s also nice to finally see some Danes!

oz
07-17-2019, 10:04 PM
[QUOTE=spruithean;583060]Yeah, I noticed that. I noticed some I-Z140 (labelled I1a2a1a1a) from Sweden (800s) and Denmark (9th-11th). A lot of the Y-Hgs are just "I1" so perhaps analysis could reveal some Z63.




Yeah maybe, there is quite a lot that isn't labeled deeper than I1a, but Z63 seems to be very uncommon in Scandinavia, it's absolutely dwarfed by the other I1 subclades and overall it's only around 1% there, so it's not all too surprising. But still out of this many samples total 442? And not even one Z63 is kinda weird.

Edit I didn't count in females, I don't know what the ratio is even if it's only 220 males that's still a big number.

deadly77
07-17-2019, 10:12 PM
So the massive Viking paper is out and has loads of I1. We're going to be busy here, especially deadly77 I hope! :)

Edit: more than 70 I1 samples at a quick count.

Alright - great news. Also oof - but fantastic. I've just got in from an evening out so let me see what's here and how the data looks.

mwauthy
07-18-2019, 04:47 AM
92, if I am counting correctly:


VK14 Russia_Ladoga_5680-12 Russia Ladoga Ladoga 10-12th centuries CE 0.162 Male I1 J1c1a
VK16 Russia_Ladoga_5680-2 Russia Ladoga Ladoga 1111+-27 0.228 Male I1 X2b4
VK20 Russia_Ladoga_5680-1 Russia Ladoga Ladoga 1062 ± 27 0.496 Male I1 H6c
VK23 Russia_Ladoga_5680-9 Russia Ladoga Ladoga 10-12th centuries CE 0.325 Male I1 U4a1a
VK29 Sweden_Skara 17 Sweden Skara Varnhem 10-12th centuries CE 3.208 Male I1 T2b3b
VK71 Denmark_Tollemosegard-BU Denmark Sealand Tollemosegård Late Germanic Iron Age/early Viking 0.174 Male I1 U5a1a
VK144 UK_Oxford_#8 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.159 Male I1 V1a1
VK148 UK_Oxford_#12 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.043 Male I1 H6a1a
VK149 UK_Oxford_#13 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.008 Male I1 H1a1
VK157 Poland_Bodzia B5 Poland Bodzia Bodzia 10-11th centuries CE 0.978 Male I1 H1c
VK163 UK_Oxford_#1 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.019 Male I1 U2e2a1a1
VK167 UK_Oxford_#5 UK Oxford St_John’s_College_Oxford 880-1000 CE 0.902 Male I1 H4a1a4b
VK179 Greenland F2 Greenland Eastern Settlement Ø029a 10-12th centuries CE 1.84 Male I1 K1a3a
VK183 Greenland F6 Greenland Eastern Settlement Ø029a 10-12th centuries CE 0.535 Male I1 T2b21
VK186 Greenland KNK-[6] Greenland Eastern Settlement Ø64 Early Norse 0.813 Male I1 H1ao
VK248 Faroe_22 Faroes Faroes Church2 16-17th centuries CE 0.076 Male I1 H49a
VK316 Denmark_Hessum sk II Denmark Funen Hessum 9-11th centuries CE 1.458 Male I1 K1a4
VK343 Oland_1021 Sweden Oland Oland 9-11th centuries CE 1.259 Male I1 H3h
VK367 Denmark_Bogovej D Denmark Langeland Bogøvej 10th century CE 1.053 Male I1 J1b1a1
VK379 Oland_1077 Sweden Oland Oland 700 CE 0.07 Male I1 U3b1b
VK380 Oland_1078 Sweden Oland Oland 9-11th centuries CE 0.106 Male I1 H27
VK388 Norway_Nordland 253 Norway Nor_North Nordland 8-16th centuries CE 0.975 Male I1 J1c5
VK407 Sweden_Skara 274 Sweden Skara Varnhem 10-12th centuries CE 0.233 Male I1 H1c21
VK410 Russia_Ladoga_5680-15 Russia Ladoga Ladoga 1107+-27 0.129 Male I1 X2b+226
VK420 Norway_Hedmark 2813 Norway Nor_South Hedmark 8-11th centuries CE 1.534 Male I1 I4a
VK482 Estonia_Salme_II-P Estonia Saaremaa Salme 8th century CE 1.085 Male I1 H1a
VK519 Norway_Nordland 4691b Norway Nor_North Nordland 6-10th centuries CE 0.217 Male I1 HV0a1
VK539 Ukraine_Shestovitsa-8870-97 Ukraine Shestovitsa Shestovitsa 10-12th centuries CE 1.574 Male I1 V
VK554 Estonia_Salme_II-L Estonia Saaremaa Salme 8th century CE 0.933 Male I1 W6a
VK190 Greenland late-0996 Greenland Eastern Settlement Ø149 1360 CE 6.495 Male I1a K1a+195
VK223 Russia_Gnezdovo 75-140 Russia Gnezdovo Gnezdovo 10-11th centuries CE 0.35 Male I1a H13a1a1c
VK295 Denmark_Hessum sk 1 Denmark Funen Hessum 9-11th centuries CE 0.57 Male I1a T1a1
VK306 Sweden_Skara 33 Sweden Skara Varnhem 10-12th centuries CE 1.052 Male I1a H15a1
VK409 Russia_Ladoga_5680-14 Russia Ladoga Ladoga 10-12th centuries CE 0.168 Male I1a H3h
VK495 Estonia_Salme_II-C Estonia Saaremaa Salme 8th century CE 1.143 Male I1a H1b
VK506 Estonia_Salme_I-3 Estonia Saaremaa Salme 8th century CE 1.233 Male I1a J1c2
VK151 UK_Oxford_#15 UK Oxford St_John’s_College_Oxford 880-1000 CE 1.142 Male I1a1 T2b4+152
VK220 Russia_Ladoga_5680-11 Russia Ladoga Ladoga 10-12th centuries CE 1.815 Male I1a1 J2b1a
VK257 UK_Dorset-3723 UK Dorset Ridgeway_Hill_Mass_Grave_Dorset 10-11th centuries CE 1.017 Male I1a1 H5a1c1a
VK352 Oland_1012 Sweden Oland Oland 9-11th centuries CE 1.149 Male I1a1 H64
VK50 Gotland_Kopparsvik-53.64 Sweden Gotland Kopparsvik 900-1050 CE 6.231 Male I1a1a1a1a H1+16189
VK279 Denmark_Galgedil AXE Denmark Funen Galgedil 10th century CE 2.393 Male I1a1b I4a
VK320 Denmark_Bogovej Grav S Denmark Langeland Bogøvej 10th century CE 1.368 Male I1a1b U5a1a1
VK400 Sweden_Skara 236 Sweden Skara Varnhem 10-12th centuries CE 1.066 Male I1a1b H1+16239
VK404 Sweden_Skara 277 Sweden Skara Varnhem 10-12th centuries CE 1.425 Male I1a1b U4a2
VK473 Gotland_Kopparsvik-126 Sweden Gotland Kopparsvik 900-1050 CE 1.396 Male I1a1b N1a1a1a1
VK165 UK_Oxford_#3 UK Oxford St_John’s_College_Oxford 880-1000 CE 1.105 Male I1a1b1 U4b1b1
VK219 Russia_Ladoga_5680-10 Russia Ladoga Ladoga 992 ± 27 1.581 Male I1a1b1 T2b6a
VK221 Russia_Ladoga_5757-14 Russia Ladoga Ladoga 911+-27 1.953 Male I1a1b1 K1d
VK297 Denmark_Hundstrup Mose sk 2 Denmark Sealand Hundstrup_Mose 670-830 CE 0.667 Male I1a1b1 J1c2h
VK315 Denmark_Bakkendrup Grav 16 Denmark Sealand Bakkendrup 850-900 CE 0.584 Male I1a1b1 T1a1b
VK488 Estonia_Salme_II-H Estonia Saaremaa Salme 8th century CE 0.901 Male I1a1b1 H5c
VK507 Estonia_Salme_I-4 Estonia Saaremaa Salme 8th century CE 0.823 Male I1a1b1 HV6
VK509 Estonia_Salme_I-6 Estonia Saaremaa Salme 8th century CE 1.328 Male I1a1b1 H1n+146
VK510 Estonia_Salme_I-7 Estonia Saaremaa Salme 8th century CE 1.525 Male I1a1b1 H10e
VK549 Estonia_Salme_II-J Estonia Saaremaa Salme 8th century CE 1.676 Male I1a1b1 T2b5a
VK553 Estonia_Salme_II-M Estonia Saaremaa Salme 8th century CE 1.264 Male I1a1b1 K1c1h
VK70 Denmark_Tollemosegard-EW Denmark Sealand Tollemosegård Late Germanic Iron Age/early Viking 6.684 Male I1a1b1a1 H7d4
VK110 Iceland_115S Iceland Hofstadir Hofstadir 10-13th centuries CE 1.792 Male I1a1b1a1 H10+(16093)
VK176 UK_Oxford_#20 UK Oxford St_John’s_College_Oxford 880-1000 CE 2.415 Male I1a1b1a1 H10
VK281 Denmark_Barse Grav A Denmark Sealand Bårse 10th century CE 2.046 Male I1a1b1a1 T2
VK296 Denmark_Hundstrup Mose sk 1 Denmark Sealand Hundstrup_Mose 660-780 CE 0.458 Male I1a1b1a1 HV6
VK511 Estonia_Salme_II-X Estonia Saaremaa Salme 8th century CE 1.701 Male I1a1b1a1 T2a1a
VK291 Denmark_Bodkergarden Grav D, sk 1 Denmark Langeland Bødkergarden 9th century CE 1.113 Male I1a1b1a4a U5a1a2b
VK98 Iceland_083 Iceland Hofstadir Hofstadir 10-13th centuries CE 2.491 Male I1a1b1a4a2 T2b3b
VK382 Oland_1132 Sweden Oland Oland 700 CE 0.06 Male I1a1b1a4a2 H3g1
VK529 Norway_Nordland 642 Norway Nor_North Nordland 8-9th centuries CE 1.813 Male I1a1b1a4a2 H7
VK547 Norway_Nordland 4727 Norway Nor_North Nordland 8-11th centuries CE 4.732 Male I1a1b1a4a2 V
VK262 UK_Dorset-3739 UK Dorset Ridgeway_Hill_Mass_Grave_Dorset 10-11th centuries CE 1.22 Male I1a2a J1c4
VK301 Denmark_Ladby Grav 4 Denmark Funen Ladby 640-890 CE 0.731 Male I1a2a R0a2b
VK532 Kragehave Odetofter XL718 Denmark Sealand Kragehave Odetofter 100 CE 4.013 Male I1a2a U2e2a1a
VK337 Oland_1064 Sweden Oland Oland 858 ± 68 CE 2.042 Male I1a2a1a1a U5a1b3a
VK357 Oland_1097 Sweden Oland Oland 1053 ± 60 CE 1.387 Male I1a2a1a1a J2b1a
VK363 Denmark_Bogovej BT Denmark Langeland Bogøvej 10th century CE 1.337 Male I1a2a1a1a U4b1a1a1
VK327 Denmark_Ribe 6 Denmark Jutland Ribe 9-11th centuries CE 1.164 Male I1a2a1a1a1a H6a1a5
VK552 Estonia_Salme_II-K Estonia Saaremaa Salme 8th century CE 1.379 Male I1a2a1a1d H10e
VK146 UK_Oxford_#10 UK Oxford St_John’s_College_Oxford 880-1000 CE 1.182 Male I1a2a1a1d1a J1c3e1
VK483 Estonia_Salme_II-V Estonia Saaremaa Salme 8th century CE 1.78 Male I1a2a1a1d1a H16
VK485 Estonia_Salme_II-O Estonia Saaremaa Salme 8th century CE 0.709 Male I1a2a1a1d1a H16
VK492 Estonia_Salme_II-B Estonia Saaremaa Salme 8th century CE 1.015 Male I1a2a1a1d1a H1b5
VK515 Norway_Nordland 4512 Norway Nor_North Nordland 10th century CE 0.636 Male I1a2a1a1d1a H52
VK524 Norway_Nordland 3708 Norway Nor_North Nordland 10th century CE 1.606 Male I1a2a1a1d1a HV0a1
VK555 Estonia_Salme_II-I Estonia Saaremaa Salme 8th century CE 1.099 Male I1a2a1a1d1a U3b1b
VK490 Estonia_Salme_II-N Estonia Saaremaa Salme 8th century CE 0.946 Male I1a2a1a1d1a1a H16
VK491 Estonia_Salme_II-Õ Estonia Saaremaa Salme 8th century CE 1.433 Male I1a2a1a1d1a1a H6a1a
VK497 Estonia_Salme_II-Ö Estonia Saaremaa Salme 8th century CE 1.447 Male I1a2a1a1d1a1a H16
VK443 Oland_1101 Sweden Oland Oland 9-11th centuries CE 2.107 Male I1a2a1a1d2 U5b2b5
VK445 Denmark_Gl Lejre-A1896 Denmark Sealand Gl._Lejre 9-11th centuries CE 1.363 Male I1a2a2 U3b
VK446 Denmark_Galgedil LS Denmark Funen Galgedil 9-11th centuries CE 1.531 Male I1a2a2 U5a1a1+16362
VK496 Estonia_Salme_II-W Estonia Saaremaa Salme 8th century CE 1.978 Male I1a2a2a H1a
VK521 Sol941 Grav900 Brondsager Torsiinre Denmark Sealand Brondsager_Torsiinre 300 CE 4.538 Male I1a2a2a H16b
VK275 Denmark_Kaargarden 217 Denmark Langeland Kaagården 10th century CE 0.448 Male I1c H

Thanks for sharing that! It’s nice to see that there are two I-Z2041 (I1a2a2) samples and two I-Z2040 (I1a2a2a) samples all four of which are parent clades of mine. I wonder if they tested deeper subclades and they came up negative, or if that was the extent of their testing for these four samples.

deadly77
07-18-2019, 08:00 AM
The longhand nomenclature was doing my head in, so I did a bit of filter and translate so I could follow. By my count, the 442 new samples in this paper, 92 are I1 or below, 2 are I and one IJ. Way more than we've ever had before. Breakdown below I1:

I1 29
I1a I-DF29 7
I1a1 I-Z2336 4
I1a1b I-Z2337 5
I1a1b1 I-L22 11
I1a1a1a1a I-M72 1
I1a1b1a1 I-P109 6
I1a1b1a4a I-Z74 1
I1a1b1a4a2 I-L813 4
I1a2a I-Z59 3
I1a2a1a1d I-CTS7362 1
I1a2a1a1a I-Z140 3
I1a2a1a1d1a I-Z73 7
I1a2a1a1a1a I-YSC0000261 1
I1a2a1a1d2 I-L1248 1
I1a2a1a1d1a1a I-L1302 3
I1a2a2 I-Z2041 2
I1a2a2a I-Z2040 2
I1c I-Z17925 1

All these assuming correct calls and reference for ISOGG tree - they say that they're using the 2019 version of the ISOGG tree. To my knowledge, there's no raw data in the form of BAM files or similar available yet to check these calls or dig a bit deeper. It appears that they used NGS and shotgun sequencing - started with 528 ancient samples and then whittled that down to 442 after removing poorly preserved and contaminated samples. From this, sequenced 376 samples and coverage between 0.1 and 11.7X, of which 216 were above 1X. Average depth of individual samples can be found in Supplementary Table 2: Sequencing statistics.

oz
07-18-2019, 08:51 AM
The longhand nomenclature was doing my head in, so I did a bit of filter and translate so I could follow. By my count, the 442 new samples in this paper, 91 are I1 or below, 2 are I and one IJ. Way more than we've ever had before. Breakdown below I1:

I1 29
I1a I-DF29 7
I1a1 I-Z2336 4
I1a1b I-Z2337 5
I1a1b1 I-L22 11
I1a1a1a1a I-M72 1
I1a1b1a1 I-P109 6
I1a1b1a4a I-Z74 1
I1a1b1a4a2 I-L813 4
I1a2a I-Z59 3
I1a2a1a1d I-CTS7362 1
I1a2a1a1a I-Z140 3
I1a2a1a1d1a I-Z73 7
I1a2a1a1a1a I-YSC0000261 1
I1a2a1a1d2 I-L1248 1
I1a2a1a1d1a1a I-L1302 3
I1a2a2 I-Z2041 2
I1a2a2a I-Z2040 2
I1c I-Z17925 1

All these assuming correct calls and reference for ISOGG tree - they say that they're using the 2019 version of the ISOGG tree. To my knowledge, there's no raw data in the form of BAM files or similar available yet to check these calls or dig a bit deeper. It appears that they used NGS and shotgun sequencing - started with 528 ancient samples and then whittled that down to 442 after removing poorly preserved and contaminated samples. From this, sequenced 376 samples and coverage between 0.1 and 11.7X, of which 216 were above 1X. Average depth of individual samples can be found in Supplementary Table 2: Sequencing statistics.

It's raining I1s haha... Even though my subclade and Ydna ancestor seemingly had nothing at all to do with this, I'm happy for you guys.. Finally a massive aDna study with I1 in the biggest spotlight.

When the raw data gets released it will be a lot to keep you busy.

JonikW
07-18-2019, 10:06 AM
I believe I1a2a1a1a1a I-YSC0000261 is also known as S1954, as many of us got as our terminal SNP from Britain's DNA back in the day. Any idea of the TMRCA for that?

deadly77
07-18-2019, 11:12 AM
I believe I1a2a1a1a1a I-YSC0000261 is also known as S1954, as many of us got as our terminal SNP from Britain's DNA back in the day. Any idea of the TMRCA for that?

Yep, that's right. Largest branch of I-Z140. Pretty much everyone who is I-YSC0000261 is I-L338 - I'm not aware of anyone who is confirmed YSC0000261+ and L338-, but a fair few of the tests stop at that point (Nat Geo, FTDNA I1 SNP pack, AncestryDNA).

YFull has the TMRCA at 3400 ybp, with data from over 100 samples, ranging from 32.65 adjusted SNPs at 4775 ybp to 16.9 adjusted SNPs at 2500 ybp. All of these at I-L338 or below. On my Age Estimation tab on my YFull hompeage, YFull has listed all of the SNPs at the I-YSC261 level twice with I-L338 level and assigned 0.5 weight to each. Similar in the Hg and SNPs tab where they use the designation: level I-L338 <-> I-YSC261 next to some of these SNPs.

romelson
07-18-2019, 11:18 AM
Converted the subclades of the hg I1 samples. Like others already said. Subclade resolution is quite bad. It's like known branches five or six years ago. But maybe there are BAM files?

35 VK50, Gotland, Kopparsvik, I1a1a1a1a = I1-M227
46 VK70, Denmark, Tollemosegard, I1a1b1a1 = I1-P109
47 VK71, Denmark, Tollemosegard, I1 = I1-M253
60 VK98, Iceland, I1a1b1a4a2 = I1-L813
87 VK144, UK, Oxford, I1 = I1-M253
91 VK148, UK, Oxford, I1 = I1-M253
92 VK149, UK, Oxford, I1 = I1-M253
94 VK151, UK, Oxford, I1a1 = I1-CTS6364
99 VK157, Poland, Bodzia, I1 = I1-M253
104 VK163, UK, Oxford, I1 = I1-M253
106 VK165, UK, Oxford, I1a1b1 = I1-L22
108 VK167, UK, Oxford, I1 = I1-M253
116 VK176, UK, Oxford, I1a1b1a1 = I1-P109
119 VK179, Greenland, I1 = I1-M253
122 VK183, Greenland, I1 = I1-M253
125 VK186, Greenland, I1 = I1-M253
128 VK190, Greenland, I1a = I1-DF29
150 VK219, Russia, Ladoga, I1a1b1 = I1-L22
151 VK220, Russia, Ladoga, I1a1 = I1-CTS6364
152 VK221, Russia, Ladoga, I1a1b1 = I1-L22
154 VK223, Russia, Gnezdovo, I1a = I1-DF29
173 VK248, Faroes, I1 = I1-M253
180 VK257, UK, Dorset, I1a1 = I1-CTS6364
185 VK262, UK, Dorset, I1a2a = I1-Z59
197 VK275, Denmark, Kaargarden, I1c = I1-Z17925
200 VK279, Denmark, Galgedil, I1a1b = I1-CTS10028
202 VK281, Denmark, Galgedil, I1a1b1a1 = I1-P109
211 VK291, Denmark, Bodkergarden, I1a1b1a4a = I1-Z74
214 VK295, Denmark, Hessum, I1a = I1-DF29
215 VK296, Denmark, Hundstrup, I1a1b1a1 = I1-P109
216 VK297, Denmark, Hundstrup, I1a1b1 = I1-L22
219 VK301, Denmark, Ladby, I1a2a = I1-Z59
222 VK306, Sweden, Skara, I1a = I1-DF29
228 VK315, Denmark, Bakkendrup, I1a1b1 = I1-L22
229 VK316, Denmark, Hessum, I1 = I-M253
233 VK320, Denmark, Bogovej, I1a1b = I1-CTS10028
239 VK327, Denmark, Ribe, I1a2a1a1a1a = I1-Z2535
248 VK337, Oland, I1a2a1a1a = I1-Z140
253 VK343, Oland, I1 = I1-M253
261 VK352, Oland, I1a1 = I1-CTS6364
265 VK357, Oland, I1a2a1a1a = I1-Z140
270 VK363, Denmark, Bogovej, I1a2a1a1a = I1-Z140
274 VK367, Denmark, Bogovej, I1 = I1-M253
281 VK379, Oland, I1 = I1-M253
282 VK380, Oland, I1 = I1-M253
283 VK382, Oland, I1a1b1a4a2 = I1-L813
301 VK400, Sweden, Skara, I1a1b = I1-CTS10028
305 VK404, Sweden, Skara, I1a1b = I1-CTS10028
308 VK407, Sweden, Skara, I1 = I1-M253
310 VK409, Russia, Ladoga, I1a = I1-DF29
311 VK410, Russia, Ladoga, I1 = I1-M253
319 VK420, Norway, Hedmark, I1 = I1-M253
340 VK443, Oland, I1a2a1a1d2 = I1-L1248
342 VK445, Denmark, Gl Lejre, I1a2a2 = I1-Z2041
343 VK446, Denmark, Galgedil, I1a2a2 = I1-Z2041
367 VK473, Gotland, Kopparsvik, I1a1b = I1-CTS10028
376 VK482, Estonia, Salme, I1 = I1-M253
377 VK483, Estonia, Salme, I1a2a1a1d1a = I1-Z73
379 VK485, Estonia, Salme, I1a2a1a1d1a = I1-Z73
382 VK488, Estonia, Salme, I1a1b1 = I1-L22
384 VK490, Estonia, Salme, I1a2a1a1d1a1a = I1-L1302
385 VK491, Estonia, Salme, I1a2a1a1d1a1a = I1-L1302
386 VK492, Estonia, Salme, I1a2a1a1d1a = I1-Z73
389 VK495, Estonia, Salme, I1a = I1-DF29
390 VK496, Estonia, Salme, I1a2a2a = I1=Z2040
391 VK497, Estonia, Salme, I1a2a1a1d1a1a = I1-L1302
395 VK506, Estonia, Salme, I1a = I1-DF29
396 VK507, Estonia, Salme, I1a1b1 = I1-L22
398 VK509, Estonia, Salme, I1a1b1 = I1-L22
399 VK510, Estonia, Salme, I1a1b1 = I1-L22
400 VK511, Estonia, Salme, I1a1b1a1 = I1-P109
404 VK515, Norway, Nordland, I1a2a1a1d1a = I1-Z73
408 VK529, Norway, Nordland, I1 = I1-M253
410 VK521, Brondsager Torsiinre, I1a2a2a = I1=Z2040
413 VK524, Norway, Nordland, I1a2a1a1d1a = I1-Z73
418 VK529, Norway, Nordland, I1a1b1a4a2 = I1-L813
421 VK532, Kragehave Odetofter, I1a2a = I1-Z59
428 VK539, Ukraine, Shestovitsa, I1=I1-M253
436 VK547, Norway, Nordland, I1a1b1a4a2 = I1-L813
438 VK549, Estonia, Salme, I1a1b1 = I1-L22
441 VK552, Estonia, Salme, I1a2a1a1d = I1-CTS7362
442 VK553, Estonia, Salme, I1a1b1 = I1-L22
443 VK554, Estonia, Salme, I1 = I1-M253
444 VK555, Estonia, Salme, I1a2a1a1d1a = I1-Z73

Spot any typos? Please reply.

deadly77
07-18-2019, 11:23 AM
It's raining I1s haha... Even though my subclade and Ydna ancestor seemingly had nothing at all to do with this, I'm happy for you guys.. Finally a massive aDna study with I1 in the biggest spotlight.

When the raw data gets released it will be a lot to keep you busy.

Indeed. I guess it's down to if you're glass half-full or glass half-empty. Many on that list are definitively not down your subclade, but there's several more that aren't defined more specifically than I1 or I-DF29. Could be a few reasons for that - coverage might not be good enough to call definitively, the software that they are using (YLeaf?) may not be reading the appropriate SNPs to make the assignment, or the authors aren't as familiar with the I1 tree to place the called SNPs to appropriate subclade. My feeling is since they're able to call I1a (I-DF29) and I1b (I-Z17925) or lower down for a lot of the samples, they would have done so rather than just I1. That suggests to me the samples that are just I1 are lower coverage than the others, but we'll have a better idea once we get into the raw data.

oz
07-18-2019, 08:19 PM
Indeed. I guess it's down to if you're glass half-full or glass half-empty. Many on that list are definitively not down your subclade, but there's several more that aren't defined more specifically than I1 or I-DF29. Could be a few reasons for that - coverage might not be good enough to call definitively, the software that they are using (YLeaf?) may not be reading the appropriate SNPs to make the assignment, or the authors aren't as familiar with the I1 tree to place the called SNPs to appropriate subclade. My feeling is since they're able to call I1a (I-DF29) and I1b (I-Z17925) or lower down for a lot of the samples, they would have done so rather than just I1. That suggests to me the samples that are just I1 are lower coverage than the others, but we'll have a better idea once we get into the raw data.

Right, it could be just an unlucky occurrence, it could be one of the lower coverage ones, or maybe it's just because this subclade was very minimal amongst the Vikings like its distribution is today amongst Scandinavians. Maybe these authors didn't even test for it which would be quite incompetent of them, but they probably did.

For now my takeaway from this is that the Z63 subclade is the most mysterious and puzzling branch of the I1 hg and hopefully some future studies will shed more light on it.

spruithean
07-18-2019, 08:38 PM
Right, it could be just an unlucky occurrence, it could be one of the lower coverage ones, or maybe it's just because this subclade was very minimal amongst the Vikings like its distribution is today amongst Scandinavians. Maybe these authors didn't even test for it which would be quite incompetent of them, but they probably did.

For now my takeaway from this is that the Z63 subclade is the most mysterious and puzzling branch of the I1 hg and hopefully some future studies will shed more light on it.

I've been waiting for more info on that Wielbark I-Z63 sample, honestly. It'd be nice to find out more. Also, there was an I-Z63 sample among the Longobards too. So it's not entirely absent from the aDNA list just quite rare.

Isn't the general agreement right now that I-Z63 was spread by Goths or other Eastern Germanic groups?

JonikW
07-18-2019, 08:39 PM
Right, it could be just an unlucky occurrence, it could be one of the lower coverage ones, or maybe it's just because this subclade was very minimal amongst the Vikings like its distribution is today amongst Scandinavians. Maybe these authors didn't even test for it which would be quite incompetent of them, but they probably did.

For now my takeaway from this is that the Z63 subclade is the most mysterious and puzzling branch of the I1 hg and hopefully some future studies will shed more light on it.

I see what you mean after looking at YFull. It seems to have a wider distribution than most. What's your theory on your own Y6228? Could it have spread out from somewhere in the Saxony region, moving south with the Lombards as well as other Germanic tribes, with some heading to Italy over time but others to France, England and up into Scandinavia?

JonikW
07-18-2019, 08:44 PM
I've been waiting for more info on that Wielbark I-Z63 sample, honestly. It'd be nice to find out more. Also, there was an I-Z63 sample among the Longobards too. So it's not entirely absent from the aDNA list just quite rare.

Isn't the general agreement right now that I-Z63 was spread by Goths or other Eastern Germanic groups?

On your last point, it's strange that so much of it ended up in Britain if so. It almost looks like it was at some kind of crossroads before the Migration Period, such as the area where the Saxons and Lombards came from.

spruithean
07-18-2019, 08:52 PM
On your last point, it's strange that so much of it ended up in Britain if so. It almost looks like it was at some kind of crossroads before the Migration Period, such as the area where the Saxons and Lombards came from.

That could very well be, Longobards and Saxons (and Frisians) had some level of interaction at a few points throughout history. I think we just need more Z63 from aDNA to really fully understand what may have happened.

JonikW
07-18-2019, 08:57 PM
That could very well be, Longobards and Saxons (and Frisians) had some level of interaction at a few points throughout history. I think we just need more Z63 from aDNA to really fully understand what may have happened.

Fully agreed. Another 90 I1 samples, this time from Iron Age Germanic lands, and a similar study of early Anglo-Saxon England should do the trick.:)

deadly77
07-18-2019, 09:31 PM
Maybe these authors didn't even test for it which would be quite incompetent of them, but they probably did.



No, they did shotgun sequencing, not SNP capture.

oz
07-18-2019, 09:33 PM
Yeah, that's where the limited data so far seems to be pointing that Z63 spread out mostly in the earlier Germanic migrations period, prior to Viking expansions. It seems to be more common in continental Europe and even England than in Scandinavia. It's very hard to venture a guess where it actually originated and when since it's so uncommon in Scandinavia, and all of this ties in with the history of all the I1 subclades because Z63 still has a very close common ancestor with other subclades. It's all an interesting puzzle that I don't have the knowledge of history and stuff and not enough aDna data yet to connect the dots.

JonikW
07-18-2019, 09:34 PM
No, they did shotgun sequencing, not SNP capture.

Does that bode well or ill for what we may discover later?

oz
07-18-2019, 09:49 PM
No, they did shotgun sequencing, not SNP capture.

I'm sure they didn't shoot at the remains, in other words I have no clue what you're saying, can you clarify your point in layman terms? Lol

deadly77
07-18-2019, 10:24 PM
Does that bode well or ill for what we may discover later?

There's advantages and disadvantages to both. SNP capture-based methods focus on specific targets in the genome with the aim to raise their relative coverage in the resulting data. This allows for the generation of data with higher coverage and higher overlaps among the SNPs that you're targetting. This is helpful in the case of poorly preserved samples (which is the case for a lot of ancient DNA), in that it can give robust haplogroup inferences. For example with the samples for the Hungarian Conqueror preprint - it verfies that two of the samples are I1 from high read of two SNPs and negative for L22. And it's a less expensive as you're cutting down on the amount of DNA that you're sequencing. The limitation is that you basically throw away all of the SNPs that you may want to read outside of those that you're targetting - back to the Hungarian Conquerer samples if you want to know if either of the two I1 samples from that preprint are I-Z58, I-Z63, I-Z17925 or some branch of I-Z2336 that isn't L22, you're SOL as everything for those just comes up as no call for all those SNPs (and a lot else).

Shotgun sequencing is less directed - basically scan everything you can in the genome (which is more intensive and therefore expensive on the sequencer), take the read ouputs and map them to the reference genome. You're getting a lot of stuff you're not looking for - say you're only interested in the Y chromosome, most of the data that you get out of the sequencer will be autosomal. But you're also going to get things that you're interested in that are outside of the range of the designed SNP capture - back to the Hungarian Conquerer samples, if they were I-Z63, shotgun sequencing would be more likely to pick that up (or something that corroborates that) than a SNP capture which isn't looking for it. One of the limitations of the shotgun compared to the SNP capture is that there's less of a guaranatee of finding the SNPs that you want most due to bad coverage or read depth in a poorly preserved sample - for example you're more likely to get low read false positives.

I prefer shotgun sequencing because I think the benefits outweigh the limitations imposed by SNP capture. If you want a direct comparison in one paper, the Lombard samples SZ45 was done by shotgun sequencing and CL63 was SNP capture, and we got a lot more information out of SZ45. But a big part of that was that SZ45 was a high quality sample with lots of coverage and multi-read SNPs. Other end of the scale was the Icelandic sample DAV-A9 or the Anglo-Saxon NO3423 where we didn't get anything further than I-DF29 as the quality wasn't as good.

I guess the modern testing analogy is Big Y vs. whole genome sequencing. Big Y is an enrichment assay, in principle similar to the SNP capture (although Big Y is way more comprehensive than the SNP capture used for ancient DNA samples by a lot of researchers), while WGS is basically the shotgun but again quality is important. A 30x WGS is better than a Big Y, but a 1x or 2x WGS is not.

But ultimately the biggest decision factor for the researcher is cost. They can get more samples sequenced (although with less data per sample). Back to the Hungarian Conquerer preprint, they may have had a choice between analyzing 5 samples with shotgun sequencing that would give them a lot more subclade data per sample, or they could do 46 samples and just get basic high level haplogroups that answered the questions that they were interested in.

deadly77
07-18-2019, 10:31 PM
I'm sure they didn't shoot at the remains, in other words I have no clue what you're saying, can you clarify your point in layman terms? Lol

Hopefully my reply to JonikW in #379 above differentiates the two. But it means they didn't intentionally exclude Z63 (or other SNPs) from their assay.

oz
07-18-2019, 10:38 PM
I see what you mean after looking at YFull. It seems to have a wider distribution than most. What's your theory on your own Y6228? Could it have spread out from somewhere in the Saxony region, moving south with the Lombards as well as other Germanic tribes, with some heading to Italy over time but others to France, England and up into Scandinavia?

It looks like Z63 is as widely distributed as I1a1 and I1a2, but I guess it's generally less common and smaller compared to them especially towards the north, I1a2 more so Northwest and I1a1 more so Scandinavia and the Baltic. As you can see that pattern on the ftdna haplotree for example. And you can't be too certain about a lot of the European regions distribution because the number of testers is small and the likelyhood of sample bias. But if it's any indication that's what it looks like. But the most confusing part to me is why it's so freakin small compared to I1a1 and I1a2 in Scandinavia? It's like 20 times or more less common in Sweden, Norway and Findland and maybe a little less in Denmark but they're not testing as much, still it looks about 10 times less common there lol.
As far as who spread it around I have no idea it could be a bunch of different groups of people. The Y6228 is as widespread as Z63 and you can't really pinpoint its origin or biggest distribution to any region. I would guess Germany and surrounds but again not enough testers too small numbers etc.

Probably wasn't spread by Vikings though haha.

deadly77
07-18-2019, 10:48 PM
I've started to add the samples from the "Population genomics of the Viking world" preprint to the Haplogroup I1 Ancient Samples Map. This will take some time as there's a lot of them - there are more than three times as many new samples as there was on there before.

Can't really add anything additional (such as what's on there in the samples from other papers) from a Y-DNA perspective until the BAM files are available, but can at least put them on the map with the haplogroup designation reported in the preprint and some summary context about the sample - the supplementary data for the preprint is rather informative and worth reading in that regard.

So far added the I-YSC0000261, I-Z140, I-P109 and I-Z2041 samples.

I also added the urm035 and urm045 from Sigtuna on there as well. Analysis not complete but enough to go on there as a work in progress.

JonikW
07-18-2019, 11:23 PM
Hopefully my reply to JonikW in #379 above differentiates the two. But it means they didn't intentionally exclude Z63 (or other SNPs) from their assay.

Are they likely to have gleaned everything possible from the 1x to 2x samples using the shotgun method or is there more to be learned by looking at the SNPs as I've seen you do in the past?

deadly77
07-18-2019, 11:57 PM
Are they likely to have gleaned everything possible from the 1x to 2x samples using the shotgun method or is there more to be learned by looking at the SNPs as I've seen you do in the past?

No - it appears that they used a program called YLeaf to do the Y-DNA assignments, so they're using software to automate the output of the Y-DNA results rather than manually review the BAM. I've seen this software as well as other similar ones referenced by researchers in some of earlier papers that I've looked at. The preprint authors also add "restricting our analysis to 26,083 biallelic SNPs from the ISOGG (International Society of Genetic Genealogy) 2019 database" in the second supplementary information file.

The ISOGG tree is rather less comprehensive and behind the trees that YFull and FTDNA use. So the authors are using a less complete reference tree, and their own supplementary information states that they're using a subset of the SNPs that are in the ISOGG tree - ie, not the full ISOGG tree.

I'm not sure how the YLeaf software accepts or rejects SNP calls. For example, if there's less than 5 reads, does it reject the SNP as not read? Less than 2? What about if there's 9 derived reads and 1 ancestral? Does it pick up one read SNPs? Does it have quality control to monitor the adjacent positions to see if there's a high level of mutation in that region? Will it accept a downstream SNP if an upstream SNP is not read (ie. Z140+ but Z60 no call)? I don't know the answer to any of these but I can anticipate a lot of circumstances where automated software will miss things.

So a combination of a less comprehensive reference tree and an automated software Y-DNA analysis. I'm pretty confident I'd be able to find more information by manually reviewing the BAM file and I probably have a better understanding of the I1 subclades. It just takes me longer to get through it than a computer. The main barrier to me is gaps in the data from lower quality samples, so I can't make a difference in that regard. But I believe I can make a better assignment in regard to reviewing the raw data that is there - that's been the case with a lot of the samples from other papers.

C.Goodell
07-19-2019, 01:59 PM
I was curious if Sigtuna 84005 has a read at position 19318850 ref is T , C = FGC12562

I tried finding the file at ena but was lost

When the data was available I was going to check VK291 in the new paper at biorivix. That sample is Z74 * as well.

deadly77
07-19-2019, 02:36 PM
I was curious if Sigtuna 84005 has a read at position 19318850 ref is T , C = FGC12562

I tried finding the file at ena but was lost

When the data was available I was going to check VK291 in the new paper at biorivix. That sample is Z74 * as well.

I had a look in the BAM file but there is no read at 19318850. Coverage is a bit patchy in this one - 1.03x according to the paper. When I was looking into the BAM file there were lots of no calls and all the calls I found were one or two reads.

Derived SNPs: Z74 1T, Z75 2A, CTS1793 1C, CTS2208 1A, CTS4791 1G, Y2562 2C, Y2565 1C, Y20288 1A

Ancestral SNPs: Y31675 1C, Y38726 1A, FGC8782 1T, Z135 1C, Y20595 2G, Y20594 2G, Y24701 1C, Y24703 1T, CTS7676 1A, Y2566 2A, L813 1A, Z720 1A

No call SNPs: CTS5476, Y2561, Y2560, Y2567, Y2563, Y20287, Y20593, Y20289, Y20596, FGC60542, Y24702, Y24704, Y24705, Y24706, Y24707, Y29654, CTS12194, CTS9167, Z718, CTS9364, FGC9478.

The BAM file for 84005 can be found here: https://www.ebi.ac.uk/ena/data/view/ERS2540884 - click on "BAM File 1" under "Submitted Files (FTP)" - it's 2.98GB so shoudln't take too long to download, based on your connection.

C.Goodell
07-19-2019, 05:10 PM
Thanks

mwauthy
07-19-2019, 05:44 PM
No - it appears that they used a program called YLeaf to do the Y-DNA assignments, so they're using software to automate the output of the Y-DNA results rather than manually review the BAM. I've seen this software as well as other similar ones referenced by researchers in some of earlier papers that I've looked at. The preprint authors also add "restricting our analysis to 26,083 biallelic SNPs from the ISOGG (International Society of Genetic Genealogy) 2019 database" in the second supplementary information file.

The ISOGG tree is rather less comprehensive and behind the trees that YFull and FTDNA use. So the authors are using a less complete reference tree, and their own supplementary information states that they're using a subset of the SNPs that are in the ISOGG tree - ie, not the full ISOGG tree.

I'm not sure how the YLeaf software accepts or rejects SNP calls. For example, if there's less than 5 reads, does it reject the SNP as not read? Less than 2? What about if there's 9 derived reads and 1 ancestral? Does it pick up one read SNPs? Does it have quality control to monitor the adjacent positions to see if there's a high level of mutation in that region? Will it accept a downstream SNP if an upstream SNP is not read (ie. Z140+ but Z60 no call)? I don't know the answer to any of these but I can anticipate a lot of circumstances where automated software will miss things.

So a combination of a less comprehensive reference tree and an automated software Y-DNA analysis. I'm pretty confident I'd be able to find more information by manually reviewing the BAM file and I probably have a better understanding of the I1 subclades. It just takes me longer to get through it than a computer. The main barrier to me is gaps in the data from lower quality samples, so I can't make a difference in that regard. But I believe I can make a better assignment in regard to reviewing the raw data that is there - that's been the case with a lot of the samples from other papers.
I’m looking forward to your future BAM analysis. Maybe there’s hope that I share more SNPs downstream of I-Z2041 and I-Z2040 with those 4 samples :)

spruithean
07-19-2019, 06:30 PM
No - it appears that they used a program called YLeaf to do the Y-DNA assignments, so they're using software to automate the output of the Y-DNA results rather than manually review the BAM. I've seen this software as well as other similar ones referenced by researchers in some of earlier papers that I've looked at. The preprint authors also add "restricting our analysis to 26,083 biallelic SNPs from the ISOGG (International Society of Genetic Genealogy) 2019 database" in the second supplementary information file.

The ISOGG tree is rather less comprehensive and behind the trees that YFull and FTDNA use. So the authors are using a less complete reference tree, and their own supplementary information states that they're using a subset of the SNPs that are in the ISOGG tree - ie, not the full ISOGG tree.

I'm not sure how the YLeaf software accepts or rejects SNP calls. For example, if there's less than 5 reads, does it reject the SNP as not read? Less than 2? What about if there's 9 derived reads and 1 ancestral? Does it pick up one read SNPs? Does it have quality control to monitor the adjacent positions to see if there's a high level of mutation in that region? Will it accept a downstream SNP if an upstream SNP is not read (ie. Z140+ but Z60 no call)? I don't know the answer to any of these but I can anticipate a lot of circumstances where automated software will miss things.

So a combination of a less comprehensive reference tree and an automated software Y-DNA analysis. I'm pretty confident I'd be able to find more information by manually reviewing the BAM file and I probably have a better understanding of the I1 subclades. It just takes me longer to get through it than a computer. The main barrier to me is gaps in the data from lower quality samples, so I can't make a difference in that regard. But I believe I can make a better assignment in regard to reviewing the raw data that is there - that's been the case with a lot of the samples from other papers.

I'm wary of the automated Y-calling software ever since the Central/South Asia paper came out, I looked through the Y-calls file for that paper for fun and there were a fair number of inconsistencies yet the program still considered single positive reads as legitimate despite 10+ negative reads.

Anyway, I saw the ancient I1 Google map and noticed you had added more pins. It's nice to see the map gain some more locations. This paper is loaded with I1, it's nice to see this finally.

JonikW
07-19-2019, 08:19 PM
I'm wary of the automated Y-calling software ever since the Central/South Asia paper came out, I looked through the Y-calls file for that paper for fine and there were a fair number of inconsistencies yet the program still considered single positive reads as legitimate despite 10+ negative reads.

Anyway, I saw the ancient I1 Google map and noticed you had added more pins. It's nice to see the map gain some more locations. This paper is loaded with I1, it's nice to see this finally.

It's a pleasure to see deadly77's map filling out. I wasn't expecting to see any additions this quickly so thanks to deadly as well as spruithean for pointing it out. I hope those Z140s in particular will be pushed a little further downstream in a few months' time.

spruithean
07-19-2019, 08:20 PM
Apparently the raw data won't be available until the paper is published in Nature. So we may be waiting quite a bit longer... sigh...

JonikW
07-19-2019, 08:54 PM
Apparently the raw data won't be available until the paper is published in Nature. So we may be waiting quite a bit longer... sigh...

I assume now that's what the three to five months meant in the link I posted last week. It said the study itself was finished, which I guess meant the preprint was ready for release. So we should have the data in time for Christmas.

deadly77
07-20-2019, 12:03 AM
I’m looking forward to your future BAM analysis. Maybe there’s hope that I share more SNPs downstream of I-Z2041 and I-Z2040 with those 4 samples :)

I'll do what I can with all the I1 samples, although it will take me a while to get through them all. I'll go through them in a similar order to that which I'm adding to the Google map - I-Z140 first because myself, JonikW, JMcB, Spruithean, deanovermont are most interested in that, then the I-P109 samples as one of the admins of that subcalde has been good to me and then I'll get to I-Z2041/Z2040 for your interest. If there were easy looking I-Z63 options for Oz and Sassoneg I'd include those too, but those will probably involve a bit of digging.

I actually misread JonikW's question, but I think I gave the answer he was more looking for. From the outside, I'm seeing four factors in what we can get from these ancient samples when they are reported in publications:

1) How old the sample is and the conditions that it's been stored in.
2) The assay that the resesearchers use - WGS or enrichment (essentially shotgun or SNP capture), read length, depth, etc.
3) How the raw data is read - SNP calls, thresholds, corroborating or disconfirming SNP calls, filtering out the false positives, whether by individual or an automated analysis.
4) Taking the read data and placing it correctly on a phylogenetic tree.

No one can affect the first point - the remains have been where they are for centuries and nothing changes that. The second point the researchers can affect but it may very much depend on the quality of the sample in point one - a high intensity sequenced low quality sample may not give much information, despite the best efforts of the researchers. Points 3 and 4 are where an independent analysis can make a difference, but points 1 and 2 are beyond control. If the assay design was not very comprehensive (such as in the Hungarian Conqueror paper), there's not too much more an independent analysis can do. Same as if the assay was comprehensive (such as in the ancient Icelanders paper) but the sample quality wasn't too great such as DAV-A9. But if there's good data (HSJ-A1, SBT-A1, SVK-A1, SZ45, etc.) an independent analysis can add a lot more compared to where the publication got to. In most cases the primary reason for the publication is not the most downstream Y-DNA subclade - it's usually just an entry in a table, so the researchers have different interests to ourselves.

So I'll do what I can, but I can only make a difference in points 3 and 4 - 1 and 2 I can't do much about so I can't promise anything.

deadly77
07-20-2019, 12:19 AM
I'm wary of the automated Y-calling software ever since the Central/South Asia paper came out, I looked through the Y-calls file for that paper for fine and there were a fair number of inconsistencies yet the program still considered single positive reads as legitimate despite 10+ negative reads.

Anyway, I saw the ancient I1 Google map and noticed you had added more pins. It's nice to see the map gain some more locations. This paper is loaded with I1, it's nice to see this finally.

Yes, I'm wary as well. I make mistakes (as I'm human) but I tend to be logical and double check if I find a conflict, while I'm not sure that an automated caller would do the same. I think the automated analysis is why SVK-A1 in the ancient Icelandic genomes paper got assigned as I1. SVK-A1 is a no call for DF29 and a one read positive for Z131. If that's the decision tree the software stops there. I looked at several SNPs downstream of Z131 and kept coming up with negatives. This didn't seem right so then I went and checked phyloequivalent SNPs for SVK-A1 and came up with much stronger positive reads for some of those. Got to thinking that SVK-A1's Z131+ result was a false positive and managed to find a lot of SNPs that corroborated a path down to I-FGC21682. I was fairly sure, but wanted a second opinion so I asked YFull to check and they agreed.

The automation is a lot quicker (and you pretty much need it for autosomal because there's just so much more data) but for now I'd rather go for the manual reviewin Y-DNA. It takes longer but I'm more sure of the readout.

Yes, I started adding the samples to the map. I can't do my own Y-DNA analysis yet but I figure that it's something I can do while waiting for BAM files. Also, it gives me a chance to read up on the archeological context of a lot of these samples. The supplementary infomation file is an absolute beast on this preprint. Credit to the authors.

deadly77
07-20-2019, 12:23 AM
It's a pleasure to see deadly77's map filling out. I wasn't expecting to see any additions this quickly so thanks to deadly as well as spruithean for pointing it out. I hope those Z140s in particular will be pushed a little further downstream in a few months' time.

The new I-Z140 samples are the first on my list for a closer look when the BAM files come out. Vested interest... ;)

JonikW
07-20-2019, 12:41 AM
Yes, I'm wary as well. I make mistakes (as I'm human) but I tend to be logical and double check if I find a conflict, while I'm not sure that an automated caller would do the same. I think the automated analysis is why SVK-A1 in the ancient Icelandic genomes paper got assigned as I1. SVK-A1 is a no call for DF29 and a one read positive for Z131. If that's the decision tree the software stops there. I looked at several SNPs downstream of Z131 and kept coming up with negatives. This didn't seem right so then I went and checked phyloequivalent SNPs for SVK-A1 and came up with much stronger positive reads for some of those. Got to thinking that SVK-A1's Z131+ result was a false positive and managed to find a lot of SNPs that corroborated a path down to I-FGC21682. I was fairly sure, but wanted a second opinion so I asked YFull to check and they agreed.

The automation is a lot quicker (and you pretty much need it for autosomal because there's just so much more data) but for now I'd rather go for the manual reviewin Y-DNA. It takes longer but I'm more sure of the readout.

Yes, I started adding the samples to the map. I can't do my own Y-DNA analysis yet but I figure that it's something I can do while waiting for BAM files. Also, it gives me a chance to read up on the archeological context of a lot of these samples. The supplementary infomation file is an absolute beast on this preprint. Credit to the authors.

Thanks for that. The supplementary material here is where most of the interest is, as always. It will be fascinating to see what the peer review process does. Inevitably there will be corrections. I don't know whether many people saw my last Z140 post, but there seems to be a small issue with VK357 that they need to address. I assume this is just a labelling oversight.

spruithean
07-20-2019, 12:53 AM
I assume now that's what the three to five months meant in the link I posted last week. It said the study itself was finished, which I guess meant the preprint was ready for release. So we should have the data in time for Christmas.

That would be a nice Christmas present!


The new I-Z140 samples are the first on my list for a closer look when the BAM files come out. Vested interest... ;)

It should be interesting to see what can be dug up for these Z140 samples. I'm secretly hoping for some A13241+ calls from these Z140 Vikings. Maybe when the paper dealing with the possible Olaf of Dublin remains comes out we'll get even more I1, and perhaps some of that will be L338 or F2642 related.


Thanks for that. The supplementary material here is where most of the interest is, as always. It will be fascinating to see what the peer review process does. Inevitably there will be corrections. I don't know whether many people saw my last Z140 post, but there seems to be a small issue with VK357 that they need to address. I assume this is just a labelling oversight.

Yeah, I had noticed that, and it is concerning. Whether it's a mistake in labelling or something else we won't know until the final print. But other than that the supplementary data is really good and it's been fascinating to read through all of this stuff (I've not yet read it all, a bit pressed for time lately).

deadly77
07-20-2019, 12:57 AM
I assume now that's what the three to five months meant in the link I posted last week. It said the study itself was finished, which I guess meant the preprint was ready for release. So we should have the data in time for Christmas.

While I don't have any inside knowledge on this paper, I've been through the process of submitting scientific publications that have been publsihed in journals on eleven occasions (albeit in a different field) - and in the process of getting a number twelve out in the near future (submitted and in review). But the process and timeline has been different every time. It's a bit more involved where I have been the primary author in comparison to a contributing author in terms of responding to reviewer comments to the associate editor of the journal. The ones where I've been the primary author were a lot more work on my part (as expected) but again it was extremely variable. Some sailed through with minor corrections, some required some dialogue with the associate editor and additional revisions, some were rejected and then submitted and published in a different journal. But all of this takes a lot of time. And it's worth doing - when a paper is peer-reviewed and published it means that several folks with good credentials have gone over this. This is a good thing, especially in today's world.

The BioRxiv system is essentially an open peer review on a paper under consideration for publication which invites comments from unsolicited reviewers. This wasn't in place when I was in grad school or postdoc, but it seems there is a chemistry equivalent ChemRixiv now which I haven't used. So there's an option to leave comments on the paper if you wish.

mwauthy
07-20-2019, 01:32 AM
I'll do what I can with all the I1 samples, although it will take me a while to get through them all. I'll go through them in a similar order to that which I'm adding to the Google map - I-Z140 first because myself, JonikW, JMcB, Spruithean, deanovermont are most interested in that, then the I-P109 samples as one of the admins of that subcalde has been good to me and then I'll get to I-Z2041/Z2040 for your interest. If there were easy looking I-Z63 options for Oz and Sassoneg I'd include those too, but those will probably involve a bit of digging.

I actually misread JonikW's question, but I think I gave the answer he was more looking for. From the outside, I'm seeing four factors in what we can get from these ancient samples when they are reported in publications:

1) How old the sample is and the conditions that it's been stored in.
2) The assay that the resesearchers use - WGS or enrichment (essentially shotgun or SNP capture), read length, depth, etc.
3) How the raw data is read - SNP calls, thresholds, corroborating or disconfirming SNP calls, filtering out the false positives, whether by individual or an automated analysis.
4) Taking the read data and placing it correctly on a phylogenetic tree.

No one can affect the first point - the remains have been where they are for centuries and nothing changes that. The second point the researchers can affect but it may very much depend on the quality of the sample in point one - a high intensity sequenced low quality sample may not give much information, despite the best efforts of the researchers. Points 3 and 4 are where an independent analysis can make a difference, but points 1 and 2 are beyond control. If the assay design was not very comprehensive (such as in the Hungarian Conqueror paper), there's not too much more an independent analysis can do. Same as if the assay was comprehensive (such as in the ancient Icelanders paper) but the sample quality wasn't too great such as DAV-A9. But if there's good data (HSJ-A1, SBT-A1, SVK-A1, SZ45, etc.) an independent analysis can add a lot more compared to where the publication got to. In most cases the primary reason for the publication is not the most downstream Y-DNA subclade - it's usually just an entry in a table, so the researchers have different interests to ourselves.

So I'll do what I can, but I can only make a difference in points 3 and 4 - 1 and 2 I can't do much about so I can't promise anything.
Any type of help from my fellow Z59 cousin will be much appreciated. Time is not an issue and I understand priorities. Thanks in advance :)

spruithean
07-21-2019, 02:32 PM
I've actually been thinking, remembering that Leslie et al concluded a considerable amount of Anglo-Saxon ancestry in Britain, yet this Viking paper concludes a fair amount of Danish-like admixture that can't be distinguished from Anglo-Saxon (due to the same population sources - just different time periods), is it not time to perhaps have a reassessment of the percentages estimated by Leslie et al for the overall Anglo-Saxon ancestry of Britain? I'm betting a fair bit of it is probably Danish in origin. But perhaps it may be too difficult to make any new estimations considering differentiating Anglo-Saxon from Dane is so far not possible...

Just rambling, still going over this paper and certainly learning quite a fair bit.

deadly77
07-21-2019, 03:35 PM
I've actually been thinking, remembering that Leslie et al concluded a considerable amount of Anglo-Saxon ancestry in Britain, yet this Viking paper concludes a fair amount of Danish-like admixture that can't be distinguished from Anglo-Saxon (due to the same population sources - just different time periods), is it not time to perhaps have a reassessment of the percentages estimated by Leslie et al for the overall Anglo-Saxon ancestry of Britain? I'm betting a fair bit of it is probably Danish in origin. But perhaps it may be too difficult to make any new estimations considering differentiating Anglo-Saxon from Dane is so far not possible...

Just rambling, still going over this paper and certainly learning quite a fair bit.

Yes - I remember that the " no clear genetic evidence of the Danish Viking occupation and control of a large part of England" in the Leslie paper was challenged a couple of years ago by Kershaw and Røyrvik https://www.cambridge.org/core/journals/antiquity/article/div-classtitlethe-people-of-the-british-isles-project-and-viking-settlement-in-englanddiv/54E19CAFF9AC2BEB39EAEC826BEDBC63for a lot of the same reasons - they came from similar start points geographically and there's not a lot of difference in the time that they came to Britain (on a genealogy time scale). There was a discussion here as well: http://sciencenordic.com/new-study-reignites-debate-over-viking-settlements-england

I haven't really gone through the autosomal DNA aspects of the new preprint yet - there's a lot to get through in this study.

JonikW
07-21-2019, 05:16 PM
Yes - I remember that the " no clear genetic evidence of the Danish Viking occupation and control of a large part of England" in the Leslie paper was challenged a couple of years ago by Kershaw and Røyrvik https://www.cambridge.org/core/journals/antiquity/article/div-classtitlethe-people-of-the-british-isles-project-and-viking-settlement-in-englanddiv/54E19CAFF9AC2BEB39EAEC826BEDBC63for a lot of the same reasons - they came from similar start points geographically and there's not a lot of difference in the time that they came to Britain (on a genealogy time scale). There was a discussion here as well: http://sciencenordic.com/new-study-reignites-debate-over-viking-settlements-england

I haven't really gone through the autosomal DNA aspects of the new preprint yet - there's a lot to get through in this study.

It's frustrating that so far we can't differentiate between the AS and slightly later Danish input. I just can't see how this could ever be resolved. It's also a crucial question on a personal level for me and my terminal SNP... Like spruithean I'd noticed the Danish contribution on the map in this study. It almost looks as if the hotspot visible in central England is more likely to in fact be a signal from the AS tribes, rather than the Danes, who settled mostly in the east and north.

mwauthy
07-21-2019, 06:23 PM
Here are some quotes from the Viking Paper that I find to be interesting. VA is short for Viking Age.

234: “Furthermore, gene flow within Scandinavia appears to be broadly northwards, dominated by Danish Vikings moving into what are now Norway and Sweden.”

246: “Thus, the south-western part of Sweden in the VA is genetically more similar to Danish VA populations than the eastern regions of mainland Sweden.”

255: “Denmark and Gotland in Sweden have the highest genetic diversity in the region, suggesting that these regions may have been centers of interaction and trade during this time.”

269: “In conclusion, the results for Gotland and Öland agree with the archeological record, suggesting that Öland and Gotland were important trading posts from the Roman period onwards.”

323: “Archeological findings and the written sources support the hypothesis that Viking back migrations and interaction between the newly settled areas and Scandinavia occurred as part of the process.”

508: “Present-day Norwegians vary between 12 and 25% in their ‘British-like’ ancestry, whilst it is still (a more uniform) 10% in Sweden.”

522 “However, we also see evidence of individuals with ancient Swedish and Finnish ancestry in the westernmost fringes of Europe, whilst Danish-like ancestry is also found in the east, defying our modern notions of historical groupings.”

527: “Our observations all suggest that the different parts of Scandinavia were not as evenly connected, as has often been assumed...In fact, our data indicate that Viking Scandinavia consisted of a limited number of transport zones and maritime enclaves.”

555: “Our findings also contradict the myth of the Vikings as peoples of pure local Scandinavian ancestry. In fact, we found many Viking Age individuals with high levels of foreign ancestry, both within and outside Scandinavia, suggesting ongoing gene flow with different peoples across Europe. Indeed it appears that some foreign peoples contributed more genetic ancestry to Scandinavia during this period than the Vikings contributed to them.”

JMcB
07-21-2019, 06:32 PM
I've actually been thinking, remembering that Leslie et al concluded a considerable amount of Anglo-Saxon ancestry in Britain, yet this Viking paper concludes a fair amount of Danish-like admixture that can't be distinguished from Anglo-Saxon (due to the same population sources - just different time periods), is it not time to perhaps have a reassessment of the percentages estimated by Leslie et al for the overall Anglo-Saxon ancestry of Britain? I'm betting a fair bit of it is probably Danish in origin. But perhaps it may be too difficult to make any new estimations considering differentiating Anglo-Saxon from Dane is so far not possible...

Just rambling, still going over this paper and certainly learning quite a fair bit.



This is just my own humble opinion but I’ve always thought that a decent portion of what is usually reported as Anglo Saxon, should really be attributed to the Danish Vikings. Partly because of the inconsistencies found in the POBI study, which was later buttressed by Kershaw’s paper, and in my own opinion, common sense. Unfortunately, I don’t think they’re going to be able to untangle the genetic similarities for quite some time.

spruithean
07-21-2019, 07:54 PM
Yes - I remember that the " no clear genetic evidence of the Danish Viking occupation and control of a large part of England" in the Leslie paper was challenged a couple of years ago by Kershaw and Røyrvik https://www.cambridge.org/core/journals/antiquity/article/div-classtitlethe-people-of-the-british-isles-project-and-viking-settlement-in-englanddiv/54E19CAFF9AC2BEB39EAEC826BEDBC63for a lot of the same reasons - they came from similar start points geographically and there's not a lot of difference in the time that they came to Britain (on a genealogy time scale). There was a discussion here as well: http://sciencenordic.com/new-study-reignites-debate-over-viking-settlements-england
I haven't really gone through the autosomal DNA aspects of the new preprint yet - there's a lot to get through in this study.

Thanks for the links. This Viking paper is a monster, and I certainly haven't gotten through all of the text or supplementary info.


It's frustrating that so far we can't differentiate between the AS and slightly later Danish input. I just can't see how this could ever be resolved. It's also a crucial question on a personal level for me and my terminal SNP... Like spruithean I'd noticed the Danish contribution on the map in this study. It almost looks as if the hotspot visible in central England is more likely to in fact be a signal from the AS tribes, rather than the Danes, who settled mostly in the east and north.

It is frustrating for the same reasons you cite (terminal Y-SNP). I've thought there was an underestimation of Danish-like ancestry in the UK for awhile considering historical events.


Here are some quotes from the Viking Paper that I find to be interesting. VA is short for Viking Age.

234: “Furthermore, gene flow within Scandinavia appears to be broadly northwards, dominated by Danish Vikings moving into what are now Norway and Sweden.”

246: “Thus, the south-western part of Sweden in the VA is genetically more similar to Danish VA populations than the eastern regions of mainland Sweden.”

255: “Denmark and Gotland in Sweden have the highest genetic diversity in the region, suggesting that these regions may have been centers of interaction and trade during this time.”

269: “In conclusion, the results for Gotland and Öland agree with the archeological record, suggesting that Öland and Gotland were important trading posts from the Roman period onwards.”

323: “Archeological findings and the written sources support the hypothesis that Viking back migrations and interaction between the newly settled areas and Scandinavia occurred as part of the process.”

508: “Present-day Norwegians vary between 12 and 25% in their ‘British-like’ ancestry, whilst it is still (a more uniform) 10% in Sweden.”

522 “However, we also see evidence of individuals with ancient Swedish and Finnish ancestry in the westernmost fringes of Europe, whilst Danish-like ancestry is also found in the east, defying our modern notions of historical groupings.”

527: “Our observations all suggest that the different parts of Scandinavia were not as evenly connected, as has often been assumed...In fact, our data indicate that Viking Scandinavia consisted of a limited number of transport zones and maritime enclaves.”

555: “Our findings also contradict the myth of the Vikings as peoples of pure local Scandinavian ancestry. In fact, we found many Viking Age individuals with high levels of foreign ancestry, both within and outside Scandinavia, suggesting ongoing gene flow with different peoples across Europe. Indeed it appears that some foreign peoples contributed more genetic ancestry to Scandinavia during this period than the Vikings contributed to them.”

Thanks for leaving the line numbers there, it makes looking for them in the text much easier. I think one of the most interesting pieces in this paper for me is that brief mention of Picts in Orkney adopting Scandinavian culture and going "Viking". It certainly wouldn't be farfetched for an Anglo-Saxon in England living under the Danelaw to go "Viking". The Last Kingdom and Uhtred of Bebbanburg anyone?


This is just my own humble opinion but I’ve always thought that a decent portion of what is usually reported as Anglo Saxon, should really be attributed to the Danish Vikings. Partly because of the inconsistencies found in the POBI study, which was later buttressed by Kershaw’s paper, and in my own opinion, common sense. Unfortunately, I don’t think they’re going to be able to untangle the genetic similarities for quite some time.

Agreed. I think it's going to be difficult for a long time to try and differentiate Anglo-Saxons from Danish Vikings (and perhaps may remain so permanently). Perhaps one day some new process will work effectively as a fine-toothed comb and determine the differences (I wish).

All of this reminds me of an old BBC program about the Vikings and they stated in the program that Anglo-Saxon and Danish were indistinguishable, that was several years ago now. :lol: not much has changed!

JonikW
07-21-2019, 08:38 PM
Here are some quotes from the Viking Paper that I find to be interesting. VA is short for Viking Age.

234: “Furthermore, gene flow within Scandinavia appears to be broadly northwards, dominated by Danish Vikings moving into what are now Norway and Sweden.”

246: “Thus, the south-western part of Sweden in the VA is genetically more similar to Danish VA populations than the eastern regions of mainland Sweden.”

255: “Denmark and Gotland in Sweden have the highest genetic diversity in the region, suggesting that these regions may have been centers of interaction and trade during this time.”

269: “In conclusion, the results for Gotland and Öland agree with the archeological record, suggesting that Öland and Gotland were important trading posts from the Roman period onwards.”

323: “Archeological findings and the written sources support the hypothesis that Viking back migrations and interaction between the newly settled areas and Scandinavia occurred as part of the process.”

508: “Present-day Norwegians vary between 12 and 25% in their ‘British-like’ ancestry, whilst it is still (a more uniform) 10% in Sweden.”

522 “However, we also see evidence of individuals with ancient Swedish and Finnish ancestry in the westernmost fringes of Europe, whilst Danish-like ancestry is also found in the east, defying our modern notions of historical groupings.”

527: “Our observations all suggest that the different parts of Scandinavia were not as evenly connected, as has often been assumed...In fact, our data indicate that Viking Scandinavia consisted of a limited number of transport zones and maritime enclaves.”

555: “Our findings also contradict the myth of the Vikings as peoples of pure local Scandinavian ancestry. In fact, we found many Viking Age individuals with high levels of foreign ancestry, both within and outside Scandinavia, suggesting ongoing gene flow with different peoples across Europe. Indeed it appears that some foreign peoples contributed more genetic ancestry to Scandinavia during this period than the Vikings contributed to them.”

Does anyone know more about line 234 and the period it refers to? I can imagine this movement happening under Knut. But in the earlier Viking heyday when the dǫnsk tunga or Danish Tongue was still used everywhere it presumably also must have occurred to some extent. There's also evidence from Norway of slightly more southerly artefact styles being adopted in the Migration Period, for example cruciform brooches, a style probably best known from the Anglian settlement of England.

Kaltmeister
07-21-2019, 10:38 PM
Here are some quotes from the Viking Paper that I find to be interesting. VA is short for Viking Age.



555: “Our findings also contradict the myth of the Vikings as peoples of pure local Scandinavian ancestry. In fact, we found many Viking Age individuals with high levels of foreign ancestry, both within and outside Scandinavia, suggesting ongoing gene flow with different peoples across Europe. Indeed it appears that some foreign peoples contributed more genetic ancestry to Scandinavia during this period than the Vikings contributed to them.”

555 indicates in my opinion that people from continental Europe were shipped to Scandinavia to establish a working class. Otherwise we would have to assume a counter-offensive from the continent to the north that never happened. In this context it is meaningful that Vikings from Sweden headed to the Baltic area - and that Eastern ancestry is strong in Sweden, peaking in Gotland, initial point of so many Viking activities. We might find out that Norway and Denmark also have ancestry from areas they invaded.

mwauthy
07-21-2019, 10:58 PM
555 indicates in my opinion that people from continental Europe were shipped to Scandinavia to establish a working class. Otherwise we would have to assume a counter-offensive from the continent to the north that never happened. In this context it is meaningful that Vikings from Sweden headed to the Baltic area - and that Eastern ancestry is strong in Sweden, peaking in Gotland, initial point of so many Viking activities. We might find out that Norway and Denmark also have ancestry from areas they invaded.

A theory of mine that needs many more samples from the Bronze Age and Early Iron Age to shed light is that the maritime areas of Scandinavia have had gene flow and continuous trade with the British Isles and North Sea and Baltic Sea coastal regions since the Bronze Age and maybe even prior. As a result, when studying subclade migrations through time or autosomal percentages its best to not discount completely backwards migrations.

JonikW
07-21-2019, 11:14 PM
A theory of mine that needs many more samples from the Bronze Age and Early Iron Age to shed light is that the maritime areas of Scandinavia have had gene flow and continuous trade with the British Isles and North Sea and Baltic Sea coastal regions since the Bronze Age and maybe even prior. As a result, when studying subclade migrations through time or autosomal percentages its best to not discount completely backwards migrations.

I agree, thinking in particular of rock carvings, that there may have been some Bronze Age cross contact. I can't immediately think of any possible evidence in the Iron Age. Maybe someone else can.

Edit: I'm referring to Scandinavian links with Britain rather than the wider Baltic, where I imagine this contact was more extensive.

Helgenes50
07-22-2019, 06:21 AM
4 of these samples are L813, 2 from Norway, 1 from Iceland and the last one from East Sweden

deadly77
07-22-2019, 08:21 AM
4 of these samples are L813, 2 from Norway, 1 from Iceland and the last one from East Sweden

Perhaps more as well. There's a few that have a designation that hasn't been well defined in the paper - eg. 29 just I1, 7 I-DF29, 4 I-Z2336, 5 I-Z2337, 1 I-Z74. Probably missed calls in the automated software capture. We'll have a better idea when we get access to the raw data in the form of BAM files.

deadly77
07-22-2019, 08:37 AM
Thanks for leaving the line numbers there, it makes looking for them in the text much easier. I think one of the most interesting pieces in this paper for me is that brief mention of Picts in Orkney adopting Scandinavian culture and going "Viking". It certainly wouldn't be farfetched for an Anglo-Saxon in England living under the Danelaw to go "Viking". The Last Kingdom and Uhtred of Bebbanburg anyone?


I rather enjoy that show - looking forward to the next series. I'm not so far along in the books - only the first two of those so far but I enjoy Cornwell's stuff. I also like how he puts a historical note at the end of the book - explains where some of the characters are genuine historical figures and which ones are fictional creations. Also with certain events, and how he may have moved time and place to fit a narrative or make it more plausible for the main characters to encounter.

While it's a work of fiction, I do agree that it wouldn't be farfetchted at all and likely that such allegiances did happen. Pretty sure the Danes weren't picky about extra swords or spears if it helped them win a battle. Also the other way as well - there's an example in the second book where Uhtred captures a Dane and offers him the chance to serve with him on the Anglo-Saxon side.

deadly77
07-22-2019, 08:39 AM
This is just my own humble opinion but I’ve always thought that a decent portion of what is usually reported as Anglo Saxon, should really be attributed to the Danish Vikings. Partly because of the inconsistencies found in the POBI study, which was later buttressed by Kershaw’s paper, and in my own opinion, common sense. Unfortunately, I don’t think they’re going to be able to untangle the genetic similarities for quite some time.

Yes, I agree this is probably the case and agree this is common sense. Thought so for a while.

JonikW
07-22-2019, 10:05 AM
Just reading this, which has some nice observations and maps:
https://indo-european.eu/2019/07/vikings-vikings-vikings-influx-of-eastern-ancestry-in-the-whole-baltic-iron-age/
I'd missed the Roman Iron Age dating of Sealand VK532, who was Z59. From the paper itself: "Three inhumation graves were recovered. One, a female dated to Early Roman Iron Age (0-200AD),
539 and the other two, a female and a male (x1718) dated to the Late Roman Iron Age (C2/C3) (200-
540 375AD)."

spruithean
07-22-2019, 10:22 AM
VK532 would be interesting to look for a deeper SNP read on, to see where on the Z59 tree he fits, autosomally VK532 is quite "Swedish-like", which I suppose makes sense.

However I'm most intrigued by the I-Z140 samples from Öland and Denmark. Interestingly Öland is sometimes associated with the Aviones tribe who are recorded as Eowan in Old English works. The Aviones with several other tribes (Anglii, Reudigni, Nuithones, Eudoses, Varini, Suardones) were part of the same group that were allegedly a Nerthus worshipping cult.

I feel like several I1 samples (downstream ones) are missing from the maps on that Indo-European blog.

deadly77
07-22-2019, 02:02 PM
VK532 would be interesting to look for a deeper SNP read on, to see where on the Z59 tree he fits, autosomally VK532 is quite "Swedish-like", which I suppose makes sense.

However I'm most intrigued by the I-Z140 samples from Öland and Denmark. Interestingly Öland is sometimes associated with the Aviones tribe who are recorded as Eowan in Old English works. The Aviones with several other tribes (Anglii, Reudigni, Nuithones, Eudoses, Varini, Suardones) were part of the same group that were allegedly a Nerthus worshipping cult.

I feel like several I1 samples (downstream ones) are missing from the maps on that Indo-European blog.

One of the guys in the I-Z140 group is Swedish and he says he has a summer house in Öland, where he is right now. He says the most important merchant port on Öland 700-1100 AD was Köpingsvik just 2 km south of his house, and sent me this link to an ongoing excavation in the south part of the island: https://www.sandbyborg.se/en/home/?fbclid=IwAR2fSXu0EzJ4Rylo7Ns8rKC4Snk5u9PX22VsSG3e RWcDAtPwoow1007Ro7c

Regarding the Indo-European blog map, it seems Carlos Quiles is still using the incorrect designations for subclades such as the Icelandic samples that we discussed earlier in this thread. Oh well.

spruithean
07-22-2019, 09:35 PM
One of the guys in the I-Z140 group is Swedish and he says he has a summer house in Öland, where he is right now. He says the most important merchant port on Öland 700-1100 AD was Köpingsvik just 2 km south of his house, and sent me this link to an ongoing excavation in the south part of the island: https://www.sandbyborg.se/en/home/?fbclid=IwAR2fSXu0EzJ4Rylo7Ns8rKC4Snk5u9PX22VsSG3e RWcDAtPwoow1007Ro7c

Regarding the Indo-European blog map, it seems Carlos Quiles is still using the incorrect designations for subclades such as the Icelandic samples that we discussed earlier in this thread. Oh well.

Thanks for that link, that looks quite interesting.

That's disappointing that he is still using the incorrect designations for those samples, hopefully in due time that will change.

deadly77
07-23-2019, 02:04 PM
Thanks for that link, that looks quite interesting.

That's disappointing that he is still using the incorrect designations for those samples, hopefully in due time that will change.

He's also included a modern I1 individual on his "Y-DNA haplogroups in Europe during the Viking expansions" map, and he's got the subclade wrong on that sample as well.

Click on the first map in the link that JonikW shared in #414 above, look towards Northern Finland where the Oulu is, there's a yellow triangle for I1a-Y18770.

Not aware of any sample in that region from previous papers, I checked the recent preprint and couldn't find anything that matched up with that.

Took me a little while to figure out what he's done. From the Ancient Fennoscandivian Genomes paper that came out in Nature Communications last year https://www.nature.com/articles/s41467-018-07483-5 among the ancient samples in that paper, there's also a modern Saami individual - Saami001 - who is reported as I1a1b3a1.

If you look up that on the 2019 ISOGG tree, closest would be I1a1b3a~ where one of the SNPs on that branch is Y18770, and YFull describes that branch as I-Y18770. Trouble is, the paper doesn't use the 2019 version of the ISOGG tree - reading the paper, they use the 2016 ISOGG tree - looking up I1a1b3a1 on that tree gets to I-L258, which makes a lot more sense.

janan
07-23-2019, 09:57 PM
I understand that the share of I1 in viking age Scandinavia was about the same as it is today. Which means that we at least know that the proliferation of I1 tok place at some earlier time.


Here are some quotes from the Viking Paper that I find to be interesting. VA is short for Viking Age.

234: “Furthermore, gene flow within Scandinavia appears to be broadly northwards, dominated by Danish Vikings moving into what are now Norway and Sweden.”

246: “Thus, the south-western part of Sweden in the VA is genetically more similar to Danish VA populations than the eastern regions of mainland Sweden.”
Well, the south-western part of Sweden was Danish until 1658... And the the sea united rather than parted during these times. So no surprise.


255: “Denmark and Gotland in Sweden have the highest genetic diversity in the region, suggesting that these regions may have been centers of interaction and trade during this time.”

269: “In conclusion, the results for Gotland and Öland agree with the archeological record, suggesting that Öland and Gotland were important trading posts from the Roman period onwards.”
Yes, agrees with what we already know. Visby at Gotland actually became the richest town in the Baltic area during early medieval time. Before that many farmers — farmannabönder — engagerad in trading and became quite wealthy.


323: “Archeological findings and the written sources support the hypothesis that Viking back migrations and interaction between the newly settled areas and Scandinavia occurred as part of the process.”
Back migrations — slaves taken as war booty? Trying to keep up the bad reputation...


527: “Our observations all suggest that the different parts of Scandinavia were not as evenly connected, as has often been assumed...In fact, our data indicate that Viking Scandinavia consisted of a limited number of transport zones and maritime enclaves.”
Makes some sense. Even though the seas surrounding the Scandinavian countries unite, distances between centers are long. On the other hand, if connections were hard to sustain, howcome language, people and culture became uniform in the NBA?


555: “Our findings also contradict the myth of the Vikings as peoples of pure local Scandinavian ancestry. In fact, we found many Viking Age individuals with high levels of foreign ancestry, both within and outside Scandinavia, suggesting ongoing gene flow with different peoples across Europe. Indeed it appears that some foreign peoples contributed more genetic ancestry to Scandinavia during this period than the Vikings contributed to them.”
Straw man, PC BS.

JonikW
07-23-2019, 11:00 PM
I understand that the share of I1 in viking age Scandinavia was about the same as it is today. Which means that we at least know that the proliferation of I1 tok place at some earlier time.


Well, the south-western part of Sweden was Danish until 1658... And the the sea united rather than parted during these times. So no surprise.


Yes, agrees with what we already know. Visby at Gotland actually became the richest town in the Baltic area during early medieval time. Before that many farmers — farmannabönder — engagerad in trading and became quite wealthy.


Back migrations — slaves taken as war booty? Trying to keep up the bad reputation...


Makes some sense. Even though the seas surrounding the Scandinavian countries unite, distances between centers are long. On the other hand, if connections were hard to sustain, howcome language, people and culture became uniform in the NBA?


Straw man, PC BS.

I agree with some of your points but among others not about back migration pointing to slaves. I was amused by their observation about a "limited number" of zones and enclaves. By definition that would apply to Scandinavia or any other defined land mass.

deadly77
07-24-2019, 08:41 AM
All 92 of the I1 samples from the Viking world preprint have now been added to the Haplogroup I1 Ancient DNA Samples Map on Google MyMaps: https://bit.ly/2Z3CJk7

Lot more than there were before this preprint. More detailed Y-DNA analysis to follow as and when the BAM files become available. No timeframe on that.

spruithean
07-24-2019, 09:44 AM
All 92 of the I1 samples from the Viking world preprint have now been added to the Haplogroup I1 Ancient DNA Samples Map on Google MyMaps: https://bit.ly/2Z3CJk7

Lot more than there were before this preprint. More detailed Y-DNA analysis to follow as and when the BAM files become available. No timeframe on that.

Awesome! The map is filling up, nice to actually see a paper report some more ancient I1 than R1b :lol:.

deadly77
07-24-2019, 07:26 PM
Awesome! The map is filling up, nice to actually see a paper report some more ancient I1 than R1b :lol:.

Aye but it's not far off. I count 92 I1 and 84 R1b. Clearly a lot of R1b around at this time as well.

spruithean
07-25-2019, 12:30 AM
Aye but it's not far off. I count 92 I1 and 84 R1b. Clearly a lot of R1b around at this time as well.

Definitely, but it is still a win for the I1 crowd, if you will.

I am really looking forward to the final print of the paper and what may be learned when the BAM files become available.

deadly77
07-25-2019, 11:04 AM
I sorted the I1 samples from the Viking preprint from highest average coverage to lowest. This gives an indicator in perhaps what we can expect when the BAM files become available:

Sample Average Depth (x) Y-DNA Haplogroup
VK70 6.684 I-P109
VK190 6.495 I-DF29
VK50 6.231 I-M227
VK547 4.732 I-L813
VK521 4.538 I-Z2040
VK532 4.013 I-Z59
VK29 3.208 I1
VK98 2.491 I-L813
VK176 2.415 I-P109
VK279 2.393 I-Z2337
VK443 2.107 I-L1248
VK281 2.046 I-P109
VK337 2.042 I-Z140
VK496 1.978 I-Z2040
VK221 1.953 I-L22
VK179 1.84 I1
VK220 1.815 I-Z2336
VK529 1.813 I-L813
VK110 1.792 I-P109
VK483 1.78 I-Z73
VK511 1.701 I-P109
VK549 1.676 I-L22
VK524 1.606 I-Z73
VK219 1.581 I-L22
VK539 1.574 I1
VK420 1.534 I1
VK446 1.531 I-Z2041
VK510 1.525 I-L22
VK316 1.458 I1
VK497 1.447 I-L1302
VK491 1.433 I-L1302
VK404 1.425 I-Z2337
VK473 1.396 I-Z2337
VK357 1.387 I-Z140
VK552 1.379 I-CTS7362
VK320 1.368 I-Z2337
VK445 1.363 I-Z2041
VK363 1.337 I-Z140
VK509 1.328 I-L22
VK553 1.264 I-L22
VK343 1.259 I1
VK506 1.233 I-DF29
VK262 1.22 I-Z59
VK146 1.182 I-Z73
VK327 1.164 I-YSC0000261
VK352 1.149 I-Z2336
VK495 1.143 I-DF29
VK151 1.142 I-Z2336
VK291 1.113 I-Z74
VK165 1.105 I-L22
VK555 1.099 I-Z73
VK482 1.085 I1
VK400 1.066 I-Z2337
VK367 1.053 I1
VK306 1.052 I-DF29
VK257 1.017 I-Z2336
VK492 1.015 I-Z73
VK157 0.978 I1
VK388 0.975 I1
VK490 0.946 I-L1302
VK554 0.933 I1
VK167 0.902 I1
VK488 0.901 I-L22
VK507 0.823 I-L22
VK186 0.813 I1
VK301 0.731 I-Z59
VK485 0.709 I-Z73
VK297 0.667 I-L22
VK515 0.636 I-Z73
VK315 0.584 I-L22
VK295 0.57 I-DF29
VK183 0.535 I1
VK20 0.496 I1
VK296 0.458 I-P109
VK275 0.448 I-Z17925
VK223 0.35 I-DF29
VK23 0.325 I1
VK407 0.233 I1
VK16 0.228 I1
VK519 0.217 I1
VK71 0.174 I1
VK409 0.168 I-DF29
VK14 0.162 I1
VK144 0.159 I1
VK410 0.129 I1
VK380 0.106 I1
VK248 0.076 I1
VK379 0.07 I1
VK382 0.06 I-L813
VK148 0.043 I1
VK163 0.019 I1
VK149 0.008 I1

Sorry, that's not perhaps the easiest to read. But it does show that a lot of the samples to the lower end of the coverage scale are just I1, so maybe chances to get further will be limited. Good news is that there are quite a lot of samples with good coverage to work with.

For comparison, the WGS samples from the Ancient Iceland paper that made it onto the YFull tree were HSJ-A1 (30.74x), SBT-A1 (6.01x), SVK-A1 (1.07x) and the ones that didn't were DAV-A9 (0.43x), SSJ-A2 (0.36x), SSG-A3 (0.26x). Of other WGS samples, the Szólád Lombard SZ45 (13.06x) got onto the YFull tree while Anglo-Saxon NO3423 (1.05x) and Sigtuna 84005 (1.03x) did not. None of the SNP capture ones made it onto the YFull tree, likely because of gaps in coverage from the design of the assay. I'd say SVK-A1 sneaked on by having good enough coverage in some of the right places. There probably isn't a hard reject below 1.07x - it'll depend on the individual sample.

So a bit of a guide to what we might realistically get from digging into the BAM files a little further by comparison to some of the samples from other papers that have been analyzed. No guarantees - all of the samples will have some gaps in coverage, and it's impossible to predict which regions and SNPs will have the gaps until the BAMs become available. But the samples with a lower average depth with in likelihood have more no calls, false positives and false negatives.

mwauthy
07-26-2019, 03:13 PM
I sorted the I1 samples from the Viking preprint from highest average coverage to lowest. This gives an indicator in perhaps what we can expect when the BAM files become available:

Sample Average Depth (x) Y-DNA Haplogroup
VK70 6.684 I-P109
VK190 6.495 I-DF29
VK50 6.231 I-M227
VK547 4.732 I-L813
VK521 4.538 I-Z2040
VK532 4.013 I-Z59
VK29 3.208 I1
VK98 2.491 I-L813
VK176 2.415 I-P109
VK279 2.393 I-Z2337
VK443 2.107 I-L1248
VK281 2.046 I-P109
VK337 2.042 I-Z140
VK496 1.978 I-Z2040
VK221 1.953 I-L22
VK179 1.84 I1
VK220 1.815 I-Z2336
VK529 1.813 I-L813
VK110 1.792 I-P109
VK483 1.78 I-Z73
VK511 1.701 I-P109
VK549 1.676 I-L22
VK524 1.606 I-Z73
VK219 1.581 I-L22
VK539 1.574 I1
VK420 1.534 I1
VK446 1.531 I-Z2041
VK510 1.525 I-L22
VK316 1.458 I1
VK497 1.447 I-L1302
VK491 1.433 I-L1302
VK404 1.425 I-Z2337
VK473 1.396 I-Z2337
VK357 1.387 I-Z140
VK552 1.379 I-CTS7362
VK320 1.368 I-Z2337
VK445 1.363 I-Z2041
VK363 1.337 I-Z140
VK509 1.328 I-L22
VK553 1.264 I-L22
VK343 1.259 I1
VK506 1.233 I-DF29
VK262 1.22 I-Z59
VK146 1.182 I-Z73
VK327 1.164 I-YSC0000261
VK352 1.149 I-Z2336
VK495 1.143 I-DF29
VK151 1.142 I-Z2336
VK291 1.113 I-Z74
VK165 1.105 I-L22
VK555 1.099 I-Z73
VK482 1.085 I1
VK400 1.066 I-Z2337
VK367 1.053 I1
VK306 1.052 I-DF29
VK257 1.017 I-Z2336
VK492 1.015 I-Z73
VK157 0.978 I1
VK388 0.975 I1
VK490 0.946 I-L1302
VK554 0.933 I1
VK167 0.902 I1
VK488 0.901 I-L22
VK507 0.823 I-L22
VK186 0.813 I1
VK301 0.731 I-Z59
VK485 0.709 I-Z73
VK297 0.667 I-L22
VK515 0.636 I-Z73
VK315 0.584 I-L22
VK295 0.57 I-DF29
VK183 0.535 I1
VK20 0.496 I1
VK296 0.458 I-P109
VK275 0.448 I-Z17925
VK223 0.35 I-DF29
VK23 0.325 I1
VK407 0.233 I1
VK16 0.228 I1
VK519 0.217 I1
VK71 0.174 I1
VK409 0.168 I-DF29
VK14 0.162 I1
VK144 0.159 I1
VK410 0.129 I1
VK380 0.106 I1
VK248 0.076 I1
VK379 0.07 I1
VK382 0.06 I-L813
VK148 0.043 I1
VK163 0.019 I1
VK149 0.008 I1

Sorry, that's not perhaps the easiest to read. But it does show that a lot of the samples to the lower end of the coverage scale are just I1, so maybe chances to get further will be limited. Good news is that there are quite a lot of samples with good coverage to work with.

For comparison, the WGS samples from the Ancient Iceland paper that made it onto the YFull tree were HSJ-A1 (30.74x), SBT-A1 (6.01x), SVK-A1 (1.07x) and the ones that didn't were DAV-A9 (0.43x), SSJ-A2 (0.36x), SSG-A3 (0.26x). Of other WGS samples, the Szólád Lombard SZ45 (13.06x) got onto the YFull tree while Anglo-Saxon NO3423 (1.05x) and Sigtuna 84005 (1.03x) did not. None of the SNP capture ones made it onto the YFull tree, likely because of gaps in coverage from the design of the assay. I'd say SVK-A1 sneaked on by having good enough coverage in some of the right places. There probably isn't a hard reject below 1.07x - it'll depend on the individual sample.

So a bit of a guide to what we might realistically get from digging into the BAM files a little further by comparison to some of the samples from other papers that have been analyzed. No guarantees - all of the samples will have some gaps in coverage, and it's impossible to predict which regions and SNPs will have the gaps until the BAMs become available. But the samples with a lower average depth with in likelihood have more no calls, false positives and false negatives.

Thanks deadly77! Both Z2040 samples look promising :)

deadly77
08-01-2019, 01:46 PM
After reading some parts of the paper a little more closely, I've reassigned samples VK482 and VK483 from I-Z73 to I-L1302. There's a rather interesting discussion in Supplementary Note 4 starting on page 16 of the second supplementary file regarding kinship analysis from the autosomal DNA data. According to the autosomal analysis, VK482 and VK483 are brothers with the samples VK490 and VK497 and all were buried relatively close together in the larger of the two ships found in the boat burials at Salme, Estonia. All four brothers have the same mtDNA haplogroup, and are close enough on Y-DNA - two are I-Z73 and two are I-L1302 - the authors comment "the slight differences in Y chromosomal haplogroup assignments in this case are likely due to the presence of ancient DNA damaged sites or insufficient genomic coverage" which is fair enough. Given all the evidence, I'm fine assigning the two I-Z73 brothers VK482 and VK483 a little further down to I-L1302. There are a few inconsistencies on the age estimate of the brothers compared to each other.

The other I-L1302 sample from Salme doesn't appear closely related to the four brothers on the autosomal analysis. One of the brothers (VK490) has a third-degree relationship with one of the other Salme samples, namely VK555 who has mtDNA haplogroup U3b1b and Y-DNA haplogroup I-Z73. Given that it's not a close relationship and there are a lot of I-Z73 examples in the Salme boat burials, I'll leave VK555 at I-Z73 for now.

Other interesting kinships among the I1 samples:

VK167 and VK168 at the St John's College, Oxford site (which has been linked with the St Brice's Day Massacre) re second degree relatives based on autosomal comparison. Given that they have the same mtDNA haplogroup (H4a1a4b) but different Y-DNA haplogroups - VK167 is I1 and VK168 is R1b1a1b1a1a1b, quite possibly half brothers who have the same mother and different fathers.

VK144 from the same St John's College, Oxford site has a second degree relationship on autosomal comparison with VK297 found across the North Sea at Galgedil, Denmark. Given the differing mtDNA haplogroups for VK279 (I4a) and VK144 (V1a1) these two could perhaps be half-brothers (with different mother) or a combination of nephew-uncle or grandfather-grandson. Based on this, VK144 may be I-Z2337 rather than just I1, although probably need a bit more data to say for sure.

VK110 (I-P109) found at Hofstaðir, Iceland shares a close relationship with two samples from the preprint: samples VK111 (mother) and VK230 (sister) and also shares same mtDNA haplogroup with these two samples, although with them being female there's no further information from a Y-DNA perspective.

VK179 (I1, mtDNA K1a3a) at Brattahlid, Greenland was reported in the preprint to be a 3rd degree relative to VK183 (also I1, different mtDNA T2b21) at the same site as well as VK 187 (female, mtDNA T2a1a) at Igaliku Kujalleq in Greenland.

Quite a few more kinships among the other non-I1 samples, so worth a read of the supplementary material - especially the Faroe Islands individuals, although the lone I1 VK248 doesn't appear to be closely related to any of those.

JMcB
08-01-2019, 02:09 PM
After reading some parts of the paper a little more closely, I've reassigned samples VK482 and VK483 from I-Z73 to I-L1302. There's a rather interesting discussion in Supplementary Note 4 starting on page 16 of the second supplementary file regarding kinship analysis from the autosomal DNA data. According to the autosomal analysis, VK482 and VK483 are brothers with the samples VK490 and VK497 and all were buried relatively close together in the larger of the two ships found in the boat burials at Salme, Estonia. All four brothers have the same mtDNA haplogroup, and are close enough on Y-DNA - two are I-Z73 and two are I-L1302 - the authors comment "the slight differences in Y chromosomal haplogroup assignments in this case are likely due to the presence of ancient DNA damaged sites or insufficient genomic coverage" which is fair enough. Given all the evidence, I'm fine assigning the two I-Z73 brothers VK482 and VK483 a little further down to I-L1302. There are a few inconsistencies on the age estimate of the brothers compared to each other.

The other I-L1302 sample from Salme doesn't appear closely related to the four brothers on the autosomal analysis. One of the brothers (VK490) has a third-degree relationship with one of the other Salme samples, namely VK555 who has mtDNA haplogroup U3b1b and Y-DNA haplogroup I-Z73. Given that it's not a close relationship and there are a lot of I-Z73 examples in the Salme boat burials, I'll leave VK555 at I-Z73 for now.

Other interesting kinships among the I1 samples:

VK167 and VK168 at the St John's College, Oxford site (which has been linked with the St Brice's Day Massacre) re second degree relatives based on autosomal comparison. Given that they have the same mtDNA haplogroup (H4a1a4b) but different Y-DNA haplogroups - VK167 is I1 and VK168 is R1b1a1b1a1a1b, quite possibly half brothers who have the same mother and different fathers.

VK144 from the same St John's College, Oxford site has a second degree relationship on autosomal comparison with VK297 found across the North Sea at Galgedil, Denmark. Given the differing mtDNA haplogroups for VK279 (I4a) and VK144 (V1a1) these two could perhaps be half-brothers (with different mother) or a combination of nephew-uncle or grandfather-grandson. Based on this, VK144 may be I-Z2337 rather than just I1, although probably need a bit more data to say for sure.

VK110 (I-P109) found at Hofstaðir, Iceland shares a close relationship with two samples from the preprint: samples VK111 (mother) and VK230 (sister) and also shares same mtDNA haplogroup with these two samples, although with them being female there's no further information from a Y-DNA perspective.

VK179 (I1, mtDNA K1a3a) at Brattahlid, Greenland was reported in the preprint to be a 3rd degree relative to VK183 (also I1, different mtDNA T2b21) at the same site as well as VK 187 (female, mtDNA T2a1a) at Igaliku Kujalleq in Greenland.

Quite a few more kinships among the other non-I1 samples, so worth a read of the supplementary material - especially the Faroe Islands individuals, although the lone I1 VK248 doesn't appear to be closely related to any of those.

As always, nice work!

This was interesting! Perhaps, not surprising but being able to find it is!


VK144 from the same St John's College, Oxford site has a second degree relationship on autosomal comparison with VK297 found across the North Sea at Galgedil, Denmark. Given the differing mtDNA haplogroups for VK279 (I4a) and VK144 (V1a1) these two could perhaps be half-brothers (with different mother) or a combination of nephew-uncle or grandfather-grandson. Based on this, VK144 may be I-Z2337 rather than just I1, although probably need a bit more data to say for sure

deadly77
08-01-2019, 04:55 PM
As always, nice work!

This was interesting! Perhaps, not surprising but being able to find it is!

Yeah, I guess that with a big dataset of 442 samples over that size of geographical area, perhaps it is not surprising that they would find some kinship between the samples.

What I found interesting on reading was how they did it - there's a variety of quality between the samples so perhaps comparing shared segments between individuals (like in our own tests) might not catch genuine kin due to both samples not having the comparable segments fully covered, so it looks like they used a couple of programs that had been reliable on NGS data that was low coverage (as low as 0.1x) in ancient DNA on previous studies. It seems that one of these programs strategy looks at a nonmatching alleles - rather than looking at how similar two samples are, more a lack of differences at key points. A bit of filtering and some assumptions (assuming autosomal DNA allele reads from the VCF homozygous, for example). The other program appears to estimate the likelihood of genotype (so there'll be some mistakes based on that) and compares the proportions of genome where the two individuals share zero, one or two alleles - so you'd expect two people who are less related to have a higher proportion of the genome with zero alleles matching, and convservely two people who are more related will have lower proportion of the genome with zero alleles matching (they'll have more matching alleles). So basically in Table S4.1, the closer k0 is to zero, the more closely related the two are and closer k0 is to 1 the less related the two individuals are.

So not as precise as the autosomal shared cM that we use to compare with other testers on our genotyped chip results in commercial testing databases, but perhaps a crude and quick way to filter out the samples from a large dataset into a more manageable list. Then can disprove some relationship options based on mismatching uniparental markers and when raw data comes available perhaps can take a more in depth look.

At any rate, they filtered the 442 down to 376 by removing the really low coverage samples, and then applied the NgsRelate tool to get down to 48 pairwise interactions where k0 was less than 0.875 - the lower the k0, the more closely related. Several of the samples have more than one pairwise relationship with more than one other sample. So the most closely related individuals are the Icelandic mother and her two children (VK110, VK111, VK230). Least closely related are VK237 and VK244 from the Faroe Islands who at k0 0.867 just sneak under the threshold.

Interesting way of approaching that - it may be common in genetic datasets but new to me.

deadly77
08-01-2019, 10:08 PM
But imagine if they had consumer DNA testing back then... "Hello customer VK144 your DNA results are ready! Click here to view your DNA matches to see who you are related to in our database..."

JonikW
08-01-2019, 10:25 PM
But imagine if they had consumer DNA testing back then... "Hello customer VK144 your DNA results are ready! Click here to view your DNA matches to see who you are related to in our database..."

I'd like to have seen the autosomal results, perhaps a few centuries earlier: Angli, 65%, Reudigni, 15%, Chauci, 10%, Langobardi, 9%. Trace regions: Cimbri <1%, Eudoses <1%.:)

JonikW
08-01-2019, 11:18 PM
...Still off topic but fun (it is the "silly season" after all). The tester should of course have the inevitable "exotic" southern Germanic Marcomanni <1%, which he either immediately latches onto and identifies with or dismisses as noise.

deadly77
08-01-2019, 11:28 PM
...Still off topic but fun (it is the "silly season" after all). The tester should of course have the inevitable "exotic" southern Germanic Marcomanni <1%, which he either immediately latches onto and identifies with or dismisses as noise.

Ha, indeed. But the the tester won't be able to distinguish between the Anglo-Saxon and Danish components of their autosomal DNA.

JMcB
08-02-2019, 03:13 AM
Ha, indeed. But the the tester won't be able to distinguish between the Anglo-Saxon and Danish components of their autosomal DNA.

Yes, but if Oswald Whiteblade and Harald Bluetooth had both tested their families, maybe we’d be able to tell by now! ;-)

deadly77
08-02-2019, 10:32 PM
Not very exciting news, but for completness...

I managed to find the AE1154 sample that was in the ancient DNA samples database that Carlos Quiles put together - I had assumed it was a mislabelling of one of the samples from the Bavarian elongated skulls paper that AED246, STR241 and STR486 were found in, but it looks like it's actually from this different paper here which looked at kinship between individuals in stone‐lined graves (which the abstract says "which first appear in Bavarian territory during the 7th century AD, are assumed to be tombs of emerging nobility"): https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.23170

The paper is not open access, but it appears that the DNA analysis wasn't exactly comprehensive - HVR I for mtDNA, autosomal STRs and Y-STRs. Which for 2017 seems rather underpowered. Nothing much further from the abstract but managed to find the dissertation of one of the authors here: https://edoc.ub.uni-muenchen.de/20640/1/Rott_Andreas.pdf

My German language translation skills are pretty much non-existent and 233 pages in German is a bit beyond my motivation, but through judicious use of ctrl+F to search for AE 1154 and some use of Google translate, it seems AE1154 is an adult male buried in the Altenerding-Klettham cemetery (just as AED246 was), buried together with a child AE 1155, possibly a grandchild. It looks like the extent of Y chromosome testing was to assign AE1154 as haplogroup I1 on the basis of the results of 16 STR results.

It seems a bit of a waste to go to all the effort of excavating remains, destructively sampling said remains and then skimping on the DNA analysis after all that with low coverage HVR I, a small number of Y STRs and autosomal STRs (7 markers), but there you go.

As I said, not very exciting, but more for completeness.

spruithean
08-05-2019, 11:17 AM
Interesting stuff. Hopefully this Viking paper can be finalized sooner than later so that Y-DNA analysis and autosomal DNA analysis can be done. It'd be really interesting to see these samples on G25 too.

I've not heard any news on the Repton Viking paper with the believed to be Olaf of Dublin & son burial. I hope that paper provides some more I1 for us to dig through.

JonikW
08-05-2019, 11:50 AM
Interesting stuff. Hopefully this Viking paper can be finalized sooner than later so that Y-DNA analysis and autosomal DNA analysis can be done. It'd be really interesting to see these samples on G25 too.

I've not heard any news on the Repton Viking paper with the believed to be Olaf of Dublin & son burial. I hope that paper provides some more I1 for us to dig through.

We should get Cnut and others from Winchester pretty soon too.
This video is up now from Barrington A, Edix Hill, Cambridgeshire. Twenty two early AS samples have been shotgun sequenced as part of a Masters project. I'm attaching a screenshot showing how they cluster (with Icelanders rather than Germans, which doesn't seem surprising to me if there were Jutes among them). No haplogroup data yet. I see there are also late AS samples from Gamlingay in Cambridgeshire on the chart and later Medieval from St Johns Divinity School.

https://youtu.be/sr2kRkiCiT0

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spruithean
08-05-2019, 12:45 PM
We should get Cnut and others from Winchester pretty soon too.
This video is up now from Barrington A, Edix Hill, Cambridgeshire. Twenty two early AS samples have been shotgun sequenced as part of a Masters project. I'm attaching a screenshot showing how they cluster (with Icelanders rather than Germans, which doesn't seem surprising to me if there were Jutes among them). No haplogroup data yet. I see there are also late AS samples from Gamlingay in Cambridgeshire on the chart and later Medieval from St Johns Divinity School.

https://youtu.be/sr2kRkiCiT0

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Thanks for sharing that video, though I'm a bit surprised at the seeming misunderstanding of "Germanic". It seems they've misunderstood it to mean "German"?

Anglo-Saxons plotting with Icelanders is not a surprise to me and seems somewhat fitting for a Scandinavian-like population. Also, forgot to add that an incoming Germanic population from Jutland & N. Germany with a Scandinavian-like genetic signal mixing with British locals could be a reasonable way to understand the plotting toward Iceland (Norse+Gaels, etc).

deadly77
08-05-2019, 01:13 PM
Interesting stuff. Hopefully this Viking paper can be finalized sooner than later so that Y-DNA analysis and autosomal DNA analysis can be done. It'd be really interesting to see these samples on G25 too.

I've not heard any news on the Repton Viking paper with the believed to be Olaf of Dublin & son burial. I hope that paper provides some more I1 for us to dig through.

No I haven't heard any news on the Repton paper either (other than what we had soon after the documentary was broadcast). There was a podcast where Cat Jarman talked with Dan Snow - if memory serves correctly there was also DNA analysis of samples in the mass grave as well as the father and son burial, although obviously the latter has got more of the publicity.

deadly77
08-05-2019, 01:19 PM
We should get Cnut and others from Winchester pretty soon too.
This video is up now from Barrington A, Edix Hill, Cambridgeshire. Twenty two early AS samples have been shotgun sequenced as part of a Masters project. I'm attaching a screenshot showing how they cluster (with Icelanders rather than Germans, which doesn't seem surprising to me if there were Jutes among them). No haplogroup data yet. I see there are also late AS samples from Gamlingay in Cambridgeshire on the chart and later Medieval from St Johns Divinity School.

https://youtu.be/sr2kRkiCiT0

32177

Good find - I'll have a watch of the video later. The samples from Edix Hill are also covered in this recent open access paper on Yersinia pestis - https://www.pnas.org/content/116/25/12363

I've looked up the samples at ENA and they appear to be there at https://www.ebi.ac.uk/ena/data/view/PRJEB29991 but to me it looks like it's just the Yersinia pestis genomes as FASTQ files rather than the human genomes. Maybe those will be added later.

deadly77
08-06-2019, 08:37 AM
Thanks for sharing that video, though I'm a bit surprised at the seeming misunderstanding of "Germanic". It seems they've misunderstood it to mean "German"?

Anglo-Saxons plotting with Icelanders is not a surprise to me and seems somewhat fitting for a Scandinavian-like population. Also, forgot to add that an incoming Germanic population from Jutland & N. Germany with a Scandinavian-like genetic signal mixing with British locals could be a reasonable way to understand the plotting toward Iceland (Norse+Gaels, etc).

I watched the video and I agree with you - I think they've misunderstood what they are calling "Germanic" or at least not defining it properly as specifically modern German population. I'm also not surprised by the plot on the PCA - I went and looked back at the Ebenesersdóttir et al 2018 Science paper on the the ancient Icelandic genomes and a similar situation there, where if you look at Figure 2A, the ancient Icleanders are a bit separated from modern Icelanders on PCA. They say "The most likely cause for this divergence of Icelanders is 1100 years of genetic drift resulting from an initial founder event and subsequent small population size". More graphs, PCAs, etc. in the Supplementary Material for that paper, although the colours that the authors use don't make the the graphs easy to read.
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spruithean
08-11-2019, 04:10 PM
I watched the video and I agree with you - I think they've misunderstood what they are calling "Germanic" or at least not defining it properly as specifically modern German population. I'm also not surprised by the plot on the PCA - I went and looked back at the Ebenesersdóttir et al 2018 Science paper on the the ancient Icelandic genomes and a similar situation there, where if you look at Figure 2A, the ancient Icleanders are a bit separated from modern Icelanders on PCA. They say "The most likely cause for this divergence of Icelanders is 1100 years of genetic drift resulting from an initial founder event and subsequent small population size". More graphs, PCAs, etc. in the Supplementary Material for that paper, although the colours that the authors use don't make the the graphs easy to read.
32206

Some PCA plots have rather difficult colours to discern from one another, thankfully the use of different shapes helps to some degree.

I found this URL to a Google Maps: https://www.google.com/maps/d/embed?mid=1t7b3zbLIrQCaAKrTxktYG8zeU7Y&ll=57.447030133306285%2C-10.588084601620011&z=4, while it isn't necessarily about ancient I1, it does contain some interesting information to dig through I suppose.

deadly77
08-14-2019, 09:52 PM
Some PCA plots have rather difficult colours to discern from one another, thankfully the use of different shapes helps to some degree.

I found this URL to a Google Maps: https://www.google.com/maps/d/embed?mid=1t7b3zbLIrQCaAKrTxktYG8zeU7Y&ll=57.447030133306285%2C-10.588084601620011&z=4, while it isn't necessarily about ancient I1, it does contain some interesting information to dig through I suppose.

That is a pretty cool map - lots of information for sure when clicking on the pin icons. I'm guessing that was made by someone in the I-P109 group based on some of the subclades in the DNA pins. Have a fairly good idea who that might be - nice work.

deadly77
08-14-2019, 10:06 PM
I decided to take the plunge and email some of the authors of some of these papers.

I sent one to the authors of the genomes of Ancient Icelanders, going through the further subclade designations I had derived for some of the I1 samples as well as my alternative assignment of SVK-A1 as I-FGC21682 under I1a rather than the paper assignment of I1b. Got back a polite email from one of the main authors saying my email was very interesting and thanks for showing interest in their paper.

Also sent one to see if I could find anything more about the eight I1 samples from the academia.edu poster abstract here https://www.academia.edu/33791135/2017_Zenczak_.....Piontek_..._Y-chromosome_haplogroup_assignment_through_next_gene ration_sequencing_of_enriched_ancient_DNA_librarie s which gets talked about a lot without much in the way of real data. Asked them if they were planning to publish the resaerch with more details or if they would be willing to release the raw data in the form of BAM files (shy bairns get nowt, as we say in Northeast England...). Got a response with "Yes we are planning to publish our results. Keep in mind that these results were from our preliminary research. Unfortunately I can't give access to the BAM files until they are published."

JonikW
08-19-2019, 10:39 AM
I'm posting a link to an unusually thought-provoking work here because many of us enjoy theorising about how our Y lines reached wherever we trace our ancestry to, and this is right up the I1 street. It's Finn Rasmussen's July 2017 "The Golden Horns: Life and Religion of the original Anglo-Saxons (http://www.google.com/url?sa=t&source=web&rct=j&url=http://www.finse.dk/goldhorns.pdf&ved=2ahUKEwj95dOz0YjkAhWaThUIHZVkB_kQFjAAegQIARAB&usg=AOvVaw0KUo-BkFNBhOFlWWnAF4tQ&cshid=1566001324828)".
I've rarely read anything on the period that's interested me so deeply. The author isn't afraid to jump off in new directions but also cites primary and modern scholarly sources frequently along the way.
It all hinges around the two famous and now destroyed gold horns from Gallehus, buried about 420, but explores the wider Migration Period Germanic world, from material culture to competing religions, place name parallels in England and Scandinavia and more. The author's Scandinavian perspective means that much, including some primary sources, was unfamiliar to me despite a lot of previous reading. When it comes to the art and artefact styles, where I'm on home ground, I had little to quibble about and gained a lot to ponder regarding the possible meanings of certain patterns and symbols in particular. The maps and illustrations are excellent too, although he could have done with a proofreader.
One takeaway with potential relevance for my own Y line (won't elaborate here but it's to do with my downstream match being an outlier in comparison with my immediate upstream ones) was the author's claim that the Heathobards were the last "Angles" to emigrate to England, leaving after 520 when Heorot, the Danish hall immortalised in Beowulf, was burned down in a conflict between the two peoples, as outlined in Beowulf and Widsith (http://anglosaxonpoetry.camden.rutgers.edu/widsith/). After that, according to the writer, the Danes gained increasing power and the Heathobard Angles finally upped sticks and left for Britain in the trail of their relatives who'd travelled generations earlier. Later, Rasmussen likens this flight to that from Harold Fair-hair's Norway to Iceland in search of land and freedom.
Linked to the Angle migrations is the author's use of the volcanic eruption of shortly before 540, and an eclipse of 413, and the possible implications for population movements and art motifs. I remember Ferguson mentioning the eruption in the context of hoard burials, but some of Rasmussen's ideas are fascinating.
It all reminded me of Michael P. Speidel's "Ancient Germanic Warriors: Warrior Styles from Trajan's Column to Icelandic Sagas" in its combination of daring statements of fact (sometimes informed speculation) and imaginative insight. If you read and enjoyed the latter book -- I've somewhat reluctantly never viewed a Roman horseman/crouching warrior gravestone in the same way since -- you'll enjoy this too; if you hated it, you'll feel the same here.
Gwyn Jones perhaps sums it up for me: "He would be a man supremely bold or learned who claimed to know the exact relationship, habitat, or even identity, of Danes, Jutes, Eruli, Heathobeards, and Angles." This particular man gets pretty close to going that far, so decide for yourselves on his conclusions. Either way, while we're waiting for the next round of I1 aDNA, download it and take a look if you're interested in where your Y forefathers may have come from.

spruithean
08-19-2019, 08:54 PM
I took a brief look earlier today, I'll dig into it hopefully later. Looks like an interesting read, if a little aggressive in its conclusions.

JMcB
08-19-2019, 09:19 PM
I'm posting a link to an unusually thought-provoking work here because many of us enjoy theorising about how our Y lines reached wherever we trace our ancestry to, and this is right up the I1 street. It's Finn Rasmussen's July 2017 "The Golden Horns: Life and Religion of the original Anglo-Saxons (http://www.google.com/url?sa=t&source=web&rct=j&url=http://www.finse.dk/goldhorns.pdf&ved=2ahUKEwj95dOz0YjkAhWaThUIHZVkB_kQFjAAegQIARAB&usg=AOvVaw0KUo-BkFNBhOFlWWnAF4tQ&cshid=1566001324828)".
I've rarely read anything on the period that's interested me so deeply. The author isn't afraid to jump off in new directions but also cites primary and modern scholarly sources frequently along the way.
It all hinges around the two famous and now destroyed gold horns from Gallehus, buried about 420, but explores the wider Migration Period Germanic world, from material culture to competing religions, place name parallels in England and Scandinavia and more. The author's Scandinavian perspective means that much, including some primary sources, was unfamiliar to me despite a lot of previous reading. When it comes to the art and artefact styles, where I'm on home ground, I had little to quibble about and gained a lot to ponder regarding the possible meanings of certain patterns and symbols in particular. The maps and illustrations are excellent too, although he could have done with a proofreader.
One takeaway with potential relevance for my own Y line (won't elaborate here but it's to do with my downstream match being an outlier in comparison with my immediate upstream ones) was the author's claim that the Heathobards were the last "Angles" to emigrate to England, leaving after 520 when Heorot, the Danish hall immortalised in Beowulf, was burned down in a conflict between the two peoples, as outlined in Beowulf and Widsith (http://anglosaxonpoetry.camden.rutgers.edu/widsith/). After that, according to the writer, the Danes gained increasing power and the Heathobard Angles finally upped sticks and left for Britain in the trail of their relatives who'd travelled generations earlier. Later, Rasmussen likens this flight to that from Harold Fair-hair's Norway to Iceland in search of land and freedom.
Linked to the Angle migrations is the author's use of the volcanic eruption of shortly before 540, and an eclipse of 413, and the possible implications for population movements and art motifs. I remember Ferguson mentioning the eruption in the context of hoard burials, but some of Rasmussen's ideas are fascinating.
It all reminded me of Michael P. Speidel's "Ancient Germanic Warriors: Warrior Styles from Trajan's Column to Icelandic Sagas" in its combination of daring statements of fact (sometimes informed speculation) and imaginative insight. If you read and enjoyed the latter book -- I've somewhat reluctantly never viewed a Roman horseman/crouching warrior gravestone in the same way since -- you'll enjoy this too; if you hated it, you'll feel the same here.
Gwyn Jones perhaps sums it up for me: "He would be a man supremely bold or learned who claimed to know the exact relationship, habitat, or even identity, of Danes, Jutes, Eruli, Heathobeards, and Angles." This particular man gets pretty close to going that far, so decide for yourselves on his conclusions. Either way, while we're waiting for the next round of I1 aDNA, download it and take a look if you're interested in where your Y forefathers may have come from.

Excellent! Thank you! As they used to say in my business; I’m in!

Plus, it also helps that it’s free. ;-)

spruithean
08-24-2019, 09:34 PM
The author certainly makes a lot of (perhaps) bold claims in regards to several topics, but it's an interesting read, which certainly makes you think about the origins of these North Sea Germanic tribes, and I guess by extension the story of I1.

spruithean
08-25-2019, 06:57 PM
Rumours of an Etruscan I1: https://anthrogenica.com/showthread.php?16487-The-Italian-Peninsula-through-Ancient-DNA/page108&p=594580#post594580

JonikW
08-25-2019, 07:27 PM
Rumours of an Etruscan I1: https://anthrogenica.com/showthread.php?16487-The-Italian-Peninsula-through-Ancient-DNA/page108&p=594580#post594580

Very interesting and thanks for posting. If it does check out I wouldn't be so surprised. I'm thinking of clues in the Bronze Age rock carvings of Norway and Sweden about contacts with the Mediterranean at that time (assuming the subclade is of the right date). I have a copy of this book (http://books.google.es/books/about/Shadows_of_a_Northern_Past.html?id=TrGAAAAAMAAJ&source=kp_book_description&redir_esc=y) at home and remember it evaluates that relationship quite extensively. I'm in sunny Spain at the moment so can't reread unfortunately. But from memory it was linked to ship forms and perhaps more. At least I remember I thought it was plausible when I read it, and the study of the sites is the best available as far as I know.

oz
08-25-2019, 08:07 PM
Rumours of an Etruscan I1: https://anthrogenica.com/showthread.php?16487-The-Italian-Peninsula-through-Ancient-DNA/page108&p=594580#post594580

I'd like it if it turns out to be legit. For the sake of diversity of the I1 progenitors, instead of all I1 having just one source of origin (North Sea, Scandinavian, Germanic). For example, maybe some of the I1 in the Balkans could be ancestors of those Etruscans, or it got to the Balkans later via the Romans, before the Goths and whatnot. History's mysteries run very deep and we're talking about things going back 5000 years ago (the approximate tmrca of I1) that's a looooong ass time for a lot of things and all kinds of migrations to happen. Adding more complexity to it only makes sense.

Not that it helps in figuring out your own deep ancestry. I wish I could know exactly who my ancestors were but that's pretty much impossible.

spruithean
08-25-2019, 08:33 PM
I'd like it if it turns out to be legit. For the sake of diversity of the I1 progenitors, instead of all I1 having just one source of origin (North Sea, Scandinavian, Germanic). For example, maybe some of the I1 in the Balkans could be ancestors of those Etruscans, or it got to the Balkans later via the Romans, before the Goths and whatnot. History's mysteries run very deep and we're talking about things going back 5000 years ago (the approximate tmrca of I1) that's a looooong ass time for a lot of things and all kinds of migrations to happen. Adding more complexity to it only makes sense.

Agreed. It'd be nice if it turned out to be a legitimate sample (not saying it isn't, just don't want to get my hopes up) of Etruscan I1. It would be interesting to see this Etruscan individuals autosomal DNA and where he may fit on a PCA. I remember when they discovered that I1 or pre-I1 (or whatever you want to call it) in Neolithic Hungary and a few individuals online pointed out that they had, for a while now, been saying that I1 is not necessarily the result of Germanic spread, but could also be the product of older movements of populations.

Whatever the case we need to get our hands on more and more samples, the Viking paper provided a good amount, but not necessarily very telling about the origins of I1 (save for the Iron Age Denmark I-Z58, which is not a surprise). Where was the ancestor of modern I1? Was he in Central Europe or somewhere else?


Not that it helps in figuring out your own deep ancestry. I wish I could know exactly who my ancestors were but that's pretty much impossible.

Indeed, I've had several theories for my own case of I1, but it's always met with the same variables, either Anglo-Saxons, Vikings or Normans or perhaps later groups or "invisible" earlier groups. It doesn't help that my branch is sparsely populated and my closest matches are downstream or on other "sibling" branches.

JonikW
08-25-2019, 10:45 PM
Agreed. It'd be nice if it turned out to be a legitimate sample (not saying it isn't, just don't want to get my hopes up) of Etruscan I1. It would be interesting to see this Etruscan individuals autosomal DNA and where he may fit on a PCA. I remember when they discovered that I1 or pre-I1 (or whatever you want to call it) in Neolithic Hungary and a few individuals online pointed out that they had, for a while now, been saying that I1 is not necessarily the result of Germanic spread, but could also be the product of older movements of populations.

Whatever the case we need to get our hands on more and more samples, the Viking paper provided a good amount, but not necessarily very telling about the origins of I1 (save for the Iron Age Denmark I-Z58, which is not a surprise). Where was the ancestor of modern I1? Was he in Central Europe or somewhere else?



Indeed, I've had several theories for my own case of I1, but it's always met with the same variables, either Anglo-Saxons, Vikings or Normans or perhaps later groups or "invisible" earlier groups. It doesn't help that my branch is sparsely populated and my closest matches are downstream or on other "sibling" branches.

What are the ages of these pending Etruscan samples? I'd be wary of thinking PCAs will tell us anything after potentially hundreds of years from the date of Y DNA arrival in that area and far from the region where we can be confident modern I1 originated. We should also expect outliers that comply with what we know of (pre)history. I agree the difficulty is in building up a big enough sample size to know what's representative. I hope you get more evidence on your own line soon. I had a recent new YFull upstream recruit who I'm hoping will add to the TMRCA picture when he's processed.

JMcB
08-26-2019, 02:59 AM
What are the ages of these pending Etruscan samples? I'd be wary of thinking PCAs will tell us anything after potentially hundreds of years from the date of Y DNA arrival in that area and far from the region where we can be confident modern I1 originated. We should also expect outliers that comply with what we know of (pre)history. I agree the difficulty is in building up a big enough sample size to know what's representative. I hope you get more evidence on your own line soon. I had a recent new YFull upstream recruit who I'm hoping will add to the TMRCA picture when he's processed.

Without wading through the thread again, I believe they are IA and that many of the samples are low quality. At least, that’s what I remember seeing him say. We’ll see. To be honest, even if it turns out to be true (and I have my doubts considering how it’s being reported), I don’t find it all that surprising.

JonikW
08-26-2019, 09:14 AM
Without wading through the thread again, I believe they are IA and that many of the samples are low quality. At least, that’s what I remember seeing him say. We’ll see. To be honest, even if it turns out to be true (and I have my doubts considering how it’s being reported), I don’t find it all that surprising.

If it does turn out be true, I've found a short paper here (http://www.academia.edu/36974280/Minoan_Greek_traders_in_Norway) that sets out evidence for Greek Bronze Age, Mycenaean and Minoan contact/influence in Scandinavia.
EDIT: this is intriguing too (http://araenil.wordpress.com/2011/06/26/evidence-of-prehistoric-connections-crete-norway/) regarding an inscription mentioned in the paper.

JMcB
08-26-2019, 02:24 PM
If it does turn out be true, I've found a short paper here (http://www.academia.edu/36974280/Minoan_Greek_traders_in_Norway) that sets out evidence for Greek Bronze Age, Mycenaean and Minoan contact/influence in Scandinavia.
EDIT: this is intriguing too (http://araenil.wordpress.com/2011/06/26/evidence-of-prehistoric-connections-crete-norway/) regarding an inscription mentioned in the paper.

While I haven’t done an in depth study on the subject, that’s also been my understanding.

Thanks for the links!

deadly77
08-30-2019, 11:06 PM
There's another Iberian pre-I1/I* to go along with BAL051. This one is Car1 from Cueva de la Carigüela in the Olade 2019 The genomic history of the Iberian Peninsula over the past 8000 years paper. Sample dated to 9700–5500 BCE. The supplementary material notes that "The archaeological excavation strongly points to a pre-Neolithic context, but several attempts to generate a radiocarbon date have not been successful." Their dating is based on Car1 plotting closely on PCA with other Iberian Mesolithic individuals (as expected for an individual who lived before the arrival of Neolithic farmers); 2.22% neanderthal ancestry (similar to other European individuals that lived around 8000 BCE); mtDNA. Although they stress that a direct radiocarbon date would provide the most accurate estimation of the age of this individual.

Anyway, this came to my attention as a few comments on Facebook pages noted that the origin point of I1 in Hunter Provyn's Phylogeographer tool was being dragged considerably southwards. Hunter said this was due to the listing of two Iberian samples that were listed as fully I1 in the Carlos Quiles dataset of ancient DNA samples. One we know about (BAL051), but the other one Car1 wasn't on my radar. I checked the Olade et al paper - the authors do not list this sample as I1 in Table S4. Olade et al list Car1/I10899 as I, but exclude some of the I2 subcaldes (xI2a1,xI2a2,xI2c). However, not being I2 doesn't make someone I1.

Given the known innacuracies in assignments of the database ancient DNA samples compiled by Carlos Quiles that we've discussed before in this thread, I decided to do what's always best - go back to the primary data of the BAM file for Car1/I10899.

Car1 is derived for 19 of the SNPs that define I1 and ancestral for 35 of the SNPs that define I1. Also not able to categorize one - for FGC2445, ancestral is C, derived is T, while the result for Car1 at ChrY(hg19):4123447 is 1A, so it's a mutation but not to the nucleotide that defines the SNP - could just be damage. As usual with a lot of these ancient samples, the rest of the I1 SNPs are no calls.

Car1 Derived I1 SNPs: Z2699 1C, Z2880 3A, Z2729 1T, Z2779 1C, CTS10338 1C, Z2885 1T, V5190/Z2742 1A, CTS11036/Z2863 1T, Z2730 1G, Z2720 1T, Z2887 1T, Z2847 1T, CTS1739 1G, Y1950 CGGA, Z2852 1T, CTS6022 1A, CTS4532 1A, Z2859 2A, Z2695 1T.

Car 1 Ancestral I1 SNPs: L840 1C, FGC7747 1T, Z2718 2C, Z2679 2T, Z2727 3C, CTS6140 1T, Y1872 1G, Z2747 1A, CTS11042 2T, Z2826 1T, Z2858 1G, V5203 2G, CTS11534 1A, Y1863 3T, CTS8394 1G, Z2825 1G, L848 1C, CTS9486 1G, Z2705 1C, Z2790 1G, Y1860 1A, Y1871 1C, FGC2427 1C, L764 1C, L1439 2C, Z2870 1T, CTS9487 1G, Z2775 1G, CTS9368 2T, Y1876 1T,Z6116 1A, Z2832 2G, CTS7386 1T, CTS8708 1T, FGC2462 1C

So as for BAL051, Car1 represents a pre-I1 lineage that likely doesn't have any modern patrilineal descendants. Not fully I1 itself, but of interest to I1 with a mixture of derived and ancestral calls among the SNPs that define the I1 haplogroup.

JonikW
08-30-2019, 11:13 PM
There's another Iberian pre-I1/I* to go along with BAL051. This one is Car1 from Cueva de la Carigüela in the Olade 2019 The genomic history of the Iberian Peninsula over the past 8000 years paper. Sample dated to 9700–5500 BCE. The supplementary material notes that "The archaeological excavation strongly points to a pre-Neolithic context, but several attempts to generate a radiocarbon date have not been successful." Their dating is based on Car1 plotting closely on PCA with other Iberian Mesolithic individuals (as expected for an individual who lived before the arrival of Neolithic farmers); 2.22% neanderthal ancestry (similar to other European individuals that lived around 8000 BCE); mtDNA. Although they stress that a direct radiocarbon date would provide the most accurate estimation of the age of this individual.

Anyway, this came to my attention as a few comments on Facebook pages noted that the origin point of I1 in Hunter Provyn's Phylogeographer tool was being dragged considerably southwards. Hunter said this was due to the listing of two Iberian samples that were listed as fully I1 in the Carlos Quiles dataset of ancient DNA samples. One we know about (BAL051), but the other one Car1 wasn't on my radar. I checked the Olade et al paper - the authors do not list this sample as I1 in Table S4. Olade et al list Car1/I10899 as I, but exclude some of the I2 subcaldes (xI2a1,xI2a2,xI2c). However, not being I2 doesn't make someone I1.

Given the known innacuracies in assignments of the database ancient DNA samples compiled by Carlos Quiles that we've discussed before in this thread, I decided to do what's always best - go back to the primary data of the BAM file for Car1/I10899.

Car1 is derived for 19 of the SNPs that define I1 and ancestral for 35 of the SNPs that define I1. Also not able to categorize one - for FGC2445, ancestral is C, derived it T, while the result for Car1 at ChrY(hg19):4123447 is 1A, so it's a mutation but not to the nucleotide that defines the SNP - could just be damage. As usual with a lot of these ancient samples, the rest of the I1 SNPs are no calls.

Car1 Derived I1 SNPs: Z2699 1C, Z2880 3A, Z2729 1T, Z2779 1C, CTS10338 1C, Z2885 1T, V5190/Z2742 1A, CTS11036/Z2863 1T, Z2730 1G, Z2720 1T, Z2887 1T, Z2847 1T, CTS1739 1G, Y1950 CGGA, Z2852 1T, CTS6022 1A, CTS4532 1A, Z2859 2A, Z2695 1T.

Car 1 Ancestral I1 SNPs: L840 1C, FGC7747 1T, Z2718 2C, Z2679 2T, Z2727 3C, CTS6140 1T, Y1872 1G, Z2747 1A, CTS11042 2T, Z2826 1T, Z2858 1G, V5203 2G, CTS11534 1A, Y1863 3T, CTS8394 1G, Z2825 1G, L848 1C, CTS9486 1G, Z2705 1C, Z2790 1G, Y1860 1A, Y1871 1C, FGC2427 1C, L764 1C, L1439 2C, Z2870 1T, CTS9487 1G, Z2775 1G, CTS9368 2T, Y1876 1T,Z6116 1A, Z2832 2G, CTS7386 1T, CTS8708 1T, FGC2462 1C

So as for BAL051, Car1 represents a pre-I1 lineage that likely doesn't have any modern patrilineal descendants. Not fullt I1 itself, but of interest to I1 with a mixture of derived and ancestral calls among the SNPs that define the I1 haplogroup.

That's great work from you again. Will you be adding him to your map with a skull and crossbones? And is there any way of adding SNP details as blurbs in these cases, or is that just too complicated?

spruithean
08-30-2019, 11:17 PM
Interesting. Thanks for posting about it, otherwise I probably wouldn't have noticed! Perhaps this is just more of a sign that pre-I1 was relatively widespread in Europe, but only one lineage of it survived to form modern I1?

deadly77
08-30-2019, 11:38 PM
Interesting. Thanks for posting about it, otherwise I probably wouldn't have noticed! Perhaps this is just more of a sign that pre-I1 was relatively widespread in Europe, but only one lineage of it survived to form modern I1?

Yes, I think that's likely. I'm also thinking that there may have been more than one bottleneck between the split from I2 and the TMRCA of I1. But of course it's invisible us in modern I1 genomes as we only inherited the survivor. And the pre-I1 samples like Car1, BAL051, SF11 are needles in the haystack (or more likely the field). If that makes sense...

There are a few other samples in the Olade paper that are I rather than I2 - although Car 1/I10988 is the only one that has the I(xI2a1,xI2a2,xI2c) designation. I added four of them to the BAM viewer while I was looking at Car1 - those were I0453, I0455, I1282, I1284 - those four were all ancestral or no call for the I1 SNPs, so no positive trace of I1 in those four.

deadly77
08-31-2019, 09:08 AM
That's great work from you again. Will you be adding him to your map with a skull and crossbones? And is there any way of adding SNP details as blurbs in these cases, or is that just too complicated?

Yes, he's on the map with a skull and crossbones. Car1 becomes the most Southern sample on the map so far.

If you click on the sample name in the left hand menu, it should zoom in to the sample in question on the map view and the left hand panel menu will bring up a short summary which has the SNP details included in the description (along with a bit about the archaelogical context, mtDNA haplogroup, a link to the original paper and anything I could find about isotopes, dates, etc.). Alternatively if you click on a pin on the map, should also replace the left hand panel menu with the short summary but without zooming in.

JonikW
08-31-2019, 09:36 AM
Yes, he's on the map with a skull and crossbones. Car1 becomes the most Southern sample on the map so far.

If you click on the sample name in the left hand menu, it should zoom in to the sample in question on the map view and the left hand panel menu will bring up a short summary which has the SNP details included in the description (along with a bit about the archaelogical context, mtDNA haplogroup, a link to the original paper and anything I could find about isotopes, dates, etc.). Alternatively if you click on a pin on the map, should also replace the left hand panel menu with the short summary but without zooming in.

I hadn't realised exactly how much you've done. That's incredibly comprehensive... I'm pleased you've put the site in your signature here. It's a uniquely valuable resource for I1 aDNA.

spruithean
08-31-2019, 03:47 PM
I hadn't realised exactly how much you've done. That's incredibly comprehensive... I'm pleased you've put the site in your signature here. It's a uniquely valuable resource for I1 aDNA.

Yeah, it is quite a large amount of work and thanks again for creating this resource Deadly!

It's actually really quite interesting to see how much it has grown since the initial creation. The Viking paper certainly provided a large amount of samples for the map.

JMcB
08-31-2019, 04:19 PM
Originally Posted by JonikW:

I hadn't realised exactly how much you've done. That's incredibly comprehensive... I'm pleased you've put the site in your signature here. It's a uniquely valuable resource for I1 aDNA.


Yeah, it is quite a large amount of work and thanks again for creating this resource Deadly!

It's actually really quite interesting to see how much it has grown since the initial creation. The Viking paper certainly provided a large amount of samples for the map.

I’ll third that Deadly! Nice work and much appreciated!

deadly77
09-01-2019, 09:02 AM
Cheers folks - it's largely born out of the discussions in this thread so thanks for all of those - it wouldn't have got to this point without you folks. I had tried some different formats such as an excel spreadsheet, but I found it difficult viewing to capture relevant detailed information without overloading among said data. I quite like the Google Maps view as it gives options for a big picture of all the samples, but has the option to isolate each of the samples one at a time for more detailed information. It came about in a discussion that I was having with Anthrogenica forum member Celt_?? and he asked me if anyone had prepared a map for ancient I1 and sent me a link to this ancient R-U152 ancient samples by R.Rocca here https://www.google.com/maps/d/viewer?mid=15zJwudMOPqf20VVXXNXkm4qydzTP3VW0&ll=49.94185809129344%2C-1.2287218813476102&z=4

I quite liked the idea, so started to put one together for I1. I think it makes finding data on specific samples a lot quicker - this thread has 47 pages and over 460 posts, so it sometimes takes me a little while to find information.

Yep, the recent Viking preprint added a heck of a lot of I1 samples. We're up to 127 I1 (and pre-I1) in total these days, and the Viking preprint accounts for 92 of those, which is two-thirds.

Stone Meadow
09-02-2019, 04:19 AM
Cheers folks - it's largely born out of the discussions in this thread so thanks for all of those - it wouldn't have got to this point without you folks. I had tried some different formats such as an excel spreadsheet, but I found it difficult viewing to capture relevant detailed information without overloading among said data. I quite like the Google Maps view as it gives options for a big picture of all the samples, but has the option to isolate each of the samples one at a time for more detailed information. It came about in a discussion that I was having with Anthrogenica forum member Celt_?? and he asked me if anyone had prepared a map for ancient I1 and sent me a link to this ancient R-U152 ancient samples by R.Rocca here https://www.google.com/maps/d/viewer?mid=15zJwudMOPqf20VVXXNXkm4qydzTP3VW0&ll=49.94185809129344%2C-1.2287218813476102&z=4

I quite liked the idea, so started to put one together for I1. I think it makes finding data on specific samples a lot quicker - this thread has 47 pages and over 460 posts, so it sometimes takes me a little while to find information.

Yep, the recent Viking preprint added a heck of a lot of I1 samples. We're up to 127 I1 (and pre-I1) in total these days, and the Viking preprint accounts for 92 of those, which is two-thirds.

Thank you so much for this outstanding work, deadly77. My father was a reasonably well known American chronicler of our family line, and in conjunction with English genealogists, four decades ago advised me that we came from Normandy through William the Conqueror's invasion of England in 1066. And that THOSE men invaded Normandy from the west coast of what is now Jutland, Denmark, a few centuries earlier.

Which brings me to today. I was scrolling through your map when I came across VIK327 I-YSC0000261 from Ribe, Jutland, Denmark, whose Y-haplogroup is an exact match for my own. I stopped and considered that I share a common ancestor with nearly half the VA persons on your list, but VIK327 is altogether more closely related.

A paternal uncle's Y-haplogroup is a few levels downstream from I-YSC0000261, at I-S1990, so I presume mine is too, but even accounting for the 1200 years since VIK327 lived still leaves plenty of room for us to have a common ancestor. Here's the weird part: my wife and I have repeatedly visited Ribe since 1980. I even purchased a copy of The Vikings of Ribe from a museum there on one of our visits.

To discover that a distant cousin, if not direct antecedent, lived there 1200 years ago is one hell of a shock!

deadly77
09-02-2019, 08:29 AM
Thank you so much for this outstanding work, deadly77. My father was a reasonably well known American chronicler of our family line, and in conjunction with English genealogists, four decades ago advised me that we came from Normandy through William the Conqueror's invasion of England in 1066. And that THOSE men invaded Normandy from the west coast of what is now Jutland, Denmark, a few centuries earlier.

Which brings me to today. I was scrolling through your map when I came across VIK327 I-YSC0000261 from Ribe, Jutland, Denmark, whose Y-haplogroup is an exact match for my own. I stopped and considered that I share a common ancestor with nearly half the VA persons on your list, but VIK327 is altogether more closely related.

A paternal uncle's Y-haplogroup is a few levels downstream from I-YSC0000261, at I-S1990, so I presume mine is too, but even accounting for the 1200 years since VIK327 lived still leaves plenty of room for us to have a common ancestor. Here's the weird part: my wife and I have repeatedly visited Ribe since 1980. I even purchased a copy of The Vikings of Ribe from a museum there on one of our visits.

To discover that a distant cousin, if not direct antecedent, lived there 1200 years ago is one hell of a shock!

Thanks - I hope you're finding this useful and helpful. Also, great to see another I-Z140 fellow on the Anthrogenica forums.

Yes, VK327 the closest one to you and me (although I'm not as far down as I-S1990) so far based on the data available. The samples with a VK prefix from the recent "Population genomics of the Viking world" preprint haven't yet made the raw data publically available. Most authors make the raw data available in the form of BAM files once the papers are officially published, so once those become available, I'll be able to download said BAM files and take a closer look at the SNPs, which may allow the assignment of a more refined phylogenetic position. But some of these ancient DNA samples are rather degraded and it's not possible to designate these confidently. Won't really know for sure until the BAM files become available. In the meantime, I've gone with the subclade assignments by the authors in the preprint. The used an automated software tool to extract Y-SNPs and used the ISOGG tree as a reference - it's likely that they missed a few SNPs that can be read in the raw data. So we might have an updated subclade for VK327 (and the other VK samples) in the near future.

Stone Meadow
09-02-2019, 03:33 PM
Thanks again, deadly77. I used a similar technique to dig down to YSC0000261. Back in 2006 I took a Y12 test from FTDNA that assigned me to I1-M253. but couldn't figure out how to use the STRs to dig deeper. Then at a family reunion in the summer of 2018 my uncle showed me his results from Genographic 2.0+, which placed him in YSC0000261. To resolve a potential NPE we decided to each take an AncestryDNA test to see if we were related, as my mother had claimed for decades that my birth certificate father was not my biological father.

AncestryDNA doesn't test specifically for one's Y-Haplogroup, but they did show us having 1809cM of matches with a largest match of 38cM, which resolved the NPE question. As interestingly, they do sample one's Y and mt genetics, and by using phylotrees and our raw data files I found both of us positive for YSC0000261 by the simple technique of looking for the defining rsid's to match subclade identities. Using the same technique I was also able to extend my old mt-Haplogroup assignment from H down to H1c9a.

It took a bit of time, but the process of discovery was rewarding itself.

Late this spring we transferred my uncle's Genographics file to FTDNA, who promptly assigned him to I-S1990. We can't get access to his Genographics raw data (the transfer goes direct), but it seems safe to say Genographics sequenced the defining SNP while AncestryDNA did not.

Stone Meadow
09-02-2019, 03:39 PM
Based on finding VIK327 I-YSC0000261 from Ribe, Jutland, Denmark, whose Y-haplogroup is an exact match for my own, I am adding a Danish flag to my profile.

JonikW
09-02-2019, 09:16 PM
Based on finding VIK327 I-YSC0000261 from Ribe, Jutland, Denmark, whose Y-haplogroup is an exact match for my own, I am adding a Danish flag to my profile.

Given your interest, I'd urge you to test Big Y or similar to help build out our tree. Like you, deadly and VK327 I'm also YSC0000261+ but I believe the TMRCA is about 3,400 ybp so a lot has happened since then. I'm S1990-, and while that takes you to about 2,400 ybp as far as I can see, that's still only just into the Iron Age so you could learn more. I enjoyed reading about your personal links to Ribe and your Danish flag decision. It's a safe bet that your ancestors were in Denmark at some stage. May I ask what part of England your line settled in and whether your surname provided any Norman origin clues? I posted here (http://anthrogenica.com/showthread.php?17089-Norman-impact-on-English-DNA) about my own Norman autosomal lines. I'm still puzzling out my Y forefather's case....

spruithean
09-03-2019, 11:42 AM
Given your interest, I'd urge you to test Big Y or similar to help build out our tree. Like you, deadly and VK327 I'm also YSC0000261+ but I believe the TMRCA is about 3,400 ybp so a lot has happened since then. I'm S1990-, and while that takes you to about 2,400 ybp as far as I can see, that's still only just into the Iron Age so you could learn more. I enjoyed reading about your personal links to Ribe and your Danish flag decision. It's a safe bet that your ancestors were in Denmark at some stage. May I ask what part of England your line settled in and whether your surname provided any Norman origin clues? I posted here (http://anthrogenica.com/showthread.php?17089-Norman-impact-on-English-DNA) about my own Norman autosomal lines. I'm still puzzling out my Y forefather's case....

That seems to be quite universal for members of Haplogroup I1 :lol:, it's just a matter of when they left!

Stone Meadow
09-03-2019, 02:56 PM
Given your interest, I'd urge you to test Big Y or similar to help build out our tree. Like you, deadly and VK327 I'm also YSC0000261+ but I believe the TMRCA is about 3,400 ybp so a lot has happened since then. I'm S1990-, and while that takes you to about 2,400 ybp as far as I can see, that's still only just into the Iron Age so you could learn more. I enjoyed reading about your personal links to Ribe and your Danish flag decision. It's a safe bet that your ancestors were in Denmark at some stage. May I ask what part of England your line settled in and whether your surname provided any Norman origin clues? I posted here (http://anthrogenica.com/showthread.php?17089-Norman-impact-on-English-DNA) about my own Norman autosomal lines. I'm still puzzling out my Y forefather's case....

The Big Y is not in my hobby budget just yet, so instead I am ordering the I1 Z2535 SNP Pack (https://www.familytreedna.com/upgrades.aspx?ot=ADV) to burrow down the subclade I already know I'm a member of.

My surname is Clayton, which genealogists James Bellarts and Elaine Rowland have traced to Robert of Caudebec, Normandy, who was awarded Clayton Manor in Lancashire in NW England after the Battle of Hastings. The Claytons mainly lived in Lancashire and Yorkshire for several hundred years before appearing in Sussex (for non-British, the south of England) about 1500. My line emigrated to New Jersey, USA, in 1677.

Robert was son of Hugh and grandson of Leofwine of Normandy. Both of the latter names are Germanic or Anglo Saxon in origin, but I don't know if they're considered Norman in particular.

JonikW
09-03-2019, 03:39 PM
The Big Y is not in my hobby budget just yet, so instead I am ordering the I1 Z2535 SNP Pack (https://www.familytreedna.com/upgrades.aspx?ot=ADV) to burrow down the subclade I already know I'm a member of.

My surname is Clayton, which genealogists James Bellarts and Elaine Rowland have traced to Robert of Caudebec, Normandy, who was awarded Clayton Manor in Lancashire in NW England after the Battle of Hastings. The Claytons mainly lived in Lancashire and Yorkshire for several hundred years before appearing in Sussex (for non-British, the south of England) about 1500. My line emigrated to New Jersey, USA, in 1677.

Robert was son of Hugh and grandson of Leofwine of Normandy. Both of the latter names are Germanic or Anglo Saxon in origin, but I don't know if they're considered Norman in particular.

Very interesting. Leofwine ("beloved friend") Is a dithematic Anglo-Saxon name, so late in period and from the higher level of English society. I haven't seen it in a Norman context before.
I hope you'll update us when you get the panel results. That sounds like a wise move.

spruithean
09-03-2019, 04:43 PM
Very interesting. Leofwine ("beloved friend") Is a dithematic Anglo-Saxon name, so late in period and from the higher level of English society. I haven't seen it in a Norman context before.
I hope you'll update us when you get the panel results. That sounds like a wise move.

Yeah, I'm somewhat perplexed by a Norman having the name Leofwine, although if the toponymy of Normandy does show there was a fair amount of Anglo-Saxon, Saxon or Anglo-Scandinavian settlements, so perhaps it is rooted in there somewhere.

Stone Meadow
09-03-2019, 07:22 PM
Very interesting. Leofwine ("beloved friend") Is a dithematic Anglo-Saxon name, so late in period and from the higher level of English society. I haven't seen it in a Norman context before.
I hope you'll update us when you get the panel results. That sounds like a wise move.

Yes, the name had been around for at least a couple hundred years before Leofwine of Normandy, though as you say in Anglo-Saxon society. I was not aware it was not known among the Normans proper. He's listed in so many places on the internet that rooting out the truth may now be impossible.

I ordered the I1 Z2535 SNP Pack this morning, so should see results in a month or so. Will let you know how it goes.

spruithean
09-03-2019, 07:32 PM
I'm not trying to deny any of the research done by your relatives or yourself, but is it possible that this family line was originally Anglo-Saxon that eventually Normanised?

JonikW
09-03-2019, 07:42 PM
I'm not trying to deny any of the research done by your relatives or yourself, but is it possible that this family line was originally Anglo-Saxon that eventually Normanised?

Only around 10% of the native population retained landholdings in some capacity by Domesday. Those that did, and families that had previously been of thegnly rank but initially lost their holdings, often thrived, so I suspect that's a possibility here.

Stone Meadow
09-03-2019, 08:22 PM
I'm not trying to deny any of the research done by your relatives or yourself, but is it possible that this family line was originally Anglo-Saxon that eventually Normanised?

Not to worry. I don't take any of it as negative. After all, I'm here to learn. My father and a distant cousin did the grunt work to tie the USA Claytons in with the Sussex Claytons. I did not get interested enough to join the effort until several years ago, by which time they had passed. My mother's father's family also has a long history of genealogy, and trace back to 3 brothers who emigrated to the USA in 1648 from Ayrshire, Scotland. I therefore decided to spend my genealogical efforts extending my mitochondrial heritage, since (at least here) that is a neglected branch of genealogy, and to me a very personal line of work, since it ties me back in time though my mother, her mother, and so on.

Building mitochondrial 'gedcoms', as it were, has proved a challenge, and I hit a wall at 1720 in Virginia, USA. The birth surnames of women often simply were not recorded, and the confirmatory links lost in time. Moreover, my mt-haplogroup, H1c9a, has proved quite uncommon: I've found one person on Anthrogenica (still too few posts here to have messaging privileges), plus a woman from New Zealand who popped up on FTDNA (tho we do not have a match on Family Finder).

JonikW
09-03-2019, 08:58 PM
Not to worry. I don't take any of it as negative. After all, I'm here to learn. My father and a distant cousin did the grunt work to tie the USA Claytons in with the Sussex Claytons. I did not get interested enough to join the effort until several years ago, by which time they had passed. My mother's father's family also has a long history of genealogy, and trace back to 3 brothers who emigrated to the USA in 1648 from Ayrshire, Scotland. I therefore decided to spend my genealogical efforts extending my mitochondrial heritage, since (at least here) that is a neglected branch of genealogy, and to me a very personal line of work, since it ties me back in time though my mother, her mother, and so on.

Building mitochondrial 'gedcoms', as it were, has proved a challenge, and I hit a wall at 1720 in Virginia, USA. The birth surnames of women often simply were not recorded, and the confirmatory links lost in time. Moreover, my mt-haplogroup, H1c9a, has proved quite uncommon: I've found one person on Anthrogenica (still too few posts here to have messaging privileges), plus a woman from New Zealand who popped up on FTDNA (tho we do not have a match on Family Finder).

You've done very well to get to 1720 on your maternal line. I've only got to the end of the 18th century but hope to test more deeply and find out more one day.
Y DNA seems much more straightforward to me when it comes to tracing ancestors on a tree, and we're accustomed to thinking of descent by surname. And like spruithean said, Denmark is likely to have played a part in most of our I1 stories and the migrations from there are well documented back into the Migration Period too.
As for maternal ancestry and the way that women were married out and mtDNA haplogroups have dispersed so widely, I've often been moved by reading chapter 22 of Finland's national epic, the Kalevala. The bride goes off to live with the bridegroom's family, from a house where she "rose from bed to butter" to "a different mother's rule" where she won't know how to "heat the fireplace as the man of the house likes". That must be the story of so many of our distant female forebears and finding out something about my late mother's V line would be a personal journey for me too.
On your I1 Claytons, you should be able to verify what's been discovered relatively easily if you ever have the time and feel up to the task.

Stone Meadow
09-04-2019, 08:04 PM
Thank you for the kind words of encouragement. When I started my maternal line inquiries I had only my mother, grandmother, and great-grandmother, all of whom I knew personally. In time I found a second cousin who had two more names. Over the past year I have tracked down 4 additional levels to the one born in 1720. I have her father's surname only, who was born in Ireland in the late 17th century and came to the US in the early 1700s.

After thinking about your verification suggestion, I realize I am more interested in the genetics questions than in building family trees, per se. To that end I think I'm going to try tracking down English Claytons who may have taken genetics testing to see if there are others with our y-Haplogroup. That will complement efforts to extend my maternal line. Still searching for more info on the origins and history of H1c9a.

Cheers, Stan

spruithean
09-05-2019, 01:25 PM
I'm also fairly interested in the genetic questions I have, more than I used to be. I suppose with the seemingly permanent brickwall for my direct paternal line it has been much more interesting to try and learn as much as possible about Haplogroup I1 and the origins of it, if I can't figure out what happened prior to the late 1700s, I'll definitely try and learn about what may have occurred prior to surnames and nations!

Kaltmeister
09-08-2019, 02:01 PM
Please mind my contribution on the relationship between EHG and I1 and their origin in the thread "I1 migration story".

deadly77
09-09-2019, 08:54 AM
Deleted

deadly77
09-13-2019, 10:05 AM
I've recently been in discussions with Hunter Provyn, the developer of the Phylogeographer/Mygrations tool regarding the ancient samples that his tool uses. I think it's a nice tool, but with any new functionality, there's going to be some teething issues and Phylogeographer definitely has had (and continues to have) some of those for sure. Patience is important for new developments, and I'm supportive of what Hunter is trying to do with Phylogeographer. I think Hunter is a fellow with the right intentions and trying to make the tool as good as he can, and he's always been receptive to comments. I've had discussions with him over a few things in the past, including updating some location tags and adding ancient samples to his database, which pulls directly from YFull for modern individuals.

Unfortunately, Hunter then decided to incorporate the dataset that had been assembled by Carlos Quiles. I can understand why he did this as it's a large dataset of over 1600 samples, with geolocation and Y-DNA haplogroup data included. Hunter asked myself and a few other haplogroup researches to look over the Carlos Quiles dataset, but the samples had already been integrated with Phylogrographer. It was disappointing to find a high error rate among the I1 samples that I reviewed. Some had the wrong location, there were examples of misreported data in papers remaining uncorrected (eg. SVK-A1 as I-Z131, CL63 as I-Z79), the wrong subclades being assigned due to a misunderstanding which year of ISOGG tree had been used by papers (eg. HSJ-A1 listed as I-A8182 rather than I-Y111864; SBT-A1 as I-S26062 rather than I-FGC74500), a sample of a modern individual (Saami001) included among ancients (and with the wrong subclade as well), and pre-I1/I* individuals with ancestral calls for I1 SNPs (SF11, BAL051, BAB5, Car1) being categorized as fully I1.

This wasn't exclusive to the I1 samples, but those are the ones that I looked at as I'm most familiar with I1. After some discussions with Hunter, it appears that other haplogroup researchers have reported similar issues with the data related to samples in other haplogroups. Any output analysis is only as good as the data input - poor or flawed data will result in poor or flawed interpretation. An example of this in particular to I1 was that the location of I-DF29 in Phylogeographer was being dragged to closer to Southwest Germany and I1 itself to Southern France due to some of these ancient samples in the Carlos Quiles dataset. After a bit of discussion, Hunter has decided to remove the Carlos Quiles database from his tool and start from scratch regarding ancient Y-DNA samples in his Phylogeographer tool. I don't think this was an easy decision, given the amount of time spent on this so far, but I think it's the right decision. Going forward, I'll be helping Hunter with ancient I1 samples in his tool and some other folks will work on the other haplogroups. Patience going forward and a few things to figure out, but at least we'll be going forward with data that should be a lot let erroneous. https://phylogeographer.com/how-haplogroup-researchers-can-add-edit-samples/?fbclid=IwAR1nThiX-aqUd6dO520I7zPn6GMkL7eQECp7sQt23NURJL13yAtAM878ZMI

spruithean
09-14-2019, 09:33 PM
Thanks for sharing. I'd been noticing that there were still rumours going about that SF11 or BAB5 or whatever pre-I1 sample was fully I1. Nice to see Mr. Provyn taking this step even though it is probably a bit of a pain considering all the work he had already done beforehand.

I'm interested to see what comes of the I1 found in Iron Age Italy (I think one was believed to be Etruscan?), it should be an interesting addition to the growing list of Ancient I1 (and pre-I1).

deadly77
09-15-2019, 09:17 AM
Thanks for sharing. I'd been noticing that there were still rumours going about that SF11 or BAB5 or whatever pre-I1 sample was fully I1. Nice to see Mr. Provyn taking this step even though it is probably a bit of a pain considering all the work he had already done beforehand.

I'm interested to see what comes of the I1 found in Iron Age Italy (I think one was believed to be Etruscan?), it should be an interesting addition to the growing list of Ancient I1 (and pre-I1).

Yes, I don't think he took the decision lightly as there had been a fair bit of work invested up to that point. I believe his initial strategy was to implement the dataset of ancient samples dataset, and then correct mistakes as they were discovered. Unfortunately, the high error rate (at least for I1 samples, although not surprisingly it became an issue for other haplogroups as well) made the task of correcting more onerous than the initial implementation, and a lot of frustration all round. As Hunter says on his website "Progress is sometimes cyclical" which I think is a good attitude.

Yes, that one will be interesting. I believe someone said the I1 sample was low quality, which would effect how much information that we can extract from the sequenced genome. Of course we won't know anything until the data is available. I was following in and out of that thread regarding the ancient I1 in Italy, although as Rozenfeld commented in post #991 "100 pages of discussion and relevant ancient DNA paper is not yet published. Is it a record?" and now it's up to 124 pages and 1236 posts. It seems sometimes that studies or samples with hints but without an actual paper or data seem to acquire a rather mythical status - such as the I1 samples Kow_55 and Mar-7 - the "Early Medieval aDNA from Poland coming soon" thread started in 2016 and went on for 245 pages and 2448 posts...

spruithean
09-16-2019, 06:22 PM
Yeah, some of these upcoming papers have taken so long to actually be released, the threads discussing them just end up being hundreds of pages long and thousands of posts about various arguments and naturally, disagreements from various people. Oh well, just the nature of things I suppose.

Finn
09-17-2019, 08:01 PM
We should get Cnut and others from Winchester pretty soon too.
This video is up now from Barrington A, Edix Hill, Cambridgeshire. Twenty two early AS samples have been shotgun sequenced as part of a Masters project. I'm attaching a screenshot showing how they cluster (with Icelanders rather than Germans, which doesn't seem surprising to me if there were Jutes among them). No haplogroup data yet. I see there are also late AS samples from Gamlingay in Cambridgeshire on the chart and later Medieval from St Johns Divinity School.

https://youtu.be/sr2kRkiCiT0

32177

Meanwhile in another part of the forum with Firemonkey's and my family's results....pointing at this? No Saxons pop up in the case of fire monkey for example...and more puzzles...

https://anthrogenica.com/showthread.php?18361-The-Danish-factor

JMcB
10-04-2019, 03:15 PM
For your possible interest.

There appears to be an I1-L258 sample in the upcoming paper:

Mittnik A., et al., Kinship-based social inequality in Bronze Age Europe

60-OBKR_117_d I-L258 I-L258 I1a1b3a1

https://edmond.mpdl.mpg.de/imeji/col...FcMTgRKNqe4Nzm


At least, according to the analysis of:

https://anthrogenica.com/showthread.php?8066-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(DISCUSSION-ONLY)&p=607295&viewfull=1#post607295


https://www.yfull.com/tree/I-L258/

The dates seem to be at odds, though. Guess we’ll have to wait and see what the paper says about this one. As far as context is concerned.

deadly77
10-04-2019, 04:41 PM
For your possible interest.

There appears to be an I1-L258 sample in the upcoming paper:

Mittnik A., et al., Kinship-based social inequality in Bronze Age Europe

60-OBKR_117_d I-L258 I-L258 I1a1b3a1

https://edmond.mpdl.mpg.de/imeji/col...FcMTgRKNqe4Nzm


At least, according to the analysis of:

https://anthrogenica.com/showthread.php?8066-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(DISCUSSION-ONLY)&p=607295&viewfull=1#post607295


https://www.yfull.com/tree/I-L258/

The dates seem to be at odds, though. Guess we’ll have to wait and see what the paper says about this one. As far as context is concerned.

Good to know - I'll keep an eye out for this paper and the associated data (which is where we can really dig into the weeds). As you say, wait and see.

spruithean
10-04-2019, 04:49 PM
Whereabouts is this I-L258 from? I guess we're still waiting for the Etruscan I1 too.

deadly77
10-04-2019, 04:53 PM
I do have a very boring post in progress. After BAL051 and Car1 turned out to pre-I1, I've been working through the 14 I samples (that were not assigned as I2) from the Olade et al 2019 Iberian paper. So far there is nothing to get excited about from a I1 perspective. Haven't finished yet, and I'll do a summary then.

If the Viking preprint samples become available, that will shove everything else to the backburner and I'll concentrate on those. I anticipate that will keep me busy for a long time.

JMcB
10-04-2019, 05:07 PM
Good to know - I'll keep an eye out for this paper and the associated data (which is where we can really dig into the weeds). As you say, wait and see.

Sorry about that, the link I added seems to have timed out.

Here’s a working version:

https://edmond.mpdl.mpg.de/imeji/collection/woFcMTgRKNqe4Nzm


Apparently there may be a fix needed, too.

https://anthrogenica.com/showthread.php?97-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(TITLES-ABSTRACTS-ONLY)&p=607257&viewfull=1#post607257

deadly77
10-04-2019, 05:17 PM
Sorry about that, the link I added seems to have times out.

Here’s a working version:

https://edmond.mpdl.mpg.de/imeji/collection/woFcMTgRKNqe4Nzm

I had downloaded those files yesterday but struggled to open them in formats that would allow me to read the data. Best I got was trying to open these with Notepad but it didn't tell me much. Best I could tell was the majority of these samples were very low coverage, so perhaps shouldn't expect much. However, any data is useful and we take what we can get :beerchug:

JMcB
10-04-2019, 05:18 PM
Whereabouts is this I-L258 from? I guess we're still waiting for the Etruscan I1 too.

Supposedly, the Lech Valley in Austria.

JMcB
10-04-2019, 05:19 PM
I had downloaded those files yesterday but struggled to open them in formats that would allow me to read the data. Best I got was trying to open these with Notepad but it didn't tell me much. Best I could tell was the majority of these samples were very low coverage, so perhaps shouldn't expect much. However, any data is useful and we take what we can get :beerchug:

Just in case you missed my later edit above, there’s supposed to be a fix:

Apparently there may be a fix needed, too.

https://anthrogenica.com/showthread.php?97-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(TITLES-ABSTRACTS-ONLY)&p=607257&viewfull=1#post607257

deadly77
10-04-2019, 05:30 PM
Whereabouts is this I-L258 from? I guess we're still waiting for the Etruscan I1 too.

I'm currently filing the Etruscan I1 along with the ones from Zenczak 2017 poster samples, as well as the Repton double grave (although so far there zero evidence that those are actually I1). I guess sometimes the anticipation makes it worse. But patience is required for publishing - I know that only too well from my own papers. The Viking preprint appeared with perhaps a few days notice beforehand, so a nice surprise that wasn't on the radar (at least on my radar).

oz
10-04-2019, 05:40 PM
This I1a1 is from EBA Austria?
For now it's still uncertain, but if there is an I1 Etruscan and I1a1 in EBA Austria that complicates the theory of all I1 in mainland Europe coming from Germanic migrations doesn't it?

deadly77
10-04-2019, 05:42 PM
This I1a1 is from EBA Austria?
For now it's still uncertain, but if there is an I1 Etruscan and I1a1 in EBA Austria that complicates the theory of all I1 in mainland Europe coming from Germanic migrations doesn't it?

I'd say wait for the data.

spruithean
10-04-2019, 05:44 PM
This I1a1 is from EBA Austria?
For now it's still uncertain, but if there is an I1 Etruscan and I1a1 in EBA Austria that complicates the theory of all I1 in mainland Europe coming from Germanic migrations doesn't it?

Besides deadly suggesting to wait for the data, because there could be errors, if it holds it could certainly be a wrench in the whole thing. I think the story for I1 is much more interesting and still needs to be fleshed out.