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oz
10-04-2019, 06:04 PM
I'd say wait for the data.

I know. But all this waiting for the data sucks.

oz
10-04-2019, 06:05 PM
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.

Certainly adds more layers to the mystery.

deadly77
10-04-2019, 07:12 PM
I know. But all this waiting for the data sucks.

It is what it is. The I1 samples from the Zenczak poster abstract on Academia.edu have been "known about" since 2017 but we have no real data. Not having the raw data had CL63 assigned to I-Z79 (in I2 rather than I1), SVK-A1 assigned to I1b rather than I-FGC21682 (so in I1a rather than I1b), BAL051 being fully I1 or the numerous inaccuracies in the Carlos Quiles blog. Having the raw data lets us look ourselves to determine the real designation.

But to my earlier point, the Viking preprint dropped in with not very much warning - I knew about it at most two days before it happened. When that came out it dwarfed our previous inventory of I1 samples. And we still don't have the raw data for that.

I'd agree with Spruithean's point - I think the I1 story is a lot more interesting and diverse compared to the data that we currently have available. I've said so several times earlier in this thread and I'd expect there to be more I1 found in places that may not be expected (and I'm looking forward to it).

I'd also point out that many subclades of I1 significantly predate Germanic migrations.

JMcB
10-04-2019, 07:48 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?

Personally, I doubt it but we’ll see. If it is valid and it’s really I-L258 it’s probably from a later time period and somehow came to light during the excavations. At least, that’s my guess. Or it’s been read incorrectly.

oz
10-04-2019, 07:51 PM
They did also label CL63 as I1a3 so maybe they just made a sloppy mistake there which hopefully won't constantly reoccur.
As to the labeling of I1 without enough snps to make up an actual I1 I don't know why that happens or how that works, is it a matter of coverage quality of the samples or some shit or because it's some dead lineage of I* and what exactly determines that.

oz
10-04-2019, 07:53 PM
Personally, I doubt it but will see. If it is valid and it’s really I-L258 it’s probably from a later time period and somehow came to light during the excavations. At least, that’s my guess. Or it’s been read incorrectly.

Yeah that's also possible, these papers should provide sufficient evidence for whatever claims they make.

JMcB
10-04-2019, 08:20 PM
Hopefully, the paper will be here soon. Although, there appears to be some issue with the Y data.

https://anthrogenica.com/showthread.php?16234-Bell-Beaker-Archaeology-and-Ancient-DNA&p=607300&viewfull=1#post607300

deadly77
10-04-2019, 10:25 PM
They did also label CL63 as I1a3 so maybe they just made a sloppy mistake there which hopefully won't constantly reoccur.
As to the labeling of I1 without enough snps to make up an actual I1 I don't know why that happens or how that works, is it a matter of coverage quality of the samples or some shit or because it's some dead lineage of I* and what exactly determines that.

I've tried to accommodate you several times over previous posts on this thread, but I'm a bit fed up of continuously repeating myself. It's all there in earlier posts on this thread, so go and have a re-read. I've added you to my "ignore list" along with Kaltmeister, so I won't see your posts in future and I won't respond any further. All the best.

oz
10-04-2019, 11:02 PM
I've tried to accommodate you several times over previous posts on this thread, but I'm a bit fed up of continuously repeating myself. It's all there in earlier posts on this thread, so go and have a re-read. I've added you to my "ignore list" along with Kaltmeister, so I won't see your posts in future and I won't respond any further. All the best.

Lol
What the hell are you even talking about? I wasn't even directly talking to you.
He put me on ignore? If your precious feelings are so fragile feel free to protect them, I don't object.

JMcB
10-05-2019, 12:06 AM
According to the General the sample is suppose to date to:

“Early Bronze Age (~2,000 BCE). Lech_EBA OBKR_117_d”

So I-L258 sounds like a mis-read. What it really is, is anyones guess.

oz
10-05-2019, 12:23 AM
According to the General the sample is suppose to date to:

“Early Bronze Age (~2,000 BCE). Lech_EBA OBKR_117_d”

So I-L258 sounds like a mis-read. What it really is, is anyones guess.

It would be very strange if it turned out positive for that clade, the age estimate on Yfull would be way off. Plus it's basically a strictly North Euro and Finland clade.

For the record, I didn't ask deadly77 anything, his feelings are too touchy today.

oz
10-05-2019, 01:24 AM
Funniest and dumbest part about him putting me on ignore is that I'm 1 out of like 3 people on this forum or anywhere really that even talk about ancient I1.

digital_noise
10-05-2019, 02:28 AM
yea thats weird.

oz
10-05-2019, 02:48 AM
If this thread was started by him I would definitely boycott it now. But JonikW started it, so if JonikW doesn't want me to post in it anymore he can feel free to say that and I'll have no problem with it whatsoever. I like it when people are honest and show true colors.

JonikW
10-05-2019, 09:03 AM
If this thread was started by him I would definitely boycott it now. But JonikW started it, so if JonikW doesn't want me to post in it anymore he can feel free to say that and I'll have no problem with it whatsoever. I like it when people are honest and show true colors.

I like how this thread has become a sounding board where we can throw I1 aDNA ideas around. I'd prefer us not to quarrel though, particularly given how few of us are into this. Deadly's excellent Maps thread has become the place where I assume samples themselves will also be posted.
I know nothing about this particular sample but if it's from the Lech River Valley in Bavaria I wouldn't be surprised to find that I1 had begun spreading out of what I assume was its Scandinavian homeland and into today's Germany by that date. I even wouldn't be surprised to find some clades in England by that time. Anyway, it'll be interesting to see if anything useful can be gleaned from the SNP data.

oz
10-05-2019, 09:57 AM
I like how this thread has become a sounding board where we can throw I1 aDNA ideas around. I'd prefer us not to quarrel though, particularly given how few of us are into this. Deadly's excellent Maps thread has become the place where I assume samples themselves will also be posted.
I know nothing about this particular sample but if it's from the Lech River Valley in Bavaria I wouldn't be surprised to find that I1 had begun spreading out of what I assume was its Scandinavian homeland and into today's Germany by that date. I even wouldn't be surprised to find some clades in England by that time. Anyway, it'll be interesting to see if anything useful can be gleaned from the SNP data.

I won't call him names and break the rules of this forum. But he thinks he's on some high horse or something because he does a few of these raw data snp checks. And he puts people on ignore for no good reason then openly discusses it on the forum, which is a really bitch ass move. He's probably the type of guy that neatly folds his underwear and sleeps with stuffed animals.

He can keep me on ignore forever and I'll never post in his thread.

As far as I1 spreading from Scandinavia down to central Europe in the EBA, anything is possible I guess but I'd rather say that's pretty unlikely given the lack of I1 in papers so far from Bronze age times. But hopefully we'll get more answers eventually.

spruithean
10-08-2019, 04:18 PM
I'm suspicious of this Lech I1-L258 sample. I would agree that it is unlikely that I1 spread out from Scandinavia to Central Europe in the Early Bronze Age, though if our TMRCA estimates are way off it could be possible, at this point who knows and we'll just have to wait it out.

I'm still waiting on the Etruscan I1 as well, and frankly I don't have the patience to scroll through the threads to find the info if it has been released.

JMcB
10-08-2019, 08:25 PM
I'm suspicious of this Lech I1-L258 sample. I would agree that it is unlikely that I1 spread out from Scandinavia to Central Europe in the Early Bronze Age, though if our TMRCA estimates are way off it could be possible, at this point who knows and we'll just have to wait it out.

I'm still waiting on the Etruscan I1 as well, and frankly I don't have the patience to scroll through the threads to find the info if it has been released.

Apparently, there were some problems with that data and the alleged call seems to be way off, considering the era in question. So I’m not optimistic about this one. Especially, as we’ve already seen enough dubious calls where I1 is concerned. Plus, now that the date of the sample has been confirmed as 2000 BCE, it’s placement becomes more questionable.

Generalissimo
10-08-2019, 09:36 PM
Apparently...I(xI1)

+ IJ FGC1564
+ I CTS5650
+ I CTS8963
- I1 M450
- I1 CTS4130
- I1 CTS4790
- I1 CTS5643^
- I1 CTS8394
- I1a1b1a1c2a1~ FGC22154
+ I1a1b1a4a1a1 L258
- I1a2a1a1d2a1c L803
- I2a1a1a1a1 CTS11229
- I2a1a1a1a1a1a1e5~ PF4398
+ I2a1a1a1a1a1a2a~ S294
- I2a1a1b2~ Y21979
- I2a1a2~ Z2587
- I2a1a2~ AM01283
- I2a1a2b S10302
- I2a1a2b CTS10494
- I2a1b1~ FGC3551

https://eurogenes.blogspot.com/2019/09/is-yamnaya-overrated.html?commentPage=5

deadly77
10-08-2019, 10:03 PM
Apparently...I(xI1)

+ IJ FGC1564
+ I CTS5650
+ I CTS8963
- I1 M450
- I1 CTS4130
- I1 CTS4790
- I1 CTS5643^
- I1 CTS8394
- I1a1b1a1c2a1~ FGC22154
+ I1a1b1a4a1a1 L258
- I1a2a1a1d2a1c L803
- I2a1a1a1a1 CTS11229
- I2a1a1a1a1a1a1e5~ PF4398
+ I2a1a1a1a1a1a2a~ S294
- I2a1a1b2~ Y21979
- I2a1a2~ Z2587
- I2a1a2~ AM01283
- I2a1a2b S10302
- I2a1a2b CTS10494
- I2a1b1~ FGC3551

https://eurogenes.blogspot.com/2019/09/is-yamnaya-overrated.html?commentPage=5

Aha - seems like a false alarm for I1. Thanks for the update.

spruithean
10-08-2019, 10:39 PM
Apparently...I(xI1)

+ IJ FGC1564
+ I CTS5650
+ I CTS8963
- I1 M450
- I1 CTS4130
- I1 CTS4790
- I1 CTS5643^
- I1 CTS8394
- I1a1b1a1c2a1~ FGC22154
+ I1a1b1a4a1a1 L258
- I1a2a1a1d2a1c L803
- I2a1a1a1a1 CTS11229
- I2a1a1a1a1a1a1e5~ PF4398
+ I2a1a1a1a1a1a2a~ S294
- I2a1a1b2~ Y21979
- I2a1a2~ Z2587
- I2a1a2~ AM01283
- I2a1a2b S10302
- I2a1a2b CTS10494
- I2a1b1~ FGC3551

https://eurogenes.blogspot.com/2019/09/is-yamnaya-overrated.html?commentPage=5

Thanks for passing this along, this makes more sense than an L258 call, that's for sure.

oz
10-09-2019, 10:53 AM
Aha - seems like a false alarm for I1. Thanks for the update.

Not exactly, because evidently it looks like it might've been a I1/I2 hybrid that probably went extinct.

spruithean
10-09-2019, 11:05 AM
Not exactly, because evidently it looks like it might've been a I1/I2 hybrid that probably went extinct.

It's probably more likely to be some form of I2 but the DNA is too degraded to make any really definitive calls. The degradation could explain the L258 call (which is probably just a result of DNA damage post-mortem).

oz
10-09-2019, 11:33 AM
It's probably more likely to be some form of I2 but the DNA is too degraded to make any really definitive calls. The degradation could explain the L258 call (which is probably just a result of DNA damage post-mortem).

Wait a minute...

Can you explain that again? I don't quite get it.

spruithean
10-09-2019, 11:59 AM
The calls only show that it is positive for L258 (I1), S294 (I2) and at the same time negative for M450 (which defines I1). Given the timing of this sample and just how much more common I2 seems to be I would bet that this is a I2 sample that either through DNA damage (over time after someone has died, their DNA degrades and false positives can appear – for various reasons like burial conditions, etc) or some other reason it has a positive call for L258.

C.Goodell
10-09-2019, 04:45 PM
Does anyone else think the math for dating SNPs is off? I think accepted practice is x 120-150 years per snp.

deadly77
10-09-2019, 04:57 PM
Rozenfeld shared a paper that was published today in the Genetic Genealogy & Ancient DNA in the News (TITLES/ABSTRACTS ONLY) thread on AG. The paper is titled "The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon" for links to the paper (which is open access, go to rozenfeld's post here https://anthrogenica.com/showthread.php?97-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(TITLES-ABSTRACTS-ONLY)&p=609103&viewfull=1#post609103

I haven't read the paper yet, but skimmed the abstract which listed "We sequenced 11 individuals (dated to 3330–1665 calibrated before common era (cal BCE)) frommodern-day Sweden, Estonia, and Poland to 0.26–3.24× coverage." Of those 11 individuals (see Table 1), 6 were females and 5 were males. They assign haplogroups to two of the males as R1a, but say they're less confident about the other three. The Supplementary Material file (often where the good stuff is) has some interesting comments regarding the Y-chromosomal DNA on pages 18-19:

"Less Y-chromosomal data was available for the remaining three males in this study (ros005, ajv54 and oll009). Therefore, we describe this data here (with marker names, position, mutation, and number of reads in brackets) without adding the information to table S5 and caution that more data is needed to confidently call haplogroups. We also examined ancestral allele states leading to R1a haplotypes (found in ber1 and poz81) among these three individuals to further strengthen an exclusion from this lineage.

The individual ros005, a male from a FBC context, likely belong to hg IJ or possibly within the I-lineage (IJ-M429*(xM304)). We found 10 derived mutations leading towards IJ
(L1155:22191266, G>C, 1 for A0'1'2'3'4; V168:17947672, G>A, 3 for A1'2'3'4; V221:7589303, G>T, 1 for A2'3'4; P97:14886273, G>T, 1 for A4=BCDEF; M213:15526751, T>C, 2 and P14:17398598, C>T, 1 for F; M522:7173143, G>A, 1 and M523:6753519, A>G, 1 for IJKLT, and finally M429:14031334, T>A, 1 and P126:21225770, C>G, 1 for IJ). We then investigated which lineages within IJ that could be excluded. As ros005 displayed ancestral alleles for J-M304 (both for M304:22749853, A>C, 1 and for P209:19179335, T>C, 2 characterizing J), we could exclude him belonging to hg J and sub-lineages therein. We could further exclude a belonging within I1-sublineages (ancestral alleles for I1- Z131:5845252, G>A, 1; I1-DF29:3626279, A>G, 1 and I1-CTS6364:16850799, A>T, 1), but not to I1-M253*(xZ131,DF29) as we had no data for that marker. Some of the sub-lineages within I2 could likely also be excluded. These were I2-L596 (L597:18887888, T>A, 1), I2-L38 (L38:15668070, A>G, 3) and I2-M223 (M223:21717307, G>A, 1). Based on ancestral allele states for ros005, we could also verify an exclusion from the R1a-lineages found in the ber1 and poz81 males (R1-M173:15026424, A>C, 3 and R1a-Z283:21976303, T>A, 2).

Individual ajv54, a male from a PWC context, likely belong to hg I2-M438 or sub-lineages therein. We found nine derived mutations leading towards I2 (L1085:2790726, T>C, 1 for A0'1'2'3'4; V168:17947672, G>A, 1 for A1'2'3'4; M42:21866840, A>T, 1 and P97:14886273, G>T, 1 for A4=BCDEF; M213:15526751, T>C, 1 for F; M578:7202703, C>T, 1 for HIJKLT; M522:7173143, G>A, 1 for IJKLT; U179:16354708, G>A, 2 for I and M438:16638804, A>G, 1 for I2). As the amount of data is quite low, and to further strengthen that ajv54 did not belong within the R1a-lineages found in ber1 and poz81 males, we list key ancestral allele states leading towards R1a (K-M526:23550924, A>C, 2; P-P295:7963031, T>G, 1; QRM74:21889767, G>A, 2; R-M207:15581983, A>G, 2 and R1a-Z645:8245045, C>T, 2).

The individual oll9, a Scandinavian Late Neolithic male from a megalithic tomb, may belong to hg I1-M253. We found 10 mutations leading in this direction (L1085:2790726, T>C, 1 and L1155:22191266, G>C, 1 for A0'1'2'3'4; V168:17947672, G>A, 1 for A1'2'3'4; P108:15426248, C>T, 1 for A2'3'4; M42:21866840, A>T, 4 and P97:14886273, G>T, 1 for A4=BCDEF; M168:14813991, C>T, 1 for CDEF; P14:17398598, C>T, 2 for F; M522:7173143, G>A, 1 for IJKLT and finally M253:15022707, C>T, 1 for I1). We note that
I1-M253 is only supported by one read involving a C to T transition. However, ancestralallele states for downstream I1-Z131 (Z131:5845252, G>A, 1) and for markers defining hg J (P209:19179335, T>C, 2), M (P399:13563083, C>T, 2 and PR2099:16328755, C>T, 1), QR (M45:21867787, G>A, 1), R1a (M420:23473201, T>A, 1 and M448:16520444, T>A, 1) and LT (P326:8467290, T>C, 1) indicate that this individual likely does not belong much further down in the phylogeny."

Worthy of looking a bit closer, especially the last one oll9. The paper says the "The genome data for the 11 investigated individuals are available at the European Nucleotide Archive (accession number PRJEB32786) - that study is there in ENA but there doesn't seem to be any data there yet. However, since the paper was just published today, they are likely in the process of uploading and data should be there soon.

spruithean
10-09-2019, 06:28 PM
Very interesting. Maybe one day we'll actually see some legitimate I1-M253 in these sorts of contexts in Scandinavia.

deadly77
10-10-2019, 11:07 AM
BAM files for PRJEB32786 are now available. I'm busy with some family events and local politics over the next few days, so likely won't get to take a look at this until next week. But they are available if someone wants to have a go.

mwauthy
10-10-2019, 12:16 PM
Does anyone else think the math for dating SNPs is off? I think accepted practice is x 120-150 years per snp.

There is no one size fits all formula that works for dating SNPs in small sample sizes because of the variability of mutation rates. I’ve seen two folks that share the same common patrilineal ancestor have 20 vs 5 combBED SNPs respectively since this common patrilineal ancestor. I’ve seen people have 29 vs 10 Big Y-700 variants since a common patrilineal ancestor.

For larger sample sizes for older subclades I do think that the 95% confidence age ranges that YFull provides gives a decent approximation. However, these ranges become too large to be helpful with smaller sample sizes with variable mutation rates as seen with the subclade I-Y125947 (800 BC - 650 AD) in my signature below.

I do think that putting certain subclade ages within a historical context (Migration Period to the Viking Age) can be somewhat helpful especially for our haplogroup because it’s distribution across Europe correlates well with Germanic and Viking expansion.

I also believe that within a genealogical timeframe paper trails and even 111 marker STR aging graphs can be more helpful than SNP aging.

If one is insistent on trying to age one’s own SNPs based on only one’s own results (a bad idea in my opinion); a very loose rule of thumb formula I think that could be somewhat helpful is to first try to predict if one has a faster vs slower average mutation rate. After assuming that I would use the formula below:

Big Y-500:
Average: 125 years per variant
Fast: 100 years per variant
Slow: 150 years per variant

Big Y-700:
Average: 75 years per variant
Fast: 50 years per variant
Slow: 100 years per variant

deadly77
10-10-2019, 05:07 PM
Well this is interesting - oll009 from the Scandinavian Battle Axe paper may be on the I-DF29 branch after initial view of the BAM. Of course, this would confirm full I1 rather than pre-I1.

There's a no call for oll009 at the SNP S438/DF29 itself, but on the YFull tree there are a few phyloequivalent SNPs on that branch. oll009 is showing derived reads for Z2891/V1614 (2T) and Z2892/CTS9848 (4G). Also no call for CTS9857/V3772 and Z2890. oll009 does have an ancestral read for Z2893 - but that's only a single read 1G. The latter could be a false negative one-read or could signify a split in the phylogenetic block of the SNPs at I-DF29 branch. I'll look to see if oll009 positive for anything downstream of I-DF29. But this is exciting for the first look at oll009's BAM. Would be the earliest I-DF29 sample found so far - dated to 1930-1750 cal BCE (95% CI) by radiocarbon dating. Paper says oll009 from a megalithic burial structure although the paper and supporting information state that oll009 from a later burial consistent with grave goods and radiocarbon dating to the Scandinavian Late Neolithic.

For completeness, I looked at the other two, but neither of those show derived reads for any of the I-DF29 SNPs, although that's not surprising in at least one of the cases. ajv54 is negative for S438/DF29 (2A), Z2890 (1T) and Z2892/CTS9848 (1C). ros005 is negative for S438/DF29 (1A) (as already noted in the paper's Supplementary Material) and Z2892/CTS9848 (3C).

spruithean
10-10-2019, 05:09 PM
Wow! That's pretty exciting, perhaps we finally have an example of I1 in Scandinavia in the Late Neolithic that could be in someway relevant to the modern lineages.

Very interesting stuff.

JMcB
10-10-2019, 06:36 PM
Well this is interesting - oll009 from the Scandinavian Battle Axe paper may be on the I-DF29 branch after initial view of the BAM. Of course, this would confirm full I1 rather than pre-I1.

There's a no call for oll009 at the SNP S438/DF29 itself, but on the YFull tree there are a few phyloequivalent SNPs on that branch. oll009 is showing derived reads for Z2891/V1614 (2T) and Z2892/CTS9848 (4T). Also no call for CTS9857/V3772 and Z2890. oll009 does have an ancestral read for Z2893 - but that's only a single read 1G. The latter could be a false negative one-read or could signify a split in the phylogenetic block of the SNPs at I-DF29 branch....

That is good news! Nice work!

Nibelung
10-10-2019, 10:23 PM
Looks like oll009 has the most European hunter-gatherer relative to its Anatolian Neolithic of any sample in the new Battle Axe paper new or previously published, perhaps suggestive of an HG-rich regional population or caste within the FBC.

oz
10-10-2019, 11:27 PM
Looks like oll009 has the most European hunter-gatherer relative to its Anatolian Neolithic of any sample in the new Battle Axe paper new or previously published, perhaps suggestive of an HG-rich regional population or caste within the FBC.

So this perhaps is indicative of FBC culture who might've had I1/I1a merging with the CWC (mostly R1a) and perhaps R1b-U106 as well, to form the BAC culture?
I don't know much about the context of these cultures and the time periods.

Also the paper states they couldn't assign any of these samples as I1 with enough confidence, correct me if I'm wrong, so how can we be too sure? We all know there's been other samples even outside of Scandinavia with similar "might be I1" snp data reads. Then there are factors of damage, contamination, it all seems very squirrelly, so I'm still skeptical about this sample too.

spruithean
10-11-2019, 12:11 AM
I'm not entirely sure what this may mean in terms of R1a and U106 but I've seen this idea thrown around with FBC merging with CWC and forming the BAC, doesn't seem like a farfetched possibility.

Always good to be skeptical, I think right now oll009 will be a tentative I-DF29 or perhaps almost DF29 until a later date in which we either get more samples from the same period or perhaps the sample is taken again and ends up being of better quality.

oll009 isn't exactly getting a positive call for DF29 itself, but is instead getting a call for some phyloequivalents. So there is a possibility that this person is in some way related to the lineage of DF29 that founded all modern DF29 lines. I think it's too early to tell at this point.

I also wouldn't be surprised if those who analyze the haplogroups for these papers are a bit more conservative in their haplogroup assignment, which is not a bad practice, it just gives us rather basal assignments. But I'd prefer that to the bizarre stuff we've seen with other papers...

deadly77
10-11-2019, 09:36 AM
Reading the supplementary information from the paper (page 18), it seems that the authors used an automated extraction tool to pull the Y-SNPs out of the sequenced data. This approach appears to be the most commonly used tactic used by the authors of most other papers. Looking up SNPs individually in the BAM file takes a fair bit of time, but allows some better judgement calls. Although could be argued that the judgement is only as good as the judge . I'd welcome anyone who can independently review and verify - the BAM file for oll009 is at European Nucleotide Archive here https://www.ebi.ac.uk/ena/data/view/SAMEA5764553

The supplementary material also notes that they are using Phylotree rather than ISOGG, FTDNA or YFull for reference tree and reference 108 in the supplementary material "A Minimal Reference Phylogeny for the Human Y Chromosome" paper published here in 2014 https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.22468

Hence the "minimal reference phylogeny", Phylotree doesn't list phyloequivalent SNPs - see here for example of the tree for I: http://www.phylotree.org/Y/tree/I.htm

As you can see, DF29 is the only SNP on that branch on Phylotree compared to CTS9857/V3772, DF29/S438, Z2891/V1614, Z2893, Z2890, Z2892/CTS9848 on the same branch in the YFull tree. My feeling is that the authors of the Scandinavian Battle Axe Paper only looked for DF29, got no call and so stopped there. They didn't report the derived calls for Z2891/V1614 or Z2892/CTS9848 because those SNPs are not on Phylotree and so their automated extraction tool wasn't programmed to look for them. That ties in with the authors reporting a negative call for DF29 for ros005 and a one-read positive for M253 in oll009 (Phylotree ony lists M253, L80, P203 for I1 compared to the 312 SNPs for YFull).

It's worth noting that six of the authors on the Scandinavian Battle Axe paper were also authors on the 2018 paper on the population genomics in Mesolithic Scandinavia which included Stora Förvar 11 where they said "Unfortunately, there was not enough Y-chromosomal data from the SF11 male to define his haplogroup" - which is quite correct based on the data available and it seems they are a bit more conservative in haplogroup assignment compared to some other authors (such as in the BAL051 paper).

So based on the automated extraction and the Phylotree reference, their output data is a one-read positive for M253 and that's it. On the basis of that, they are quite right not to assign I1 with any confidence. I would do the same. But since they've made the raw data available at ENA (link at the top of the post) and we have a more comprehensive reference in the YFull tree, then we can take a look and assign I1 with a bit more confidence. In particular, will be able to take a look at more of the 312 SNPs that are on the I1 branch and that should give more confidence in I1 once I've looked at those.

deadly77
10-11-2019, 09:52 AM
teepean47 (using YLeaf V2) and Pribislav are also reporting oll009 as I1a/DF29 in the Genetic Genealogy & Ancient DNA in the News (DISCUSSION ONLY) thread in the Ancient DNA section in posts #2886 and #2889.
https://anthrogenica.com/showthread.php?8066-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(DISCUSSION-ONLY)&p=609641&viewfull=1#post609641
https://anthrogenica.com/showthread.php?8066-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(DISCUSSION-ONLY)&p=609688&viewfull=1#post609688

Pribislav
10-11-2019, 10:46 AM
teepean47 (using YLeaf V2) and Pribislav are also reporting oll009 as I1a/DF29 in the Genetic Genealogy & Ancient DNA in the News (DISCUSSION ONLY) thread in the Ancient DNA section in posts #2886 and #2889.
https://anthrogenica.com/showthread.php?8066-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(DISCUSSION-ONLY)&p=609641&viewfull=1#post609641
https://anthrogenica.com/showthread.php?8066-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(DISCUSSION-ONLY)&p=609688&viewfull=1#post609688

I have these calls at DF29 level:

Z2892/CTS9848+ C>G (4 reads)

Z2891/V1614+ C>T (2 reads)

Z2893- G>A (1 read)

The last one could be false negative due to aDNA damage.

EDIT:

I see now you already got the same results in post #531.

EDIT 2:

Did you mean 4G (not 4T) at Z2892/CTS9848? I have G as a derived allele at that position (hg19: 19100590).

deadly77
10-11-2019, 10:57 AM
I have these calls at DF29 level:

Z2892/CTS9848+ C>G (4 reads)

Z2891/V1614+ C>T (2 reads)

Z2893- G>A (1 read)

The last one could be false negative due to aDNA damage.

Excellent - I have exactly the same (see #531 above). And I also have the same thoughts regarding the latter one as a false negative - could also be a consequence of it being a unreliable one-read - my own WGS has 21A reads and 1G read for Z2893.

If oll009 is derived for anything downstream of I-DF29, that may confirm. I've been looking but haven't found anything - all ancestral or no call except Y11204 is 1A (derived) on the I-Y11205 branch. However, I'm not confident in that assignment as it's only a one-read and there's contradictory ancestral reads for at least 5 phlyoequivalent SNPs on that branch (including some that are more than one-read).

mwauthy
10-11-2019, 12:28 PM
Well this is interesting - oll009 from the Scandinavian Battle Axe paper may be on the I-DF29 branch after initial view of the BAM. Of course, this would confirm full I1 rather than pre-I1.

There's a no call for oll009 at the SNP S438/DF29 itself, but on the YFull tree there are a few phyloequivalent SNPs on that branch. oll009 is showing derived reads for Z2891/V1614 (2T) and Z2892/CTS9848 (4T). Also no call for CTS9857/V3772 and Z2890. oll009 does have an ancestral read for Z2893 - but that's only a single read 1G. The latter could be a false negative one-read or could signify a split in the phylogenetic block of the SNPs at I-DF29 branch. I'll look to see if oll009 positive for anything downstream of I-DF29. But this is exciting for the first look at oll009's BAM. Would be the earliest I-DF29 sample found so far - dated to 1930-1750 cal BCE (95% CI) by radiocarbon dating. Paper says oll009 from a megalithic burial structure although the paper and supporting information state that oll009 from a later burial consistent with grave goods and radiocarbon dating to the Scandinavian Late Neolithic.

For completeness, I looked at the other two, but neither of those show derived reads for any of the I-DF29 SNPs, although that's not surprising in at least one of the cases. ajv54 is negative for S438/DF29 (2A), Z2890 (1T) and Z2892/CTS9848 (1C). ros005 is negative for S438/DF29 (1A) (as already noted in the paper's Supplementary Material) and Z2892/CTS9848 (3C).

Based on modern distributions of I1a I’ve always theorized that it must have originated in Southern Sweden in Skåne County. Nice to see that we are finally getting some ancient dna corroboration.

deadly77
10-11-2019, 12:56 PM
Did you mean 4G (not 4T) at Z2892/CTS9848? I have G as a derived allele at that position (hg19: 19100590).

Yes, indeed I did. I looked back at the notes I was making on my excel spreadsheet and I had it as 4G from the BAM. I guess I typed 4T when writing the post in Anthrogenica and the correct allele didn't make the transition. Too much time looking at a computer screen yesterday:doh:. I'll edit #531 to correct that - thanks for pointing that out.
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JMcB
10-11-2019, 02:22 PM
Excellent - I have exactly the same (see #531 above). And I also have the same thoughts regarding the latter one as a false negative - could also be a consequence of it being a unreliable one-read - my own WGS has 21A reads and 1G read for Z2893.

If oll009 is derived for anything downstream of I-DF29, that may confirm. I've been looking but haven't found anything - all ancestral or no call except Y11204 is 1A (derived) on the I-Y11205 branch. However, I'm not confident in that assignment as it's only a one-read and there's contradictory ancestral reads for at least 5 phlyoequivalent SNPs on that branch (including some that are more than one-read).

Once again, thank you! This is very interesting news! And thank you also to Pribislav and teepean47!

mwauthy
10-11-2019, 02:58 PM
Once again, thank you! This is very interesting news! And thank you also to Pribislav and teepean47!

Even if olloo9 is part of an extinct transition branch between I1 and I1a that would still be really cool and informative because he would be our first confirmed fully I1 ancient sample.

deadly77
10-11-2019, 03:33 PM
Even if olloo9 is part of an extinct transition branch between I1 and I1a that would still be really cool and informative because he would be our first confirmed fully I1 ancient sample.

Both are possibilities - oll009 could be fully I-DF29 or a transition point that splits the branch. We can't really say for sure with the data we have as it's not conclusive enough - two derived SNPs, one contradictory ancestral SNP (although one-read and may not be valid) and three no calls on that branch. Confirming a downstream branch would give weight to fully I-DF29. I'm working through those (almost done) but nothing that confirms anything downstream with any confidence so far.

Not sure what you mean by first confirmed fully I1 ancient sample. We have over 100 that are confirmed fully I1 from being part of downstream subclades, athough all of those are from more recent times from 5th to 17th century. Perhaps that depends how you define "ancient" - I'm using it in a very loose sense for the purposes of my Haplogroup I1 Ancient DNA Samples Map, where "ancient" is essentially anything that's "not modern". I couldn't think of a better way to phrase it but open to suggestions. Or perhaps you mean first as in the oldest in terms of age rather than the order in which they have been published and analyzed.

But yes, this is currently the earliest confirmed fully I1 sample by quite some way. And yes, it is really cool.

spruithean
10-11-2019, 04:03 PM
I think mwauthy might just mean that oll009 is the first confirmed I1 sample that isn't pre-I1 from the Nordic Bronze Age era. The other possible ones were the ones from the Late Neolithic to the Nordic Bronze Age (those RISE samples that are pre-I1 on your Ancient I1 map).

This is pretty exciting news, so it's looking like oll009 is I1, and possibly I1a?

mwauthy
10-11-2019, 04:06 PM
Both are possibilities - oll009 could be fully I-DF29 or a transition point that splits the branch. We can't really say for sure with the data we have as it's not conclusive enough - two derived SNPs, one contradictory ancestral SNP (although one-read and may not be valid) and three no calls on that branch. Confirming a downstream branch would give weight to fully I-DF29. I'm working through those (almost done) but nothing that confirms anything downstream with any confidence so far.

Not sure what you mean by first confirmed fully I1 ancient sample. We have over 100 that are confirmed fully I1 from being part of downstream subclades, athough all of those are from more recent times from 5th to 17th century. Perhaps that depends how you define "ancient" - I'm using it in a very loose sense for the purposes of my Haplogroup I1 Ancient DNA Samples Map, where "ancient" is essentially anything that's "not modern". I couldn't think of a better way to phrase it but open to suggestions. Or perhaps you mean first as in the oldest in terms of age rather than the order in which they have been published and analyzed.

But yes, this is currently the earliest confirmed fully I1 sample by quite some way. And yes, it is really cool.

You are correct. I didn’t clarify what I meant by “ancient.” What I think of when I think of “ancient” are timeframes that come close to the tmrca of said subclade in question.

Thanks again for your BAM analysis. I’m either too stupid or too lazy to do it myself ;)

mwauthy
10-11-2019, 07:51 PM
Ftdna on their Haplotree only lists 3 phyloequivalent SNPs for DF29 (CTS9857, CTS9848, and Z2891). If Ftdna doesn’t recognize Z2893 as being phyloequivalent then maybe its ancestral value is not relevant in the case of oll009?

deadly77
10-12-2019, 09:06 AM
This is pretty exciting news, so it's looking like oll009 is I1, and possibly I1a?

I would say so. I've been willing to classify some of the other ancient samples as I-DF29/I1a, such as the Anglo-Saxon NO3423, the Icleandic DAV-A9, the Bavarians AED249 and STR241, Scandinavian urm045, colonist US14 on similar levels of evidence from the SNP calls. I haven't had a chance to look at the SNPs on the I1 level yet as I'm still working through the SNPs one level below I-DF29, but I'm pretty sure oll009 will be positive for quite a few of the 312 I1 SNPs.

I'm going to say that oll009 is I-DF29/I1a as in my opinion the evidence from the raw data is strong enough. Others may be skeptical - that's up to them. But for me the data is conclusive so far.

deadly77
10-12-2019, 09:27 AM
You are correct. I didn’t clarify what I meant by “ancient.” What I think of when I think of “ancient” are timeframes that come close to the tmrca of said subclade in question.

Thanks again for your BAM analysis. I’m either too stupid or too lazy to do it myself ;)

Gotcha - I have been trying to think of better name for my map, but the "Haplogroup I1 DNA Samples of Non-Modern Era Individuals" doesn't have much of a ring to it.

You're welcome regarding the BAM analysis. It's not actually that difficult to do and it's something I've largely taught myself but most of the tools are freely available and most people could probably handle doing it as it's not too technical. If there's interest, I could do a thread on how I do it with example screenshots in the future. I'm not saying it's the best way to analyze BAM files, but it works for me. It is time consuming though, so working against the laziness may be the biggest barrier.

deadly77
10-12-2019, 10:06 AM
Ftdna on their Haplotree only lists 3 phyloequivalent SNPs for DF29 (CTS9857, CTS9848, and Z2891). If Ftdna doesn’t recognize Z2893 as being phyloequivalent then maybe its ancestral value is not relevant in the case of oll009?

I wouldn't read too much into that. FTDNA's haplotree is built largely from their customers testing data, so SNPs that aren't captured well in their tests won't show. I had a look at some results that I have access to, and I can see that Z2893 is no call in a YElite test and a Big Y Y700 test, while my WGS picks it up. It's probable that the Y enrichment assay before sequencing doesn't cover this position well. Some testers might get a result and some might not. It's at position ChrY position (Hg19):22544398 or ChrY position (Hg38):20382512, which is little outside what YSEQ defines as the DYZ19 region (chrY:20054914..20351054 (DYZ19 125 bp repeat region)). I don't have a Big Y Y500 to check but coverage but I imagine Z2893 isn't covered well in those. Z2893 is also not included in the I-M253 SNP pack.

YFull have more WGS and more ancient samples than the FTDNA haplotree (which has zero WGS), so in my opinion they have more comprehensive relevant data.

Looking back through my notes on other ancient I1 samples, there are a few examples where there have been false negative one-read SNPs on the I-DF29 branch. urm035 from the Sigtuna paper was a low coverage sample that had derived calls for DF29 and Z2892 / CTS9848 but an ancestral call for Z2893. Also CL63 from the Collegno Langobard cemetery has confirmed Z63 with strong 10T reads, but has a negative one-read SNP for DF29 with 1A - based on the Z63 result, we can say the one-read negative DF29 is false. And there's the Icelandic SVK-A1 false positive Z131 which contradicts the actual placement at I-FGC21682.

Looking at my own YElite, there are 16 one-read novel SNPs but when I cross reference with my WGS, one out of the 16 turns out to be genuine while the other 15 are shown to be mostly ancestral when viewed with the greater read depth of the WGS. So one-reads can be real or they can be false, but without corroborating information, really can't be sure.

deadly77
10-12-2019, 01:05 PM
Quick stats (because it's relatively easy to do in YFull's "Groups" view) on the I1-Z140 group at YFull - 201 members, 21 positive for Z2893, zero negative for Z2893, 180 no-call for Z2893.

DF29 in contrast seems to be more readily covered with only 2 no-calls out of the 201, 8 ambiguous and the rest positive. The ambiguous calls all seem to be low read (eg. 3 reads) where one aberrant allele is likely the throw the quality score off.

Z2892/CTS9848 22 derived, the rest no-call (179).
Z2891/V1614 all derived except for one that was a no call, so 200/201 positive.
CTS9857/V3772 all derived except 7 no calls and 2 ambiguous.
Z2890 has 41 derived, 3 ambiguous, the rest no call.

mwauthy
10-12-2019, 03:53 PM
I wouldn't read too much into that. FTDNA's haplotree is built largely from their customers testing data, so SNPs that aren't captured well in their tests won't show. I had a look at some results that I have access to, and I can see that Z2893 is no call in a YElite test and a Big Y Y700 test, while my WGS picks it up. It's probable that the Y enrichment assay before sequencing doesn't cover this position well. Some testers might get a result and some might not. It's at position ChrY position (Hg19):22544398 or ChrY position (Hg38):20382512, which is little outside what YSEQ defines as the DYZ19 region (chrY:20054914..20351054 (DYZ19 125 bp repeat region)). I don't have a Big Y Y500 to check but coverage but I imagine Z2893 isn't covered well in those. Z2893 is also not included in the I-M253 SNP pack.

YFull have more WGS and more ancient samples than the FTDNA haplotree (which has zero WGS), so in my opinion they have more comprehensive relevant data.

Looking back through my notes on other ancient I1 samples, there are a few examples where there have been false negative one-read SNPs on the I-DF29 branch. urm035 from the Sigtuna paper was a low coverage sample that had derived calls for DF29 and Z2892 / CTS9848 but an ancestral call for Z2893. Also CL63 from the Collegno Langobard cemetery has confirmed Z63 with strong 10T reads, but has a negative one-read SNP for DF29 with 1A - based on the Z63 result, we can say the one-read negative DF29 is false. And there's the Icelandic SVK-A1 false positive Z131 which contradicts the actual placement at I-FGC21682.

Looking at my own YElite, there are 16 one-read novel SNPs but when I cross reference with my WGS, one out of the 16 turns out to be genuine while the other 15 are shown to be mostly ancestral when viewed with the greater read depth of the WGS. So one-reads can be real or they can be false, but without corroborating information, really can't be sure.

Thanks for the explanation. I suppose those are the same reasons why Ftdna only lists around 70 phyloequivalent SNPs for I-M253 while YFull lists around 311.

In case your curious there were no results for I-Z2893 in my Big Y-500 test.

Lastly, it would be cool if it’s not too much work if you created a training thread with screenshots showing the steps needed to check a location on the Y chromosome for one of these ancient samples. For the future of this hobby it would be beneficial to have multiple folks capable of doing this.

deadly77
10-12-2019, 08:56 PM
Thanks for the explanation. I suppose those are the same reasons why Ftdna only lists around 70 phyloequivalent SNPs for I-M253 while YFull lists around 311.

In case your curious there were no results for I-Z2893 in my Big Y-500 test.

Lastly, it would be cool if it’s not too much work if you created a training thread with screenshots showing the steps needed to check a location on the Y chromosome for one of these ancient samples. For the future of this hobby it would be beneficial to have multiple folks capable of doing this.

Yeah, I think there's generally a lot more focus on the downstream branches as that's where the customers apply their scrutiny on who they match the most closely and where they differ. Not a lot of people look at the far up roots of those lineages. But indeed - the Big Y Y500 had a lot of areas of the Y chromosome that it misses, leading to no calls, one reads, ambiguous, etc. which likely means that there may not be consistency between different samples. The Big Y Y700 has significantly more coverage which adds a lot of SNPs in regions that Big Y Y500 didn't cover well, and also cleans up a lot of the poor reads in the well covered regions as well. Result is that a lot of SNPs being discovered in Big Y Y700 tests are being tagged as "novel" variants, but some of them are phyloequivalent SNPs to upstream branches. I believe FTDNA is moving these SNPs over to where they should be, but it's a going to take them a while - much longer than the hg19 to hg38 conversion of a couple of years ago.

I remember looking at their haplotree a few weeks ago and seeing 70 or 75 phyloequivalent SNPs on the I-M253 branch, but I've taken a look today and they are now listing "+293" variants on that branch. So it seems like they are making progress in filling out there haplotree.

But even though the Big Y Y700 is better than the Big Y Y500, it's not perfect and it still misses some things. And while Z2893 is way up the tree on the I-DF29, there's no guarantee that the Big Y Y700 doesn't miss important SNPs downstream. WGS has better horizontal coverage over the Y chromosome, so I think it's a better test. I understand it's not for everyone, especially the prices at the more reliable providers.

I'll try and put something together regarding BAM analysis. I would like another few pairs of eyes on some of these - if anything it's great for verification if different people come to the same conclusion. It's just a case of finding time to write up and do it. But it's probably worth doing.

deadly77
10-13-2019, 07:36 PM
Back to oll009, I've been through the SNPs at the level below I-DF29 and there's nothing conclusive for anything downstream. The only SNPs that oll009 is derived for are Y11204 with 1A read and A5729 with 1A read. Obviously these two results conflict each other and neither is especially reliable. There's no corroborating reinforcement from phyloequivalent SNPs as Y11869, Y11210, Y11210 (2T), Y24622, Y32359, Y11868 and Y11864 on the I-Y11205 branch are ancestral in the former case; and Y16802 (3G), A5734 and A5716 (2A) on the I-A5679 branch are ancestral in latter case. There's also S10066 with 1G, 1A read which is ambiguous but neither read is for the derived allele (T) for that SNP.

Everything else is ancestral or no call, so I-DF29 is as far as oll009 goes on the data available.

I looked at ajv54 and ros005 from the same paper in parallel since it's easy to load tracks from several BAM files into the IGV. No derived calls for any of these SNPs in either of these samples. All SNPs are ancestral or no call. But that's not surprising as Pribislav tagged these two as I2.

deadly77
10-13-2019, 07:48 PM
I had a brief look at the alleged I1 that turned out to be not I1 from #519. OBKR_117 was the only one listed as Y-DNA I from the supplementary information of the Mittnik "Kinship-based social inequality in Bronze Age Europe" paper. BAM files are now available at ENA, but apparently there are four BAM files for OBKR_117. Loaded all four in the IGV and took a look at SNP L258.
33866
33867
Not sure why there are four BAM files - may have been done with different techniques - such as shotgun or SNP capture, or may be separate mtDNA. :noidea:
Looks the first and fourth ones have a one-read for L258 - so chance of being a false positive result, especially in light of the ancestral I1 SNPs upstream.
Scanned out a bit and these four BAM files had very poor coverage. Checked the 6 SNPs at the I-DF29 and no call for all of them.

deadly77
10-14-2019, 01:56 PM
oll009 from the recent Scandinavian Battle Axe paper has pretty decent coverage of the SNPs on the I1 branch so far - checked 50 out of the >300 and 25 are derived, some with multiple reads. All good corroboration for oll009 being haplogroup I1.

deadly77
10-25-2019, 10:45 AM
Finished working through the I1-level SNPs for oll009. oll009 has good coverage for a lot of these SNPs, with many positions read. He's derived for 130 of the I1 SNPs, including several that have multiple reads - for example Z2816/CTS8170 has 5 derived T reads.

Derived I1-level SNPs: Z2699/FGC2430 2C, Z2844 1G, Y1831/FGC2468 1A, L840 1G, Z2706/CTS1220 1G, Z2841 1C, Z2856 1C, Z2714/FGC2425 1A, FGC7747 1G, Z2718 1T, Z2701/CTS571 1C, Z2855 1A, Z2781/CTS4790 1T, Z2802/CTS6221 1T, Z2679/CTS136 2G, Z2727 2T, Z2785/CTS5247 3C, Z2751/L841/YSC0000257 1A, Z2700/CTS565 1C, Z2737 1T, Y1868/FGC2444/S111/V1623 2A, Z2798/CTS6109 1T, Y1958 ATTTTTTTG, PAGE123/PAGES00123/Z2763 1G, L495/Z2788/Z2788.2 1T, Z2846 2G, Z2733 2T, CTS7121/Z2808 1A, Z2824/CTS9010 1A, FGC2422/Z2715 1T, CTS11042/S66 2C, FGC33327 1A, Z2882/YSC0000301 1C, L123 2T, Z2811/CTS7477 2C, CTS2970/Z2760 1T, CTS1266/Z2707 1C, Z2730 1G, Z2722 2T, CTS1755/Z2750 2T, CTS2644/Z2757 1A, FGC3441/Y1935 1G, Y1951 GA ins, FGC3444 1A, Z2816/CTS8170 5T, CTS9518/Z2831 2T, CTS313/Z2681 1C, CTS6992 3T, CTS2732/Z2758 2A, CTS9749/Z2833 1G, L81 1C, CTS10613/Z2840 1C, L848/Z2877/YSC0000299 1G, FGC2433 3A, Z2805/CTS6629 1A, M253 1T, Z2723 1T, Z2862 1C, Z2847 1T, CTS8716/Z2822 1T, FGC10275 2T, CTS6006/Z2795 1A, Z2745 1T, Z2812/CTS7652 1T, Z2790/CTS5643 1A, Z2878/L843/YSC0000273 2G, Z2738 1G, Z2874/CTS11751 2C, Z2772/CTS4327 1C, FGC2438/S108/Y1864 1G, CTS5891/Z2793 1G, Z2759/CTS2738 2A, FGC2427/Z2713 1A, Y1886 2C, Z2734 2C, Z2736 2T, Z2852 1T, CTS2410/Z2755 2A, Z2864/L509 2G, Z2861 1A, Z2784/CTS5167 4T, Z2809/CTS7267 1C, CTS209/Z2680/V1092 1G, L1439 2A, Y1879/FGC2436 3G, Z2872/CTS11552 1A, CTS4130/Z2769/V2932 2G, CTS10140/Z2837 1A, Y1932/S2007 1G, Z2794/CTS5993 1A, Z2834/CTS10062 1A, CTS8597/Z2819 1T, Z2732 1G, CTS641/Z2702 1T, FGC2452/Y1852 1A, FGC2431/Z2710 1C, CTS9845 3G, Y1891/FGC7748 2G, CTS9368/Z2827 1G, Y1876 2A, Z2828/CTS9405 3G, Y1837/FGC2461 2T, Z2853 1C, CTS11675/Z2873 3T, FGC2470/Y1930 1G, CTS10556 1A, Z2854 1A, Y1840/FGC3440 2A, FGC2478/Y1917 1A, Y1842/FGC2448 1G, Z17955/Y1918/FGC2464 1T, CTS2044 1G, Z2686/FGC2450 1C, Y1859/FGC2442 1T, FGC2454/Y1833 1A, CTS11166/Z2867 1A, Y1926/FGC2484 1A, Z2687 1G, Y1940/FGC3443 1T, Z2721 1T, Z2691 1T, CTS12609/Z2889 1G, Z2851 1G, Y1853 1A, Y1883/S2013/FGC2472 1T, Y1873 1T, Z2731 2A , Z2774/CTS4344 2C, Z2729 2T, CTS8468 1A.

There were also 14 of the I1-level SNPs that I tagged as ambiguous. There were a couple that had an allele that was neither derived or ancestral - CTS5408/Z2786 had 1A (Anc:C, Der:G) and FGC2434/Z2696 had 1T (Anc:G, Der:C) - these are both one-read SNPs and likely to be false reads. There were twelve more where different alleles were read at the same position: Z2726 2G, 1A, Z2770/CTS4189 2A 1C, Z2708/CTS1393 1A 1T, CTS6022/Z2796 2A 1G, FGC2441 1G 1A, Z2740 2G 2A, CTS11214/Z2868 4G 3C, Y1870/FGC2460 4C 1T, FGC2482/Y1919 1C 1G, Z2815/CTS8107 3T 1G, CTS7988 5C 2T, Y1947/FGC3437 1G 1A. Some of these I'd have a bit more confidence in - the Y1870/FGC2460 4C 1T could probably be called as actually derived with the 1T representing a false read. The example of Y1947/FGC3437 1G 1A a bit less so.

There were also a seven SNPs on the I1-level branch that had the ancestral allele - Z2746 2A, CTS3029 1T, FGC2445/Z2688 1C, Y1916/FGC2477 1G, CTS4387 1G, Z2683 1C, Z2804/CTS6547 2C, FGC7871/Y1906 1G. Most of these are one-read SNPs and perhaps represent false negative calls. Z2746 has 2A reads, but the position ChrY(hg19):13626434 would locate this SNP in the centromere where the p and q branches cross over which is prone to recombination events.

I'm satisfied from the SNP calls that oll009 can be considered fully I1. The evidence is strong and consistently corroborated across many of the SNPs at the I1-level, and supported by the two derived SNPs at the I-DF29 level, while the evidence against in the form of ancestral reads at I1-level SNPs is less convincing given the low quality of thre reads and regions that some of these SNPs are found in. It's also a small number of ancestral SNPs given the good horizontal coverage across oll009's genome.

I had a look at ajv54 and ros005 in parallel to oll009 while looking at the BAM files. Similar to oll009, these two had good horizontal coverage of the Y chromosome. ajv54 had a single derived I1-level SNP FGC2422/Z2715 with a 1T read, although ajv54 is ancestral for 138 of the I1-level SNPs (as well as 5 ambiguous), so FGC2422/Z2715 is likely to be a false positive. ros005 did not have any derived reads at the I1 level - all ancestral or no call.

spruithean
10-27-2019, 09:00 PM
Awesome, nice to see a legitimate I1 from Late Neolithic Scandinavia, perhaps it gives more support for the other pre-I1 RISE individuals (from roughly the same period) as being fully I1, despite the lack of supporting data in their samples.

deadly77
10-27-2019, 10:33 PM
Awesome, nice to see a legitimate I1 from Late Neolithic Scandinavia, perhaps it gives more support for the other pre-I1 RISE individuals (from roughly the same period) as being fully I1, despite the lack of supporting data in their samples.

Yeah, it's quite possible that some of these RISE samples are full I1. SF11, BAL051, Car1 are a lot easier to categorize at pre-I1 due to the SNPs in their genomes that are the ancestral alleles on the I1 branch and being dated before the I1 TMRCA. Given that BAB5 predates the I1 TMRCA, BAB5 most likely has ancestral SNPs at the I1 branch level, but we don't know for sure. The RISE samples are much more of a grey area given the dates of those samples but I'm wary of assigning them full I1 status based on the data available. For me it's not strong enough to be sure as it's a really low number of SNPs where a lot of them are one-read. I put these ones on my map with a question mark in brown, as opposed to the skull and crossbones in black for the more confidently assigned pre-I1 samples.

I'm not entirely consistent - the two I1 samples from the Hungarian Conquerer preprint SzO/540 and K2/26 also have pretty poor coverage and not many I1 SNPs covered, and no derived I1 subclade SNPs. These are dated to well after the I1 TMRCA, but of course some branches of pre-I1 may have been around for quite a while after the I1 TMRCA - just not around today - or at least not in any of the Y-DNA databases of contemporary individuals at a level of testing which would show that.

But yes, this one was a nice find from this time period. Torsten Günther noted on Twitter that this paper has been in the making for at least six years and there have been several professional and personal reasons among the authors why this got delayed or other projects had higher priorities at the time.

deadly77
10-28-2019, 08:00 AM
Decided to change the icons for the two Hungarian Conqueror samples to brown with question mark, due to lack of I1-level SNPs read by an enrichment assay that wasn't really worthy of the name. Also noticed that the Haplogroup I1 Ancient DNA Samples Map is up over 5000 views (5168 right now, to be precise).

mwauthy
11-06-2019, 12:15 AM
YFull now has all009 on their Haplotree as I-DF29* so that’s pretty cool confirmation even though I was convinced with deadly77’s analysis as well.

deadly77
11-06-2019, 12:51 AM
YFull now has all009 on their Haplotree as I-DF29* so that’s pretty cool confirmation even though I was convinced with deadly77’s analysis as well.

Excellent - thanks for pointing that out. I had sent YFull an email with the paper, a link to the BAM file and my analysis of the SNPs that I'd compiled from the BAM file on October 26th. I hoped this might be included given that it's a shotgun sequenced sample with reasonable horizontal coverage. I hadn't heard back from them but happy to see oll009 on there.

Interesting on that YFull tree that if you hover your cursor over the "i" next to oll009, there's a small pop-up that says "I-DF29*, I-Z63*, I-BY151*" - perhaps YFull has found something a bit further downstream. In my own analysis, I had Z63 as a no call. I didn't check anything below that as pretty worn out going through all of the 312 I1 level SNPs, all of the I-DF29 level and all of the branches one level below that.

Looking up BY151 in oll009's BAM file, there's a one-read positive 1A at that position. Not sure if that's strong enough to assign without other corroborating SNPs. It may be that YFull is just noting it for now. I guess watch this space. Although should point out that BY151 at ChrY position (Hg19):22305998/ChrY position (Hg38):20144112 is in the DYZ19 region and YFull has given BY151 a 1-star SNP rating - so I'm not sure why I-BY151 is used as a branch on the YFull tree given that YFull's FAQ regarding their star rating system. Given that it's a one-read, one-star SNP in the DYZ19 region, may not be reliable. Of course if other derived SNPs that corroborate are found, we can revise accordingly.

It looks like YFull also added ber1 from the same paper to R-Y2395* branch in R1a.

mwauthy
11-06-2019, 01:14 AM
Excellent - thanks for pointing that out. I had sent YFull an email with the paper, a link to the BAM file and my analysis of the SNPs that I'd compiled from the BAM file on October 26th. I hoped this might be included given that it's a shotgun sequenced sample with reasonable horizontal coverage. I hadn't heard back from them but happy to see oll009 on there.

Interesting on that YFull tree that if you hover your cursor over the "i" next to oll009, there's a small pop-up that says "I-DF29*, I-Z63*, I-BY151*" - perhaps YFull has found something a bit further downstream. In my own analysis, I had Z63 as a no call. I didn't check anything below that as pretty worn out going through all of the 312 I1 level SNPs, all of the I-DF29 level and all of the branches one level below that.

Looking up BY151 in oll009's BAM file, there's a one-read positive 1A at that position. Not sure if that's strong enough to assign without other corroborating SNPs. It may be that YFull is just noting it for now. I guess watch this space. Although should point out that BY151 at ChrY position (Hg19):22305998/ChrY position (Hg38):20144112 is in the DYZ19 region and YFull has given BY151 a 1-star SNP rating - so I'm not sure why I-BY151 is used as a branch on the YFull tree given that YFull's FAQ regarding their star rating system. Given that it's a one-read, one-star SNP in the DYZ19 region, may not be reliable. Of course if other derived SNPs that corroborate are found, we can revise accordingly.

It looks like YFull also added ber1 from the same paper to R-Y2395* branch in R1a.

Thanks for sending that info to YFull. I think YFull’s notation implies there is not enough evidence to rule out or confirm al009 as being I-Z63* or I-BY151*

I’ve seen similar notation in other subclades when there was a discrepancy between a Big Y-700 subclade downstream and a Big Y-500 kit. Since the Big Y-500 kit didn’t have coverage of the Big Y-700 subclade they couldn’t rule it out as being possibly positive for it.

deadly77
11-06-2019, 01:30 AM
Thanks for sending that info to YFull. I think YFull’s notation implies there is not enough evidence to rule out or confirm al009 as being I-Z63* or I-BY151*

I’ve seen similar notation in other subclades when there was a discrepancy between a Big Y-700 subclade downstream and a Big Y-500 kit. Since the Big Y-500 kit didn’t have coverage of the Big Y-700 subclade they couldn’t rule it out as being possibly positive for it.

Makes sense.

deadly77
11-06-2019, 11:54 AM
Slightly off-topic, but since we're discussing YFull, I noticed that YFull have added a new "chart view" option in addition to the normal and "scientific" view. May need to use the zoom in and out and scrolling to see the area that you want to look at. A little bit like the tree style charts that Eupedia put out, but these ones are up to date. Screenshots from I-Z140, but you can apply the chart view to any of the branches.
344093441034411

JMcB
11-07-2019, 09:42 PM
I was just quickly scanning through the new Roman paper supplemental and saw the following:

An intriguing haplogroup observed in Late Antiquity is I-M253 (I1), which is quite common in present-day northern Europe (at 25-40% frequency in Scandinavia)(75–77), relatively rare in mainland Italy (~4%) and completely absent in Sardinia (78). It is estimated that the I-M253 haplogroup arose 3,200-5,000 years ago in northern Europe (79), so the presence of this haplogroup in Imperial Rome could possibly reflect migration from the north into central Italy. R110, the individual who carries the I-M253 comes from Crypta Balbi, a site that used to be a theater courtyard in the Imperial era and transformed for other purposes in Late Antiquity. Interestingly, Lombard-associated ornaments have been excavated at this site, pointing to connections with central Europe. Additionally, five of the seven individuals from this site, including R110, are classified by ChromoPainter into a cluster with more haplotype sharing with central/northern Europeans. Therefore, the I-M253 haplotype observed in Late Antiquity is consistent with the increasing genetic influence from central European populations detected by other analyses (e.g., PCA, f-statistics, qpAdm).

https://science.sciencemag.org/content/sci/suppl/2019/11/06/366.6466.708.DC1/aay6826_Antonio_SM.pdf

JMcB
11-07-2019, 10:23 PM
Slightly off-topic, but since we're discussing YFull, I noticed that YFull have added a new "chart view" option in addition to the normal and "scientific" view. May need to use the zoom in and out and scrolling to see the area that you want to look at. A little bit like the tree style charts that Eupedia put out, but these ones are up to date. Screenshots from I-Z140, but you can apply the chart view to any of the branches.
344093441034411

I really like that new feature. Especially, the simple view, which allows you to see how subclades descend more easily. It also allows me to fool around on my iPad and add some additional subcllades in my area that YFull and FT don’t know about, or haven't processed yet.

I-A13241 (click simple chart):

https://www.yfull.com/chart/tree/I-A13241/


And with my additions:

34459


Let’s hope people keep sending their Bam (or VCF files, if that’s actually allowed) to YFull. After FT’s new (and I think punitive) Bam file tax.

deadly77
11-07-2019, 11:48 PM
I was just quickly scanning through the new Roman paper supplemental and saw the following:

An intriguing haplogroup observed in Late Antiquity is I-M253 (I1), which is quite common in present-day northern Europe (at 25-40% frequency in Scandinavia)(75–77), relatively rare in mainland Italy (~4%) and completely absent in Sardinia (78). It is estimated that the I-M253 haplogroup arose 3,200-5,000 years ago in northern Europe (79), so the presence of this haplogroup in Imperial Rome could possibly reflect migration from the north into central Italy. R110, the individual who carries the I-M253 comes from Crypta Balbi, a site that used to be a theater courtyard in the Imperial era and transformed for other purposes in Late Antiquity. Interestingly, Lombard-associated ornaments have been excavated at this site, pointing to connections with central Europe. Additionally, five of the seven individuals from this site, including R110, are classified by ChromoPainter into a cluster with more haplotype sharing with central/northern Europeans. Therefore, the I-M253 haplotype observed in Late Antiquity is consistent with the increasing genetic influence from central European populations detected by other analyses (e.g., PCA, f-statistics, qpAdm).

https://science.sciencemag.org/content/sci/suppl/2019/11/06/366.6466.708.DC1/aay6826_Antonio_SM.pdf

Interesting - I'll take a closer look at R110 when the BAM files become available. Paper says they will be available at ENA under accession number PRJEB32566. Nothing there yet, but sometimes takes a few hours to get uploaded there once published. There are 44 of the samples at NCBI under that accession number, but R110 isn't one of them. R110 added to the ancient samples map.

deadly77
11-08-2019, 08:02 AM
Looking at the excel file and Table S2, there's a second I1 in the Ancient Rome paper - sample R1286 is listed as I-M253. This one is listed as Medieval and radiocarbon dated to 1411 - 1447 calCE and from the Cancelleria - The Basilica of San Lorenzo in Damaso site.

deadly77
11-09-2019, 09:37 AM
Okay, BAM files for all of the samples from the Ancient Rome paper are now at European Nucleotide Archive, so I've downloaded the BAM files for R110 and R1286.

After the great horizontal coverage of oll009, these two look a bit more sparse on the first few SNPs looked at so far. Of the I-DF29 SNPs, R110 is derived for CTS9857/V3772 with 1T read, no call for the rest. R1286 is no call for all I-DF29 level SNPs.

For the larger branches of I-DF29, both are no call for Z58. R110 is ancestral (1A) for Z2336 / CTS6364, no call for Y2592 and Y2593 - R1286 is no call for all three I-Z2336 SNPs. For Z63, R110 is a no call at that position, but R1286 has an ambiguous call with both the derived and ancestral allele equally at Z63 - 1A and 1T, so it's read but not conclusive. Both are ancestral for Z140 - R110 has 1G, R1286 has 3G.

I'll have a more in depth look later, but out with the family and then going to the football this afternoon.

deadly77
11-09-2019, 11:09 AM
Aha - R1286 is most likely I-P109. He's one-read derived with 1T for P109 itself, but that's strengthened by a good 4G read derived call for CTS11651/Z2338 upstream. So we can more confidently assign the earlier ambiguous Z63 to ancestral. R110 is not the same Y-lineage - he's ancestral for P109 (1C), as well as Z2337/CTS10028 (2T), Z2336/CTS6364 (1A).

JonikW
11-09-2019, 11:28 AM
Aha - R1286 is most likely I-P109. He's one-read derived with 1T for P109 itself, but that's strengthened by a good 4G read derived call for CTS11651/Z2338 upstream. So we can more confidently assign the earlier ambiguous Z63 to ancestral. R110 is not the same Y-lineage - he's ancestral for P109 (1C), as well as Z2337/CTS10028 (2T), Z2336/CTS6364 (1A).

Excellent work and great to see these two on your Ancient DNA Samples Map already. Much appreciated.

deadly77
11-09-2019, 11:53 AM
Excellent work and great to see these two on your Ancient DNA Samples Map already. Much appreciated.

A little further down with S1286 from I-P109 - he's at least I-S14887.

JMcB
11-09-2019, 04:18 PM
Excellent work and great to see these two on your Ancient DNA Samples Map already. Much appreciated.

Indeed! I was just going to go through the supplemental looking for the details on R1286 and then I clicked on Deadly’s map and it was all in there already. Nice!!!

Pribislav
11-09-2019, 08:21 PM
R110 is below Z63!

R110; 400-600 AD; Crypta Balbi; Late Antiquity; I1-Z63>BY151>FGC81364>S2078>S2077>Y2245>Y7234 (https://www.yfull.com/tree/I-Y7234/)

No calls at Y7666 level, 7 ancestral SNPs at Y7663 level.

spruithean
11-09-2019, 08:40 PM
R110 is below Z63!

R110; 400-600 AD; Crypta Balbi; Late Antiquity; I1-Z63>BY151>FGC81364>S2078>S2077>Y2245>Y7234 (https://www.yfull.com/tree/I-Y7234/)

No calls at Y7666 level, 7 ancestral SNPs at Y7663 level.

Interesting, the Lombard CL63 is also I-Y2245.

Pribislav
11-09-2019, 08:43 PM
More details:


R110; 400-600 AD; Crypta Balbi; Late Antiquity; I1-Z63>BY151>FGC81364>S2078>S2077>Y2245>Y7234 (https://www.yfull.com/tree/I-Y7234/)

This was a tricky one, no calls at Z63, BY151 and FGC81364 levels, then FGC9506+ at S2078 level and Y4102/FGC9504+ at S2077 level. Then again no calls at Y2245 level, and then all 6 derived SNPs at Y7234 level:

Y7234/FGC14479+ C>T (1 read)

Y7235/FGC14480+ C>T (1 read)

FT72052+ C>T (1 read)

Y7510/FGC14490+ G>A (1 read)

Y7511/FGC14485+ C>G (1 read)

Y7239/FGC14497+ G>A (2 reads)

No calls at Y7666 level, and 7 ancestral SNPs at Y7663 level.

Pribislav
11-09-2019, 08:58 PM
A little further down with S1286 from I-P109 - he's at least I-S14887.

R1286 should also be S14887>Y4115:

Y4115/FGC13270+ A>T (1 read)

He has only ancestral calls for all 6 downstream subclades.

deadly77
11-09-2019, 10:48 PM
More details:

Nice work Pribislav - I had not dug down to far into R110, but it was quite clear he wasn't I-Z58 or I-Z2336.

deadly77
11-09-2019, 10:55 PM
R1286 should also be S14887>Y4115:

Y4115/FGC13270+ A>T (1 read)

He has only ancestral calls for all 6 downstream subclades.

This was pretty much where I had got to before going out for the football game (4-0 win). I looked at the downstream subclades and ran into a few negatives, but haven't looked at all of the phyloequivalent SNPs yet to rule everything out. Given that Y4115 was a one read I may have gone back up a level, but haven't done so yet.

Aroon1916
11-09-2019, 11:06 PM
This is completely off topic and my apologies.

I just want to say how great this thread is. My father's haplogroup is I1 M253 Z63 Y6375. I don't know much about it except for what I have found on Eupedia.

We have traced his paternal lineage back to Northern Ireland. His paternal great great grandfather was born (most likely) in County Cavan around 1813 and emigrated to Ontario, Canada around 1840. We have been unable to trace anything beyond this. The family name is Hewitt but have no idea how long they were in Ireland or if the family originally came from England or Scotland. One theory was that they were Huguenots. But enough of that.

You are a knowledgeable and dedicated group on this thread. Proud to be connected to the I1 crowd.

oz
11-10-2019, 10:55 AM
R110 is below Z63!

R110; 400-600 AD; Crypta Balbi; Late Antiquity; I1-Z63>BY151>FGC81364>S2078>S2077>Y2245>Y7234 (https://www.yfull.com/tree/I-Y7234/)

No calls at Y7666 level, 7 ancestral SNPs at Y7663 level.

That's great!

What about those rumors of allegedly Etruscan I1?

Pribislav
11-10-2019, 11:33 AM
That's great!

What about those rumors of allegedly Etruscan I1?

There was only one male Etruscan sample in this paper, and he is J2b2-CTS6190 (https://www.yfull.com/tree/J-CTS6190/).

spruithean
11-10-2019, 01:12 PM
That's great!

What about those rumors of allegedly Etruscan I1?

The Etruscan was likely not I1 to begin with, sort of like that error that was made with the Lech Valley sample.

JonikW
11-13-2019, 10:38 AM
There are two I1 samples in the new Hun, Avar and Conquering Hungarian period paper, both L22 unsurprisingly. They are: SzO/540, early Avar period 7th century, and K2/26, Conqueror period 9th to 10th century.

https://www.nature.com/articles/s41598-019-53105-5

Add: SzO/540 was autosomally European with a trace of East Asian while K2/26 was somewhat more East Asian than European.

deadly77
11-13-2019, 11:25 AM
There are two I1 samples in the new Hun, Avar and Conquering Hungarian period paper, both L22 unsurprisingly. They are: SzO/540, early Avar period 7th century, and K2/26, Conqueror period 9th to 10th century.

https://www.nature.com/articles/s41598-019-53105-5

Add: SzO/540 was autosomally European with a trace of East Asian while K2/26 was somewhat more East Asian than European.

This is the final published paper of the preprint that came out in April earlier this year (with raw data released around the same time. I reviewed the BAM files for SzO/540 and K2/26 back in #242 on page 25 of this thread https://anthrogenica.com/showthread.php?13783-Ancient-I-M253-samples-list&p=559642&viewfull=1#post559642

Unfortunately, these samples are not very useful in terms of the data that can be obtained from the BAM file. The researchers used a very poor enrichment assay that was only designed to capture 168 Y-SNPs. All we can really say for sure about SzO/540 and K2/26 is that they are both I1 and negative for L22. It's no call/no read for pretty much anything else. There might be some hits that are close by in position to one of the targeted 168 Y-SNPs, for example, L1287 is picked up with one or two negative reads in both despite not being on the list, but most ones I looked at were no call.

The autosomal DNA is also poor - they only targeted 61 autosomal SNPs for things like eye and hair colour, lactase persistence, etc. The MDS plots in the paper are based on Y chromosome haplogroup distributions rather than autosomal - I don't believe they did any autosomal comparison - probably 61 autosomal SNPs isn't much to get a meaningful comparison with any sample outside of this paper.

JonikW
11-13-2019, 11:45 AM
This is the final published paper of the preprint that came out in April earlier this year (with raw data released around the same time. I reviewed the BAM files for SzO/540 and K2/26 back in #242 on page 25 of this thread https://anthrogenica.com/showthread.php?13783-Ancient-I-M253-samples-list&p=559642&viewfull=1#post559642

Unfortunately, these samples are not very useful in terms of the data that can be obtained from the BAM file. The researchers used a very poor enrichment assay that was only designed to capture 168 Y-SNPs. All we can really say for sure about SzO/540 and K2/26 is that they are both I1 and negative for L22. It's no call/no read for pretty much anything else. There might be some hits that are close by in position to one of the targeted 168 Y-SNPs, for example, L1287 is picked up with one or two negative reads in both despite not being on the list, but most ones I looked at were no call.

The autosomal DNA is also poor - they only targeted 61 autosomal SNPs for things like eye and hair colour, lactase persistence, etc. The MDS plots in the paper are based on Y chromosome haplogroup distributions rather than autosomal - I don't believe they did any autosomal comparison - probably 61 autosomal SNPs isn't much to get a meaningful comparison with any sample outside of this paper.

Well, that had completely vanished from my mind. Must be getting old... Thanks for all that. Disappointing that they have the L22 designation in the published paper then.
I'm beginning to lose hope of anyone carrying out a good Migration Period study of Northwest Europe at this stage, particularly given the Zeitgeist and its understandable wish to highlight diversity on the ground in the past. Unlike Rome or even the Vikings, the early Anglo-Saxons and similar are not obvious candidates for this approach, and as you may have seen there's even a push to rename the period in England to avoid any dodgy connotations. There's always hope of the occasional micro study of a cemetery I suppose, particularly where this might have something fitting to say about gender, identity and power. Otherwise funding might be a serious difficulty...

deadly77
11-13-2019, 03:30 PM
Well, that had completely vanished from my mind. Must be getting old... Thanks for all that. Disappointing that they have the L22 designation in the published paper then.
I'm beginning to lose hope of anyone carrying out a good Migration Period study of Northwest Europe at this stage, particularly given the Zeitgeist and its understandable wish to highlight diversity on the ground in the past. Unlike Rome or even the Vikings, the early Anglo-Saxons and similar are not obvious candidates for this approach, and as you may have seen there's even a push to rename the period in England to avoid any dodgy connotations. There's always hope of the occasional micro study of a cemetery I suppose, particularly where this might have something fitting to say about gender, identity and power. Otherwise funding might be a serious difficulty...

Ha, well the Y-DNA analysis from that paper wasn't very memorable, so perhaps that's why it vanished from your mind.

I'm not sure how much these things cost, but clearly it's not inexpensive. We have some idea how much whole genome sequencing for a modern individual costs based on the prices of commercial tests, but obviously the process of the extraction of DNA is going to be a bit different - no ancient remains are spitting into a tube, so there's got to be some grinding of up of bones, extraction of DNA, etc. under clean conditions which would require some expertise, facilities, reagents, all of which costs money. And then there's access to the remains, excavation or exhumation, permissions, ownership...

Regarding funding had a look at some of the acknowledgements sections of some of the papers we've looked at to see who is funding some of these studies:

The Population Genomics of the Viking world preprint had: "This work was supported by the Mærsk Foundation, the Lundbeck Foundation, the Novo Foundation, the Danish National Research Foundation, KU2016, and the Wellcome Trust (grant nos. WT104125MA). The authors thank the iPSYCH Initiative, funded by the Lundbeck Foundation (grant nos. R102-A9118 and R155-2014-1724), for supplying SNP frequency estimates from the present-day Danish population for comparison with Viking Age samples" and in addition to this, several of the individual researchers acknowledged support from fellowships: "SR was supported by the Novo Nordisk Foundation (NNF14CC0001). FR was supported by a Villum Young Investigator Award (project no. 000253000)...G.S. and E.C. were supported by a Marie Skłodowska-Curie Individual Fellowship “PALAEO-ENEO”, a project funded by the European Union EU Framework Programme for Research and Innovation Horizon 2020 (Grant Agreement number 751349). RM was supported by an EMBO Long-Term Fellowship (ALTF 133-2017)."
The Ancient Iceland paper had " S.S.E. and V.B.G. received grants from The Research Fund of University of Iceland for doctoral studies. M.S.-V. and A.J. received a grant from EUROTAST Marie Curie Framework Programme 7 Initial Training Network (290344). M.S.E. received a grant from the Icelandic Research Fund (163428-051). The work was partly funded (E.G. and G.L.C.) by a Career Development Award (13/CDA/2223) from Science Foundation Ireland and Swedish Research Council (Dnr 2016-02349), Swedish Research
Council for Health, Working Life and Welfare (Dnr 2013-0194), and Swedish Brain Foundation (FO2017-0076)." as well as a note "Authors affiliated with deCODE Genetics are employed by the company, which is owned by Amgen, Inc" under competing interests since 14 of the authors had affliation with deCODE - although I believe deCODE has since been spun-off and no longer owned by Amgen.
Anglo-Saxon paper containing NO3423 had "This study makes use of data generated by the Wellcome Trust Case Control Consortium. A full list of the investigators who contributed to the generation of the data is available from www.wtccc.org.uk. Funding for the project was provided by the Wellcome Trust under award 076113. We wish to acknowledge the DJEI/DES/SFI/HEA Irish Centre for High-End Computing (ICHEC) for the provision of computational facilities and support. This study has been financed by the BEAN project of the Marie Curie ITN (grant number 289966). M.D.T. was funded by ERC Investigator grant 295729-CodeX."
Recent Ancient Rome paper: "This project was partially supported by National Science Foundation Graduate Research Fellowships (M.L.A. and D.J.C.); Stanford Interdisciplinary Graduate Fellowship and grants from the Stanford Archaeology Center and Stanford Anthropology Dept (H.M.M.); Howard Hughes Medical Institute (Z.G. and J.K.P.); and an MIUR grant (Project D15D18000410001) (G.M.)."
Hungarian Conqueror paper: "This work was supported by grants from the National Research, Development and Innovation Office (K-124350 to TT) and The House of Árpád Programme (2018–2023) Scientific Subproject: V.1. Anthropological-Genetic portrayal of Hungarians in the Arpadian Age to TT."
Birger Magnusson paper: "We thank Agnar Helgason at deCODE Genetics in Iceland for letting us use his unpublished program PhyloNet version 5. AG was supported by the Royal Swedish Academy of Science."
Sigtuna: "The project was supported by Riksbankens Jubileumsfond (RJ_M13_0904:1) and Swedish Research Council (VR_2013-04959). Sequencing was conducted at the Uppsala University SNP&SEQ Technology Platform. Computations were performed at UPPMAX resources (Uppsala Multidisciplinary Centre for Advanced Computational Science) under projects b2013203, b2013240, b2015307, and b2016056."

Although there are no papers yet (presumably because this is dated from September this year), the homepage of Stephan Schiffels at MPI has this announcement on the award of a grant that you might find interesting... and also gives an indication of the kind of money involved http://www.stephanschiffels.de/posts/2019-09-23-erc-funded.html

JonikW
11-13-2019, 03:54 PM
Ha, well the Y-DNA analysis from that paper wasn't very memorable, so perhaps that's why it vanished from your mind.

I'm not sure how much these things cost, but clearly it's not inexpensive. We have some idea how much whole genome sequencing for a modern individual costs based on the prices of commercial tests, but obviously the process of the extraction of DNA is going to be a bit different - no ancient remains are spitting into a tube, so there's got to be some grinding of up of bones, extraction of DNA, etc. under clean conditions which would require some expertise, facilities, reagents, all of which costs money. And then there's access to the remains, excavation or exhumation, permissions, ownership...

Regarding funding had a look at some of the acknowledgements sections of some of the papers we've looked at to see who is funding some of these studies:

The Population Genomics of the Viking world preprint had: "This work was supported by the Mærsk Foundation, the Lundbeck Foundation, the Novo Foundation, the Danish National Research Foundation, KU2016, and the Wellcome Trust (grant nos. WT104125MA). The authors thank the iPSYCH Initiative, funded by the Lundbeck Foundation (grant nos. R102-A9118 and R155-2014-1724), for supplying SNP frequency estimates from the present-day Danish population for comparison with Viking Age samples" and in addition to this, several of the individual researchers acknowledged support from fellowships: "SR was supported by the Novo Nordisk Foundation (NNF14CC0001). FR was supported by a Villum Young Investigator Award (project no. 000253000)...G.S. and E.C. were supported by a Marie Skłodowska-Curie Individual Fellowship “PALAEO-ENEO”, a project funded by the European Union EU Framework Programme for Research and Innovation Horizon 2020 (Grant Agreement number 751349). RM was supported by an EMBO Long-Term Fellowship (ALTF 133-2017)."
The Ancient Iceland paper had " S.S.E. and V.B.G. received grants from The Research Fund of University of Iceland for doctoral studies. M.S.-V. and A.J. received a grant from EUROTAST Marie Curie Framework Programme 7 Initial Training Network (290344). M.S.E. received a grant from the Icelandic Research Fund (163428-051). The work was partly funded (E.G. and G.L.C.) by a Career Development Award (13/CDA/2223) from Science Foundation Ireland and Swedish Research Council (Dnr 2016-02349), Swedish Research
Council for Health, Working Life and Welfare (Dnr 2013-0194), and Swedish Brain Foundation (FO2017-0076)." as well as a note "Authors affiliated with deCODE Genetics are employed by the company, which is owned by Amgen, Inc" under competing interests since 14 of the authors had affliation with deCODE - although I believe deCODE has since been spun-off and no longer owned by Amgen.
Anglo-Saxon paper containing NO3423 had "This study makes use of data generated by the Wellcome Trust Case Control Consortium. A full list of the investigators who contributed to the generation of the data is available from www.wtccc.org.uk. Funding for the project was provided by the Wellcome Trust under award 076113. We wish to acknowledge the DJEI/DES/SFI/HEA Irish Centre for High-End Computing (ICHEC) for the provision of computational facilities and support. This study has been financed by the BEAN project of the Marie Curie ITN (grant number 289966). M.D.T. was funded by ERC Investigator grant 295729-CodeX."
Recent Ancient Rome paper: "This project was partially supported by National Science Foundation Graduate Research Fellowships (M.L.A. and D.J.C.); Stanford Interdisciplinary Graduate Fellowship and grants from the Stanford Archaeology Center and Stanford Anthropology Dept (H.M.M.); Howard Hughes Medical Institute (Z.G. and J.K.P.); and an MIUR grant (Project D15D18000410001) (G.M.)."
Hungarian Conqueror paper: "This work was supported by grants from the National Research, Development and Innovation Office (K-124350 to TT) and The House of Árpád Programme (2018–2023) Scientific Subproject: V.1. Anthropological-Genetic portrayal of Hungarians in the Arpadian Age to TT."
Birger Magnusson paper: "We thank Agnar Helgason at deCODE Genetics in Iceland for letting us use his unpublished program PhyloNet version 5. AG was supported by the Royal Swedish Academy of Science."
Sigtuna: "The project was supported by Riksbankens Jubileumsfond (RJ_M13_0904:1) and Swedish Research Council (VR_2013-04959). Sequencing was conducted at the Uppsala University SNP&SEQ Technology Platform. Computations were performed at UPPMAX resources (Uppsala Multidisciplinary Centre for Advanced Computational Science) under projects b2013203, b2013240, b2015307, and b2016056."

Although there are no papers yet (presumably because this is dated from September this year), the homepage of Stephan Schiffels at MPI has this announcement on the award of a grant that you might find interesting... and also gives an indication of the kind of money involved http://www.stephanschiffels.de/posts/2019-09-23-erc-funded.html

Thanks for that: very informative. I see they kick off on that new project with a nod to diversity, and a focus on Celtic Central Europe should end up ticking a few of those boxes as well as throwing up some interesting results for us. I guess the problem for the Germanic Migration Period in the west - at least inside the tribes themselves - is that the most "diversity" on offer is a little R1a among the I1 and U106. ;)

deadly77
11-13-2019, 04:15 PM
Thanks for that: very informative. I see they kick off on that new project with a nod to diversity, and a focus on Celtic Central Europe should end up ticking a few of those boxes as well as throwing up some interesting results for us. I guess the problem for the Germanic Migration Period in the west - at least inside the tribes themselves - is that the most "diversity" on offer is a little R1a among the I1 and U106. ;)

Indeed - I think that that project will definitely tick a few boxes. It also jogged my memory about this one from October about a Wellcome Trust grant awarded to Pontus Skoglund at the Francis Crick Institute in London - this should tick a few more boxes: https://www.crick.ac.uk/news/2019-10-25_uncovering-5000-years-of-genetic-evolution-from-the-stone-age-to-the-21st-century

spruithean
11-16-2019, 10:07 PM
Indeed - I think that that project will definitely tick a few boxes. It also jogged my memory about this one from October about a Wellcome Trust grant awarded to Pontus Skoglund at the Francis Crick Institute in London - this should tick a few more boxes: https://www.crick.ac.uk/news/2019-10-25_uncovering-5000-years-of-genetic-evolution-from-the-stone-age-to-the-21st-century

Should be interesting!

Hopefully we see that paper with the father and son Viking duo from Repton. It's been a long time since we first heard about it.

JonikW
11-16-2019, 11:16 PM
Should be interesting!

Hopefully we see that paper with the father and son Viking duo from Repton. It's been a long time since we first heard about it.

Thanks for the reminder. Knut and Co from Winchester should be coming our way too. Definitely a few I1 candidates there.

mwauthy
11-17-2019, 02:58 PM
Indeed - I think that that project will definitely tick a few boxes. It also jogged my memory about this one from October about a Wellcome Trust grant awarded to Pontus Skoglund at the Francis Crick Institute in London - this should tick a few more boxes: https://www.crick.ac.uk/news/2019-10-25_uncovering-5000-years-of-genetic-evolution-from-the-stone-age-to-the-21st-century

This study will hopefully shed some light on which I1 subclades were Migration Period vs Viking Age. Maybe some Iron Age I1 will pop up in the British Isles too which would be a fascinating find.

spruithean
11-17-2019, 05:49 PM
This study will hopefully shed some light on which I1 subclades were Migration Period vs Viking Age. Maybe some Iron Age I1 will pop up in the British Isles too which would be a fascinating find.

Yeah, here's hoping we get that sort of detail. That question is an old one and it would be nice to get a rather definitive answer, though I honestly wouldn't be surprised if that never gets answered!

deadly77
11-17-2019, 10:09 PM
This study will hopefully shed some light on which I1 subclades were Migration Period vs Viking Age. Maybe some Iron Age I1 will pop up in the British Isles too which would be a fascinating find.

My hunch is that it's unlikely that there will be such clear separation between the two - I think it's more likely that we find the same subclades in both and there will be considerable overlap so we won't get anything definitive. But we'll see - we can assess better if that's the case with more data - which will come out of this.

RP48
11-18-2019, 12:24 AM
For someone new to this discussion it would help to have a brief summary at some point with links to important data. It’s very interesting but I can not digest 60 pages. Not a demand by any means!

JonikW
11-18-2019, 12:29 AM
For someone new to this discussion it would help to have a brief summary at some point with links to important data. It’s very interesting but I can not digest 60 pages. Not a demand by any means!

The best summary of aDNA data for I1 is deadly's Ancient DNA Samples Map. Just follow the link in his signature. The thread here is also worth digesting when you have time.

RP48
11-18-2019, 01:39 AM
The best summary of aDNA data for I1 is deadly's Ancient DNA Samples Map. Just follow the link in his signature. The thread here is also worth digesting when you have time.

I never noticed the link! Thank you!

spruithean
11-18-2019, 01:38 PM
I definitely agree that deadly77's ancient I1 map is a good place to start. With various links to the papers that feature the ancient samples. It's also a lot easier to digest the info in his map than the 60 page thread!

Pribislav
11-18-2019, 02:31 PM
I should have all the samples sorted by subclade in this ancient I1-M253 spreadsheet (https://drive.google.com/file/d/1VhXRd1RtHGXdeyvhUT3WdkrNcr4o2Eun/view?usp=sharing). If anyone notice mistakes in SNP assignments, or samples missing from the spreadsheet, feel free to post it here.

deadly77
11-18-2019, 05:22 PM
I should have all the samples sorted by subclade in this ancient I1-M253 spreadsheet (https://drive.google.com/file/d/1VhXRd1RtHGXdeyvhUT3WdkrNcr4o2Eun/view?usp=sharing). If anyone notice mistakes in SNP assignments, or samples missing from the spreadsheet, feel free to post it here.

Nice work Pribislav - I have a few on my map that aren't on your spreadsheet, but they are low data ones. Birger Magnusson and his son Erik entombed at Varnhem Abbey - it's an earlier paper and the researchers only tested one SNP (M253) relevant to I1. But that's the same level of testing to BAB5, which is on the spreadsheet. On that note, I had listed BAB5 and the RISE samples from the Allentoft 2015 paper as pre-I1/I* - there's no ancestral I1-level SNPs as for SF11, BAL051, Car1 but I think if more were tested on BAB5 it would fall into that category given the date. The paucity of data in the RISE samples means it's difficult to say either way, so I've decided to be more conservative in their classification.

The samples urm035 and urm045 from the Sigtuna paper weren't assigned a haplogroup in the manuscript. On going through the BAM files, the samples are low coverage with lots of no calls, but I'm satisfied that they cover enough derived reads for the I1 level SNPs. For subclades, urm035, picked up DF29 1G, Z2892 / CTS9848 1G as well as an ancestral call for Z2893 1G; urm045 had Z2893 1A, Z2892 / CTS9848 1G, Z61 1T. They're one-read SNPs, but given the low coverage, I think that might be as far as it goes for these two.

The other ones are AE 1154 in Altenerding-Klettham and there are seven I1 samples from a skeleton collective from 4th - 5th centuries in the village of Görzig - although all of these are from a small number of STRs - no SNPs tested, so it's up to you if you include them.

I hadn't included the ME_7 or KO_55 samples as I'm yet to find a reliable source for the data. Do you have anything?

Regarding US14, the "colonist" found at Shohola Creek, Indian Cabin Ridge, Pennsylvania, I noticed that there were a couple of mentions of Z73 in some tables in that paper, but I haven't been able to verify that in the BAM file. I found US14 was no call for Z73 and the phyloequivalent SNPs at I-Z73: Z73, FGC8675, CTS743, L1301, CTS12940, FGC8671, Z2896, Y2926, Z2899, Z2901, FGC8668, FGC8669, S2137, V1812, V3142 and also upstream levels with no calls for CTS9352, CTS9477, Z2895, CTS7362, Z2903, FGC8667, Z60, Z61, CTS8647, Z62, Z59, Z58. Only downstream SNP I found was a one read for DF29+, but I'm satisfied that he's I1 with derived reads for 29 of the 312 SNPs on the I1 level. But I couldn't find anything that verified US14 as I-Z73. Could you check the BAM file and see if I missed anything?

JonikW
11-24-2019, 07:32 PM
I see deadly77 has finally disappeared from my list of 100 YFull SNP matches today. Good to see more S12289 testers, who have brought this about, but sad to see him go. Sadly only a couple of the new testers have the flags that I always enjoy for what they can potentially add to the picture of ancient movements.

deadly77
11-24-2019, 10:31 PM
I see deadly77 has finally disappeared from my list of 100 YFull SNP matches today. Good to see more S12289 testers, who have brought this about, but sad to see him go. Sadly only a couple of the new testers have the flags that I always enjoy for what they can potentially add to the picture of ancient movements.

Aha, but you're still on my list of SNP matches at YFull, JonikW. I guess that's because I have less close matches.

You could always send your matches without the flags a message by clicking on the envelope icon next to their YFull ID and ask them if they would consider adding a flag.

Interesting things going on at the base of I-L338. YFull appear to have grouped two of the L338+/S12289- subclades together with a new branch point at I-A12974. It seem a bit of an odd choice. In the groups view, 3 of the kits below I-Y12329 are listed positive (all though not all with read quality 100) with one n/a, while the two kits at I-Y33691 have ambiguous reads for the SNP A12974. In my own results, the SNP A12974 is ambiguous (18A, 27T). ChrY position (Hg38):10125784 would put it in the centromere as YSEQ defines it (and so wouldn't be available in their catalogue for Sanger sequencing). Five of my SNPs on the "Hg and SNPs" tab are listed at the I-A12974* level are listed but four of them are one star. "Age estimation" tab also has some of the SNPs listed more than once but weighted between I-L338 and I-YSC261 level or between I-A12974 and my kit number. Perhaps YFull aren't yet sure of some of the placements and things at this level will change in the future.

deadly77
11-27-2019, 12:25 PM
There's two main methods of ancient DNA analysis - "shotgun" sequencing which is similar in principle to a WGS or the "SNP Capture" enrichment assay approach, most commonly the 1240K SNP capture assay used by the Reich group and others. There's advantages and disadvantages to both approaches - we discussed a bit earlier in this thread around post #379 and there's a good discussion of merits and drawbacks of each in Kivisild's 2017 review in Human Genetics here https://link.springer.com/article/10.1007/s00439-017-1773-z which is worth a read.

Bringing it up again as Wing Genealogist very kindly extracted the Y-SNPs that are included in the design of the assay - see post here https://anthrogenica.com/showthread.php?18691-1240K-Y-SNPs&p=612520&viewfull=1#post612520 and spreadsheet here https://docs.google.com/spreadsheets/d/1wCWqyy8-jWU5-ZtNjKXXU1k-rTh8TZNO4tl6W2mE-pQ/edit?usp=sharing

I volunteered to identify I1 SNPs to the spreadsheet, since I have them in hg19 position, and I was also curious how extensive the 1240k SNP capture assay was at covering the I1 SNPs.

Of the 312 phyloequivalent SNPs at the I1 branch (before subclades), the 1240k SNP capture covers 149 of those (48%) - that's a lot more than I thought having looked at several ancient I1 samples where 1240k SNP capture was used. DNA damage/fragmentation was likely a bigger factor than SNP capture assay.

At I-DF29 level, 3 SNPs (DF29/S438, Z2891/V1614, Z2891/V1614) are covered, while other three are not, so that's 50%.

Of the three main I-DF29 downstream branches, I-Z58 and I-Z63 are covered by their single SNP (no phyloequivalent SNPs on those branches) while for I-Z2336, Z2336/CTS6364 is covered while phyloequivalents Y2592 and Y2593 are not.

I'm not going to go through all 2123 subclades and 7555 SNPs that are on the YFull tree, but I can take a look if anyone's especially interested in anything in particular. Or you can take a look on Wing Genealogist's spreadsheet if you know hg19 position for the SNP of interest. I would guess that more lately discovered SNPs and subclades are less likely to be in the 1240k SNP capture assay.

General takeaway is that there's more than enough I1 SNPs in the 1240k SNP capture assay to identify ancient remains as at least I1. Lack of calls in several samples that we know about are probably more due to damage to the sample in the centuries or millenia post-mortem, how it's been stored (temperature, acidic soil, etc.) than the assay. 1240k SNP capture may be less good at covering downstream branches.

mwauthy
11-27-2019, 07:05 PM
There's two main methods of ancient DNA analysis - "shotgun" sequencing which is similar in principle to a WGS or the "SNP Capture" enrichment assay approach, most commonly the 1240K SNP capture assay used by the Reich group and others. There's advantages and disadvantages to both approaches - we discussed a bit earlier in this thread around post #379 and there's a good discussion of merits and drawbacks of each in Kivisild's 2017 review in Human Genetics here https://link.springer.com/article/10.1007/s00439-017-1773-z which is worth a read.

Bringing it up again as Wing Genealogist very kindly extracted the Y-SNPs that are included in the design of the assay - see post here https://anthrogenica.com/showthread.php?18691-1240K-Y-SNPs&p=612520&viewfull=1#post612520 and spreadsheet here https://docs.google.com/spreadsheets/d/1wCWqyy8-jWU5-ZtNjKXXU1k-rTh8TZNO4tl6W2mE-pQ/edit?usp=sharing

I volunteered to identify I1 SNPs to the spreadsheet, since I have them in hg19 position, and I was also curious how extensive the 1240k SNP capture assay was at covering the I1 SNPs.

Of the 312 phyloequivalent SNPs at the I1 branch (before subclades), the 1240k SNP capture covers 149 of those (48%) - that's a lot more than I thought having looked at several ancient I1 samples where 1240k SNP capture was used. DNA damage/fragmentation was likely a bigger factor than SNP capture assay.

At I-DF29 level, 3 SNPs (DF29/S438, Z2891/V1614, Z2891/V1614) are covered, while other three are not, so that's 50%.

Of the three main I-DF29 downstream branches, I-Z58 and I-Z63 are covered by their single SNP (no phyloequivalent SNPs on those branches) while for I-Z2336, Z2336/CTS6364 is covered while phyloequivalents Y2592 and Y2593 are not.

I'm not going to go through all 2123 subclades and 7555 SNPs that are on the YFull tree, but I can take a look if anyone's especially interested in anything in particular. Or you can take a look on Wing Genealogist's spreadsheet if you know hg19 position for the SNP of interest. I would guess that more lately discovered SNPs and subclades are less likely to be in the 1240k SNP capture assay.

General takeaway is that there's more than enough I1 SNPs in the 1240k SNP capture assay to identify ancient remains as at least I1. Lack of calls in several samples that we know about are probably more due to damage to the sample in the centuries or millenia post-mortem, how it's been stored (temperature, acidic soil, etc.) than the assay. 1240k SNP capture may be less good at covering downstream branches.


Thanks for the info! Going forward the two SNPs I care most about identifying in ancient I1 are:

I-Z382 (Nordic Bronze Age)
Hg 19: 3680849 : G to C

I-FGC24357 (Nordic Iron Age)
Hg 19: 17709753: G to A

deadly77
11-27-2019, 07:17 PM
Thanks for the info! Going forward the two SNPs I care most about identifying in ancient I1 are:

I-Z382 (Nordic Bronze Age)
Hg 19: 3680849 : G to C

I-FGC24357 (Nordic Iron Age)
Hg 19: 17709753: G to A

Z382 is covered in the 1240k SNP capture assay. Phyloequivalent SNPs Y2171/FGC24330 and Z2037 at the I-Z382 level are not covered. FGC24357 is not covered.

Not that this guarantees that Z382 would definitely be read in a 1240k SNP capture assay for an ancient sample. But there's a better chance of having a result here.

mwauthy
11-27-2019, 07:39 PM
Z382 is covered in the 1240k SNP capture assay. Phyloequivalent SNPs Y2171/FGC24330 and Z2037 at the I-Z382 level are not covered. FGC24357 is not covered.

Not that this guarantees that Z382 would definitely be read in a 1240k SNP capture assay for an ancient sample. But there's a better chance of having a result here.


Thanks! There were two ancient I1 samples in the Viking Paper that tested positive for I-Z2040 which is the parent clade of I-Z382 . When the data is eventually released for those samples hopefully we will get confirmation for I-Z382 which is missing from the Isogg Haplotree.

deadly77
11-28-2019, 12:11 AM
Thanks! There were two ancient I1 samples in the Viking Paper that tested positive for I-Z2040 which is the parent clade of I-Z382 . When the data is eventually released for those samples hopefully we will get confirmation for I-Z382 which is missing from the Isogg Haplotree.

Ah - this won't apply to the VK samples from the Viking preprint as the researchers from that paper used shotgun sequencing rather than the 1240k SNP capture assay.

Huh, didn't realize that Z382 wasn't on the ISOGG tree. I'm not sure what the procedure for getting SNPs on the ISOGG tree involves. There should be enough evidence from several samples to have Z382 added to ISOGG tree. Ybrowse lists 30 derived reads by Sanger sequencing and there must be enough Big Y that are derived for this SNP. That is, unless there is some other reason why ISOGG did not accept this SNP. Perhaps contact the ISOGG administrator and ask them.

But yes, we'll have a better idea when the BAM files become available. Even if Z382 is no call, there may be reads for phyloequivalent or downstream SNPs that would provide information by proxy.

deadly77
12-23-2019, 06:07 PM
I've been working with Hunter Provyn to get some of the ancient I1 samples into his Phylogeographer tool. The tool uses the YFull tree as it's main data source, but you can see the supplemental ancient samples here https://phylogeographer.com/ancient-samples-map/ with a filter for haplogroup (rough filter for now).

So far, updated the locations for the five I1samples on the YFull tree, then added additional samples for SSJ-A2, SSG-A3, DAV-A9 (Iceland); 84005, urm035, urm045 (Sigtuna); NO3423 (Anglo-Saxon); AED249, STR486 (Bavaria); CL63 (Collegno); R110, R1286 (Rome).

For the pre-I1 samples BAL051, SF11, Car1, RISE175, RISE179, RISE210, BAB5 we're trying a slightly different approach - we've added these samples as haplogroup I and also included the positive and negative I1 SNPs into the dataset and then adjust the algorithm to account for that so that such samples don't pull the origin point of I1 as much as they were before. The tool doesn't yet support the logic for splitting clades by positives and negative SNPs, but going to give this a try and see how it works going forward.

Not added to Phylogeographer.com: SzO/540 and K2/26 from Hungarian conqueror paper, STR241 from Bavaria or US14 from Pennsylvania as they are all pretty low coverage. And US14 would likely throw the geographical skew a bit as well. Likewise Birger Magnusson and his son Erik entombed at Varnhem Abbey where they only tested M253. Also didn't include AE 1154, E864/I or the samples from the skeleton collective from 4th - 5th centuries in the village of Görzig as those were STR data only with no SNPs.

Also not included yet: the VK samples from the Population genomics of the Viking World preprint. Since we don't have the BAM files for these samples yet, the actual subclade may change after review and I'd rather not add all of these samples twice (since there are a lot of them).

Bollox79
12-24-2019, 07:42 PM
I've been working with Hunter Provyn to get some of the ancient I1 samples into his Phylogeographer tool. The tool uses the YFull tree as it's main data source, but you can see the supplemental ancient samples here https://phylogeographer.com/ancient-samples-map/ with a filter for haplogroup (rough filter for now).

So far, updated the locations for the five I1samples on the YFull tree, then added additional samples for SSJ-A2, SSG-A3, DAV-A9 (Iceland); 84005, urm035, urm045 (Sigtuna); NO3423 (Anglo-Saxon); AED249, STR486 (Bavaria); CL63 (Collegno); R110, R1286 (Rome).

For the pre-I1 samples BAL051, SF11, Car1, RISE175, RISE179, RISE210, BAB5 we're trying a slightly different approach - we've added these samples as haplogroup I and also included the positive and negative I1 SNPs into the dataset and then adjust the algorithm to account for that so that such samples don't pull the origin point of I1 as much as they were before. The tool doesn't yet support the logic for splitting clades by positives and negative SNPs, but going to give this a try and see how it works going forward.

Not added to Phylogeographer.com: SzO/540 and K2/26 from Hungarian conqueror paper, STR241 from Bavaria or US14 from Pennsylvania as they are all pretty low coverage. And US14 would likely throw the geographical skew a bit as well. Likewise Birger Magnusson and his son Erik entombed at Varnhem Abbey where they only tested M253. Also didn't include AE 1154, E864/I or the samples from the skeleton collective from 4th - 5th centuries in the village of Görzig as those were STR data only with no SNPs.

Also not included yet: the VK samples from the Population genomics of the Viking World preprint. Since we don't have the BAM files for these samples yet, the actual subclade may change after review and I'd rather not add all of these samples twice (since there are a lot of them).

Yes Dr. Iain McDonald of my DF98 group is also working with Hunter etc! Interesting to see what shows up so far for my subgroup so far under DF98 i.e. FGC14823 - there are a few more SNPs under that that are not on YFull... but for FGC14823 it gets us into the Nordic Bronze Age via the SNP migration path... naturally I am interested in anything on SSG-A3 (which I figured out must be grave 4 at that site as grave 3 is in fact a female with female burial goods via the archaeological paper I found on that site and grave 4 the male with male burial goods i.e. A3 since he has a Y-chromo!).

Under FGC14823 is the little group with 6drif-3 from York... and others at Big Tree (looks to be Northern European at the moment, but really need more samples - the German match with my surname Weaver is 95% conf int from 500 to 1400 years ago I think via Dr. Iain - that surname clusters around the Rhineland, but their MDKA has a middle name much more common in Northern Germany - in the words of Dr. Iain himself: "By themselves, those three and six mutations equate to a relationship of about 300 to 1340 years ago. But when combined with your STR differences, it places it at around 450 to 1220 years ago (with 95% confidence) or around 560 to 1020 years ago (with 68% confidence). So it looks like you probably share a family origin at some point during the late Middle Ages."): https://www.ytree.net/DisplayTree.php?blockID=1329

Concerning the Viking paper raw data - any idea when that might come out? I am curious to see the sub groups of both the two DF96 guys (one from Denmark and one from mass grave in England if I remember correctly) and the DF98 guy from Skara - since I have a couple Swedes in my little group maybe he might be in that!

Cheers,
Charlie Cathal Dubh

oz
12-28-2019, 06:20 AM
Are there any kurgan burial mounds remains from Scandinavia tested for Adna yet? I heard there's a lot of them from the BA period. Why hasn't anyone done that yet? It might be more relevant than the Vikings study, which is great. But we still don't know much about how I1 became the most common lineage in Scandinavia.

deadly77
12-28-2019, 01:17 PM
Yes Dr. Iain McDonald of my DF98 group is also working with Hunter etc! Interesting to see what shows up so far for my subgroup so far under DF98 i.e. FGC14823 - there are a few more SNPs under that that are not on YFull... but for FGC14823 it gets us into the Nordic Bronze Age via the SNP migration path... naturally I am interested in anything on SSG-A3 (which I figured out must be grave 4 at that site as grave 3 is in fact a female with female burial goods via the archaeological paper I found on that site and grave 4 the male with male burial goods i.e. A3 since he has a Y-chromo!).

Under FGC14823 is the little group with 6drif-3 from York... and others at Big Tree (looks to be Northern European at the moment, but really need more samples - the German match with my surname Weaver is 95% conf int from 500 to 1400 years ago I think via Dr. Iain - that surname clusters around the Rhineland, but their MDKA has a middle name much more common in Northern Germany - in the words of Dr. Iain himself: "By themselves, those three and six mutations equate to a relationship of about 300 to 1340 years ago. But when combined with your STR differences, it places it at around 450 to 1220 years ago (with 95% confidence) or around 560 to 1020 years ago (with 68% confidence). So it looks like you probably share a family origin at some point during the late Middle Ages."): https://www.ytree.net/DisplayTree.php?blockID=1329

Concerning the Viking paper raw data - any idea when that might come out? I am curious to see the sub groups of both the two DF96 guys (one from Denmark and one from mass grave in England if I remember correctly) and the DF98 guy from Skara - since I have a couple Swedes in my little group maybe he might be in that!

Cheers,
Charlie Cathal Dubh

Ah, that's good to hear. I've seen Hunter and Iain mention each other. Although I1 and R1b have a rather different route into Europe until a certain point, I do think that they have a shared history (especially R-U106) and seem to be found together a lot, even if they aren't connected through Y-phylogeny.

Regarding SSG-A3, I'm sticking with that sample name rather than the archaeological grave 4 - I think you're correct that there was a mislabelling, but all of the genetic data, including BAM files is tied to SSG-A3, so I'm keeping consistent with that.

I don't see any of the 6DRIF samples from York on the Phylogeographer map. It doesn't appear at YFull, so you may need to add it as a supplemental sample. Hunter has made the process a lot easier, but you may need to contact him and register for an account to submit and edit samples. I haven't looked into the BAM file for 6DRIF-3 but the I1 Anglo-Saxon sample from the same paper looks like it was just below what YFull accepts. Mean coverage of NO3423 was 1.05x, while 6DRIF-3 was 1.67x. I had asked YFull about NO3423 after looking myself and Vladimir said the quality of sample was really low, although he was kind enough to send me a report of the positive and negative SNPs that they read. Don't know if anyone asked YFull about 6DRIF3 (or any of the other Roman samples from that paper). 6DRIF-3 has the highest mean coverage of all the samples from that paper, so most likely to get on if you ask them.

Regrading the Viking preprint - no idea on an actual date. One of the authors has said they will release BAM files when officially published as a paper, rather than current form as a preprint. You can read some comments by one of the authors (Ashot Margaryan) when asked about this on biorvix here https://www.biorxiv.org/content/10.1101/703405v1. They mention a "resubmission" which indicates that reviewers may have sent the original manuscript back to the authors for rewriting, etc. This is a normal part of the peer review process. It's a big paper (especially when you consider the supplementary files) so it's not unexpected. But publication is probably not imminent.

JonikW
12-28-2019, 02:16 PM
Are there any kurgan burial mounds remains from Scandinavia tested for Adna yet? I heard there's a lot of them from the BA period. Why hasn't anyone done that yet? It might be more relevant than the Vikings study, which is great. But we still don't know much about how I1 became the most common lineage in Scandinavia.

This isotopes study (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0219850) featured some. Discussion on this site back in the summer suggested we might get aDNA results as a follow-up.

deadly77
02-02-2020, 09:23 AM
The SZ45 ancient sample (6th Century Lombard cemetery, Szólád, modern day Hungary) has moved onto new branch I-FGC21810 on the YFull tree below I-FGC21819 with YF01673. 36150

deadly77
02-04-2020, 11:59 AM
I added another ancient I1 to the map (link in my signature). This one comes from the big Olade et al paper on the Iberian Peninsula from the Reich group published last year in Science https://science.sciencemag.org/content/363/6432/1230

Sample I12033 was reported in the paper as Y-DNA haplogroup I. The paper dates this sample to 500-600 CE based on archaeological context and linked the samples in this location to Visigoths. They analyzed 9 individuals from the 58 burials at this site. Of those 9, four were females and the males were BT (low coverage), E1b1b1a1b1a, R1b1a1a2a1, J2a and I - quite a diverse bunch.

I've been digging through the "I" samples in this paper to see if any of them are positive for any of the I1 SNPs (see pre-I1 sample Car1/I10899 from the same paper, also listed as I). After looking through the BAM file, I12033 is positive for three of the I1 level SNPs Z2679 1G, Y1868 1A, Z2705 1T.

I12033 doesn't have great coverage - all of the other >300 SNPs except for the three listed in the paragraph above on the I1 level were not read. I looked for downstream SNPs and all the ones at the I-DF29 level were not read, ditto for quite a few of the early branches of I-Z2336 and I-Z58. I12033 is negative for Z63, so that probably rules that out (with the caveat that it's a one read at this position). I'm pretty sure that this sample is fully I1 given the dating, but in consistency with similar low coverage samples such as the RISE samples from the Allentoft 2015 paper and the Hungarian conqueror paper, I've labelled on the map as brown with "?" that I use for probable I1.

The supporting information (page 32-33) of the paper has a bit more about the site: "The Pla de l’Horta villa is located in Sarrià de Ter, around four kilometers from the city of Girona, and therefore it should be considered a fundus that belonged to the suburbium of Gerunda. It was constructed in the middle of the 1st century BCE. The residential part underwent substantial alterations in the Flavian and Severan periods, on both occasions with notable use of mosaic floors. In the industrial district of this settlement
we can identify the area of the wine presses, especially from the 4th century CE, which is the last phase for which there is evidence on the villa. However, due to the villa’s considerable size, we can deduce that it probably had a large industrial area that has not yet been excavated to the north of the structures that have been discovered.
Immediately to the north of this area, a necropolis associated with the villa has been found, with a funerary building and a series of tombs. This site clearly belongs to the villa, which would subsequently be extended in the Visigoth period. The samples that have been analyzed correspond to this Visigothic phase. Several types of burials can be seen, from a simple grave to a cist. The number of burials identified (58), as well as the results of the analysis, demonstrate the persistence and importance of the habitat, even though it has not yet been identified archaeologically. The grave goods and the typology of the tombs point to a Visigothic origin of the individuals."

spruithean
02-05-2020, 12:19 AM
I added another ancient I1 to the map (link in my signature). This one comes from the big Olade et al paper on the Iberian Peninsula from the Reich group published last year in Science https://science.sciencemag.org/content/363/6432/1230

Sample I12033 was reported in the paper as Y-DNA haplogroup I. The paper dates this sample to 500-600 CE based on archaeological context and linked the samples in this location to Visigoths. They analyzed 9 individuals from the 58 burials at this site. Of those 9, four were females and the males were BT (low coverage), E1b1b1a1b1a, R1b1a1a2a1, J2a and I - quite a diverse bunch.

I've been digging through the "I" samples in this paper to see if any of them are positive for any of the I1 SNPs (see pre-I1 sample Car1/I10899 from the same paper, also listed as I). After looking through the BAM file, I12033 is positive for three of the I1 level SNPs Z2679 1G, Y1868 1A, Z2705 1T.

I12033 doesn't have great coverage - all of the other >300 SNPs except for the three listed in the paragraph above on the I1 level were not read. I looked for downstream SNPs and all the ones at the I-DF29 level were not read, ditto for quite a few of the early branches of I-Z2336 and I-Z58. I12033 is negative for Z63, so that probably rules that out (with the caveat that it's a one read at this position). I'm pretty sure that this sample is fully I1 given the dating, but in consistency with similar low coverage samples such as the RISE samples from the Allentoft 2015 paper and the Hungarian conqueror paper, I've labelled on the map as brown with "?" that I use for probable I1.

The supporting information (page 32-33) of the paper has a bit more about the site: "The Pla de l’Horta villa is located in Sarrià de Ter, around four kilometers from the city of Girona, and therefore it should be considered a fundus that belonged to the suburbium of Gerunda. It was constructed in the middle of the 1st century BCE. The residential part underwent substantial alterations in the Flavian and Severan periods, on both occasions with notable use of mosaic floors. In the industrial district of this settlement
we can identify the area of the wine presses, especially from the 4th century CE, which is the last phase for which there is evidence on the villa. However, due to the villa’s considerable size, we can deduce that it probably had a large industrial area that has not yet been excavated to the north of the structures that have been discovered.
Immediately to the north of this area, a necropolis associated with the villa has been found, with a funerary building and a series of tombs. This site clearly belongs to the villa, which would subsequently be extended in the Visigoth period. The samples that have been analyzed correspond to this Visigothic phase. Several types of burials can be seen, from a simple grave to a cist. The number of burials identified (58), as well as the results of the analysis, demonstrate the persistence and importance of the habitat, even though it has not yet been identified archaeologically. The grave goods and the typology of the tombs point to a Visigothic origin of the individuals."

Interesting. I'm hoping that more I1 Visigoths are found, or even Suebi. I would also like to see some aDNA from the Vandals.

deadly77
02-05-2020, 11:05 AM
Interesting. I'm hoping that more I1 Visigoths are found, or even Suebi. I would also like to see some aDNA from the Vandals.

The visigoths from Pla de l’Horta villa in this paper appear to be a rather diverse bunch with regard to Y-DNA haplogroups. Although they only sampled 9 out of the 58 graves. Not sure if that's because the remains were in a bad state, DNA was too damaged or if they felt that they had enough for a representative sample. There's also the likelihood that the BT (low coverage) sample I12029 may be positive for SNPs which would allow a more refined haplogroup assignment (such as urm035 and urm045 in the Sigtuna paper).

I've been through a few of the I samples from this paper, but the majority of them so far don't have any positive results for SNPs on the I1 level. The vast majority of SNPs in these I samples are no calls with a few that are negative. Most of these samples would probably turn out to be I2, but at least we got Car1 as a pre-I1 and I12033 as a probable I1. Some of the samples designated BT, CT, CF, F, etc. may be too, but for these I'm not sure the juice is worth the squeeze.

Pribislav
02-05-2020, 12:51 PM
It's worth mentioning that three yet unpublished Roman samples from Serbia are I1.

The one from Viminacium, dated 0-300 AD, is just I1. The other two, from Mediana (labeled Serbia_Gepid) and Timacum Minus, dated 300-500 AD, are I1a2a1a and I1a2a1a2, respectively. Unfortunately, I don't know which version of ISOGG tree has been used, so they could be Z58>CTS8647>Z140 and Z58>CTS8647>Z140>S2169 (ISOGG 2016) or Z58>CTS8647 and Z58>CTS8647>A11141/S26062 (ISOGG 2017). The former is more probable IMO.

spruithean
02-05-2020, 12:57 PM
Potential for a Gepid to be S2169?! If that gets confirmed that’ll be a rather interesting surprise.

Do you have a link to this paper?

deadly77
02-05-2020, 02:18 PM
It's worth mentioning that three yet unpublished Roman samples from Serbia are I1.

The one from Viminacium, dated 0-300 AD, is just I1. The other two, from Mediana (labeled Serbia_Gepid) and Timacum Minus, dated 300-500 AD, are I1a2a1a and I1a2a1a2, respectively. Unfortunately, I don't know which version of ISOGG tree has been used, so they could be Z58>CTS8647>Z140 and Z58>CTS8647>Z140>S2169 (ISOGG 2016) or Z58>CTS8647 and Z58>CTS8647>A11141/S26062 (ISOGG 2017). The former is more probable IMO.

Interesting. What's the source of this unpublished data? Is it a preprint or a poster?

Pribislav
02-05-2020, 04:32 PM
Potential for a Gepid to be S2169?! If that gets confirmed that’ll be a rather interesting surprise.

Do you have a link to this paper?

The paper isn't out yet, hopefully we'll see it this year.


Interesting. What's the source of this unpublished data? Is it a preprint or a poster?

The source is a supplementary spreadsheet from the upcoming paper by Harvard. It's not even in the preprint yet, but the sequencing and subsequent analyses are done.

deadly77
02-05-2020, 05:09 PM
Is the Viminacium sample the one listed as VIM_2 in the 2018 PNAS paper on elongated skulls? https://www.pnas.org/content/115/13/3494/tab-figures-data

EDIT: Ah, must be a different one. Looked up VIM_2 in the Reich anno file and that one is listed as R1b1.

Pribislav
02-05-2020, 07:30 PM
Is the Viminacium sample the one listed as VIM_2 in the 2018 PNAS paper on elongated skulls? https://www.pnas.org/content/115/13/3494/tab-figures-data

EDIT: Ah, must be a different one. Looked up VIM_2 in the Reich anno file and that one is listed as R1b1.

Yes, it's a different one, although he's also featured in the spreadsheet. Of 28 newly reported male samples from Viminacium (excluding VIM_2), only 1 is I1. But that shouldn't come as a surprise since they only sequenced skeletons from earlier Roman necropoli. A shame really, since there are hundreds of excavated Gepid skeletons from Viminacium.

spruithean
02-06-2020, 01:16 PM
Yes, it's a different one, although he's also featured in the spreadsheet. Of 28 newly reported male samples from Viminacium (excluding VIM_2), only 1 is I1. But that shouldn't come as a surprise since they only sequenced skeletons from earlier Roman necropoli. A shame really, since there are hundreds of excavated Gepid skeletons from Viminacium.

Is there any source (like a poster or something) for these 3 I1 individuals from Serbia? I’d be interested to see. If not I suppose we wait for the publication.

Sort of disappointing that there is a treasure trove of aDNA with those Gepid skeletons and not much testing has been done. Probably one of the more interesting Migration Period Germanic groups for me, at least.

deadly77
04-04-2020, 08:53 AM
I had been working through the remaining haplogroup I samples in Olade et al's 2019 paper in Science on the Iberian Peninsula to see if there was any more nuggets of I1 to dig out after I12033 and I10899/Car1 had a small number of derived SNPs at the I1 level (discussed above in the thread or go to map in my signature for these).

Of the remaining samples designated I or IJK from the paper that I was able to run, none of them have derived/positive results for SNPs on the I1 level. All are negative or no call for those SNPs. Most likely these are I2. For anyone who is interested in the calls:

I0453, negative for 2 SNPs: Z2844 (1C), Z2775 (1G).
I0455, negative for 4 SNPs: Z2727 (1C), Y1860 (1A), CTS4295 (1A), Y1876 (1T).
I1282, negative for 9 SNPs: Z2726 (1A), Z2756 (1A), FGC2422 (1C), L347 (1C), L848 (3C), FGC2445 (2C), Z6116 (1A), Z2695 (1G), Z2683 (1C).
I1284, negative for 7 SNPs: Z2843 (1T), Z2779 (1T), Z2826 (1T), Z2887 (1C), Z2790 (1G), Z2708 (1C), CTS5891 (1C).
I1970, negative for 22 SNPs: FGC7747 (1T), Z2751 (2T), Z2850 (1A), CTS3268 (2T), FGC2422 (1C), CTS3506/Z2765 (1A), FGC33327 (1T), Z2857 (1T), CTS11783 (1T), L347 (1C), CTS10613 (1G), Z2839 (1A), CTS7751 (1C), Z2860 (1C), CTS6022 (1G), CTS4532 (2G), L1439 (2C 1G - derived is A, so 2 reads for ancestral, 1 read for a mutation to a different allele), Z2859 (1G), FGC2445 (1C), Z2806/CTS6765 (2T), Z2683 (1C), CTS8708 (1T).
I3575, negative for 32 SNPs: L840 (1C), Z2880 (1G), FGC7747 (1T), Z2802 (1G), Z2727 (1C), Z2729 (2C), Z2751 (2T), L80 (1A), Z2883 (1C), Z2823 (1G), Z2747 (1A), Z2885 (1C), CTS3268 (1T), Z2698/FGC2435 (2T), Z2848 (1C), CTS1755/Z2750 (1C), FGC3444 (1G), CTS6992 (1C), S63 (2A), L81 (1A), Z2805 (1T), CTS7949 (1C), Z2878 (1A), FGC2427 (1C), CTS4295 (1C), CTS4532 (1G), L764 (2C), L1439 (1G - neither ancestral or derived), FGC2441 (1A), Z2870 (1T), Z2859 (1G), CTS9368 (1T), Z2683 (1C).
I6543, negative for 8 SNPs: L840 (1C), Z2781 (1G), Y1868 (1G), L123 (1C), L848 (1C), FGC2433 (1G), Z2878 (1A), CTS4532 (1G).
I7645, negative for 7 SNPs: Z2729 (2C), CTS3506/Z2765 (1A), CTS1266 (1A), L848 (1C), Z2887 (1C), Z2861 (1G), Z2854 (1T).
I8153, negative for 6 SNPs: L118 (1A), FGC3444 (1G), L764 (1C), Z2859 (1G), Z6116 (1A), Z2683 (1C).
I10286, negative for 4 SNPs: CTS3268 (1T), CTS11036/Z2863 (1C), Z2848 (1C), Z2832 (1G).

No call for other SNPs on the I1 level. Couldn't get the BAM files for samples I10278 or I11604.

So, more book-keeping than positive results from an I1 perspective.

ph2ter
04-11-2020, 11:05 AM
https://i.imgur.com/oHNCATJ.png

ph2ter
04-11-2020, 06:21 PM
With terminal SNP:

https://i.imgur.com/T7V45eP.png

deadly77
04-12-2020, 09:29 AM
With terminal SNP:

https://i.imgur.com/T7V45eP.png

Just be aware that there are some errors in the Indo-European.eu compiled dataset - for the I1 samples:

I-A8200 is not the terminal SNP for Icelandic Pre-Christian non-migrant SSJ-A2. The correct terminal is I-Z74. The mistake arises from conversion of the longhand version of the subclade (eg. I1a1b3) reported in a paper into the shorthand name (I-SNP), as the ISOGG tree changes the definition between different years. The current 2019-2020 ISOGG tree lists I1a1b3 with SNPs A8178, A8182, A8200, A8204, while the 2016 version of the ISOGG tree had I1a1b3 with SNP Z74, which are different branches on the YFull tree. The authors of the Ebenesersdóttir et al. Science paper on the ancient Iceland genomes specify that they used the 2016 ISOGG tree. So I-A8182 (I1->I-DF29->I-Y2592->I-Z2336->I-Z2337->I-A8182 (phyloequivalent to A8200) versus I-Z74 (I1->I-DF29->I-Y2592->I-Z2336->I-Z2337->I-S6346->I-L22->I-Y3549->I-CTS6868->I-Z74) - quite different branches that separated between 4600 and 3500 years ago.
Same issue with Saami Contemporary sample Saami001 which isn't I-A8191 - again from converting I1a1b3a1 using a later version of the ISOGG tree than the 2016 version which should lead to I-L258. Although this is a modern sample used in the paper to compare to genome data from 11 ancient individuals, so not really an ancient sample itself.
CL63 is listed as I-Z79. Z79 is a SNP in I2 haplogroup, and this is a mistake by the authors of the Amorim et al 2018 paper, copied onto the indo-european.eu list without checking the data. Anyway, CL63 is negative for Z79 when reviewing the BAM file and actually the correct assignment from analyzing the BAM file is I-Y2245. Also seems to be duplicated as in the indo.european.eu list as CL36 (with the same wrong information) so it appears twice.

Location for NO3423 should be closer to Norton Bishopmill in Teeside at 54.59552, -1.30755, while the location in the indo-european.eu list uses Driffield Terrace, York which is the location for 7 other Roman samples in the same Martiniano et al 2016 paper - see Supplementary Figure 1 https://www.nature.com/articles/ncomms10326. Some of the locations for the Icelandic samples using the coordinates listed in the indo-european.eu list look like they are a bit off - compare to the map in Fig 1 of the Ebenesersdóttir et al 2018 Science paper https://science.sciencemag.org/content/360/6392/1028

For some of the samples, can get to a more downstream subclade by analysis of the BAM file than what are listed - SSG-A3 I-CTS6868, DAV-A9 I-DF29, NO3423 I-DF29, SZ45 I-FGC21810, etc. see the link in my signature for a map with SNP calls and BAM files for all are publically available for checking.

The indo-eurpoean.eu list also includes several samples as I1 that I'd categorize as pre-I1 in between the branch away from I2 but prior to the TMRCA of modern I1 as they include derived and ancestral calls for the SNPs that define I1 - these are SF11, Car1/I10899, BAL051. I guess it's a matter of characterization but the indo-european.eu list includes M253 as a positive SNP result for SF11, which is incorrect (SF11 is a no call for M253). There's also a few other samples which I'd say there's not enough data to call as I1 or pre-I1 due to a lot of no calls which are listed as I1. But I guess that's a matter of debate in how I1 is defined.

oz
04-12-2020, 12:54 PM
Yea I thought the terminal SNP map has some mislabeling. And those really old I1 aren't actually I1, more like pre-I1 that might've ended up as dead end lineages.

mwauthy
04-12-2020, 03:25 PM
Yea I thought the terminal SNP map has some mislabeling. And those really old I1 aren't actually I1, more like pre-I1 that might've ended up as dead end lineages.


Yeah any “I1” found outside of Sweden prior to the Bronze Age is suspicious to me and is most likely some extinct “pre-I1” lineage. Even the gentleman in the Ftdna I1 Project that is negative for I-DF29 and I-Z17954 is from Sweden.

oz
04-12-2020, 04:04 PM
Yeah any “I1” found outside of Sweden prior to the Bronze Age is suspicious to me and is most likely some extinct “pre-I1” lineage. Even the gentleman in the Ftdna I1 Project that is negative for I-DF29 and I-Z17954 is from Sweden.

Yeah Sweden could very well be the "urheimat" of I1 but we don't know that for sure yet. There's some basal lineages in places outside of Sweden too on Ftdna and Yfull. Plus on Ftdna the number of people who tested downstream of I1 is the highest in Sweden, Finland and Norway. Look at their total number of I1 and then look at their subclade numbers, and compare that with Germany and England for example, almost half of them aren't downstream of I1.

deadly77
04-13-2020, 10:48 AM
Carlos Quiles said on the YFull Facebook page that he would correct the I1 samples in his indo-european.eu list where there were mistakes, so if you replot the map with the new data once he's done that, it should resolve the inaccuracies. Although that only applies to the I1 samples - I haven't checked other haplogroups but I would expect that there would be some inaccuracies due to similar issues, so it would be worth having those checked as well against the primary data.

deadly77
04-23-2020, 09:08 AM
There's been quite a bit of interest in the "Ancient genomes from present-day France unveil 7,000 years of its demographic history" thread over in the Ancient DNA section that Generalissimo posted yesterday here https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=661138&viewfull=1#post661138with links to BAM files https://www.ebi.ac.uk/ena/data/view/PRJEB36529

The paper itself or a preprint doesn't appear to have been published yet, but R.Rocca shared the abstract in the thread as well as a comment from Arza on the Eurogenes blog that there was a single I1 in the Iron Age. R. Rocca noted that the samples are low coverage in #35, but also that BES1248 was the I1. Generalissimo also shared the Y-calls for the samples from this paper https://drive.google.com/open?id=1Tq46HJRJT-OQPEkppRKuizR9TfYUzDEU

Looking at BES1248, it does look like this is the I1 sample, with 13 derived calls among the I1 level SNPs. All are one read, but they are consistently corroborating each other, so that's a good sign. There's only one derived downstream SNP listed S10350 - again one read.

I've had a look in the BAM file for BES1248 and as R.Rocca said in the Ancient DNA thread, it's pretty low coverage with a lot of no calls. There is a derived read for S10350, but on checking the SNPs at upstream levels, BES1248 has ancestral allele for the SNPs S22349 (1C) at I-FGC24354 branch and Y5394 (1G), FGC11745 / Y5396 (1T) at I-Y5384 branch. These results give me less confidence for the derived call for S10350 - perhaps this is a false positive, although with all of these one read, then that's not necessarily confident either. BES1248 is no call for all other upstream SNPs between I1 and S10350, including Z58 and all the SNPs at the I-DF29 level. For what it's worth, the list of Y-calls also lists derived reads for FGC5488, ZS8666 in haplogroup J as well as Z35554, Y19887 in haplogroup Q. Possibly recurrent SNPs, but more likely one read false positives.

Ancestral values from the Y-calls list on the following I1 subclade SNPs:

CTS6364
Y11141
Y10701
Y7283
Y18320
SK1235
Y18314
A10905
A10912
Y10636
Y19808
Y22501
Y22496
Y30874
Y29648
Y11266
A8583
Y17613
A5338
P109
FGC21814
FGC21599
Y6374
Y15573
Y15572
Y15574
FGC16691
FGC16686
FGC21792
FGC21733
Y20203
Y18385
S10200
Y4378
FGC14194
FGC14184
FGC22029
FGC22035
FGC22044
FGC22033
FGC21919
FGC21933
Y31123
Y30036
FGC22053
FGC21974
FGC21975
FGC22128
A7627
FGC22115
Y22478
Y22483
Y22477
A5571
Y13482
Z133.1
Z44217
Y17381
Y13390
Y24707
Y30548
Y31093
Y20593
Y20596
CTS2208
FGC12551
FGC15300
FGC15306
Y29620
Y19672
Y15039
BY3429
Y16704
BY3464
Y22916
Y32167
Y32162
Y22403
S6443
Y23149
Y23050
Y24486
Y24631
Y24632
FGC54064
Y24790
Y11554
Y11561
Y10643
Y3602
Y3601
Y15033
Y3605
Y20849
FGC41727
FGC41737
FGC10450
A8194
A8204
Y17265
Y17253
Z4727
L338
BY463
A12726
S2189
Y3153
CTS940
CTS2987
CTS7397
Y3650
A10216
S2170
A1352
A1520
Y6368
Y7140
Y7485
Y6896
A11346
A14539
A14531
Y10890
Y7278
A1609
FGC23829
FGC23831
FGC23814
FGC23809
L1302
Y13052
BY211
Y23575
BY497
Y23339
Y23338
Y23141
Y22410
Y15025
Y15024
Y17247
Y21061
CTS5668
Z44261
Y21977
Y15930
Y13048
Y25790
Y21713
Y32136
FGC22166
A482
Z44267
BY1741
Y7233
Y15516
S22349
Y5388
Y5394
S4672
CTS10863
A6588
Y20400
Y20391
CTS4560
CTS802
A12080
A12079
Y16456
BY1400
A6469
A8694
A6476
Y11875
Y23125
Y23121
FGC9534
S12223
Y14348
Y14536
Y14540
FGC14856
FGC14482
Y21531
Y24753
Y16437
Y16439
Y17340
BY13534
A8238
Y7059
Y7079
Y7072
Y7077
Y21372
Y21370
Y14657
CTS8178
S11545
Y15571
A5746
BY13674
A5742
Y16964
Y24620
Y18799
FGC31809
FGC31811
FGC24020
Y11249
Y16410
Y16414
CTS5510
CTS3429
Y18119
Z44271
A9628
FGC45110
A8788
FGC37297
Y19288

Quite probably consistent with I1 though - been through 200 of the I1 level SNPs and BES1248 and he's derived for 16 of those with one ambiguous and no ancestral. All of these are one read so far. However, the low coverage of this sample may make it difficult to confidently assign a subclade below I1.

deadly77
04-23-2020, 10:17 AM
BES1248 derived for 19 of the SNPs at the I1 level branch (all one read), ambiguous for 1 SNP (1N read), no call for the rest. Calls:

L842/YSC0000264/Z2789 1T
Z2714/FGC2425 1A
Z2718 1T
Z2727 1T
Z2729 1T
L841/YSC0000257/Z2751 1A
Y1962 Insertion of C
Z2798/CTS6109 1T
Y1958 Insertion of T
Z2866/CTS11126 1G
CTS11783/Z2876 1C
CTS6992 1T
Z2705/CTS883 1T
Z2678/CTS40 1T
Z2790/CTS5643 1N
Z2878/L843 / YSC0000273 1G
L75 1A
Z2732 1G
FGC2452/Y1852 1A
CTS12191/Z2888 1T

mwauthy
04-23-2020, 02:34 PM
There's been quite a bit of interest in the "Ancient genomes from present-day France unveil 7,000 years of its demographic history" thread over in the Ancient DNA section that Generalissimo posted yesterday here https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=661138&viewfull=1#post661138with links to BAM files https://www.ebi.ac.uk/ena/data/view/PRJEB36529

The paper itself or a preprint doesn't appear to have been published yet, but R.Rocca shared the abstract in the thread as well as a comment from Arza on the Eurogenes blog that there was a single I1 in the Iron Age. R. Rocca noted that the samples are low coverage in #35, but also that BES1248 was the I1. Generalissimo also shared the Y-calls for the samples from this paper https://drive.google.com/open?id=1Tq46HJRJT-OQPEkppRKuizR9TfYUzDEU

Looking at BES1248, it does look like this is the I1 sample, with 13 derived calls among the I1 level SNPs. All are one read, but they are consistently corroborating each other, so that's a good sign. There's only one derived downstream SNP listed S10350 - again one read.

I've had a look in the BAM file for BES1248 and as R.Rocca said in the Ancient DNA thread, it's pretty low coverage with a lot of no calls. There is a derived read for S10350, but on checking the SNPs at upstream levels, BES1248 has ancestral allele for the SNPs S22349 (1C) at I-FGC24354 branch and Y5394 (1G), FGC11745 / Y5396 (1T) at I-Y5384 branch. These results give me less confidence for the derived call for S10350 - perhaps this is a false positive, although with all of these one read, then that's not necessarily confident either. BES1248 is no call for all other upstream SNPs between I1 and S10350, including Z58 and all the SNPs at the I-DF29 level. For what it's worth, the list of Y-calls also lists derived reads for FGC5488, ZS8666 in haplogroup J as well as Z35554, Y19887 in haplogroup Q. Possibly recurrent SNPs, but more likely one read false positives.

Ancestral values from the Y-calls list on the following I1 subclade SNPs:

CTS6364
Y11141
Y10701
Y7283
Y18320
SK1235
Y18314
A10905
A10912
Y10636
Y19808
Y22501
Y22496
Y30874
Y29648
Y11266
A8583
Y17613
A5338
P109
FGC21814
FGC21599
Y6374
Y15573
Y15572
Y15574
FGC16691
FGC16686
FGC21792
FGC21733
Y20203
Y18385
S10200
Y4378
FGC14194
FGC14184
FGC22029
FGC22035
FGC22044
FGC22033
FGC21919
FGC21933
Y31123
Y30036
FGC22053
FGC21974
FGC21975
FGC22128
A7627
FGC22115
Y22478
Y22483
Y22477
A5571
Y13482
Z133.1
Z44217
Y17381
Y13390
Y24707
Y30548
Y31093
Y20593
Y20596
CTS2208
FGC12551
FGC15300
FGC15306
Y29620
Y19672
Y15039
BY3429
Y16704
BY3464
Y22916
Y32167
Y32162
Y22403
S6443
Y23149
Y23050
Y24486
Y24631
Y24632
FGC54064
Y24790
Y11554
Y11561
Y10643
Y3602
Y3601
Y15033
Y3605
Y20849
FGC41727
FGC41737
FGC10450
A8194
A8204
Y17265
Y17253
Z4727
L338
BY463
A12726
S2189
Y3153
CTS940
CTS2987
CTS7397
Y3650
A10216
S2170
A1352
A1520
Y6368
Y7140
Y7485
Y6896
A11346
A14539
A14531
Y10890
Y7278
A1609
FGC23829
FGC23831
FGC23814
FGC23809
L1302
Y13052
BY211
Y23575
BY497
Y23339
Y23338
Y23141
Y22410
Y15025
Y15024
Y17247
Y21061
CTS5668
Z44261
Y21977
Y15930
Y13048
Y25790
Y21713
Y32136
FGC22166
A482
Z44267
BY1741
Y7233
Y15516
S22349
Y5388
Y5394
S4672
CTS10863
A6588
Y20400
Y20391
CTS4560
CTS802
A12080
A12079
Y16456
BY1400
A6469
A8694
A6476
Y11875
Y23125
Y23121
FGC9534
S12223
Y14348
Y14536
Y14540
FGC14856
FGC14482
Y21531
Y24753
Y16437
Y16439
Y17340
BY13534
A8238
Y7059
Y7079
Y7072
Y7077
Y21372
Y21370
Y14657
CTS8178
S11545
Y15571
A5746
BY13674
A5742
Y16964
Y24620
Y18799
FGC31809
FGC31811
FGC24020
Y11249
Y16410
Y16414
CTS5510
CTS3429
Y18119
Z44271
A9628
FGC45110
A8788
FGC37297
Y19288

Quite probably consistent with I1 though - been through 200 of the I1 level SNPs and BES1248 and he's derived for 16 of those with one ambiguous and no ancestral. All of these are one read so far. However, the low coverage of this sample may make it difficult to confidently assign a subclade below I1.


Wow very interesting! I’m positive for I-S10350 myself. Do we have a more specific date from the Iron Age? Do we have a specific location in France? Although only 1 call for S10350 and a contradictory call at S22349 is far from conclusive.

My theory is that I-S10350 originated near northern coastal Germany around 2500-1500 years ago with a primary migration of his descendants to the British Isles during the Migration Period. With a few descendants being absorbed into the Netherlands and Belgium on their journey to the British Isles.

JonikW
04-23-2020, 02:44 PM
Wow very interesting! I’m positive for I-S10350 myself. Do we have a more specific date from the Iron Age? Do we have a specific location in France? Although only 1 call for S10350 and a contradictory call at S22349 is far from conclusive.

My theory is that I-S10350 originated near northern coastal Germany around 2500-1500 years ago with a primary migration of his descendants to the British Isles during the Migration Period. With a few descendants being absorbed into the Netherlands and Belgium on their journey to the British Isles.

Dates and locations haven't been released yet. It'll be interesting if this sample turns out to be Belgic, given Caesar's musings on the tribe. Some members of that grouping may indeed have crossed the Rhine from the area you mention, if we can believe his account. About time we had a new sample, and nice work from deadly77 as always.

spruithean
04-23-2020, 02:47 PM
Dates and locations haven't been released yet. It'll be interesting if this sample turns out to be Belgic, given Caesar's musings on the tribe. Some members of that grouping may indeed have crossed the Rhine from the area you mention, if we can believe his account. About time we had a new sample, and nice work from deadly77 as always.

I'm hoping the pre-print is released soon, should be interesting to look at! Perhaps this I1 sample will give some credence to Caesar's views on some of the Belgic tribes. I'm not sure how much this changes overall for I1 as a whole though, considering the timing and the various rather Germanic-looking branches.

mwauthy
04-23-2020, 03:06 PM
Hi Deadly! S10350 is not downstream of Y5384. So the only contradictory read is S22349 at the FGC24354 branch.

deadly77
04-23-2020, 03:42 PM
Hi Deadly! S10350 is not downstream of Y5384. So the only contradictory read is S22349 at the FGC24354 branch.

You are correct - looks like I misread a line when scrolling up the YFull tree - should really have followed the breadcrumbs at the top. I covered the SNPs at I-FGC24356, I-FGC24357, I-FGC24354 - all no calls apart from S10350 and S22349 - then I took my wrong turn at I-Y5384. I'll check I-S16414 and I-S26361 and see what any of those turn out as. I got I-Z382 to I-Z58 - all no calls.

Thanks for pointing that out.

mwauthy
04-23-2020, 04:16 PM
You are correct - looks like I misread a line when scrolling up the YFull tree - should really have followed the breadcrumbs at the top. I covered the SNPs at I-FGC24356, I-FGC24357, I-FGC24354 - all no calls apart from S10350 and S22349 - then I took my wrong turn at I-Y5384. I'll check I-S16414 and I-S26361 and see what any of those turn out as. I got I-Z382 to I-Z58 - all no calls.

Thanks for pointing that out.


My pleasure! Thanks for checking all those SNPs.

This is probably not relevant regarding the reliability of the two aforementioned SNPs but here is my data regarding their read accuracy. Both SNPs only have a 3 star rating with YFull: S10350 is combBED while S22349 is not. S10350 appears to have slightly more read accuracy.

Big Y-500 Data:
S22349 76 A 3 C
S10350 89 A 3 G

Big Y-700 Data:
S22349 13 A 1 C
S10350 43 A

deadly77
04-23-2020, 05:06 PM
The SNPs at the I-S16414 and I-S26361 branches were all no call.

I checked the SNPs that are downstream of I-S10350 - any of those would potentially corroborate S10350+ if positive, although they wouldn't contradict S10350+ if negative. Most were no call, and three were negative:

A15022 1C
Y20429/YFS030526 1T
BY11021 1C

mwauthy
04-23-2020, 05:28 PM
The SNPs at the I-S16414 and I-S26361 branches were all no call.

I checked the SNPs that are downstream of I-S10350 - any of those would potentially corroborate S10350+ if positive, although they wouldn't contradict S10350+ if negative. Most were no call, and three were negative:

A15022 1C
Y20429/YFS030526 1T
BY11021 1C


The Ftdna Haplotree is more comprehensive than the YFull Haplotree so here is a list of all phyloequivalent SNPs downstream of Z59 up to S10350 and their HG38 base pair locations if you want to check these additional SNPs for reads. Thanks!

Z2041 (15459136 T to C)
FGC24331 (3219515 C to T)

Z2040 (13530261 G to T)
Z2039 (11682999 G to T)

Z382 (3812808 G to C)
FGC24330 (6602156 A to G)
Z2037 (5317864 G to A)

S26361 (26480398 C to A)
FGC24335 (3826443 T to A)
FGC35282 (4266363 C to T)
S18588 (14524412 G to C)

S16414 (12678908 A to G)
FGC24348 (9855427 T to A)

S22349 (17379708 C to A)
FGC24354 (14915899 T to G)
FGC24334 (3383721 T to C)
FGC24362 (20062896 C to T)
FGC24370 (20976741 G to T)

FGC24357 (15597873 G to A)
BY34649 (20108550 C to G)

FGC24347 (9545224 A to C)
FGC24336 (3888790 C to G)

FGC24356 (15516796 A to G)

S10350 (7692669 G to A)

deadly77
04-23-2020, 05:55 PM
The Ftdna Haplotree is more comprehensive than the YFull Haplotree so here is a list of all phyloequivalent SNPs downstream of Z59 up to S10350 and their HG38 base pair locations if you want to check these additional SNPs for reads. Thanks!

Z2041 (15459136 T to C)
FGC24331 (3219515 C to T)

Z2040 (13530261 G to T)
Z2039 (11682999 G to T)

Z382 (3812808 G to C)
FGC24330 (6602156 A to G)
Z2037 (5317864 G to A)

S26361 (26480398 C to A)
FGC24335 (3826443 T to A)
FGC35282 (4266363 C to T)
S18588 (14524412 G to C)

S16414 (12678908 A to G)
FGC24348 (9855427 T to A)

S22349 (17379708 C to A)
FGC24354 (14915899 T to G)
FGC24334 (3383721 T to C)
FGC24362 (20062896 C to T)
FGC24370 (20976741 G to T)

FGC24357 (15597873 G to A)
BY34649 (20108550 C to G)

FGC24347 (9545224 A to C)
FGC24336 (3888790 C to G)

FGC24356 (15516796 A to G)

S10350 (7692669 G to A)

Thanks for the list. I went through and checked the ones that are on FTDNA but not YFull - all of these are no calls in the BAM file. While FTDNA, YSEQ, FGC and YFull are operating primarily with the hg38 reference, most academic studies are using hg19 reference - so far the Ancient Iceland paper is the only one I have seen where the ancient samples were mapped to hg38. Thankfully the YFull database includes hg19 and hg38 coordinates for all the SNPs in their database, and your list is easier to read than the FTDNA public haplotree.

So I guess we're left with the two contradicting calls for S10350+ and S22349- due to the low coverage in the BAM. Perhaps once we get the paper it will include the dating of BES1248's remains and maybe that can be compared to the subclade age estimate for I-S10350 to see if that matches up or if BES1248 turns out to be too early. But at least we can be fairly sure he's on the I1/pre-I1 branch.

mwauthy
04-23-2020, 06:00 PM
Thanks for the list. I went through and checked the ones that are on FTDNA but not YFull - all of these are no calls in the BAM file. While FTDNA, YSEQ, FGC and YFull are operating primarily with the hg38 reference, most academic studies are using hg19 reference - so far the Ancient Iceland paper is the only one I have seen where the ancient samples were mapped to hg38. Thankfully the YFull database includes hg19 and hg38 coordinates for all the SNPs in their database, and your list is easier to read than the FTDNA public haplotree.

So I guess we're left with the two contradicting calls for S10350+ and S22349- due to the low coverage in the BAM. Perhaps once we get the paper it will include the dating of BES1248's remains and maybe that can be compared to the subclade age estimate for I-S10350 to see if that matches up or if BES1248 turns out to be too early. But at least we can be fairly sure he's on the I1/pre-I1 branch.


Could “BES” be shorthand for the city where the sample was found? Maybe Besançon?

JonikW
04-23-2020, 08:04 PM
Could “BES” be shorthand for the city where the sample was found? Maybe Besançon?


I wondered the same and that was the only possibility I could find too last night using the index in some Celtic books (there was one in Germany that I forget now). If this is the only "BES" sample it might suggest a small but significant site rather than one with multiple remains.

JonikW
04-23-2020, 09:37 PM
A bit more speculation: first to add by way of a caveat that I know nothing about archaeological finds in Besançon if that's what this turns out to be. But it's solely mentioned in my books in connection with Caesar, who aimed to fend off a local incursion by the Germanic Suebi there, who must have had a decent share of M253 in their ranks. From the Gallic Wars (Penguin edition): "During the few days that they spent near Besançon to lay in a stock of corn and other provisions, the soldiers began to question the Gauls and merchants there, who talked about the enormous stature, incredible courage, and splendid military training of the Germans. Some affirmed that on many occasions when they had met them in battle, the very expression on their faces and the fierce glance of their eyes were more than they could endure."
Not much to distract us on the I1 front so I'm enjoying thinking over the possibilities here, and the Suebi seem to have been a force to be reckoned with in that part of France in the first century BC. Of course there are many other Bes- place names in France, if that's even the naming convention used with this sample. I look forward to the preprint.:)

mwauthy
04-23-2020, 10:59 PM
A bit more speculation: first to add by way of a caveat that I know nothing about archaeological finds in Besançon if that's what this turns out to be. But it's solely mentioned in my books in connection with Caesar, who aimed to fend off a local incursion by the Germanic Suebi there, who must have had a decent share of M253 in their ranks. From the Gallic Wars (Penguin edition): "During the few days that they spent near Besançon to lay in a stock of corn and other provisions, the soldiers began to question the Gauls and merchants there, who talked about the enormous stature, incredible courage, and splendid military training of the Germans. Some affirmed that on many occasions when they had met them in battle, the very expression on their faces and the fierce glance of their eyes were more than they could endure."
Not much to distract us on the I1 front so I'm enjoying thinking over the possibilities here, and the Suebi seem to have been a force to be reckoned with in that part of France in the first century BC. Of course there are many other Bes- place names in France, if that's even the naming convention used with this sample. I look forward to the preprint.:)


Thanks for sharing that Jonik! Very interesting! I agree with you that at this point it’s a lot of speculation, but it’s fun and informative regardless :)

At a 95% confidence interval YFull says that I-S10350 could be as old as 2500 years before present so an Iron Age sample is definitely possible especially if it’s closer to Caesar’s time.

Personally, I have 31 Big Y-700 SNPs since Mr. I-S10350. If we average 73 years per Big Y-700 SNP we’re looking at 2263 years before present which might be awe fully close.

deadly77
04-24-2020, 11:10 AM
I've been trying to have a look around this site https://www.inrap.fr/projets/recherche so see if there was any archaeological context or location that could be linked to BES1248, since the Ancestra project conducted the ancient DNA studies. However, a combination of Google translate and decades old (and admittedly underused) GCSE level French hasn't yet paid any dividends. A lot of interesting stuff on there - just haven't found anything that I've been able to link to BES1248.

mwauthy
04-25-2020, 05:55 PM
I did a random google search and found this:

http://www.historycy.org/index.php?showtopic=184053&pid=1878520&st=3285&#entry1878520

Not sure if I’m reading this correctly but there are 3 locations associated with BES1248, but the only one from France is Upper Normandy. This would coincide nicely with the Belgae tribes that were known to also live across the English Channel in England if this sample is truly indeed positive for I-S10350?

JMcB
04-25-2020, 06:44 PM
That appears to be someone’s population analysis.

https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=662098&viewfull=1#post662098

mwauthy
04-25-2020, 06:54 PM
That appears to be someone’s population analysis.

https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=662098&viewfull=1#post662098

Thanks! Those population analysis would suggest a Northern France origin.

JonikW
04-25-2020, 07:53 PM
That appears to be someone’s population analysis.

https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=662098&viewfull=1#post662098

Thanks JMcB for putting a pointer here. Where you said "The three closest modern populations for each sample from the Iron and Bronze Ages, by my population averages:" were you going to add those?

JMcB
04-25-2020, 08:04 PM
Thanks! Those population analysis would suggest a Northern France origin.

Which wouldn’t be surprising in this circumstance. Nevertheless, it does explain why you were seeing three populations associated with BES1248. At the end of the day, we’ll have to wait for the paper.

JMcB
04-25-2020, 08:08 PM
Thanks JMcB for putting a pointer here. Where you said "The three closest modern populations for each sample from the Iron and Bronze Ages, by my population averages:" were you going to add those?

Hello JonikW, My mistake, I should have put those in quotation marks. Those were the original poster’s comments in Polish as rendered by Google’s translator. Not anything said by me.

JonikW
04-25-2020, 08:08 PM
Thanks JMcB for putting a pointer here. Where you said "The three closest modern populations for each sample from the Iron and Bronze Ages, by my population averages:" were you going to add those?

Thanks! My mistake then and thanks for posting. I'm not checking the other thread so would have missed it.

JonikW
05-15-2020, 06:51 PM
Thanks! Those population analysis would suggest a Northern France origin.

jstephan's excellent work here (http://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=666546#post666546) at #97 suggests to me that the BES sample may indeed be Belgic if they were a "Celtic" Gaulish population group with admixture from folk who also went on to contribute to the Anglo-Saxons. Interesting.

jstephan
05-15-2020, 07:01 PM
jstephan's excellent work here (http://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=666546#post666546) at #97 suggests to me that the BES sample may indeed be Belgic if they were a "Celtic" Gaulish population group with admixture from folk who also went on to contribute to the Anglo-Saxons. Interesting.

Excellent work is David and the people from Ancestra and all the ones who processed the samples! I just simply ran already processed samples against modern populations. But thanks JonikW.

JMcB
05-15-2020, 08:03 PM
jstephan's excellent work here (http://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=666546#post666546) at #97 suggests to me that the BES sample may indeed be Belgic if they were a "Celtic" Gaulish population group with admixture from folk who also went on to contribute to the Anglo-Saxons. Interesting.

See ph2ter’s mapping of the same, also:

https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=666635&viewfull=1#post666635

JonikW
05-15-2020, 09:01 PM
See ph2ter’s mapping of the same, also:

https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=666635&viewfull=1#post666635

Thanks JMcB. I think we can be pretty confident then that this sample is from a Belgic site (once again ph2ter's maps prove a wonderful resource for aDNA as well as modern samples). It's still disappointing that there's apparently only one sample from this site in the study. If it's Belgic and I-M253+, that's fascinating for us I1 people but regrettable because aDNA has the potential to fully test at the autosomal level Caesar's statement regarding the reported movement across the Rhine. So if this proves to be a standout elite burial, as seems likely to me, it will tell us less about the Germanic/Celtic genetic breakdown -- and the prevalence of I1 at that time -- than samples from a cross-section of society would. That's a shame but doesn't detract of course from this sample's welcome addition to the I1 aDNA picture.

JonikW
05-15-2020, 11:50 PM
Adding this separately in the interest of fairness to those who hit the thanks button before. I've been mulling this over a bit since. pht2er's map suggests a level of population continuity in the Belgic region that I would scarcely have thought possible this morning. I'd add though that given the later dispersement of some of the sample's potential source populations in the north (thinking among other things of Bede's belief -- which has some arguable archaeological backing -- regarding a drain to England from Angeln, and so conceivably more widely) we'd need more Iron Age data for a full understanding of his relationship to the neighbouring peoples of the time. Alongside his status and how long his various lines had been in the area where he was buried, that muddies the waters a bit further for I1 implications among others. Anyone know when we can read the paper and unlock more?

JMcB
05-16-2020, 02:42 AM
Adding this separately in the interest of fairness to those who hit the thanks button before. I've been mulling this over a bit since. pht2er's map suggests a level of population continuity in the Belgic region that I would scarcely have thought possible this morning. I'd add though that given the later dispersement of some of the sample's potential source populations in the north (thinking among other things of Bede's belief -- which has some arguable archaeological backing -- regarding a drain to England from Angeln, and so conceivably more widely) we'd need more Iron Age data for a full understanding of his relationship to the neighbouring peoples of the time. Alongside his status and how long his various lines had been in the area where he was buried, that muddies the waters a bit further for I1 implications among others. Anyone know when we can read the paper and unlock more?


At this point, you can request a copy here:

https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=666272&viewfull=1#post666272

… with a hat tip to Angle.

My results have been spotty when asking on previous occasions but you never know! Hopefully, it’s a sign the paper is coming out soon.

deadly77
05-24-2020, 12:19 AM
Rozenfeld has reported this preprint on Biorxiv on A systematic investigation of human DNA preservation in medieval skeletons https://www.biorxiv.org/content/10.1101/2020.05.20.106971v1 in this post on the Ancient DNA sub forum here: https://anthrogenica.com/showthread.php?97-Genetic-Genealogy-amp-Ancient-DNA-in-the-News-(TITLES-ABSTRACTS-ONLY)&p=669021&viewfull=1#post669021

Sample KRA004 from Krakauer Berg, near Peißen, Saxony-Anhalt, Germany is listed as I1a2a1a1d, although it seems when they sampled from other parts of the skeleton outside the petrous bone, there was a less precise assignment on that data (see Table 3). Table 4 lists him as a 15 year old male, 14C dates (AD, Cal 2-sigma) 1284-1392.

The preprint says they are using the ISOGG list of diagnostic SNPs (current as of 26 November 2019), so assuming the current 2019-20 version of the ISOGG tree, I1a2a1a1d corresponds to I-CTS7362.

Data availability says Sequence data is available through the European Nucleotide Archive under accession number PRJEB36983 (released upon publication). Nothing there yet i ENA and probably not until paper is published. After that perhaps we can verify I-CTS7362 and maybe dig a little deeper. However, it seems this is a 1240k SNP capture sample so further data may be limited.

mwauthy
05-26-2020, 03:16 PM
I received a response from the scientist in charge of the sample BES1248. It’s from a site very much in the south of France at Bessan, La Monediére from the second century B.C.

Unfortunately, she couldn’t provide any more information regarding Y chromosome SNP calls. Based on the quality of the sample and the approach they took this is all we have to work with at this point in time. A different approach taken in the future that targets the Y chromosome could possibly yield better coverage.

Based on the above information I’m leaning more heavily now on the sample not actually being positive for I-S10350. However, since BES1248 is genetically more similar to people from the north of France maybe he wasn’t actually born in the South of France in which case I-S10350 could still be a possibility?
If the Teutones and Ambrones could fight the Romans in 102 BC at the Battle of Aquae Sextiae all the way south in Aix-en-Provence, France maybe BES1248 is not so far displaced after all?

Lastly, she said the study pertaining to this sample will be released in the next few days on PNAS. I didn’t ask but I’m assuming that’s “Proceedings of the National Academy of Sciences?”

oz
05-26-2020, 04:35 PM
Second century BC still seems a little bit surprising and early for I1 in Southern France. Hopefully they will provide some useful information on the nature of this grave and the grave site.

mwauthy
05-26-2020, 04:49 PM
Second century BC still seems a little bit surprising and early for I1 in Southern France. Hopefully they will provide some useful information on the nature of this grave and the grave site.


It is interesting that there is an oppidum in Bessan. However, according to Wikipedia the Greeks had been there since 600 BC.

JMcB
05-26-2020, 04:57 PM
I received a response from the scientist in charge of the sample BES1248. It’s from a site very much in the south of France at Bessan, La Monediére from the second century B.C.

Unfortunately, she couldn’t provide any more information regarding Y chromosome SNP calls. Based on the quality of the sample and the approach they took this is all we have to work with at this point in time. A different approach taken in the future that targets the Y chromosome could possibly yield better coverage.

Based on the above information I’m leaning more heavily now on the sample not actually being positive for I-S10350. However, since BES1248 is genetically more similar to people from the north of France maybe he wasn’t actually born in the South of France in which case I-S10350 could still be a possibility? If the Teutones and Ambrones could fight the Romans in 102 BC at the Battle of Aquae Sextiae all the way south in Aix-en-Provence, France maybe BES1248 is not so far displaced after all?

Lastly, she said the study pertaining to this sample will be released in the next few days on PNAS. I didn’t ask but I’m assuming that’s “Proceedings of the National Academy of Sciences?”

I’m inclined to agree. I think his autosomal results are a better indicator of his ancestry, then where he was finally laid to rest. People have always traveled far and wide.

The paper is out but unfortunately you need a subscription.

deadly77
05-26-2020, 07:09 PM
The paper is out but unfortunately you need a subscription.

The Supporting Information is available and there are 55 pages to go through. Can download here under the Download Appendix (pdf) link on this page: https://www.pnas.org/content/early/2020/05/20/1918034117/tab-figures-data

Thanks to mwauthy's correspondence with one of the authors, we know that BES1248 is from south of France at Bessan, La Monediére. The supporting information has this about the archaeological context of that site:

At La Monédière (Bessan, Hérault), a burial complex used in the course of the second century BCE
yielded a small collection of burials.
The site of La Monédière is the place of a Gallic fortified settlement occupied between the early sixth
century and the end of the fifth century BCE. Covering an area of nearly 4 ha, this settlement
occupies a slight relief on the right bank of the Hérault river. Its foundation appears closely linked to
very early contacts made in this part of the Gulf of Lyon with the Mediterranean societies and the
establishement, at the mouth of the Herault, of the Agde littoral counter which is roughly 6 km away.
The trading activities, indicated by the abundance of products imported from the Greek or Etruscan
world, are generally at a level higher than that observed in neighboring establishments. The quantity of
amphora reveal the involvement of this site in trade networks uniting the coast and the interior, as
well as its role in the redistribution of the products transported from the Mediterranean within the
framework of Mediterranean trade, by land or waterways. Benefiting from a favorable geographical
position, La Monédière stands as an essential market place and a privileged meeting place between
natives and Greeks, to such an extent that the question of the in situ installation of a community
appears Hellenic. Its occupation is interrupted towards the end of the 5th century BCE at the moment
of the founding of the colony of Agde/Agathè by Marseilles. In the course of the second century BCE,
the site is revisited. At this time, a funeral complex yields a small collection of burials associated with
a very poorly known settlement, which could be an integral part of the chôra of the Agathe colony.

mwauthy
05-27-2020, 03:45 AM
The Supporting Information is available and there are 55 pages to go through. Can download here under the Download Appendix (pdf) link on this page: https://www.pnas.org/content/early/2020/05/20/1918034117/tab-figures-data

Thanks to mwauthy's correspondence with one of the authors, we know that BES1248 is from south of France at Bessan, La Monediére. The supporting information has this about the archaeological context of that site:

At La Monédière (Bessan, Hérault), a burial complex used in the course of the second century BCE
yielded a small collection of burials.
The site of La Monédière is the place of a Gallic fortified settlement occupied between the early sixth
century and the end of the fifth century BCE. Covering an area of nearly 4 ha, this settlement
occupies a slight relief on the right bank of the Hérault river. Its foundation appears closely linked to
very early contacts made in this part of the Gulf of Lyon with the Mediterranean societies and the
establishement, at the mouth of the Herault, of the Agde littoral counter which is roughly 6 km away.
The trading activities, indicated by the abundance of products imported from the Greek or Etruscan
world, are generally at a level higher than that observed in neighboring establishments. The quantity of
amphora reveal the involvement of this site in trade networks uniting the coast and the interior, as
well as its role in the redistribution of the products transported from the Mediterranean within the
framework of Mediterranean trade, by land or waterways. Benefiting from a favorable geographical
position, La Monédière stands as an essential market place and a privileged meeting place between
natives and Greeks, to such an extent that the question of the in situ installation of a community
appears Hellenic. Its occupation is interrupted towards the end of the 5th century BCE at the moment
of the founding of the colony of Agde/Agathè by Marseilles. In the course of the second century BCE,
the site is revisited. At this time, a funeral complex yields a small collection of burials associated with
a very poorly known settlement, which could be an integral part of the chôra of the Agathe colony.


On page 49 of the supplementary pdf there is a chart showing a Neolithic I1? I’m assuming that’s probably some intermediary pre-I1 extinct line?

deadly77
05-27-2020, 07:09 AM
On page 49 of the supplementary pdf there is a chart showing a Neolithic I1? I’m assuming that’s probably some intermediary pre-I1 extinct line?

Good catch - hadn't caught that in the earlier lists of haplogroups. Went back and looked at some of the summaries in the Ancient DNA section on AG and several of the summaries included Iron Age, Bronze Age, Bell beaker and didn't include the Neolithic samples.

Can't really assess if that Neolithic I1 is some intermediary pre-I1 extinct line just on Figure S 5.1. As we've seen from the various pre-I1 that we know about in published papers, there's considerable variance in how different authors call this (I1 vs. I) in summarized data. I'm happy to have a look at the BAM file if I know which one it is - the idea of hunting through 36 low coverage Neolithic samples blind, not so keen. In this regard, the mentioned Dataset S10, Dataset S11 may be useful in narrowing that down. I don't see those currently in the SI section - not sure if they will be added later or if they are only available to those who have purchased access to the journal.

Any chance you could ask the scientist in charge of the sample BES1248 that you corresponded with earlier if she can clarify which sample is the Neolithic I1?

oz
05-27-2020, 11:05 AM
Why don't we rename the pre I1 just I1 and M253 I1a and Df29 I1a1 to avoid the confusion?
Would that make sense?

JonikW
05-27-2020, 12:45 PM
Good catch - hadn't caught that in the earlier lists of haplogroups. Went back and looked at some of the summaries in the Ancient DNA section on AG and several of the summaries included Iron Age, Bronze Age, Bell beaker and didn't include the Neolithic samples.

Can't really assess if that Neolithic I1 is some intermediary pre-I1 extinct line just on Figure S 5.1. As we've seen from the various pre-I1 that we know about in published papers, there's considerable variance in how different authors call this (I1 vs. I) in summarized data. I'm happy to have a look at the BAM file if I know which one it is - the idea of hunting through 36 low coverage Neolithic samples blind, not so keen. In this regard, the mentioned Dataset S10, Dataset S11 may be useful in narrowing that down. I don't see those currently in the SI section - not sure if they will be added later or if they are only available to those who have purchased access to the journal.

Any chance you could ask the scientist in charge of the sample BES1248 that you corresponded with earlier if she can clarify which sample is the Neolithic I1?

So the two samples we have on the datasheet in addition to BES1248, using tables S1-1 and S5-1:

Sample ID Cx161: y haplogroup (capture) I1a2b4~. I-FGC3466. Mt haplogroup H1.
Middle Neolithic 2 (5340 +/ 30BP).
ZAC Agora, Cugnaux, Haute-Garonne.

Sample ID FAD9: y haplogroup (capture) I1a2a1a1a3a2b~. I-A11354. Mt haplogroup K1b1a1.
Early Bronze Age (3490 +/- 30BP).
Dolmen des Fades, Pépieux, Aude.

JonikW
05-27-2020, 01:15 PM
I see the ~5,300 ybp Neolithic sample's FGC3466 falls under S5619 (formed 4,600 ybp; TMRCA 3,800 ybp, YFull).

oz
05-27-2020, 01:28 PM
I see the ~5,300 ybp Neolithic sample's FGC3466 falls under S5619 (formed 4,600 ybp; TMRCA 3,800 ybp, YFull).

Is that under Z58?
So after all these years and hundreds if not thousands of ancient DNA samples across Europe we come to find out Z58 (and possibly other I1a's) might've originated in Neolithic France? That's truly amazing.
And I guess the tmrca estimates aren't reliable.

mwauthy
05-27-2020, 02:20 PM
So the two samples we have on the datasheet in addition to BES1248, using tables S1-1 and S5-1:

Sample ID Cx161: y haplogroup (capture) I1a2b4~. I-FGC3466. Mt haplogroup H1.
Middle Neolithic 2 (5340 +/ 30BP).
ZAC Agora, Cugnaux, Haute-Garonne.

Sample ID FAD9: y haplogroup (capture) I1a2a1a1a3a2b~. I-A11354. Mt haplogroup K1b1a1.
Early Bronze Age (3490 +/- 30BP).
Dolmen des Fades, Pépieux, Aude.


Do you have access to the BAM files for those 2 samples deadly77? I’m curious what your thoughts are regarding the matter.

deadly77
05-27-2020, 03:04 PM
Do you have access to the BAM files for those 2 samples deadly77? I’m curious what your thoughts are regarding the matter.

I had a look at PRJEB38152 in European Nucleotide Archive here https://www.ebi.ac.uk/ena/data/view/PRJEB38152 and I couldn't find either Cx161 or FAD9.

mwauthy
05-27-2020, 03:38 PM
Why don't we rename the pre I1 just I1 and M253 I1a and Df29 I1a1 to avoid the confusion?
Would that make sense?


Instead of “pre-I1” I would use I-I1.

JonikW
05-27-2020, 04:41 PM
I see the ~5,300 ybp Neolithic sample's FGC3466 falls under S5619 (formed 4,600 ybp; TMRCA 3,800 ybp, YFull).

If this Cugnaux guy really does turn out to be what they say, we'll all be pondering how he got so far south. He or his Y ancestor could have been anything from a lone traveller to an enslaved spoil of war passed over a long distance, or -- perhaps the most intriguing possibility -- part of a cultural group that had made its way south. This is interesting from a study called "Enclosing the Neolithic (http://www.academia.edu/37746745/Mid-Late_neolithic_enclosures_in_the_South_of_France)", edited by Alex Gibson, because it does point to potential links or influences between Cugnaux and cultures much nearer Scandinavia (where we might most expect to find Neolithic I1) in the forms of the LBK, Rössen (http://en.m.wikipedia.org/wiki/R%C3%B6ssen_culture) and Michelsberg cultures.

It says: "The Chassean enclosures of the south of France are [rare …] The most complete
and recently published results come from the site of Villeneuve-Tolosane/Cugnaux (Gandelin 2011) [...] These southern enclosures appeared later than their counterparts in northern France which were constructed from the end of the Early Neolithic (Villeneuve-Saint-Germain/Middle Neolithic I transition) and are based on LBK models present in Germany and Belgium from the end of the 6th millennium. BC. These were developed in the Cerny Culture and the Chambon Group in the Paris Basin and in the Rössen culture further to the east and their
morphology and sizes vary. It is during the Middle Neolithic II that enclosures become widespread among the northern
Chassean cultures, the Michelsberg culture and the Noyen group [...] Several hypotheses have been proposed to explain the appearance of these sites in southern France [...] The first concerns security and protection (defense of a settlement, conflict between groups, protection of livestock etc) whilst the second is more symbolic or ritualistic (cultural, funerary, display etc)."

I can also see a couple of studies involving isotopes and this site. The only one I can access, "Southern French Neolithic Populations: Isotopic Evidence for Regional Specificities in Environment and Diet", suggests some outlier burials, including in Cugnaux, of people who had moved around during their lifetimes. This range seems to be restricted to Garonne, Languedoc and Catalonia though and of course doesn't tell us where any of the Cugnaux ancestors would have originated.

It concludes: "The presence of outlier individuals whose isotopic data are unique might reveal population mobility, as suggested by other authors in relation to archaeological evidence (flint supply, Vaquer, personal communication)."

I look forward to further developments on this sample for sure.

Edit: added bold for emphasis

oz
05-27-2020, 04:55 PM
Who cares what someone decides to call these haplogroups, they're just some letters and numbers someone gave them, honestly I don't care what they call it. I just suggested a practical solution.

Back to what JonikW shared, if these I1a2+ turn out to be legit, what does that mean for the Scandinavian I1a? Are they Neolithic France Jr. now? Lol...

What does it mean for all the I1 all over Europe and elsewhere...do you question the Germanic expansion as the culprit?
Doesn't really seem feasible, because in that case wouldn't they have found I1a samples before at least nearby France somewhere which predate the Germanic migrations? France isn't an island to suggest that I1a was isolated there forever and expanded from there in the late Neolithic or something. If you look at Neolithic hgs that have been found so far and if we compare it with I2 the closest relative, it's been found everywhere in all time periods in big numbers. G2 as well and a bunch of others.

mwauthy
05-27-2020, 05:24 PM
Based on modern distributions I don’t think this sample would negate a Scandinavian origin for I-DF29 but I do think it would make us have to reassess our current understanding of I-DF29 mutation rates and when various dispersals out of Scandinavia occurred for various patrilineal lines. I-Z138/I-Z139 does have a very strong Western European distribution and would be a logical great candidate for an early exit out of Scandinavia.

JonikW
05-27-2020, 05:25 PM
There seems to be a fourth I1 sample, in Table S5-2, with the sample ID GOX287. Who the heck is he? Am I the only one who's confused by the way this study and dataset are presented?:\ Add: I can see some interesting SNPs, starting with S1954. Some look relatively recent, for example: S2298 formed 2200 ybp, TMRCA 1200 ybp.

GOX287's SNPs:
"I-L157.1/etc*(xCTS6364,S1954,CTS1148,Y7198,A10216,A1357,Y63 68,A196,A14544,FGC22406,A1616,A9117,FGC23813,S2137 ,S22055,Y22019,Y21567,S2332,FGC12754,Y29671,Y7927, S22349,Y30577,Y6086,CTS6400,A6573,S10967,FGC43922, Y7052,A12054,BY851,S6270,FGC19401,A6849,Y23129,FGC 9544,Y6229,FGC14843,FGC14485,Y6393,Y24747,Y17338,A 8235,BY13512,Y23358,Y19675,Y21370,Y14660,Y13962,Y8 331,S15818,Y15777,Y15882,FGC15551,Y11206,Y18800,FG C24027,Y16703,S2298,Z44274,Y19408,A9728,A9606,A830 2,A8789)"

oz
05-27-2020, 06:04 PM
There seems to be a fourth I1 sample, in Table S5-2, with the sample ID GOX287. Who the heck is he? Am I the only one who's confused by the way this study and dataset are presented?:\ Add: I can see some interesting SNPs, starting with S1954. Some look relatively recent, for example: S2298 formed 2200 ybp, TMRCA 1200 ybp.

GOX287's SNPs:
"I-L157.1/etc*(xCTS6364,S1954,CTS1148,Y7198,A10216,A1357,Y63 68,A196,A14544,FGC22406,A1616,A9117,FGC23813,S2137 ,S22055,Y22019,Y21567,S2332,FGC12754,Y29671,Y7927, S22349,Y30577,Y6086,CTS6400,A6573,S10967,FGC43922, Y7052,A12054,BY851,S6270,FGC19401,A6849,Y23129,FGC 9544,Y6229,FGC14843,FGC14485,Y6393,Y24747,Y17338,A 8235,BY13512,Y23358,Y19675,Y21370,Y14660,Y13962,Y8 331,S15818,Y15777,Y15882,FGC15551,Y11206,Y18800,FG C24027,Y16703,S2298,Z44274,Y19408,A9728,A9606,A830 2,A8789)"

Who is this guy supposed to be? Y6229 is under Y6228.

JonikW
05-27-2020, 06:10 PM
Who is this guy supposed to be? Y6229 is under Y6228.

I can't see any mention of him elsewhere in the material, but he's in a table with other samples from the study so looks like he is too. Please tell me if I'm wrong...

37764

Edit: added a fuller screenshot

JMcB
05-27-2020, 06:16 PM
There seems to be a fourth I1 sample, in Table S5-2, with the sample ID GOX287. Who the heck is he? Am I the only one who's confused by the way this study and dataset are presented?:\ Add: I can see some interesting SNPs, starting with S1954. Some look relatively recent, for example: S2298 formed 2200 ybp, TMRCA 1200 ybp.

GOX287's SNPs:
"I-L157.1/etc*(xCTS6364,S1954,CTS1148,Y7198,A10216,A1357,Y63 68,A196,A14544,FGC22406,A1616,A9117,FGC23813,S2137 ,S22055,Y22019,Y21567,S2332,FGC12754,Y29671,Y7927, S22349,Y30577,Y6086,CTS6400,A6573,S10967,FGC43922, Y7052,A12054,BY851,S6270,FGC19401,A6849,Y23129,FGC 9544,Y6229,FGC14843,FGC14485,Y6393,Y24747,Y17338,A 8235,BY13512,Y23358,Y19675,Y21370,Y14660,Y13962,Y8 331,S15818,Y15777,Y15882,FGC15551,Y11206,Y18800,FG C24027,Y16703,S2298,Z44274,Y19408,A9728,A9606,A830 2,A8789)"

Perhaps, it’s my tired eyes but I can’t find him in the main index. Be that as it may, this is turning out to be an interesting study for us.

mwauthy
05-27-2020, 06:25 PM
There seems to be a fourth I1 sample, in Table S5-2, with the sample ID GOX287. Who the heck is he? Am I the only one who's confused by the way this study and dataset are presented?:\ Add: I can see some interesting SNPs, starting with S1954. Some look relatively recent, for example: S2298 formed 2200 ybp, TMRCA 1200 ybp.

GOX287's SNPs:
"I-L157.1/etc*(xCTS6364,S1954,CTS1148,Y7198,A10216,A1357,Y63 68,A196,A14544,FGC22406,A1616,A9117,FGC23813,S2137 ,S22055,Y22019,Y21567,S2332,FGC12754,Y29671,Y7927, S22349,Y30577,Y6086,CTS6400,A6573,S10967,FGC43922, Y7052,A12054,BY851,S6270,FGC19401,A6849,Y23129,FGC 9544,Y6229,FGC14843,FGC14485,Y6393,Y24747,Y17338,A 8235,BY13512,Y23358,Y19675,Y21370,Y14660,Y13962,Y8 331,S15818,Y15777,Y15882,FGC15551,Y11206,Y18800,FG C24027,Y16703,S2298,Z44274,Y19408,A9728,A9606,A830 2,A8789)"


I’m confused as well since one of the charts only shows the Iron Age BES1248 I1. Then there’s another graphic showing 1 Neolithic I1 and 1 Iron Age I1 but no Bronze Age I1. Then there’s another data set with 4 different I1?

oz
05-27-2020, 06:34 PM
I can't see any mention of him elsewhere in the material, but he's in a table with other samples from the study so looks like he is too. Please tell me if I'm wrong...

37763

I don't really have a clue. Is it another really ancient one? This is the strangest paper for ancient I1 by far. I wonder if more will start popping up now in future studies. Maybe it was just very elusive before, stayed low key.

JonikW
05-27-2020, 07:17 PM
I don't really have a clue. Is it another really ancient one? This is the strangest paper for ancient I1 by far. I wonder if more will start popping up now in future studies. Maybe it was just very elusive before, stayed low key.

The long-promised Reich paper on Iron Age Britain will be fascinating for many reasons, one of which is whether it turns up any I1, or any U106 for that matter. Looks like anything's up for grabs after this French study. It really highlights the difficulties of drawing conclusions about our I1 ancestors and how they got to where we ended up today. That said, there are five testers on my twig of the tree now and we're all either Eastern England, Northern England or Scandinavia with shared TMRCAs in the Early Medieval period, so I doubt whether I have any personal surprises in store.

deadly77
05-27-2020, 08:22 PM
There seems to be a fourth I1 sample, in Table S5-2, with the sample ID GOX287. Who the heck is he? Am I the only one who's confused by the way this study and dataset are presented?:\ Add: I can see some interesting SNPs, starting with S1954. Some look relatively recent, for example: S2298 formed 2200 ybp, TMRCA 1200 ybp.

GOX287's SNPs:
"I-L157.1/etc*(xCTS6364,S1954,CTS1148,Y7198,A10216,A1357,Y63 68,A196,A14544,FGC22406,A1616,A9117,FGC23813,S2137 ,S22055,Y22019,Y21567,S2332,FGC12754,Y29671,Y7927, S22349,Y30577,Y6086,CTS6400,A6573,S10967,FGC43922, Y7052,A12054,BY851,S6270,FGC19401,A6849,Y23129,FGC 9544,Y6229,FGC14843,FGC14485,Y6393,Y24747,Y17338,A 8235,BY13512,Y23358,Y19675,Y21370,Y14660,Y13962,Y8 331,S15818,Y15777,Y15882,FGC15551,Y11206,Y18800,FG C24027,Y16703,S2298,Z44274,Y19408,A9728,A9606,A830 2,A8789)"

I'd interpret this sample as being negative for the SNPs listed in the brackets by the nature of the x in front of all of these. Also, several of these are mutually exclusive - for example S1954, A196 and Y7198 are all on different branches of the I-Z140 group and can't allbe positive without conflicting each other.

Compare with BES1248 in Table S5-2, listed as I-FGC9452* (xCTS6364, Z4727, S1289, etc...) checked a few of these in brackets and all negative for BES1248.

I couldn't find FGC9452 on the YFull or FTDNA trees, but it is on the ISOGG tree on the I1 branch level (ie, not subclade) and it's at ChrY position (Hg38):10112707 close to the centromere.

deadly77
05-27-2020, 09:12 PM
Instead of “pre-I1” I would use I-I1.

Ultimately it won't affect how these are reported in manuscripts or supplementary material from scientific papers unless the people who write those papers adopt the terminology. And as we can see, different authors are not consistent across the field as it is. Some researchers will call a pre-I1 sample as I1, some will call it as I, some will say not enough information to define a haplogroup - examples of all these situations are in published papers. None of them use the term pre-I1 as it is. I'm not particularly fond of the I-I1 designation as to me it reads ambiguous. I definitely think using longhand nomenclature that ISOGG uses for branches and then applying those labels to different branches to what ISOGG uses adds to confusion.

I'm not necessarily married to term pre-I1, and started using it back around post #118 on this thread because there wasn't really an existing label at the time to reflect that these samples were after the split from I2 but before the MRCA of modern I1 individuals in a terms of a phylogenetic tree. Other options could be I, I*, I(xI2). I'm happy to adopt another term for the map and in conversation if it makes sense and there's a consensus. If not I'll just continue to use pre-I1 on the map and in my own definitions.

JonikW
05-27-2020, 09:38 PM
I'd interpret this sample as being negative for the SNPs listed in the brackets by the nature of the x in front of all of these. Also, several of these are mutually exclusive - for example S1954, A196 and Y7198 are all on different branches of the I-Z140 group and can't allbe positive without conflicting each other.

Compare with BES1248 in Table S5-2, listed as I-FGC9452* (xCTS6364, Z4727, S1289, etc...) checked a few of these in brackets and all negative for BES1248.

I couldn't find FGC9452 on the YFull or FTDNA trees, but it is on the ISOGG tree on the I1 branch level (ie, not subclade) and it's at ChrY position (Hg38):10112707 close to the centromere.

Thanks very much for that. I always value your opinion, as you know, so do you have a further take on this sample? He seems to have a lot of valid markers, so why is the pretty uninformative I-L157.1 highlighted here and why might he have been excluded from the main study if that's actually the case?

deadly77
05-27-2020, 10:02 PM
Thanks very much for that. I always value your opinion, as you know, so do you have a further take on this sample? He seems to have a lot of valid markers, so why is the pretty uninformative I-L157.1 highlighted here and why might he have been excluded from the main study if that's actually the case?

I don't see his sample among the BAM files at ENA, so there's no raw data for me to verify any of these SNPs (or any other I1-related SNPs). The description of I-L157.1 is as you say pretty uninfomative - it's a bit like saying I1 or I-M253, although I'm not sure why they called out L157 specifically (positive result for that one, and that's what they're using to define I1?). But without the BAM file to check corroborating SNPs on the I1 level, can't really say anything to confirm or disprove anything to do with this sample.

As JMcB says above in #684, I'm struggling to find any mention of sample GOX287 in the paper, supplementary information or spreadsheets outside of a single mention in Table S5-2. Might just be same as him in that my eyes are tired and better to try again tomorrow.

deadly77
05-27-2020, 10:15 PM
I think there might be two datasets in this paper, that were analyzed differently. Paper says "we genetically analyzed 243 unique individuals sampled from 54 different archeological sites, enriching for both complete mitochondrial genomes and a panel of 120 nuclear single-nucleotide polymorphisms (SNPs) including Y-chromosome SNPs, as well as a partially overlapping dataset of 58 low-coverage genomes" - so the 58 samples had what's equivalent to a low read-depth WGS, and the majority of 243 samples had the equivalent of a chip test which covered a few designated SNPs (autosomal and Y - but like say a 23andme test) and a full mitochondrial sequence. Perhaps this is why the majority of samples don't have a BAM file - only 58 of them do (which matches the numbers at ENA).

Pribislav
05-27-2020, 10:45 PM
For samples which weren't shotgun sequenced they captured 47 regions on Y-chromosome totaling 4715 base pairs. I don't know how many phylogenetically relevant SNPs are in those regions in total, but in table S5-1 it can be seen that sample with largest number of valid SNPs (1360) is BOU11, but most of the rest have bellow 500.

mwauthy
05-27-2020, 10:59 PM
I'd interpret this sample as being negative for the SNPs listed in the brackets by the nature of the x in front of all of these. Also, several of these are mutually exclusive - for example S1954, A196 and Y7198 are all on different branches of the I-Z140 group and can't allbe positive without conflicting each other.

Compare with BES1248 in Table S5-2, listed as I-FGC9452* (xCTS6364, Z4727, S1289, etc...) checked a few of these in brackets and all negative for BES1248.

I couldn't find FGC9452 on the YFull or FTDNA trees, but it is on the ISOGG tree on the I1 branch level (ie, not subclade) and it's at ChrY position (Hg38):10112707 close to the centromere.


It is a bizarre designation. You’re correct that I-FGC9452 is not on the Ftdna or YFull Haplotree. It’s simply listed as I1~ on the Isogg tree. What does the ~ even mean?

JonikW
05-27-2020, 11:10 PM
For samples which weren't shotgun sequenced they captured 47 regions on Y-chromosome totaling 4715 base pairs. I don't know how many phylogenetically relevant SNPs are in those regions in total, but in table S5-1 it can be seen that sample with largest number of valid SNPs (1360) is BOU11, but most of the rest have bellow 500.

Interesting. In the case of GOX287 though, he was shotgun sequenced and has 5,653 valid SNPs.

spruithean
05-28-2020, 02:25 AM
Just trying to catch up on all this here!

Wow! This is rather big stuff for I1. I thought BES1248 would be from somewhere in the north of France. I'm quite surprised, especially given his Z58 grouping. I wonder what this might mean for I-Y7198 lineages.

JMcB
05-28-2020, 03:19 AM
Just trying to catch up on all this here!

Wow! This is rather big stuff for I1. I thought BES1248 would be from somewhere in the north of France. I'm quite surprised, especially given his Z58 grouping. I wonder what this might mean for I-Y7198 lineages.


Judging from his autosomal readings, I suspect he was from the North and ended up in the South. Unfortunately, his subclade appears to be in doubt at this point, too.

https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=666635&viewfull=1#post666635


I’m curious about these two early samples:

FAD9 — I-A11354 — https://www.yfull.com/tree/I-A11341/

An Early Bronze Age Z140 sample (1893-1700 BC) in Southern France.

&

Cx161 — FGC3466 — https://www.yfull.com/tree/I-S5619/

An Middle Neolithic sample (4314-4052 BC) also in Occitanie.


These are pretty early, I hope they check out.


Hopefully, Deadly will get his hands on their Bam files in the near future.

deadly77
05-28-2020, 07:42 AM
It is a bizarre designation. You’re correct that I-FGC9452 is not on the Ftdna or YFull Haplotree. It’s simply listed as I1~ on the Isogg tree. What does the ~ even mean?

It is a bit bizarre, but it's not unique. The Anglo-Saxon NO3423 from Martiniano et al Nat. Commun 2016 was listed as I1-S107, and there's usually many posts on the I-M253 facebook page from folks who have run data through the Morley haplogroup predictor and got "I-L759" and they ask about it as a subclade. Both of these SNPs are in the block of >300 SNPs on the I1 branch before diversification but it essentially means I-M253 - ie, I1 without a defined subclade.

Perhaps the authors didn't want to use the designation I-M253 unless the sample was actually positive for M253 the SNP itself. I checked position ChrY(hg19):15022707 and it's a no call in BES1248's BAM file. So perhaps they picked one of the phyloquivalent SNPs that he's positive for to use instead. So I-FGC9452 for BES1248 and and I-L127.1 for GOX287. But it actually just means I1 with no confirmed subclade.

For what it's worth, I'm positive for FGC9452 (19C) and L127.1 (23G) as an I1 person.

deadly77
05-28-2020, 08:05 AM
Just trying to catch up on all this here!

Wow! This is rather big stuff for I1. I thought BES1248 would be from somewhere in the north of France. I'm quite surprised, especially given his Z58 grouping. I wonder what this might mean for I-Y7198 lineages.

I don't think there's enough evidence to confirm BES1248 in the I-Z58 group. He has a one read positive in his BAM file for S10350, but that's contradicted by a one read negative for S22349, which is a phyloequivalent SNP on the I-FGC24354 branch three steps up. Both of these can't be right and phylogenetically consistent with each other and BES1248 is no call for all other SNPs between I-S10350 back to the I1, including I-Z58 and I-DF29 branch. If there were more SNPs in this lineage that were positive or negative, that may swing it one way or another, but all no calls makes that decision more difficult.

I think it's safer ground to categorize him as at the basic I1 level, where there's more corroborating evidence - 19 positive SNPs at the I1 level (20 if you include FGC9452) that are all in agreement with each other. I guess it's accuracy versus precision. I1 with no defined subclade is more accurate. I-S10350 (or Z58) is more precise but has a high possibility of not being very accurate based on the evidence available.

deadly77
05-28-2020, 08:22 AM
Judging from his autosomal readings, I suspect he was from the North and ended up in the South. Unfortunately, his subclade appears to be in doubt at this point, too.

https://anthrogenica.com/showthread.php?20136-Ancient-genomes-from-present-day-France-unveil-7-000-years-of-its-demographic-history&p=666635&viewfull=1#post666635


I’m curious about these two early samples:

FAD9 — I-A11354 — https://www.yfull.com/tree/I-A11341/

An Early Bronze Age Z140 sample (1893-1700 BC) in Southern France.

&

Cx161 — FGC3466 — https://www.yfull.com/tree/I-S5619/

An Middle Neolithic sample (4314-4052 BC) also in Occitanie.


These are pretty early, I hope they check out.


Hopefully, Deadly will get his hands on their Bam files in the near future.

Not sure BAM files will be available for these ones, given the method of DNA analysis used, although that depends on the details. If it's a genotyped chip test - like a custom version of the arrays used by 23andme, Ancestry, etc. then I think it's unlikely that there will be a BAM file and we'll only get a BAM file for the 58 low coverage shotgun sequenced samples such as BES1248. If it's a SNP capture similar to what the researchers in the Avar burials used, we may get a BAM with a lot of holes in it. Or if the SNPs results came from a Sanger (similar to a YSEQ single SNP test) then perhaps that could be assembled into a BAM file. The latter two cases mean we're unlikely to get anything "new" from the data, but perhaps can confirm the calls rather than taking them on trust from a spreadsheet.

If not a BAM file (in the case of a genotyped chip test) then hopefully we can look at some of the other calls and see if the final ones are phylogenetically consistent. My AncestryDNA test has positive SNPs for Z1842 (haplogroup J), CTS616 (haplogroup I2), M307/P203 (haplogroup O) but those single SNPs alone don't define me as any of those haplogroups. Can verify these are false positives by looking at upstream negatives - for example, I'm negative for L134/PF4539, M304, L60/S6, M267, Z2215, Z1828 in haplogroup J which contradict the positive resut for Z1842. So if we could get something similar for FAD9 or Cx161 then we can be a bit more confident.

oz
05-28-2020, 08:40 AM
Just trying to catch up on all this here!

Wow! This is rather big stuff for I1. I thought BES1248 would be from somewhere in the north of France. I'm quite surprised, especially given his Z58 grouping. I wonder what this might mean for I-Y7198 lineages.

Actually it's not that big. Even if this oldest sample is correct it's still pretty much around the age estimate of the TMRCA for I1 or older by maybe 500 years. Who and what guarantees that their dating methods are totally accurate.
And second, unless they find more I1 at least between the area of France and Scandinavia before the Bronze age then this study might've have just discovered nothing more than extinct lineages and these samples might also be contaminated.
Let's see if this gets backed up by more I1 samples that might get discovered in future studies. Although I still find it pretty odd that there is virtually zero I1 anywhere else in Europe before around 5000 ybp.

JMcB
05-28-2020, 02:18 PM
Not sure BAM files will be available for these ones, given the method of DNA analysis used, although that depends on the details. If it's a genotyped chip test - like a custom version of the arrays used by 23andme, Ancestry, etc. then I think it's unlikely that there will be a BAM file and we'll only get a BAM file for the 58 low coverage shotgun sequenced samples such as BES1248. If it's a SNP capture similar to what the researchers in the Avar burials used, we may get a BAM with a lot of holes in it. Or if the SNPs results came from a Sanger (similar to a YSEQ single SNP test) then perhaps that could be assembled into a BAM file. The latter two cases mean we're unlikely to get anything "new" from the data, but perhaps can confirm the calls rather than taking them on trust from a spreadsheet.

If not a BAM file (in the case of a genotyped chip test) then hopefully we can look at some of the other calls and see if the final ones are phylogenetically consistent. My AncestryDNA test has positive SNPs for Z1842 (haplogroup J), CTS616 (haplogroup I2), M307/P203 (haplogroup O) but those single SNPs alone don't define me as any of those haplogroups. Can verify these are false positives by looking at upstream negatives - for example, I'm negative for L134/PF4539, M304, L60/S6, M267, Z2215, Z1828 in haplogroup J which contradict the positive resut for Z1842. So if we could get something similar for FAD9 or Cx161 then we can be a bit more confident.

Let’s hope the latter is the case. What’s your intuition on these two samples? They seem to be too early to be true and I’m one who thinks the ancients traveled a lot more than we think. The Z140 appears to be a little too far down the tree for that time period. Any thoughts?

deadly77
05-28-2020, 03:38 PM
Let’s hope the latter is the case. What’s your intuition on these two samples? They seem to be too early to be true and I’m one who thinks the ancients traveled a lot more than we think. The Z140 appears to be a little too far down the tree for that time period. Any thoughts?

My intuition is to pause and not get too excited about these two samples for now until we know more. There's a lot of information in the paper, supplementary information and datasets that have come together over the last few days in a piecemeal fashion and it's not well organized for easy reading. I'm a bit wary that these samples are listed in one datasheet but the Y-DNA data doesn't seem to be much discussed much elsewhere outside of that.

It's reminding me a bit of the supposed I-L258 sample “Early Bronze Age (~2,000 BCE). Lech_EBA OBKR_117_d” from the Mittnik A., et al., Kinship-based social inequality in Bronze Age Europe paper that had quite a few people excited for a while but with concerns that the TMRCA didn't match up (posts above in the forum between #489 on Page 49 and#525 on Page 53 above) until Generalissimo shared (post #519 on page 52 above) that this sample was negative for five I1 level SNPs to go along with the positive result from L258 and also a positive result for I2a1a1a1a1a1a2a~ S294. Later found the L258 SNP result was a one read false positive from the BAM file (see post #556 on page 56).

deadly77
05-28-2020, 03:59 PM
...and that's not to say that FAD9 isn't actually I-A11354 or Cx161 isn't actually I-FGC3466. Just that I'd like to assess more evidence for or against either situation than we currently have available.

JMcB
05-28-2020, 04:09 PM
Well, it wouldn’t be the first time we’ve been on a wild goose chase. So your caution is advisable! I’m skeptical about these but perhaps, I’m wrong.

Thanks for all of your help!

JonikW
05-29-2020, 08:30 PM
Another big paper on French aDNA is out. Looks like no further Neolithic surprises for us. https://advances.sciencemag.org/content/6/22/eaaz5344

oz
05-29-2020, 08:50 PM
Another big paper on French aDNA is out. Looks like no further Neolithic surprises for us. https://advances.sciencemag.org/content/6/22/eaaz5344

Damn you're quick, I was just about to post it too.

JMcB
05-29-2020, 09:23 PM
Another big paper on French aDNA is out. Looks like no further Neolithic surprises for us. https://advances.sciencemag.org/content/6/22/eaaz5344

Thankfully, it’s not behind a paywall either.

oz
05-29-2020, 11:59 PM
Just adds more skepticism that I1 and even less likely I1a2 was found in Neolithic and EBA South France. And the C1a and H2 lineages didn't have much luck in surviving the post Neolithic age in Europe.

JonikW
05-30-2020, 12:54 AM
Just adds more skepticism that I1 and even less likely I1a2 was found in Neolithic and EBA South France. And the C1a and H2 lineages didn't have much luck in surviving the post Neolithic age in Europe.

Or if they do prove to be I1 it bolsters the case that they were outliers who had travelled a long distance. The BES sample looks firmly Belgic for example, based on modelling on this forum.

oz
05-30-2020, 03:48 AM
Or if they do prove to be I1 it bolsters the case that they were outliers who had travelled a long distance. The BES sample looks firmly Belgic for example, based on modelling on this forum.

Yeah maybe they liked vacationing or retiring in that Southern region of France since the Neolithic, who knows...
Me personally though, I would prefer Croatia or Greece.

janan
06-01-2020, 11:49 AM
Intriguing though when you consider that the entire Atlantic European cost at middle neolithic got connected through the common megalithic culture. All the way from southernmost Spain to Västergötland in Sweden. By migration? Which way?

Riverman
06-01-2020, 06:26 PM
Intriguing though when you consider that the entire Atlantic European cost at middle neolithic got connected through the common megalithic culture. All the way from southernmost Spain to Västergötland in Sweden. By migration? Which way?

The most likely scenario right now is that somewhere in France a strong Mesolithic community adopted Cardial farmer cultural elements and, one way or another, took Neolithic wives. This clan survived and developed its own characteristics, being on the long run successful and expanded in different directions. First hints come from the recent paper on French Neolithics. I think the results of this paper (https://advances.sciencemag.org/content/6/22/eaaz5344) are of importance for the whole debate:

However, the situation is different in today’s France, where we observe not only the highest HG ancestry proportion overall when compared to other regions in Europe but it is also found in the oldest individuals from the southern sites of PEN and LBR. This observation is also supported by uniparental markers. Y chromosome lineages in western early farmers in the southern region are exclusively derived from HG (I2a; table S5 and text S5). In contrast, mitochondrial DNA results show a more universal Neolithic diversity profile, as previously reported [i.e., (4, 5)], with only two haplotypes (U5 and U8) that are potentially of HG origin (table S4 and text S4).

[...]

Two individuals from the Middle Neolithic OBN site located immediately west of the Rhine (Fig. 1A) also show a high proportion of the HG ancestry component (OBN B), in contrast to LBK sites east of the Rhine. To quantify the extra-HG proportion, we modeled LBK from Germany as a mixture of Anatolia_Neolithic and European_HG, and subsequently OBN subgroups as a more proximal mixture model of LBK and European_HG. We find this model well supported (table S11), and obtained up to 31.8% of excess HG ancestry for OBN B. Given the absence of a strong HG contribution in LBK groups east of the Rhine, we assume this to be a local contribution during the centuries following the arrival of first farmers. Moreover, male individuals from OBN carry exclusively the Y chromosome haplogroups I2a1a2 and C1a2b, attributed to HG groups (text S5), providing further evidence for a greater amount of the HG contribution in this region.



Archaeological research has argued for increased interaction between incoming farmers and indigenous HG in the western Mediterranean during a second stage of the Neolithization process and especially in areas with higher HG population densities, e.g., the Tosco-Emilian Apennine and Po plain (18). We are now able to confirm that these contacts left a traceable biological signal during the Neolithic expansion in southern France. From an archaeological perspective, this suggests that HG have contributed to the clear changes observed within the material culture postdating the pioneer phase.


Note that ICC individuals from the eastern Adriatic coast have only a very small amount of HG ancestry with a greater affinity to central European groups (see table S8). This fits with the hypothesis of a differentiation of technical traditions within material cultures observed from both sides of Apennine Mountains in Italy: an Adriatic tradition connected to the Balkans and a Tyrrhenian one whose origin is still unknown (41). It is tempting to associate such a strong HG component on the Tyrrhenian side with the characteristic/specific pottery traditions observed in this same region and to consider these original traditions the result of a HG reinterpretation (41). However, the scarcity of genomic data available from central and southern Italy currently does not allow this hypothesis to be tested directly.
Moreover, ICC individuals from the Iberian Peninsula also carry less HG ancestry. Together, this rejects the hypothesis that ICC-associated individuals represent a uniform genetic horizon per se and argues for more regionally nuanced scenarios of interaction.


In accordance with the established chronology of first Neolithic settlements in the French territory, the overlapping/synchronous date estimates obtained for southern ICC sites are consistent with the signal of a first HG contribution in the south of France, followed by a subsequent northward expansion of groups carrying this HG legacy

So here we have such a case, a forager clan taking Neolithic wives and adopting the Neolithic culture. From this or a similar group the shift from G2/H2/T to I2a was initiated on a grand scale.

Figure S13 is interesting, showing which alliances were formed and that G2 and H2 marched in the West together (from other studies we know T participated as well, compare with Cassidy):
https://advances.sciencemag.org/content/suppl/2020/05/21/6.22.eaaz5344.DC1/aaz5344_SM.pdf

Also:

We caution that because the amount of HG ancestry is very low in many Neolithic groups (<10%), it remains difficult to characterize the ultimate source reliably. Nevertheless, our admixture patterns from supported models show clear geographic signals. Neolithic groups associated with the LBK in central Europe (Hungary, Austria, and Germany) carry a small HG proportion, which was likely derived from admixture with HG individuals of the EHG-WHG cline and could have occurred in southeastern Europe during a preceding phase of the Neolithic expansion around 6000–5400 BCE. When using f-statistics of the form f4(Mbuti, test; BDB001, KO1) with our new Mesolithic genome (BDB001) from the Middle-Elbe-Saale region in central Germany as a geographically local HG proxy (instead of using Loschbour, which is located west of the Rhine), we do not find support for a local attraction for LBK groups, but the same pattern as for Loschbour (fig. S5C). This suggests that additional gene flow from neighboring Loschbour-like HG such as BDB001 in central Europe was negligible in the first Neolithic groups. However, the German Baalberge group (4000–3500 BCE) shows a marked increase of such HG ancestry, as well as individuals from the Blätterhöhle group, as has been suggested (5, 6), compared to a combination of both KO1-like and Loschbour-like ancestries for LBK groups (6). We can now show that this increase in WHG ancestry (up to 21.3 ± 1.5% in Baalberge; table S13) is driven by either local Loschbour-like ancestry or an expansion of farming groups from the west carrying this signal during the fifth millennium BCE, as suggested by archaeological data (36). For all studied Neolithic groups west of the Rhine, we observe a different pattern with a higher HG ancestry proportion, even for earliest groups that appears to be of a local (Loschbour-like) HG origin, consistent with archaeological data (2).

So the small amount of HG ancestry before the expansion of HG dominated groups from the West and possibly North is different and came from the early contacts of farmers with SEE foragers.

Particularly interesting is the continuity of I2a Neolithic clans in Southern France through the ages. They established themselves and stood their ground. By 4000 BC the G2/H/T clans were reduced to a few places or lower percentages in Europe.

Cassidy wrote in her thesis that she believes most of the HG reemergence is local, but notes that this can't be said for sure, and there are also opinions and relations pointing to a common source for the I2a/WHG expansion. For the later developments, I think, this is important too:

Cardial Ware is seen in the Limburg and La Hoguette pottery styles, found inland along the western fringes of LBK’s early distribution (Thorpe 2003; Hofmann 2016). These ceramic types, thought to be the result of indigenous interaction with more southern Impressed Ware groups, may have predated the arrival of LBK in some regions, and indeed are clearly replaced by LBK ware in many areas at a later date, including the southern Netherlands (~5,300 BC) (Cunliffe 2008).


Its intriguing that the British Neolithic is close to Rössen and Michelsberg (I2a:E1b alliance) and TRB comes from the same root most likely, as did the Atlantic Megalithic. From the fusion of Mesolithic, Cardial and LBK traditions in France. Now where the HG lineage first came up, the most successful and expansive group, is debatable, but going after the recent studies France is now in the focus.

JonikW
06-05-2020, 08:58 AM
This Scandinavia paper was posted in the Ancient DNA section and is interesting for its lack of I1: "The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders"

https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.24079

As a reminder: "The PWC appear in the archeological record between approximately 3400 and 2400 BCE... It has now been shown that there is a strong genetic similarity between individuals from PWC contexts and chronologically older Scandinavian Mesolithic hunter‐gatherer individuals"

Interestingly, the study was restricted to Gotland. I wonder what a coastal mainland site of this culture would show. I1 must have been out there in parts of Scandinavia, but still awaiting a Bronze Age expansion. Here's the breakdown:

"We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene‐pools…

"We successfully retrieved Y‐chromosomal haplotypes from six of the PWC males, while two additional males were typed previously (Table 1, Supporting Table S7) (Günther et al., 2018; Skoglund, Malmström, et al., 2014). All males, both from typical PWC burials (n = 4) and from “BAC influenced ” burials (n = 3), belonged to haplogroup I, and individuals with greater genome coverage displayed haplogroups I2a1a and I2a1b lineages."

EDIT: Added observation and clarity

Kaltmeister
06-05-2020, 03:02 PM
JonikW: I agree that the Pitted Ware Culture is a likely habitat for haplogroup I1, especially on the northern parts of the Norwegian coast. I1 and I2 may have merged here to the SHG admixture - my expectation is that EHG represents the I1 component, and the relation EHG/WHG mirrors the relation of I1 and I2.

Riverman
06-05-2020, 03:45 PM
To me its not that interesting whether I1 was in Scandinavia too in Mesolithic times, but more interesting where the I1 branch survived and expanded from which is now dominant in the region. That must not be the same.

oz
06-05-2020, 06:27 PM
And we still don't have any clear, solid evidence in ancient dna so far to answer any of these questions. It's just getting weird and frustrating at this point.

Riverman
06-05-2020, 07:04 PM
And we still don't have any clear, solid evidence in ancient dna so far to answer any of these questions. It's just getting weird and frustrating at this point.

That's the fate of the "late bloomers" E-V13 and I1, which seem to have come from a fairly late and rapid expansion. ;)

oz
06-05-2020, 08:37 PM
That's the fate of the "late bloomers" E-V13 and I1, which seem to have come from a fairly late and rapid expansion. ;)

Yeah something like that. E-V13 and I2-CTS10228 are quite a mystery as well. But in my opinion I1 for now takes the title as the biggest phantom of ancient DNA in Europe. Mostly because it is a haplogroup that split from I-M170 over 20 thousand years ago. All things considered, that's pretty miraculous if it only started to expand 4-5 thousand years ago or later. Yet we still can't even locate the source of this expansion with any conclusive Adna evidence.

Riverman
06-06-2020, 09:05 AM
Yeah something like that. E-V13 and I2-CTS10228 are quite a mystery as well. But in my opinion I1 for now takes the title as the biggest phantom of ancient DNA in Europe. Mostly because it is a haplogroup that split from I-M170 over 20 thousand years ago. All things considered, that's pretty miraculous if it only started to expand 4-5 thousand years ago or later. Yet we still can't even locate the source of this expansion with any conclusive Adna evidence.

To me its almost for certain it expanded in the Nordic Bronze Age. In this time and sphere it rose to a leading clan and elite lineage, which it wasn't before probably. The exact path up to this point is the mystery and the main candidates to me are right now it came with farmers from France or the Pannonia-Carpathian Basin either to Poland/Unetice or directly to Northern Europe or was a forager turned farmer lineage in Northern Europe. When the first hits come in, if the resolution is not high enough, it might still not be the solution, because I1 could have been thinly spread in many people, like E-V13, before the big success in the NBA.

oz
06-06-2020, 06:03 PM
At this point it's still all guess work, we don't really know. And who knows if we will ever really find out. You'd think the Scandinavians would be more interested in this particular subject but I haven't seen one paper or study released yet where they specifically try to figure out the I1 question.

JonikW
06-06-2020, 07:35 PM
At this point it's still all guess work, we don't really know. And who knows if we will ever really find out. You'd think the Scandinavians would be more interested in this particular subject but I haven't seen one paper or study released yet where they specifically try to figure out the I1 question.

I was hoping that Eske Willerslev would have done a really good and broad Danish/Scandinavian study by now given that he's Danish, partly based in Copenhagen and at the forefront of aDNA. What I'd love to see is a study ranging from the Nordic Bronze to Iron Age with loads of quality I1 samples. Even an FTDNA Big Y advertising campaign in Scandinavia would suit me right now.

oz
06-06-2020, 08:16 PM
I was hoping that Eske Willerslev would have done a really good and broad Danish/Scandinavian study by now given that he's Danish, partly based in Copenhagen and at the forefront of aDNA. What I'd love to see is a study ranging from the Nordic Bronze to Iron Age with loads of quality I1 samples. Even an FTDNA Big Y advertising campaign in Scandinavia would suit me right now.

On second thought though, Scandinavias aren't really an exception with the lack of geeking out interest over these haplogroups. No one really is, even in this a academia Adna world. All they really do is present the data of the uniparentals (and sometimes not the most accurately) but they don't release some special studies dedicated completely to them.
Why that is, I'm not really sure. Perhaps they just don't think they're really that important. But in my opinion they are key in tracing the migrations if anything and can provide clues.
But it makes me wonder if our male egos overestimate the importance of the Y haplogroup.

Nevertheless I still find it interesting and would love to trace the history and migration of my distant male ancestors. It would just be nice to know that, regardless of how relevant or irrelevant it might be.

oz
06-06-2020, 08:52 PM
And speaking of that I'm waiting for my results on ftdna from the PR683 snp pack that I ordered. Not expecting much or too deep of a terminal snp but it should at least assign me to some subclades that have a tmrca at least as young as 2500 ybp on Yfull. One of the subclades the Y37939 looks like the most common Z63 in Finland, while the sibling branch Y7627 is found in Iceland and Norway. Although there's not that many testers either unfortunately, but if I'm not mistaken with the limited information I've found, the clades under Y6228 seem to be the most common type of Z63 in the Nordic countries and Central and East Europe.

Riverman
06-07-2020, 01:34 PM
On second thought though, Scandinavias aren't really an exception with the lack of geeking out interest over these haplogroups. No one really is, even in this a academia Adna world. All they really do is present the data of the uniparentals (and sometimes not the most accurately) but they don't release some special studies dedicated completely to them.
Why that is, I'm not really sure. Perhaps they just don't think they're really that important. But in my opinion they are key in tracing the migrations if anything and can provide clues.
But it makes me wonder if our male egos overestimate the importance of the Y haplogroup.

Nevertheless I still find it interesting and would love to trace the history and migration of my distant male ancestors. It would just be nice to know that, regardless of how relevant or irrelevant it might be.

Its because it tells you throughout human history male clans, patriarchal and patrilinear, were the primary agents for the spread of cultures and genes. They consider it, most of the time, when it seems necessary for the bigger picture, but they don't make it an important part of their work and writings because of that. Its not part of the narrative they want to sell to the public and the media is ready to pick up in a positive or even just neutral way. If they do, it might be in a rather negative and biased way ("bad patriarchy, bad guys").

Besides autosomal DNA is the safer way to prove close relationships and migrations, as well as genetic frequency changes, which is the main interest of the current research.

Echo
06-12-2020, 03:59 AM
I was hoping that Eske Willerslev would have done a really good and broad Danish/Scandinavian study by now given that he's Danish, partly based in Copenhagen and at the forefront of aDNA. What I'd love to see is a study ranging from the Nordic Bronze to Iron Age with loads of quality I1 samples. Even an FTDNA Big Y advertising campaign in Scandinavia would suit me right now.
he best is texting him via mail I think.

JonikW
06-25-2020, 12:07 AM
In case you guys miss this in the ancient DNA discussion section, courtesy of RCO. Max Planck are recruiting a Research Group Leader. This is from the job description:

"This project aims to study the population shifts related to cultures such as Pannonians, Romans, Goths, Huns, Longobards, Gepids, Avars, Bulgars, Slavs and Franks in the Carpathian Basin in 400-900 CE. HistoGenes will analyse ~6,000 ancient human samples from this region with cutting edge scientific methods and contextualize the interpretation of these data in their archaeological and historical setting."

That's a heck of a lot of samples... I look forward to eventually seeing Goth, Longobard, Gepid and Frank Y chromosome results in particular. Should be a fair bit of I1 there.

spruithean
06-25-2020, 12:21 AM
In case you guys miss this in the ancient DNA discussion section, courtesy of RCO. Max Planck are recruiting a Research Group Leader. This is from the job description:

"This project aims to study the population shifts related to cultures such as Pannonians, Romans, Goths, Huns, Longobards, Gepids, Avars, Bulgars, Slavs and Franks in the Carpathian Basin in 400-900 CE. HistoGenes will analyse ~6,000 ancient human samples from this region with cutting edge scientific methods and contextualize the interpretation of these data in their archaeological and historical setting."

That's a heck of a lot of samples... I look forward to eventually seeing Goth, Longobard, Gepid and Frank Y chromosome results in particular. Should be a fair bit of I1 there.

Really looking forward to seeing aDNA from Gepids. Earlier posts in this thread discuss some I1 among Gepids in Serbia IIRC.

oz
06-25-2020, 02:10 AM
In case you guys miss this in the ancient DNA discussion section, courtesy of RCO. Max Planck are recruiting a Research Group Leader. This is from the job description:

"This project aims to study the population shifts related to cultures such as Pannonians, Romans, Goths, Huns, Longobards, Gepids, Avars, Bulgars, Slavs and Franks in the Carpathian Basin in 400-900 CE. HistoGenes will analyse ~6,000 ancient human samples from this region with cutting edge scientific methods and contextualize the interpretation of these data in their archaeological and historical setting."

That's a heck of a lot of samples... I look forward to eventually seeing Goth, Longobard, Gepid and Frank Y chromosome results in particular. Should be a fair bit of I1 there.

Holy shit! How long will that take? Is it gonna be published all as one study or multiple different papers over an x amount of years?
6,000 samples all from the Carpathian Basin 400-900 ad? That would be as big of an Adna project as we'll ever see. Almost sounds too promising and too good to be true.

spruithean
06-30-2020, 01:45 AM
Holy shit! How long will that take? Is it gonna be published all as one study or multiple different papers over an x amount of years?
6,000 samples all from the Carpathian Basin 400-900 ad? That would be as big of an Adna project as we'll ever see. Almost sounds too promising and too good to be true.

Yeah, here's hoping something doesn't come up that prevents this from being completed...

oz
08-27-2020, 11:46 PM
Pribislav posted this in another thread, the paper isn't published and there's no pre-print or anything yet but it's part of some upcoming big study on Roman and Medieval age in Balkans and surrounds I guess. Apparently a few I1s have been found already in Serbia.

Viminacium - 28 (labeled Serbia_Roman):

E x 13 (L618 x 6; L618>V13 x 3; Z830 x 1; Z830>M123 x 1; Z1902 x 1; M96 x 1)

G x 5 (PF3148 x 1; PF3148>L91 x 1; P303 x 1; L497 x 1; L497>Z1815 x 1)

R1b x 3 (Z2103 x 1; U106 x 1; U152>L2>Z367 x 1)

R1a x 2 (Z2124>Z2122 x 1; Z2124>Z2123 x 1)

J x 2 (M304 x 1; L24 x 1)

T x 1 (M184)

I1 x 1 (M253)

I2 x 1 (L596)


Timacum Minus, Slog necropolis - 10 (labeled Serbia_Roman):

E x 3 (M35 x 1; L618 x 1; L618>V13 x 1)

J x 3 (M304 x 1; M410 x 1; M241 x 1)

R1b x 2 (Z2103 x 1; Z2103>CTS1450 x 1)

G x 1 (CTS342>FGC12126)

I1 x 1 (Z58>CTS8647)


Timacum Minus, Kuline necropolis - 5 (labeled Serbia_Early_Middle_Age):

I2 x 2 (M423 x 2)

E x 1 (L618)

J x 1 (M304)

R1b x 1 (P312>DF99)


Lepenski Vir - 2:

E x 1 (M35) - Serbia_Roman

J x 1 (M102) - Serbia_Medieval


Mediana - 2 (labeled Serbia_Gepid):

G x 1 (P287)

I1 x 1 (Z58>CTS8647)


Gomolava - 1 (labeled Serbia_Medieval):

I2 x 1 (M423>L621>CTS4002)

JMcB
08-28-2020, 02:42 AM
Pribislav posted this in another thread, the paper isn't published and there's no pre-print or anything yet but it's part of some upcoming big study on Roman and Medieval age in Balkans and surrounds I guess. Apparently a few I1s have been found already in Serbia.

Viminacium - 28 (labeled Serbia_Roman):

E x 13 (L618 x 6; L618>V13 x 3; Z830 x 1; Z830>M123 x 1; Z1902 x 1; M96 x 1)

G x 5 (PF3148 x 1; PF3148>L91 x 1; P303 x 1; L497 x 1; L497>Z1815 x 1)

R1b x 3 (Z2103 x 1; U106 x 1; U152>L2>Z367 x 1)

R1a x 2 (Z2124>Z2122 x 1; Z2124>Z2123 x 1)

J x 2 (M304 x 1; L24 x 1)

T x 1 (M184)

I1 x 1 (M253)

I2 x 1 (L596)


Timacum Minus, Slog necropolis - 10 (labeled Serbia_Roman):

E x 3 (M35 x 1; L618 x 1; L618>V13 x 1)

J x 3 (M304 x 1; M410 x 1; M241 x 1)

R1b x 2 (Z2103 x 1; Z2103>CTS1450 x 1)

G x 1 (CTS342>FGC12126)

I1 x 1 (Z58>CTS8647)


Timacum Minus, Kuline necropolis - 5 (labeled Serbia_Early_Middle_Age):

I2 x 2 (M423 x 2)

E x 1 (L618)

J x 1 (M304)

R1b x 1 (P312>DF99)


Lepenski Vir - 2:

E x 1 (M35) - Serbia_Roman

J x 1 (M102) - Serbia_Medieval


Mediana - 2 (labeled Serbia_Gepid):

G x 1 (P287)

I1 x 1 (Z58>CTS8647)


Gomolava - 1 (labeled Serbia_Medieval):

I2 x 1 (M423>L621>CTS4002)

Thanks for the heads up Oz!

I’ll have to check this thread out and see what the up coming paper is.

https://anthrogenica.com/showthread.php?21442-E-V13-in-Bulgarian-Iron-Age&p=695643&viewfull=1#post695643


Edit: With some follow ups:

https://anthrogenica.com/showthread.php?21442-E-V13-in-Bulgarian-Iron-Age&p=695698&viewfull=1#post695698


https://anthrogenica.com/showthread.php?21442-E-V13-in-Bulgarian-Iron-Age&p=695709&viewfull=1#post695709

spruithean
08-28-2020, 02:19 PM
Nice to see some more ancient I1, especially a Gepid. I hope we get more Gepid samples.

deadly77
08-28-2020, 03:15 PM
This sounded familiar - I thought Pribislav had mentioned these samples earlier in this ancient I1 thread so went back and checked - post #619 on page 62 in February https://anthrogenica.com/showthread.php?13783-Ancient-I-M253-samples-list&p=644012&viewfull=1#post644012

Salamander
09-15-2020, 10:23 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.


Hi, this is my first post on this forum. Pardon me for joining this thread very late, but I found it very useful and I’d like to tease out one aspect. Maybe it will be helpful for some of the other guests who are having trouble interpreting DNA test results.

Stone Meadow’s post mentioned his ancestor Leofwine of Normandy. There is an online genealogy which lists Sir Thomas de Clayton born in England around the 1500s as a direct male descendent of his. By chance, Sir Thomas de Clayton appears as the ancestor of a 7-step match of mine in my FTDNA test. So I was excited to see this post because it potentially linked me to a known individual deep into the Middle Ages.

My FTDNA Y-111 test says I am S1990. My documented direct male genealogy goes back to Ireland but hits a wall around the late 1700s. At the 111-marker level, FTDNA lists only one match for me – an exact match with someone of the same surname as me (King). There are no other matches listed, even at different steps. But at the 67-marker view many more matches appear, and one of those lists Sir Thomas de Clayton as his ancestor.

FTDNA’s “TiP” says there is an 86 per cent chance of this person and I having a common ancestor within 16 generations (say 600 years?) and a 95 per cent chance within 20 generations (say 1000 years?). At first glance this would appear to suggest there’s a pretty good chance that I also am descended from Leofwine of Normandy.

However, at the 67-marker level I have a number of closer contacts whose ancestors came from much further afield. These include a 5-step match with someone harking from Neumark in eastern Germany, and a couple of 6-step matches pointing to Sweden. This would tend to suggest that the King and Clayton lines join up further back than Leofwine.

So my question is: based on all of this, can I probably trace my descent to Leofwine of Normandy, or have I misinterpreted the guidance on years to most recent common ancestor? Or is the fact that I am looking at 67-marker results rather than 111-marker results skewing my interpretation? Also, will I have to test at a higher level (say Y-700), or to put my results into other providers in order to understand this better?

mwauthy
09-16-2020, 08:10 PM
I noticed that their is an article on National Geographic today referring to the Viking study. Does this mean we’re closer to being able to analyze the raw data to search for deeper SNP calls?


https://api.nationalgeographic.com/distribution/public/amp/history/2020/09/scientists-raid-viking-dna-explore-genetic-roots

deadly77
09-16-2020, 08:19 PM
I noticed that their is an article on National Geographic today referring to the Viking study. Does this mean we’re closer to being able to analyze the raw data to search for deeper SNP calls?


https://api.nationalgeographic.com/distribution/public/amp/history/2020/09/scientists-raid-viking-dna-explore-genetic-roots

Yes - the paper has now been published (it's mentioned in the Ancient DNA section on Anthrogenica) and it's in Nature https://www.nature.com/articles/s41586-020-2688-8.epdf?sharing_token=m06OGzNYwNnANcCCnoShiNRgN0jAj Wel9jnR3ZoTv0OtPvex4nPtepui57w-C83dyFy9GqVA3aAzEttqQ2i38BqQeP2IXzWohVq0B1qBvkiWgG aG7vjYeMDQJp99vsRGARmvElOfumNcqhDYzd49m_pMYYaclkEn mc5Fzvq5bTxg5MOquH_eL10594sAitq1LTteGnRRdJlNqLCOzH fp-4VAcY7F0KI9nUl0WRoGS9M7R5ji-4ORqoZWHeD6J8yywRbOXPtjAySVItj3fdYKuO-baHQeu58-YIOi2QT0XYKieyjGbCQ9fiZsOa_W7oJxCsPmt_dtqtqS3qYYI2 yEFw%3D%3D&tracking_referrer=www.theguardian.com&fbclid=IwAR1oI5U2wORGEvYGlUufB006KBNcN0J_9aR-25LvrZ_W-XIvjHrJYtEAY_g

BAM files are available at European Nucleotide Archive under project PRJEB37976 here https://www.ebi.ac.uk/ena/browser/view/PRJEB37976

I'm downloading VK327's BAM file now. It's going really slow. Not sure if that's due to my internet connection or if ENA is getting a lot of traffic.

mwauthy
09-16-2020, 09:28 PM
Yes - the paper has now been published (it's mentioned in the Ancient DNA section on Anthrogenica) and it's in Nature https://www.nature.com/articles/s41586-020-2688-8.epdf?sharing_token=m06OGzNYwNnANcCCnoShiNRgN0jAj Wel9jnR3ZoTv0OtPvex4nPtepui57w-C83dyFy9GqVA3aAzEttqQ2i38BqQeP2IXzWohVq0B1qBvkiWgG aG7vjYeMDQJp99vsRGARmvElOfumNcqhDYzd49m_pMYYaclkEn mc5Fzvq5bTxg5MOquH_eL10594sAitq1LTteGnRRdJlNqLCOzH fp-4VAcY7F0KI9nUl0WRoGS9M7R5ji-4ORqoZWHeD6J8yywRbOXPtjAySVItj3fdYKuO-baHQeu58-YIOi2QT0XYKieyjGbCQ9fiZsOa_W7oJxCsPmt_dtqtqS3qYYI2 yEFw%3D%3D&tracking_referrer=www.theguardian.com&fbclid=IwAR1oI5U2wORGEvYGlUufB006KBNcN0J_9aR-25LvrZ_W-XIvjHrJYtEAY_g

BAM files are available at European Nucleotide Archive under project PRJEB37976 here https://www.ebi.ac.uk/ena/browser/view/PRJEB37976

I'm downloading VK327's BAM file now. It's going really slow. Not sure if that's due to my internet connection or if ENA is getting a lot of traffic.


Awesome! Looks like you’re going to be a busy man in the near future :)

Any additional info you can provide on the two I-Z2041 samples (VK445 and VK446) and the two I-Z2040 samples (VK496 and VK521) would be much appreciated :)

deadly77
09-16-2020, 10:41 PM
Awesome! Looks like you’re going to be a busy man in the near future :)

Any additional info you can provide on the two I-Z2041 samples (VK445 and VK446) and the two I-Z2040 samples (VK496 and VK521) would be much appreciated :)

Ah yes - I am going to be busy man in the near future, but not with analyzing these BAM files. Big project on at my new workplace, and they pay me so that takes priority. I won't have much bandwidth to look at the majority of these anytime soon. I will get through them but my approach to analyzing BAM files is rather manual and as a result is slow. Pribislav seems to be able to this a lot quicker than I do and his analysis is always sound, so he will probably get to it before I do. My priority list is the I-Z140 samples first , then the I-P109 samples and then I'll get to your I-Z2041 and I-Z2040 samples. But don't expect anything from me anytime soon on those four.

mwauthy
09-16-2020, 10:52 PM
Ah yes - I am going to be busy man in the near future, but not with analyzing these BAM files. Big project on at my new workplace, and they pay me so that takes priority. I won't have much bandwidth to look at the majority of these anytime soon. I will get through them but my approach to analyzing BAM files is rather manual and as a result is slow. Pribislav seems to be able to this a lot quicker than I do and his analysis is always sound, so he will probably get to it before I do. My priority list is the I-Z140 samples first , then the I-P109 samples and then I'll get to your I-Z2041 and I-Z2040 samples. But don't expect anything from me anytime soon on those four.


No problem! I completely understand the prioritization. I’m actually in the process of downloading VK521 right now because it seems the most promising to me. The downloading process is quite slow and tedious. Any advice for how a layman should approach looking at these?

deadly77
09-16-2020, 11:08 PM
No problem! I completely understand the prioritization. I’m actually in the process of downloading VK521 right now because it seems the most promising to me. The downloading process is quite slow and tedious. Any advice for how a layman should approach looking at these?

I've tried downloading the I-Z140 samples - very slow. I've got VK327 and VK363 but Vk357 and VK337 are taking ages. I actually went out for a couple of hours and still not done.

I can only talk about how I do it - there may be other (perhaps better) ways. I'd advise downloading the IGV from the Broad Institute for viewing the files. The user guides are pretty good. Once you have the file use IGVtools to index the BAM file (most of the time ENA includes a index file but I didn't see one for these files). Make sure the index file is in the same folder as the BAM. Load up the relevant reference genome (hg19 or hg38 - check paper for which one is the right one - most ancient genomes are mapped to hg19) in IGV, load the BAM file, select ChrY and then browse by position per SNP. Use YFull or Genetic Homeland as reference for position of SNPs as they include hg38 and hg19 position while YBrowse and FTDNA just list hg38 position. Sorry that I'm not able to give a detailed step-by-step - unfortunately I really don't have the bandwidth now to go through the details. But this is essentially my approach and it works for me. There is a fair bit of trial and error, but probably you'll learn more by doing it.

JMcB
09-16-2020, 11:42 PM
Ah yes - I am going to be busy man in the near future, but not with analyzing these BAM files. Big project on at my new workplace, and they pay me so that takes priority. I won't have much bandwidth to look at the majority of these anytime soon. I will get through them but my approach to analyzing BAM files is rather manual and as a result is slow. Pribislav seems to be able to this a lot quicker than I do and his analysis is always sound, so he will probably get to it before I do. My priority list is the I-Z140 samples first , then the I-P109 samples and then I'll get to your I-Z2041 and I-Z2040 samples. But don't expect anything from me anytime soon on those four.

As always, thank you for all of your efforts and also for supplying a link to the paper! When I looked before it appeared inaccessible.

spruithean
09-17-2020, 12:01 AM
This is very exciting! It'll be really interesting to see the autosomal DNA of these samples!

Nibelung
09-17-2020, 03:47 AM
So we finally have the Viking paper! I look forward to watching I1's much deserved discussion of its reign during that era.

deadly77
09-17-2020, 05:47 AM
VK327 is S12289+ and looks like he's on at least the I-Y8333 branch as he's A1841/Y28952+ with two T reads. So this rules out the branches of myself, JonikW and StoneMeadow for VK327. I'll get a closer look this evening after I finish work.

Riverman
09-17-2020, 08:22 AM
So my question is: based on all of this, can I probably trace my descent to Leofwine of Normandy, or have I misinterpreted the guidance on years to most recent common ancestor? Or is the fact that I am looking at 67-marker results rather than 111-marker results skewing my interpretation? Also, will I have to test at a higher level (say Y-700), or to put my results into other providers in order to understand this better?

I had no really close match, but from what I gathered Tip is pretty much useless and unless you have a very close match by STR's, its not reliable. If you really want to know and be sure, also being prepared for the future, with comparisons to ancient DNA and new matches, there is no way around BigY or a similar test. Doesn't mean you get the information for right now, if there is a lack of samples in, but its the only way to go to get to know all the important aspects of your paternal lineage.

Salamander
09-17-2020, 09:47 AM
I had no really close match, but from what I gathered Tip is pretty much useless and unless you have a very close match by STR's, its not reliable. If you really want to know and be sure, also being prepared for the future, with comparisons to ancient DNA and new matches, there is no way around BigY or a similar test. Doesn't mean you get the information for right now, if there is a lack of samples in, but its the only way to go to get to know all the important aspects of your paternal lineage.

Thanks for that. I will do the BigY when I can. In case others are interested there were significant occurrences of specific surnames in my 67-marker matches, at the 5, 6, and 7-step levels. Apart from the Claytons, quite a few of Baylor, Phipps, Compton/Crumpton, Hitchcock/Hickok, Tate and Gordon. But only the last two listed Irish antecedents.

spruithean
09-17-2020, 01:50 PM
Hi, this is my first post on this forum. Pardon me for joining this thread very late, but I found it very useful and I’d like to tease out one aspect. Maybe it will be helpful for some of the other guests who are having trouble interpreting DNA test results.

Stone Meadow’s post mentioned his ancestor Leofwine of Normandy. There is an online genealogy which lists Sir Thomas de Clayton born in England around the 1500s as a direct male descendent of his. By chance, Sir Thomas de Clayton appears as the ancestor of a 7-step match of mine in my FTDNA test. So I was excited to see this post because it potentially linked me to a known individual deep into the Middle Ages.

My FTDNA Y-111 test says I am S1990. My documented direct male genealogy goes back to Ireland but hits a wall around the late 1700s. At the 111-marker level, FTDNA lists only one match for me – an exact match with someone of the same surname as me (King). There are no other matches listed, even at different steps. But at the 67-marker view many more matches appear, and one of those lists Sir Thomas de Clayton as his ancestor.

FTDNA’s “TiP” says there is an 86 per cent chance of this person and I having a common ancestor within 16 generations (say 600 years?) and a 95 per cent chance within 20 generations (say 1000 years?). At first glance this would appear to suggest there’s a pretty good chance that I also am descended from Leofwine of Normandy.

However, at the 67-marker level I have a number of closer contacts whose ancestors came from much further afield. These include a 5-step match with someone harking from Neumark in eastern Germany, and a couple of 6-step matches pointing to Sweden. This would tend to suggest that the King and Clayton lines join up further back than Leofwine.

So my question is: based on all of this, can I probably trace my descent to Leofwine of Normandy, or have I misinterpreted the guidance on years to most recent common ancestor? Or is the fact that I am looking at 67-marker results rather than 111-marker results skewing my interpretation? Also, will I have to test at a higher level (say Y-700), or to put my results into other providers in order to understand this better?

I would be very wary of a 67 marker match, especially once it becomes quite close to being a low probability of a shared recent common ancestor. I say this because I have several 67 marker matches to individuals with ancestors who originated not too far from where my paternal lineage is believed to have come from. Initially, I would have assumed a recent connection, but Big Y testing has shown that the connection is much further back in time and definitely before the advent of surnames.

I'm not sure who this Leofwine of Normandy fellow is? The name Leofwine is a rather Old English (Anglo-Saxon) given name, that I wouldn't expect to see in Normandy. Do the various genealogies for the Claytons have good sources and documentation back to this Leofwine?


So we finally have the Viking paper! I look forward to watching I1's much deserved discussion of its reign during that era.

It's been a fairly long wait for this paper to officially be released, it'll be nice to see some I1 in the discussions now.

deadly77
09-17-2020, 03:49 PM
Looks like some are appearing on the YFull tree already. Among the I1 samples, they have added VK70 at I-Y6374 (under I-P109) and VK70 at I-Y22923 (under I-M227). Probably will add more in stages and likely best to find by opening up basic level haplogroup and using ctrl+F to search for "VK".

deadly77
09-17-2020, 04:24 PM
VK327 is negative for PH4523 (2G) which likely rules out I-PH4462 branch and negative for FT166204 (1C) on the I-A4637 branch although that's only a one read SNP and he's no call for the rest of the SNPs on the I-A4637 branch (although negative for A4642 on the branch I-A4638 downstream. Also negative for A7322 (1G), FT124056 (1C) and Y185625 (1G) on the I-Y185625 branch.

He is positive for BY466/Z44259 which corroborates the A1841/Y28952+. I guess we'll put him at I-Y8334* and he branches off from the other samples at YFull at that point. May check FTDNA's tree later for branches that aren't on YFull.