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JonikW
03-18-2018, 01:10 PM
I'm hoping that a few people here are interested in ancient I1 results. The latest Germanic aDNA paper (behind a paywall at https://www.sciencedirect.com/science/article/pii/S0305440318300505) includes an elderly I1 male from Altenerding-Klettham in southern Germany. I haven't accessed the paper but assume this is the male aged 60+ from Altenerding-Klettham, buried with a spatha and other grave goods, who also features in the recent Bavaria elongated skulls paper (no Y DNA data released). We also had two I1 individuals in the recent Langobard study and I may have missed others...
Has anyone here got an up-to-date list of ancient I1 samples, perhaps with subclades and other useful info? If someone has the data to kick things off, maybe we could post more results on this thread as they are published in future.
Thanks

spruithean
03-18-2018, 01:56 PM
Thanks for sharing!

I was unaware that the Langobard samples were I1, I assume this individual in Altenerding-Klettham was an Alemanni?

I'm not aware of any up-to-date ancient I1 samples and their possible subclades. I hope someone has one!

Pribislav
03-18-2018, 02:16 PM
This is what I have so far:

StoraFörvar11 5500-5250 BC Stora Förvar cave, Stora Karlsö Island Sweden SHG pre-I1-M253 (xL121) Skoglund 2014

BAB5 5300-4900 BC* Balatonszemes-Bagódomb Hungary LBKT_Neolithic I1-M253 Szécsényi-Nagy 2014

RISE179 2010-1776 BC Abekĺs I Sweden Nordic_LN I1-M253 Allentoft 2015

RISE207 1493-1302 BC Angmollan Sweden Nordic_BA I1-M253 Allentoft 2015

RISE210 1432-1292 BC Ängamöllan Sweden Nordic_BA I1-M253? Allentoft 2015

RISE175 1395-1132 BC Abekĺs I Sweden Nordic_BA I1-M253 Allentoft 2015

KO_55 100-300 AD Kowalewko Poland Wielbark_Culture I1a3a1a1a-M253>DF29>Z63>BY151>S2078>S2077>Y2245>L1237 Zenczak 2017

NO3423 550-650 AD Norton on Tees Great Britain Anglo-Saxon I1-M253 Martiniano 2016

SZ45 600-650 AD Szolad Hungary Langobard I1a1b1-M253>DF29>Z2336>Z2337>L22 Amorim 2018

ME_7 1000-1200 AD Markowice Poland Medieval I1a2a2a5-M253>DF29>Z58>Z59>Z2041>Z2040>Z382>Y5384 Zenczak 2017

rms2
03-18-2018, 02:22 PM
The oldest I-M253 I could find at Jean M's Ancestral Journeys/Ancient Eurasian DNA web site was BAB 5 from Balatonszemes-Bagodomb in Hungary. I don't see an age estimate on it, but it dates to the Neolithic Period and belonged to the LBK Transdanubia culture (LinearBandKeramik).

Oops! I see Pribislav beat me to it! Sorry. Too slow, I guess.

JonikW
03-18-2018, 03:18 PM
This is what I have so far:

StoraFörvar11 5500-5250 BC Stora Förvar cave, Stora Karlsö Island Sweden SHG pre-I1-M253 (xL121) Skoglund 2014

BAB5 5300-4900 BC* Balatonszemes-Bagódomb Hungary LBKT_Neolithic I1-M253 Szécsényi-Nagy 2014

RISE179 2010-1776 BC Abekĺs I Sweden Nordic_LN I1-M253 Allentoft 2015

RISE207 1493-1302 BC Angmollan Sweden Nordic_BA I1-M253 Allentoft 2015

RISE210 1432-1292 BC Ängamöllan Sweden Nordic_BA I1-M253? Allentoft 2015

RISE175 1395-1132 BC Abekĺs I Sweden Nordic_BA I1-M253 Allentoft 2015

KO_55 100-300 AD Kowalewko Poland Wielbark_Culture I1a3a1a1a-M253>DF29>Z63>BY151>S2078>S2077>Y2245>L1237 Zenczak 2017

NO3423 550-650 AD Norton on Tees Great Britain Anglo-Saxon I1-M253 Martiniano 2016

SZ45 600-650 AD Szolad Hungary Langobard I1a1b1-M253>DF29>Z2336>Z2337>L22 Amorim 2018

ME_7 1000-1200 AD Markowice Poland Medieval I1a2a2a5-M253>DF29>Z58>Z59>Z2041>Z2040>Z382>Y5384 Zenczak 2017

The other I1 Lombard sample was from the cemetery at Collegno, northern Italy, dated 580-630CE in the paper. He was I1a3 Z79 and is labelled as sample ID number CL63.
From the paper: "Unlike at Szólád, we find evidence of only one other individual (CL63) that is of predominant central/northern ancestry that does not belong to the major kindred unit (though our sampling of this cemetery is not as complete as Szólád)."

Pribislav
03-18-2018, 04:11 PM
The other I1 Lombard sample was from the cemetery at Collegno, northern Italy, dated 580-630CE in the paper. He was I1a3 Z79 and is labelled as sample ID number CL63.
From the paper: "Unlike at Szólád, we find evidence of only one other individual (CL63) that is of predominant central/northern ancestry that does not belong to the major kindred unit (though our sampling of this cemetery is not as complete as Szólád)."

The problem is Z79 is downstream of I2, not I1. So something is not right with CL63, whether they've mistaken haplogroup assignment or SNP.

JonikW
03-18-2018, 04:19 PM
The problem is Z79 is downstream of I2, not I1. So something is not right with CL63, whether they've mistaken haplogroup assignment or SNP.

I just realised that myself... So he was either I1a3 or Z79. Has anyone checked the raw files for CL63?

JonikW
03-18-2018, 07:25 PM
Also found this, Zenczak 2017:

https://www.academia.edu/33791135/2017_Zenczak_.....Piontek_..._Y-chromosome_haplogroup_assignment_through_next_gene ration_sequencing_of_enriched_ancient_DNA_librarie s

"Here, we present the analysis of Y-chromosome obtained from seventeen, not yet reported, ancient male samples excavated from different burial sites in Poland: Kowalewko (Roman Iron Age), Maslomecz (Roman Iron Age), Legowo (early Middle Ages) and Niemcza (early Middle Ages)...

We successfully assigned haplogroups to sixteen individuals. Eight belonged to haplogroup I1 (I-M253). Three of them belonged to the sub-branch I1a3a1a1a (I-L1237) and one to I1a2a (I-Z59). I1 is the most common haplogroup in present day Scandinavia, and it is found in all places invaded by ancient Germanic tribes and Vikings."

And this, Harthun 2016:

https://anthrogenica.com/showthread.php?6635-Holy-Roman-Empire-amp-Migration-Period-Ancient-DNA-from-Germany&p=144929&viewfull=1#post144929

These remains from Görzig (Saxony-Anhalt) date from the 4th and 5th centuries. Seven out of the 12 males were I1. No subclades given.

spruithean
03-18-2018, 08:18 PM
I wish some of these samples (notably Hungary, Nordic LN, Nordic BA and Anglo-Saxon at Teesside) had some degree of subclade testing. I'd be curious to see how many were Z140, L22 or some other subclade.

Looks like a fair chunk of I1 regardless of the subclade is found in areas settled by Germanic tribes or in areas where the eventual Germanic people would appear, not very surprising! :P

JonikW
03-18-2018, 09:21 PM
I wish some of these samples (notably Hungary, Nordic LN, Nordic BA and Anglo-Saxon at Teesside) had some degree of subclade testing. I'd be curious to see how many were Z140, L22 or some other subclade.

Looks like a fair chunk of I1 regardless of the subclade is found in areas settled by Germanic tribes or in areas where the eventual Germanic people would appear, not very surprising! :P

Yes, I assume we were responsible for the 30 percent or so of non-Indo European vocabulary in early Germanic languages, when the R1b and R1a peoples joined with us to create "Germanic" cultures.

JonikW
03-27-2018, 02:09 PM
According to a thread in the ancient DNA section of this site, these three samples from the Bavaria 6th century elongated skulls paper were I1.
AED249 I1 L840
STR486 I1 L840
STR241 I1 L840
STR486 is the individual I mentioned at the start of this thread. L840 doesn't appear to be on the official tree unless I've missed it. But it's available on yseq as a SNP found in a P109 tester. That would make it L22+ and so may have arrived in Bavaria not long before after a long folk movement from the Vistula region or elsewhere in the north. But the presence of L22 in early medieval southern Germany would also seem to open the possibility that these people had arrived in the region earlier. If so, their population group may even account for some L22 in Britain, and so predating the Vikings. This could have been via a route down the Rhine and across with the Anglo-Saxon migrations (as southern German Pottery finds at the Sancton cemetery, for example, attest) or perhaps even earlier via the settlements of "laeti" (settlers with military obligations) from Germania under the Romans. For example Fraomar and his Alemmanic "numerus", which was settled somewhere in Britannia in 372. Alongside laeti, we know that veterans of every stripe from legionaries to barbarian auxiliaries often married local women during service abroad and never returned home.

spruithean
03-27-2018, 02:15 PM
According to YFull and ISOGG L840 is within the 300 something SNPs associated with I-M253.

EDIT: According to my Big Y results I am positive for L840 and I am Z140+. Though it is apparently not on the Haplotree. Ybrowse position is chrY:18,672,817..18,672,817

JonikW
03-27-2018, 02:23 PM
According to YFull and ISOGG L840 is within the 300 something SNPs associated with I-M253.

EDIT: According to my Big Y results I am positive for L840 and I am Z140+. Though it is apparently not on the Haplotree. Ybrowse position is chrY:18,672,817..18,672,817

Ah, great! Scratch my L22 idea then... Wonder if someone will try to get more subclades.

Flatiron
03-27-2018, 03:11 PM
According to YFull's analysis of my Full Genomes test, I am positive at I1 and also for the I1 equivalent SNPs of M253 and L840. YFull estimates the age of these mutations as 4415 ybp. M253 and L840 are rated 5 star by YFull.

vettor
03-27-2018, 06:00 PM
According to a thread in the ancient DNA section of this site, these three samples from the Bavaria 6th century elongated skulls paper were I1.
AED249 I1 L840
STR486 I1 L840
STR241 I1 L840
STR486 is the individual I mentioned at the start of this thread. L840 doesn't appear to be on the official tree unless I've missed it. But it's available on yseq as a SNP found in a P109 tester. That would make it L22+ and so may have arrived in Bavaria not long before after a long folk movement from the Vistula region or elsewhere in the north. But the presence of L22 in early medieval southern Germany would also seem to open the possibility that these people had arrived in the region earlier. If so, their population group may even account for some L22 in Britain, and so predating the Vikings. This could have been via a route down the Rhine and across with the Anglo-Saxon migrations (as southern German Pottery finds at the Sancton cemetery, for example, attest) or perhaps even earlier via the settlements of "laeti" (settlers with military obligations) from Germania under the Romans. For example Fraomar and his Alemmanic "numerus", which was settled somewhere in Britannia in 372. Alongside laeti, we know that veterans of every stripe from legionaries to barbarian auxiliaries often married local women during service abroad and never returned home.

one needs to clarify where they came from , if it was the Oder river area, then they where Lombards, if the came from lower vistula region then they where Goths

Flatiron
03-27-2018, 07:04 PM
I just looked for the SZ45 information in the 2018 Amorim et al paper, but I could not find anything showing a SZ mutation path leading to L22. Maybe I missed it? Or was the information from another source?

spruithean
03-30-2018, 10:09 AM
I believe the information is coming from raw BAM files for these aDNA individuals. At least that's what I'm gathering from reading other threads.

JonikW
03-30-2018, 10:27 AM
I believe the information is coming from raw BAM files for these aDNA individuals. At least that's what I'm gathering from reading other threads.

That's correct, apart from STR486 mentioned at the start of this thread, which is confirmed. I read on another site on the day the paper was posted that one of the finds was an elderly I1 male. This turns out to be STR486, aged 60+ and buried with a spatha and other gear.

Bollox79
04-30-2018, 12:10 AM
That's correct, apart from STR486 mentioned at the start of this thread, which is confirmed. I read on another site on the day the paper was posted that one of the finds was an elderly I1 male. This turns out to be STR486, aged 60+ and buried with a spatha and other gear.

I have asked Alex Williamson to take a look at the samples from Collegno who were only reported to L151 or L52 who are kindred (Germanic Fara here - either agnatic line of descent or a band of brothers or men who traveled in a group with their associates - I think that is what we are seeing in these migration era cemeteries) who are kindred to CL84, a Northern European male who is U106+. These other four I asked Alex to look at if there are in fact BAM or Fastq files... are very Northern European and 1st generation/phase like CL84. I would like to know if they are also U106+.

In addition to that I took a look at the I-M223 (the majority of the I haplogroups for the Szolad samples and the founding male/oldest male who was SZ13 correct?) and that group called ZS20 seems to be very Scandinavian with a presence in the Isles. Depending on the dating of the downstream SNPs under ZS20 - they may come from a Northern Germanic (well it's a certainly) population group who also got over to the Isles (depending on the dating of SNPs again) either with Romans or as Vikings? Or in the Anglo-Saxon period? I am not familiar with this group though or their SNP dating as I am with my own DF98 group etc. I think that these I-M223 samples in Szolad can give us a bit of info on the U106 guys who were buried near them etc and were as Northern European as them. We have to figure these guys were on the move... I'm positive they all probably came from Northern Germany and/or Scandinavia... it's just the particulars we have to figure out (with keeping the SNP dating in mind).

Also there were some I haplogroup guys in the Munich paper... that you guys are discussing in this thread. At least two U106 samples ALH 1 (who is also DF96 brother group to DF98 Wettin) is Z156+ and also AED 106 is Z156+ because he is Z305 (which is downstream of Z156). These SNPs are not as common in Scandinavia as L48 and Z18... but all of these U106 guys from the Baiuvarii paper are very Northern European - placing autosomally with either Scandinavians, Northern Dutch, or Northern German in a K36 PCA. I'm trying to figure out if these Z156 guys around Munich (and keep in mind the Langobards were L48 and Z18 instead of Z156) came from the North and through the West aka Western Germanic groups while the Langobards were more North and then around the East after the collapse of the Hunnic Empire. We must keep in mind that the burials looked at around Munich are dated from 1st phase (both AED or Alternerding were 1st phase so max period 450 to about 500 AD) and one Straubing (STR 316) was 2nd phase so about 500-550 AD... and the Langobard cemetery at Szolad was 560s 570s AD for one generation I think... and the one at Collegno was 1st phase about 570s AD...

P.S. Alex took a look at the U106 guys from around Munich and here is where we are at now:

AED (Altenerding-Klettham cemetery) 106: U106+ (possibly based on BAM analysis kit run by several people and Yleaf for the Z305 result - update: 3 reads for U106 and one for Z305 per Alex W.) - Z381+, Z156+, Z305+)?: Male aged 60+. Grave goods included: spatha, belt, bag, vessel, glass. Burial dated based on grave goods/burial rite to circa 480 - 510 AD. Clusters autosomally in a K36 PCA near Saxony and NE Germany. Phase 1 burial (mid 400s - early 500s AD). Number of grave goods: 10 per the paper “Diet and Mobility in Early Medieval Bavaria: A case study of Carbon and Nitrogen stable isotopes.”

AED (Altenerding-Klettham cemetery) 92: U106+ (per BAM analysis - update: 35 reads(!) for U106 per Alex W.): Male aged 20-30. Grave goods included: spatha, seax, lance, shield, belt, bag. Burial dated based on grave goods/burial rite to circa 480-510 AD. Clusters autosomally in a K36 PCA very near Mecklenburg-Vorpommern in NE Germany (almost on top of it). Edit: Phase 1 burial (mid 400s - early 500s AD). Number of grave goods: 23 (the highest number of grave goods in this cemetery of the samples looked at in the paper Diet and Mobility in Early Medieval Bavaria: A case study of Carbon and Nitrogen stable isotopes).

ALH (Altheim cemetery) 1: U106+, (ALH 1 has now been found positive for the following SNPs by Alex Williamson: R-M269>U106/S21>Z2265> Z381/S263>S264/Z156>S265/Z304>DF96>FGC13326>S22047 ). Male aged 50-60+. Grave goods included: Grave was disturbed/robbed. Burial dated based on grave goods/burial rite: Undateable, but other graves ALH 2, 3, and 10 were carbon dated in the range of roughly 260-535 AD (using lowest and highest estimates). Clusters autosomally in a K36 PCA in between Norway, Denmark, and Northern Netherlands/Friesland.

STR (Straubing-Bajuwarenstraße cemetery) 316: U106+(based on BAM file analysis - update: 4 reads for U106 per Alex W.). Male aged 40-60. Grave goods included: belt, bag, vessel. Burial dated based on grave goods/burial rite to circa 480-510 AD. Clusters autosomally in a K36 PCA between North Norway and Norwegians and somewhat near ALH 1. Phase 2 burial (1st half of 6th cent: 500-550 AD) and 7 grave goods per the paper “Diet and Mobility in Early Medieval Bavaria: A case study of Carbon and Nitrogen stable isotopes.”

STR (Straubing-Bajuwarenstraße cemetery) 393: U106+(based on BAM file analysis - update: 11 reads for U106 per Alex W.). Male aged 40-55. Grave goods included: spatha. Burial dated based on grave goods/burial rite to circa 460 – 530 AD. Clusters autosomally in a K36 PCA near Central East Prussia. No info from paper “Diet and Mobility in Early Medieval Bavaria: A case study of Carbon and Nitrogen stable isotopes.”

Edit: The reason I mention the haplogroup I samples in addition to my U106 group samples... is that I think these groups were traveling in tandem or at least that appears for certain with the Langobards... and these groups could or would have come from similar areas? I don't think it's chance that they are all Northern European and buried with similar traditions and they were not kindred or related in some way..>! The different distributions of these different groups must mean something!!

Additional edit: Many of the Munich U106ers were also looked at in this paper: Diet and Mobility in Early Medieval Bavaria: A case study of Carbon and Nitrogen stable isotopes... and their isotopes and diet analysis were fairly normal - not outliers - for their local area. Per the elongated skull paper I think they look like they are migrants - i.e. they are very Northern European in their autosomal, but per their isotopes they look rather normal, average, and local for those cemeteries around Munich. I think we would find more diet and isotope outliers among the women with the elongated skulls. Does this mean that marriages with or perhaps even taking wives that were more Eastern... that these men buried around Munich had connections with the East... or did they come from a more Western or Northern with Northern Euro autosomal and settled in the area, but retained their Northern European autosomal character by not mixing much with locals, but became local per their isotope and diet? Some of the Germanic tribes had been near or on the Rhine since 200 or 300s AD... here I'm referencing an event or group like the Alamanni and their capture of the Agri Decumates in 260 AD. Why would these guys around Munich appear so Northern European per their autosomal, but local per their isotopes and diet?

One more edit hah: The origins of the Baiuvarii - at least in the papers I've been reading and some in German that I had to translate - seem to think that the origin of the Baiuvarii had several different tribes involved in eventually becoming a somewhat united tribe or group of people. This seems to be reflected in the burials around Munich - that the early 1st phase grave goods have more hand-made and individual characteristics (like different tribes living near each other) and the later phases start to have a more common, mass produced character in their grave goods ;-).

spruithean
06-05-2018, 06:18 PM
Here is a list of the Haplogroup I1 samples in the recent Iceland Study.

SBT-A1 Medieval Iceland, I1a2a1a2-F2642 ~75% Gaelic, ~25% Norse
SVK-A1 Medieval Iceland, I1b-Z131 ~100% Norse
SSG-A3 Medieval Iceland, I1-M253 ~50% Norse, ~50% Gaelic
HSJ-A1 Medieval Iceland, I1a1b3b-L813 ~60% Norse, ~20% Gaelic
SSJ-A2 Medieval Iceland, I1a1b3-Z74 ~90% Norse ~10% Gaelic
DAV-A9 Medieval Iceland, I1-M253 ~100% Norse

JonikW
06-05-2018, 06:29 PM
I'm so pleased you posted that spruithean, especially with the population group breakdown. Good work. I take it that the I-M253-only samples are unlikely to have good enough coverage for anyone to be able identify subclades.

spruithean
06-05-2018, 11:02 PM
I'm so pleased you posted that spruithean, especially with the population group breakdown. Good work. I take it that the I-M253-only samples are unlikely to have good enough coverage for anyone to be able identify subclades.

There might be some errors in the estimations of their ethnic breakdowns.

I agree, I suspect most of the samples have a fair amount of ancient DNA damage. The M253 only samples had SNP calls of ~100-130, while the F2642, Z131, L813, Z74 had calls of ~140-900.

Nice to see an old sample of an I1-Z140+F2642+ individual.

JonikW
08-24-2018, 07:24 AM
Adding to this thread an I1 individual from the Krzewinska et al study on Sigtuna (10th to 12th century Sweden). 84005 from Cemetery 1 was I1a1b3 (I-Z74*). He was one of six individuals with "strontium values and genetic variation that agreed with a local origin".

spruithean
08-24-2018, 06:10 PM
Adding to this thread an I1 individual from the Krzewinska et al study on Sigtuna (10th to 12th century Sweden). 84005 from Cemetery 1 was I1a1b3 (I-Z74*). He was one of six individuals with "strontium values and genetic variation that agreed with a local origin".

I noticed this the other day, but thought nothing of it initially, quite exciting to find a new I1 in the aDNA list! It's also quite interesting that both this Swedish and another Icelandic sample are on the I-Z74 branch of the tree.

The_Lyonnist
08-30-2018, 10:23 PM
Has we found Z17925?

spruithean
08-30-2018, 11:49 PM
Has we found Z17925?

Not to my knowledge, but it is only a matter of time until we find more ancient I1 whether they be DF29 or non-DF29 clades.

Helgenes50
08-31-2018, 05:35 AM
I noticed this the other day, but thought nothing of it initially, quite exciting to find a new I1 in the aDNA list! It's also quite interesting that both this Swedish and another Icelandic sample are on the I-Z74 branch of the tree.

Most of the Z74 clades are Swedish and Finnish.
Some of them are Norwegian, these are the different branches we see for the greatest number in the British Isles and Iceland. The first Z74 was probably an East or South Swede.

mwauthy
08-31-2018, 12:01 PM
Not to my knowledge, but it is only a matter of time until we find more ancient I1 whether they be DF29 or non-DF29 clades.

I wonder how long cremation was practiced in Scandinavia prior to Christianity and if that could be a cause for the lack of ancient I1a samples?

spruithean
08-31-2018, 12:24 PM
I wonder how long cremation was practiced in Scandinavia prior to Christianity and if that could be a cause for the lack of ancient I1a samples?

That definitely has an influence on the search for ancient I1. Hopefully we can still find a good amount despite cremation practices.

Helgenes50
08-31-2018, 12:45 PM
That definitely has an influence on the search for ancient I1. Hopefully we can still find a good amount despite cremation practices.

The case is similar with the ancestors of the Celts, the Urnfield culture

JonikW
08-31-2018, 01:03 PM
Cremation was never universal in the Germanic world of course. The Vikings, for example, practised inhumation as well as cremation, although the latter was more common. Admittedly, the trend does limit things for some periods and places. Can DNA be extracted from some cremated bone using new technology? For years I read that it would be impossible to test the Scandinavian bog bodies but saw recently somewhere that this might soon be possible.
I've posted these pics that I snapped at a Viking exhibition in Norway before on a separate thread.

25627

25626

claudefrancis
09-03-2018, 02:11 PM
Hi every body



I know that I am part of I-M253 I would like to give you some date to
to understand my origin. Can you help me?

file raw data FTDNA transfert (Geno 2.0 NG)

Eurogenes K13


# Population Percent
1 North_Atlantic 36.19
2 East_Med 18.39
3 West_Med 18.16
4 Baltic 15.93
5 West_Asian 6.85
6 Red_Sea 1.88
7 Siberian 0.88
8 East_Asian 0.72
9 Oceanian 0.44
10 Northeast_Africa 0.39
11 Amerindian 0.16

I observe that 1+4 = 51% and 2+3 = 36%

My paternal line live in nord France: influence scandinavian (Danish + Norvegian) maybe (viking) ?????? or germans tribus

My mothernal line live in south Italy influence west asian maybe

All my paternal family are very high, blond, white skin and blue/green eyes

Paternal line: L1(I-m253)>DF29>Z58>I-Z138>S2293>S6277>S6275
Maternal line J1c2

Thanks for your help

mwauthy
09-03-2018, 04:46 PM
Hi every body



I know that I am part of I-M253 I would like to give you some date to
to understand my origin. Can you help me?

file raw data FTDNA transfert (Geno 2.0 NG)

Eurogenes K13


# Population Percent
1 North_Atlantic 36.19
2 East_Med 18.39
3 West_Med 18.16
4 Baltic 15.93
5 West_Asian 6.85
6 Red_Sea 1.88
7 Siberian 0.88
8 East_Asian 0.72
9 Oceanian 0.44
10 Northeast_Africa 0.39
11 Amerindian 0.16

I observe that 1+4 = 51% and 2+3 = 36%

My paternal line live in nord France: influence scandinavian (Danish + Norvegian) maybe (viking) ?????? or germans tribus

My mothernal line live in south Italy influence west asian maybe

All my paternal family are very high, blond, white skin and blue/green eyes

Paternal line: L1(I-m253)>DF29>Z58>I-Z138>S2293>S6277>S6275
Maternal line J1c2

Thanks for your help

I1-S2675 was formed 4600 years ago almost certainly in Scandinavia and has a common ancestor around 3600 years ago almost certainly in Scandinavia. I1-Z138 is a common West Germanic Branch. It arrived in Northern France probably with the Franks or Normans. You need to do deeper Y chromosome testing to see what kind of matches you have 1500-1000 years ago if you want to figure out if it’s most likely Frankish or Norman.

cleerje
09-04-2018, 01:04 AM
Your y dna profile is almost the same as mine: I-M253>DF29>Z58>Z138>Z139>Z2293>>S6277>S6270>S6275. My last name, Cleere, is Middle English derived from the Norman-French name Clere. They probably migrated from Normandy to England after the Norman conquest of England in 1066 and settled in East Anglia. My autosomal DNA profile indicates a strong North Sea (Danish, Swedish) origin, as well as French influence. I suggest you join the I-Z138 group project. They may be able to help you out and they can add one more name to the S6270/S6275 grouping.

rozenfeld
09-04-2018, 01:36 AM
Can DNA be extracted from some cremated bone using new technology?


As of 2017 it was impossible:

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170940

authun
09-09-2018, 03:23 PM
According to a thread in the ancient DNA section of this site, these three samples from the Bavaria 6th century elongated skulls paper were I1.
AED249 I1 L840
STR486 I1 L840
STR241 I1 L840
STR486 is the individual I mentioned at the start of this thread. L840 doesn't appear to be on the official tree unless I've missed it. But it's available on yseq as a SNP found in a P109 tester. That would make it L22+ and so may have arrived in Bavaria not long before after a long folk movement from the Vistula region or elsewhere in the north. But the presence of L22 in early medieval southern Germany would also seem to open the possibility that these people had arrived in the region earlier. If so, their population group may even account for some L22 in Britain, and so predating the Vikings. This could have been via a route down the Rhine and across with the Anglo-Saxon migrations (as southern German Pottery finds at the Sancton cemetery, for example, attest) or perhaps even earlier via the settlements of "laeti" (settlers with military obligations) from Germania under the Romans. For example Fraomar and his Alemmanic "numerus", which was settled somewhere in Britannia in 372. Alongside laeti, we know that veterans of every stripe from legionaries to barbarian auxiliaries often married local women during service abroad and never returned home.

The decoration of the urns on the early cremation cemetaries in the Yorkshire Wolds, at Sancton, Londesbrough, Newbold and so on show the strongest stylistic affinities with those from Angeln and the island of Fyn according to JNL Myres. Later he was looking for evidence of Alemannic laeti and in relation to the village of Almondbury, ( Alemennberig in DB ) as a site. The accepted etymology means Stronghold of All Men but this is insecure and it is pretty much like saying 'nowhere in particular ville'. Stronghold of the Alemann makes more sense although there are some linguistic difficulties, apparantly. Myres points out that in 306, Crocus, who is described as "Alamannorum rege," plays a key role in the accession of Constantine at York. (Aurelius Victor). Doubtless he had a large contingent of men who may have been rewarded by being given grants of land. However, the only alamannic archaeology is one brooch, in east Yorkshire. This doesn't discount the hypothesis. They probably had roman equipment, but it means it cannot be proven.

Other evidences for Alemannic settlement in England are:

276 - 279 Probus defeats alemannic insurection around the Rhine and along with their leader Igillus "sent [them] to Britain, where they settled, and were subsequently very serviceable to the emperor when any insurrection broke out." (Zosiumus)

372 Valentinian sends the Alamannic Fraomarius of the Bucinobantes (an alamannic canton), along with other Alamannic troops commanded by Bitheridius and Hortarius, to Britain. (Ammianus Marcellinus)

However, it has not been possible to identify where they were settled in Britain.

Very recently, thirteen individuals interred at the Alemannic cemetary at Niederstotzingen were tested:

Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard (http://advances.sciencemag.org/content/4/9/eaao1262)

The NRY analyis is given in supplementary data table s9 (http://advances.sciencemag.org/highwire/filestream/206951/field_highwire_adjunct_files/0/aao1262_SM.pdf) but this shows that they all belonged to R1b1a or below except one who belonged to G2a2.


The bavarian case of ancient I1 might be explained by germanic groups from the Vistula but also by Lombards from the Elbe in the north of Germany.:

25773

JonikW
09-09-2018, 05:12 PM
Additionally, in Anglo-Saxon Pottery and the Settlement of England, 1969, Myres mentions in this context a wider “group of place-names in the West Riding containing the element ‘Almond’”. In this part of Yorkshire, he adds, there are such older survivals as Elmet and Loidis, or Leeds, whereas names in the East Riding went on to be “heavily overlaid by Anglian and Scandinavian settlement”. A large part of the Castle Hill fort at Almondbury remains unexcavated so if this was an Alemanni base in England there could be some I1 waiting for us. Interesting in this context that Malcolm Todd pointed out that the Alemanni reused Iron Age hillforts in their homeland, so who knows?

authun
09-09-2018, 06:35 PM
Castle Hill was excavated in 1970. The surprise was that what we had been told at school, in the 1960s, is that it wasn't the site of the Brigantine fort where Cartumandua handed Caractacus over to the romans. This was an idea which went back as far as Camden in his book Britannia written in the 1577. The iron age settlement was abandonned around 400BC, probably due to an underground coal seam burning. It was so hot, the rock was vitrified. Structures such as houses or the wooden pallisade can suddenly burst into flame, anything wooden which is piled into the ground is at danger. Myres' suggested that the hill fort was still highly defensible and one reason why Alamanni might be given land nearby, in Almondbury, was to ensure that Britons didn't re-occupy it. It's a good site with commanding views and steep sides. The normans were the first to reoccupy it when Ilbert de Lacy built a motte and bailey there. No signs of the settlement in Almondbury itself though. All the flat land has been built over.

There were anglo saxons in the area though. My favourite piece of graffito comes from a nearby church - Eoh woro htae - carved into the stonework, eoh wrote this. Eoh must have been bored with the sermon. Still, I live in hope that something older will be found. Recently, it was discovered that the vicus of the roman fort at nearby Slack, was still inhabited in the 4th century. It had been assumed that it was abandonned when the fort was abandonned in or around 140AD. A conduit supplying water to the site was found to have been constructed around the start of the 4th century. So, there are still new discoveries to be made. This is the place Camden assumed to be Camulodunum.

JonikW
09-09-2018, 07:15 PM
Castle Hill was excavated in 1970. The surprise was that what we had been told at school, in the 1960s, is that it wasn't the site of the Brigantine fort where Cartumandua handed Caractacus over to the romans. This was an idea which went back as far as Camden in his book Britannia written in the 1577. The iron age settlement was abandonned around 400BC, probably due to an underground coal seam burning. It was so hot, the rock was vitrified. Structures such as houses or the wooden pallisade can suddenly burst into flame, anything wooden which is piled into the ground is at danger. Myres' suggested that the hill fort was still highly defensible and one reason why Alamanni might be given land nearby, in Almondbury, was to ensure that Britons didn't re-occupy it. It's a good site with commanding views and steep sides. The normans were the first to reoccupy it when Ilbert de Lacy built a motte and bailey there. No signs of the settlement in Almondbury itself though. All the flat land has been built over.

There were anglo saxons in the area though. My favourite piece of graffito comes from a nearby church - Eoh woro htae - carved into the stonework, eoh wrote this. Eoh must have been bored with the sermon. Still, I live in hope that something older will be found. Recently, it was discovered that the vicus of the roman fort at nearby Slack, was still inhabited in the 4th century. It had been assumed that it was abandonned when the fort was abandonned in or around 140AD. A conduit supplying water to the site was found to have been constructed around the start of the 4th century. So, there are still new discoveries to be made. This is the place Camden assumed to be Camulodunum.

Excellent! Are you from Yorkshire? I believe there was talk of applying for a lottery grant to excavate the rest of Castle Hill a couple of years ago (much of it was untouched by the earlier investigation). I don't know if that's still a possibility though...

authun
09-09-2018, 10:41 PM
Yes, it's on the otherside of the valley from where I live. The archaeology is nothing to get too excited about though, but it is always possible that something may be found. There used to be a 19th century pub and car park on the hill but this was illegally demolished by the Thandi Brothers who started to erect a hotel without planning permission. They were ordered to remove the partially built structure which left the big blot that you can see in the photo below. Now some new hotel cum visitor centre is going to be built on that spot, one which is more like the original listed building. That this the area where they have started excavations. Their first find was a 19th century bottle :-)

The tower was built on the site of the motte and bailey to celebrate Queen Victoria's Jubilee. On this photograph, just to the right of the top of the tower, you can see some darker green rectangular crop marks. That is where one of the de Lacy's had their manor house. On the otherisde of the central divide, where it is empty, there was an attempt to build a village in the middle ages, but that failed. Some aerial photos show crop marks which show a rectangular grid layout.

25782

Bollox79
09-10-2018, 08:29 AM
The decoration of the urns on the early cremation cemetaries in the Yorkshire Wolds, at Sancton, Londesbrough, Newbold and so on show the strongest stylistic affinities with those from Angeln and the island of Fyn according to JNL Myres. Later he was looking for evidence of Alemannic laeti and in relation to the village of Almondbury, ( Alemennberig in DB ) as a site. The accepted etymology means Stronghold of All Men but this is insecure and it is pretty much like saying 'nowhere in particular ville'. Stronghold of the Alemann makes more sense although there are some linguistic difficulties, apparantly. Myres points out that in 306, Crocus, who is described as "Alamannorum rege," plays a key role in the accession of Constantine at York. (Aurelius Victor). Doubtless he had a large contingent of men who may have been rewarded by being given grants of land. However, the only alamannic archaeology is one brooch, in east Yorkshire. This doesn't discount the hypothesis. They probably had roman equipment, but it means it cannot be proven.

Other evidences for Alemannic settlement in England are:

276 - 279 Probus defeats alemannic insurection around the Rhine and along with their leader Igillus "sent [them] to Britain, where they settled, and were subsequently very serviceable to the emperor when any insurrection broke out." (Zosiumus)

372 Valentinian sends the Alamannic Fraomarius of the Bucinobantes (an alamannic canton), along with other Alamannic troops commanded by Bitheridius and Hortarius, to Britain. (Ammianus Marcellinus)

However, it has not been possible to identify where they were settled in Britain.

Very recently, thirteen individuals interred at the Alemannic cemetary at Niederstotzingen were tested:

Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard (http://advances.sciencemag.org/content/4/9/eaao1262)

The NRY analyis is given in supplementary data table s9 (http://advances.sciencemag.org/highwire/filestream/206951/field_highwire_adjunct_files/0/aao1262_SM.pdf) but this shows that they all belonged to R1b1a or below except one who belonged to G2a2.


The bavarian case of ancient I1 might be explained by germanic groups from the Vistula but also by Lombards from the Elbe in the north of Germany.:

25773

Graves 1, 3a, 6, 9, 12b, 12c were all R1b-U106 at Niederstotzingen - and positive for a subgroup called Z319 that is shared with the "Longobard" sample from Szolad, Hungary called SZ 11!

Speaking of the Elbe - I think there is a bit of evidence for the sub groups of Z304 (under Z156 under U106 etc) to have a connection with the Elbe area based on the fact that we found Z305 (Z305-307 is ancestral of Z304) and DF96 (which is under Z304) in the Baiuvarii at Altenerding and Altheim near Munich and there is a connection in pottery from there (and around the Roman forts such as Straubing - we had two U106ers at Straubing also) and pottery from along the Elbe. Add to that my sub group of DF98 (which is the brother group of DF96 and associated with the Saxon/Elbe House of Wettin from Wettin, Thuringia) associated with a very old noble family like the Wettins - I think we might see a possible origin for some of the DF98/DF96ers somewhere around the Elbe ;-).

Also plenty of evidence for the L48 group to be also associated with that type of origin and movement...

here are the two Szolad samples that were under L48 that is under U106:

SZ 2: R-M269>U106/S21>Z2265>Z381/S263>Z301/S499>L48>Z9>Z30/S271>Z2>Z7>Z8>ZZ58 by A. Williamson (Wayne K also ran SZ 2 in HG38 assemblies for this sample and found it Z8+, but not ZZ58+): male aged 2-3 years of age. Stress markers and selection of relevant pathologies: Cribra orbitalia; periosteal lesions maxilla. Autosomal: 90%+ CEU+GBR 10% FIN

SZ 11: R-M269>U106/S21>Z2265>Z381/S263>Z301/S499>L48>Z9>Z347>Z328> FGC10367>Z319>S1734>~2222759 2-T-A>FGC13489>hg38:20038474-A-C by A. Williamson: male aged 35-45 years of age. Skull shape: Hyperdolichocrany. Height: 175.5 ± 3.5 cm. Grave goods: Lance. Stress markers and selection of relevant pathologies: Cribra orbitalia; healed right hip and right humerus fracture; osteoarthritis; spondylosis; periodontitis. Autosomal: 100% CEU+GBR

and the Niederstotzingen samples:

c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 1, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 3a, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 6, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 9, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 12b, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 12c, U106/S21> Z2265> Z381/S263>Z301/S499>L48>Z9>Z347> Z328>FGC10367>Z319

Graves 1, 3a, 6, 9, and 12b all have DNA evidence per the new paper that they are 1st or 2nd step relations - 12c does not, but is still the same male paternal line at least to the Z319 marker... I have yet to update my google doc with the archaeological info for the Niederstotzingen guys...

Bollox79
09-10-2018, 08:42 AM
Yes, it's on the otherside of the valley from where I live. The archaeology is nothing to get too excited about though, but it is always possible that something may be found. There used to be a 19th century pub and car park on the hill but this was illegally demolished by the Thandi Brothers who started to erect a hotel without planning permission. They were ordered to remove the partially built structure which left the big blot that you can see in the photo below. Now some new hotel cum visitor centre is going to be built on that spot, one which is more like the original listed building. That this the area where they have started excavations. Their first find was a 19th century bottle :-)

The tower was built on the site of the motte and bailey to celebrate Queen Victoria's Jubilee. On this photograph, just to the right of the top of the tower, you can see some darker green rectangular crop marks. That is where one of the de Lacy's had their manor house. On the otherisde of the central divide, where it is empty, there was an attempt to build a village in the middle ages, but that failed. Some aerial photos show crop marks which show a rectangular grid layout.

25782

authun,

What is your interpretation of the York "Gladiator" burial ground SW of York called Driffield Terrace on "The Mount?" Have you heard of that place? I think it's just as likely (especially now we have so much U106 turning up in Germanic Migration burials) that they might have been POWs or auxiliary soldiers or something - both the samples 3drif-16 and 6drif-3 were in the DNA study and 3drif-16 is DF96 like the Baiuvarii from Altheim and 6drif-3 - well you can see the SNPs I share with him in my signature! I have found a lot of evidence for a high profile cemetery on "The Mount" here under info on Roman burials of York: https://www.british-history.ac.uk/rchme/york/vol1/pp67-110 and also here with the inscriptions found if you search "the mount" in the find/search function: https://www.british-history.ac.uk/rchme/york/vol1/pp111-135

Cheers!

JonikW
09-10-2018, 10:10 AM
Graves 1, 3a, 6, 9, 12b, 12c were all R1b-U106 at Niederstotzingen - and positive for a subgroup called Z319 that is shared with the "Longobard" sample from Szolad, Hungary called SZ 11!

Speaking of the Elbe - I think there is a bit of evidence for the sub groups of Z304 (under Z156 under U106 etc) to have a connection with the Elbe area based on the fact that we found Z305 (Z305-307 is ancestral of Z304) and DF96 (which is under Z304) in the Baiuvarii at Altenerding and Altheim near Munich and there is a connection in pottery from there (and around the Roman forts such as Straubing - we had two U106ers at Straubing also) and pottery from along the Elbe. Add to that my sub group of DF98 (which is the brother group of DF96 and associated with the Saxon/Elbe House of Wettin from Wettin, Thuringia) associated with a very old noble family like the Wettins - I think we might see a possible origin for some of the DF98/DF96ers somewhere around the Elbe ;-).

Also plenty of evidence for the L48 group to be also associated with that type of origin and movement...

here are the two Szolad samples that were under L48 that is under U106:

SZ 2: R-M269>U106/S21>Z2265>Z381/S263>Z301/S499>L48>Z9>Z30/S271>Z2>Z7>Z8>ZZ58 by A. Williamson (Wayne K also ran SZ 2 in HG38 assemblies for this sample and found it Z8+, but not ZZ58+): male aged 2-3 years of age. Stress markers and selection of relevant pathologies: Cribra orbitalia; periosteal lesions maxilla. Autosomal: 90%+ CEU+GBR 10% FIN

SZ 11: R-M269>U106/S21>Z2265>Z381/S263>Z301/S499>L48>Z9>Z347>Z328> FGC10367>Z319>S1734>~2222759 2-T-A>FGC13489>hg38:20038474-A-C by A. Williamson: male aged 35-45 years of age. Skull shape: Hyperdolichocrany. Height: 175.5 ± 3.5 cm. Grave goods: Lance. Stress markers and selection of relevant pathologies: Cribra orbitalia; healed right hip and right humerus fracture; osteoarthritis; spondylosis; periodontitis. Autosomal: 100% CEU+GBR

and the Niederstotzingen samples:

c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 1, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 3a, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 6, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 9, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 12b, U106/S21>Z2265> Z381/S263>Z301/S499> L48> Z9> Z347> Z328> FGC10367>Z319> S1734>FGC363>FGC23165>FGC23143
c. 580-630s AD, Niederstotzingen, Baden-Württemberg, Grave 12c, U106/S21> Z2265> Z381/S263>Z301/S499>L48>Z9>Z347> Z328>FGC10367>Z319

Graves 1, 3a, 6, 9, and 12b all have DNA evidence per the new paper that they are 1st or 2nd step relations - 12c does not, but is still the same male paternal line at least to the Z319 marker... I have yet to update my google doc with the archaeological info for the Niederstotzingen guys...

Thanks Bollox. Given that this is an I1 thread have you discovered anything about the individual mentioned back in the first ever post?

Bollox79
09-10-2018, 10:46 AM
Thanks Bollox. Given that this is an I1 thread have you discovered anything about the individual mentioned back in the first ever post?

JonikW,

As far as I know for now... they still stand at what they were - you are talking about the samples from Straubing and Altenerding correct?

AED249 I1 L840
STR486 I1 L840
STR241 I1 L840

I will keep my eye out for any grave goods attributed to those exact graves as I search for more and more via the internet and google - as I have found some interesting reproductions of grave goods from Altendering and Straubing - but none so far from our U106 or your I1 guys :-(. I can try and run past Alex Williamson who I always ask to take a look at the raw data - I can ask him if he can try and get a few more SNPs out of the three I1 guys via e-mail... I'll send him a message and see what he says ok?

In my google doc I keep for ancient and med U106+ samples, I'd eventually like to include a section listing the other samples of Northern European ancestry like the I1 guys (or R1a) from the Baiuvarii and I2a guys from Szolad - there was one I1 guy at Szolad correct and possibly one at Collegno? Ok did a quick check and CL63 from Collegno is I1a3. I'm not terribly familiar with I subgroups... SZ45 at Szolad was I1a1b1. SZ 12, 14, and 24 were I2a2a1, SZ 43 was I2a2a1a2a1a, SZ 3 was I2a2a1b2a2, and SZ 13, 22, and 7 were I2a2a1b2a2a2 - for a total of 9 I guys - but mostly I2a2a1...

Mainly I would like to have a note on the Y-DNA groups of Northern European men buried near or "with" the U106+ men... or in the same cemetery etc... I just finished up my write up for the Niederstotzingen guys today... and one guy from the Sigtuna paper urm160...

Speaking of the Sigtuna paper: 84005 was I1a1b3(I-Z74∗) and grt036 was I2a2/2b (I-M436∗)...

Edit: JonikW I fired off an e-mail to Alex... will see if he has time to check the Baiuvarii guys!

authun
09-10-2018, 11:08 AM
Yes, I used to study in York during the 1970s but at that time, the Coppergate Dig was the big buzz. The headless roman burials on the Mount were excavated much later of course but I did read up on them. At that time the speculation was that they were gladiators and then later genomic and isotopic tests were undertaken. The last time I ever read anything though was a couple of years ago, summarised here: https://www.york.ac.uk/news-and-events/news/2016/research/headless-romans/

My personal interest has always been Anglo Scandinavian York however, and of course the surrounds. Also, as I am P109, I tend to read more on northern european and Scandinavian history. Yorkshire is rich in norse stone scultpures, many of which appear now as part of the fabric in church walls. It's great fun spotting them. There is of course the need to read up on the earlier romans though. A few years ago I saw the 6th legion stone in the church at Escombe. This is a very early anglo saxon church dating to around 670-675 which used stone robbed from the ruins of the roman fort at Binchester. The roman interest is therefore secondary to the anglo scandinavian interest.

I retain some interest in roman britain because the recent excavations at the vicus belonging to the roman fort at Slack may be of major importance. It looks as if a mansio was built there and this might have become an important centre in the Kingdom of Elmet. I'd like to think it was the place where Hereric hid from Aethelfrith. It is on the York to Chester road. Edwin was being protected in Gwyned at that time. The roman interest is there as the prelude to the period I like to study.

The layout of the fort and the vicus:

25789


The proposed site of the Mansio, the fort had long gone by the time this was erected. It just appears here for positioning purposes.

25790


What remains to be found however is the graveyard. The corresponding fort at Castleshaw on the other side of the pennines too has a graveyeard, somewhere. Neither have yet been found.

JonikW
09-10-2018, 02:01 PM
JonikW,

As far as I know for now... they still stand at what they were - you are talking about the samples from Straubing and Altenerding correct?

AED249 I1 L840
STR486 I1 L840
STR241 I1 L840

I will keep my eye out for any grave goods attributed to those exact graves as I search for more and more via the internet and google - as I have found some interesting reproductions of grave goods from Altendering and Straubing - but none so far from our U106 or your I1 guys :-(. I can try and run past Alex Williamson who I always ask to take a look at the raw data - I can ask him if he can try and get a few more SNPs out of the three I1 guys via e-mail... I'll send him a message and see what he says ok?

In my google doc I keep for ancient and med U106+ samples, I'd eventually like to include a section listing the other samples of Northern European ancestry like the I1 guys (or R1a) from the Baiuvarii and I2a guys from Szolad - there was one I1 guy at Szolad correct and possibly one at Collegno? Ok did a quick check and CL63 from Collegno is I1a3. I'm not terribly familiar with I subgroups... SZ45 at Szolad was I1a1b1. SZ 12, 14, and 24 were I2a2a1, SZ 43 was I2a2a1a2a1a, SZ 3 was I2a2a1b2a2, and SZ 13, 22, and 7 were I2a2a1b2a2a2 - for a total of 9 I guys - but mostly I2a2a1...

Mainly I would like to have a note on the Y-DNA groups of Northern European men buried near or "with" the U106+ men... or in the same cemetery etc... I just finished up my write up for the Niederstotzingen guys today... and one guy from the Sigtuna paper urm160...

Speaking of the Sigtuna paper: 84005 was I1a1b3(I-Z74∗) and grt036 was I2a2/2b (I-M436∗)...

Edit: JonikW I fired off an e-mail to Alex... will see if he has time to check the Baiuvarii guys!

Thanks! Anything you can find out on any I1 samples that accompany U106 would be very helpful and also illuminate your own excellent work on kinship groups, status and so on, I imagine. I hope to see some more posts from you on the I1 section in future. Your U106 efforts are truly commendable. It's great to have authun on board with his insights too.

Bollox79
09-11-2018, 06:18 AM
Thanks! Anything you can find out on any I1 samples that accompany U106 would be very helpful and also illuminate your own excellent work on kinship groups, status and so on, I imagine. I hope to see some more posts from you on the I1 section in future. Your U106 efforts are truly commendable. It's great to have authun on board with his insights too.

JonikW,

I heard back from Alex... and this is what he had to say about the three I1 guys from the Baiuvarii paper - I hope it helps a bit at least:

"I took a look at the 3 men you mentioned. They are targeted capture sequencing, which only looks at specific locations, rather than the whole genome. There isn't much there. I don't care much for this type of test. I generally work from the data on my own tree. I don't have much of an I branch on my tree, so I had to use the ISOGG tree.

STR486 - I1a. Apart from the various I1 reads, he is positive for V1614/Z2891 (1 read) and CTS9848 Z2892 (1 read).
AED249 - I1a. Apart from the various I1 reads, he is positive for DF29/S438 (1 read)
STR241 - I1. Can't find anything beyond I1."

Once again credit to Alex for teasing out a few more SNPs - I don't know if those for STR486 or AED249 match any of your SNPs or any other I1 guy's SNPs? Alex and I are not very familiar with the I tree - we are mainly R1b guys - he is P312 and I am U106 etc... hope it helps and makes up for me clogging up your I thread with U106 stuff - but then again I consider us (I and U106 - and R1a even in some areas) to be the uber Northern European paternal lines ;-p.

Cheers,
Charlie

Edit: JonikW you should start your own google doc for ancient and medieval results for haplogroup I1 (and I2?)... it's pretty easy and google docs is awesome in that it saves everything you do so as you do it... You could start with the three from the Baiuvarii paper - now you have the SNPs they are positive for (though maybe mention it was only targeted sequencing - limited data) and get the archeological data from the paper to add to it ;-)!

JonikW
09-11-2018, 08:49 AM
JonikW,

I heard back from Alex... and this is what he had to say about the three I1 guys from the Baiuvarii paper - I hope it helps a bit at least:

"I took a look at the 3 men you mentioned. They are targeted capture sequencing, which only looks at specific locations, rather than the whole genome. There isn't much there. I don't care much for this type of test. I generally work from the data on my own tree. I don't have much of an I branch on my tree, so I had to use the ISOGG tree.

STR486 - I1a. Apart from the various I1 reads, he is positive for V1614/Z2891 (1 read) and CTS9848 Z2892 (1 read).
AED249 - I1a. Apart from the various I1 reads, he is positive for DF29/S438 (1 read)
STR241 - I1. Can't find anything beyond I1."

Once again credit to Alex for teasing out a few more SNPs - I don't know if those for STR486 or AED249 match any of your SNPs or any other I1 guy's SNPs? Alex and I are not very familiar with the I tree - we are mainly R1b guys - he is P312 and I am U106 etc... hope it helps and makes up for me clogging up your I thread with U106 stuff - but then again I consider us (I and U106 - and R1a even in some areas) to be the uber Northern European paternal lines ;-p.

Cheers,
Charlie

Edit: JonikW you should start your own google doc for ancient and medieval results for haplogroup I1 (and I2?)... it's pretty easy and google docs is awesome in that it saves everything you do so as you do it... You could start with the three from the Baiuvarii paper - now you have the SNPs they are positive for (though maybe mention it was only targeted sequencing - limited data) and get the archeological data from the paper to add to it ;-)!

Nice work Charlie. Much appreciated. Please pass on thanks from users of this thread! I'll check out those SNPs and really should compile a database unless anyone who's more expert feels like giving it a go...

claudefrancis
09-11-2018, 01:19 PM
Hi again

I have father line S6275 (nord France) and mother line J1C2 (center Italy)


Yesderday I decide to work for 2 approach

I buy to FTDNA – S20289 pack + BY1 pack + A6397 pack

After the results I will buy other under pack if necessary

I buy the same day Y-DNA67

But for FTDNA I am S6275 but I don't understand S6270 was not confirm ?

Thanks for your help

JonikW
09-11-2018, 01:55 PM
Hi again

I have father line S6275 (nord France) and mother line J1C2 (center Italy)


Yesderday I decide to work for 2 approach

I buy to FTDNA – S20289 pack + BY1 pack + A6397 pack

After the results I will buy other under pack if necessary

I buy the same day Y-DNA67

But for FTDNA I am S6275 but I don't understand S6270 was not confirm ?

Thanks for your help

I'm sure someone will help Claudefrancis. Could you post on a different thread so we can keep this for ancient discussion?:)

claudefrancis
09-11-2018, 03:16 PM
Dear JonikW,


sure I will open a thread of I-Z58 maybe under I-M253

spruithean
09-11-2018, 07:13 PM
JonikW,

I heard back from Alex... and this is what he had to say about the three I1 guys from the Baiuvarii paper - I hope it helps a bit at least:

"I took a look at the 3 men you mentioned. They are targeted capture sequencing, which only looks at specific locations, rather than the whole genome. There isn't much there. I don't care much for this type of test. I generally work from the data on my own tree. I don't have much of an I branch on my tree, so I had to use the ISOGG tree.

STR486 - I1a. Apart from the various I1 reads, he is positive for V1614/Z2891 (1 read) and CTS9848 Z2892 (1 read).
AED249 - I1a. Apart from the various I1 reads, he is positive for DF29/S438 (1 read)
STR241 - I1. Can't find anything beyond I1."

Once again credit to Alex for teasing out a few more SNPs - I don't know if those for STR486 or AED249 match any of your SNPs or any other I1 guy's SNPs? Alex and I are not very familiar with the I tree - we are mainly R1b guys - he is P312 and I am U106 etc... hope it helps and makes up for me clogging up your I thread with U106 stuff - but then again I consider us (I and U106 - and R1a even in some areas) to be the uber Northern European paternal lines ;-p.

Cheers,
Charlie

Edit: JonikW you should start your own google doc for ancient and medieval results for haplogroup I1 (and I2?)... it's pretty easy and google docs is awesome in that it saves everything you do so as you do it... You could start with the three from the Baiuvarii paper - now you have the SNPs they are positive for (though maybe mention it was only targeted sequencing - limited data) and get the archeological data from the paper to add to it ;-)!

Just to adjust the nomenclature for a quick reference (for myself, and anyone who gets confused by alternate SNPs), STR486, is likely I-DF29, along with AED249. I'm curious about STR241, perhaps he was also DF29 (likely, considering 99% of I1 is descended from DF29, with the small minority belonging to non-DF29).

deadly77
09-13-2018, 04:20 PM
I just realised that myself... So he was either I1a3 or Z79. Has anyone checked the raw files for CL63?

I realize that this is several months after the question was asked regarding the other I1 Lombard sample was from the cemetery at Collegno, northern Italy, dated 580-630CE in the paper, but it popped up again on the I-M253 Facebook page today.

You're quite right - Z79 is a SNP that is part of the I2 haplogroup.

I had a look at the supporting information for the paper at https://www.nature.com/articles/s41467-018-06024-4#Sec23 - if you click on Supplementary Data 3 it will bring up an excel file which has more information.

Looking at CL63 they list him as positive for Z79. I checked the position number 17147721 and that's correct for Z79 at using the hg19 reference. However, CL63 is negative for pretty much all of the upstream I2 SNPs that I can see - negative for L460, M438, etc. Then if you go and look at the I1 SNPs, CL63 is positive for several of those, including M253 and several of those in the big block of >300 SNPs that defines I1 before branching into subclades. He's positive for DF29 and negative for L22, P109, Z63.

My feeling is that the Z79 SNP in CL63 is a false positive read and CL63 is I1 and not I2 based on the other SNPs. But I'm not sure about their haplogroup assignments - they list P109 as I2 and also I1a3 is Z63 (which he's negative for). Perhaps they're using an earlier version of the ISOGG naming convention?

The other I1 individual in that study SZ45 also positive for a lot of the I1 SNPs. However, if I'm reading the data correctly, they've listed said individual as derivative for both L22 and Z63 so at least one of them must be wrong. Perhaps they are making calls for SNPs based on a low number of reads.

deadly77
09-13-2018, 04:32 PM
I also received an email today from Hunter Provyn's Mygrations project (until recently this was called Phylogeograper). He's collecting locations and SNPs for ancient DNA into a shared document to add to his database as supplemental samples https://phylogeographer.com/supplemental-samples/ or directly to an online excel spreadsheet here https://docs.google.com/spreadsheets/d/1OttVBg8z-EIVKTG-PTo-XvzSEdqxKx8Uf2p6YjSe5jo/edit#gid=546343050

spruithean
09-13-2018, 10:01 PM
I realize that this is several months after the question was asked regarding the other I1 Lombard sample was from the cemetery at Collegno, northern Italy, dated 580-630CE in the paper, but it popped up again on the I-M253 Facebook page today.

You're quite right - Z79 is a SNP that is part of the I2 haplogroup.

I had a look at the supporting information for the paper at https://www.nature.com/articles/s41467-018-06024-4#Sec23 - if you click on Supplementary Data 3 it will bring up an excel file which has more information.

Looking at CL63 they list him as positive for Z79. I checked the position number 17147721 and that's correct for Z79 at using the hg19 reference. However, CL63 is negative for pretty much all of the upstream I2 SNPs that I can see - negative for L460, M438, etc. Then if you go and look at the I1 SNPs, CL63 is positive for several of those, including M253 and several of those in the big block of >300 SNPs that defines I1 before branching into subclades. He's positive for DF29 and negative for L22, P109, Z63.

My feeling is that the Z79 SNP in CL63 is a false positive read and CL63 is I1 and not I2 based on the other SNPs. But I'm not sure about their haplogroup assignments - they list P109 as I2 and also I1a3 is Z63 (which he's negative for). Perhaps they're using an earlier version of the ISOGG naming convention?

The other I1 individual in that study SZ45 also positive for a lot of the I1 SNPs. However, if I'm reading the data correctly, they've listed said individual as derivative for both L22 and Z63 so at least one of them must be wrong. Perhaps they are making calls for SNPs based on a low number of reads.

Thank for you passing this along, that certainly shakes things up. CL63, could very well be I-DF29 instead of I-Z79. That's some good news (possibly) for the rather large DF29 crowd.

I hope they can fix these errors, especially with the mislabeling of P109 and I2! Not to mention the positive results for L22 and Z63, which is clearly not possible...

oz
09-13-2018, 10:17 PM
Why would they put such confusing inacurate labels that don't even make sense? I'm all sorts of confused about this.

spruithean
09-13-2018, 10:30 PM
Why would they put such confusing inacurate labels that don't even make sense? I'm all sorts of confused about this.

Probably a combo of low quality reads and human error.

deadly77
09-13-2018, 11:03 PM
Probably a combo of low quality reads and human error.

I'd agree it's likely a combination of both. False positives can definitely arise from a low number of reads (eg. 1 or 2) which is why the more reliable NGS tests read multiple times. Perhaps getting into the primary data would help, but I'm not at the level of technical know-how myself yet and I'm not sure my current computer is powerful enough to handle that. It would be great if some of the BAM files these samples could make their way over to YFull.

Another possibility is that the DNA over time has degraded to a point where the data is just all they can get from it.

But yes, some of the assignment of SNPs and haplogroups as well as positive results for mutually exclusive descendant branches raises some red flags from looking at the supplementary data as opposed to just taking the manuscript at face value. I'm rather surprised that it wasn't caught in peer review.

25896

JonikW
09-14-2018, 07:53 AM
I'd agree it's likely a combination of both. False positives can definitely arise from a low number of reads (eg. 1 or 2) which is why the more reliable NGS tests read multiple times. Perhaps getting into the primary data would help, but I'm not at the level of technical know-how myself yet and I'm not sure my current computer is powerful enough to handle that. It would be great if some of the BAM files these samples could make their way over to YFull.

Another possibility is that the DNA over time has degraded to a point where the data is just all they can get from it.

But yes, some of the assignment of SNPs and haplogroups as well as positive results for mutually exclusive descendant branches raises some red flags from looking at the supplementary data as opposed to just taking the manuscript at face value. I'm rather surprised that it wasn't caught in peer review.

25896

Has anyone ever sent an aDNA BAM file to YFull, I wonder? What we need is a rich I1 person to help out. Anyone have Warren Buffett's contact details?;) On a more serious note, this does have worrying implications for how much we will learn about subclades as more ancient samples come in, particularly for those of us who are interested in potential matches. It also raises alarms about the peer review process. There were obviously no I1 or I2 people involved in this particular case, that's for sure.

deadly77
09-14-2018, 03:38 PM
Has anyone ever sent an aDNA BAM file to YFull, I wonder? What we need is a rich I1 person to help out. Anyone have Warren Buffett's contact details?;) On a more serious note, this does have worrying implications for how much we will learn about subclades as more ancient samples come in, particularly for those of us who are interested in potential matches. It also raises alarms about the peer review process. There were obviously no I1 or I2 people involved in this particular case, that's for sure.

I don't know if anybody sends ancient DNA BAM files to YFull. The majority of their database is from customer submissions and you can tell which ones these are because they have a YF prefix to the kit. But they do include data from other sources - you can usually tell these ones because they have a different kit prefix (HG for anonymous donors from the 1000 genomes project, ERS from an academic paper on Sardinians, etc.). They have a list of them here on their website: https://www.yfull.com/paper/list/

I had another look at the Lombard Cemeteries paper in question and at the end it says under Data Availability "Sequencing data (as processed BAM files) are available from the NCBI sequence readarchive (SRA) database under accession # SRP132561 (1240 capture data) andSRP132581 (WGS data)." - it may just be as simple as sending YFull an email and asking them if they can download the BAM from there for this and other papers. But I don't have any idea if this is the best way (or even a way...).

JonikW
09-14-2018, 09:31 PM
I don't know if anybody sends ancient DNA BAM files to YFull. The majority of their database is from customer submissions and you can tell which ones these are because they have a YF prefix to the kit. But they do include data from other sources - you can usually tell these ones because they have a different kit prefix (HG for anonymous donors from the 1000 genomes project, ERS from an academic paper on Sardinians, etc.). They have a list of them here on their website: https://www.yfull.com/paper/list/

I had another look at the Lombard Cemeteries paper in question and at the end it says under Data Availability "Sequencing data (as processed BAM files) are available from the NCBI sequence readarchive (SRA) database under accession # SRP132561 (1240 capture data) andSRP132581 (WGS data)." - it may just be as simple as sending YFull an email and asking them if they can download the BAM from there for this and other papers. But I don't have any idea if this is the best way (or even a way...).

That link was interesting. I wonder whether some of those studies paid YFull for its services. After all, it might make sense in some cases. I notice the Reich stuff isn't there.

deadly77
10-06-2018, 01:22 PM
I decided to try and get my hands dirty with looking at some of these in more detail. I was most interested in SBT-A1 from the Science 2018 paper by Ebenesersdóttir et al. which reported the genomes of 27 ancient Icelanders. With a more recent paper, I thought the coverage might be more extensive and the paper listed SBT-A1 as I1a2a1a2, which would make him I-F2642/S2169. I'm I-Z140 but on a different branch down I-L338, and I figured some of my fellow Z140+ folks on here would be interested in SBT-A1 as well. :)

I downloaded the BAM file for SBT-A1, which is freely available, and I started looking at the data using the Broad Institute’s Integrated Genomics Viewer (IGV). The coverage of the Y chromosome looks to be a lot less that what we expect from looking at our own Big Y, YElite or WGS tests. Some areas of the Y chromosome are not well covered by whatever analysis method the researchers used and some portions are not covered at all. Please bear that in mind there are going to be a few holes from no calls and one read SNPs.

So, in checking for the SNP that we’re interested in, SBT-A1 is indeed F2642+, but it’s only one read for A. One-read SNPs can be false positives, so decided to check a few others – Z140+ (again 1 read), M253+ (4 positive reads). For the SNPs that are currently phyloequivalent for F2642, SBT-A1 is a no call for S2163, 1 read positive for S2155 and Z4725 plus some good positive reads for CTS3521 (12G) and CTS9191 (6T). So, despite the one read for F2642, I believe we can be reasonably confident from the other SNPs that SBT-A1 is F2642+.

What I really wanted to get into was looking at the subclades downstream of F2642. Started out with the most populated subclades – SBT-A1 is clearly CTS6772- (11C) and a no call for Y1966. SBT-A1 is also Y1884- (2C) and a no call for Y1843 and Y1854. SBT-A1 is also A1925- (2T). So that rules out a lot of the people in the project looking for a long distant Icelandic relative - sorry Spruithean and JMcB - he's quite far away from your branch:\

We do have a small group of six folks in the FTDNA Z140 project that are positive for Y1854 but negative for Y1843 or Y1884, so based on the no call for Y1854 in SBT-A1, I started looking around those. It looks like a couple of those have Big Y and one has FGC’s YElite. The FGC YElite results had a series of novel SNPs which I thought were worth looking for in SBT-A1’s BAM file, and quite a few of them match up with those. 15 of these SNPs are no calls, 10 SNPs are negative but for 12 of these SNPs SBT-A1 is positive, although some I would say are less confident as they are one read SNPs or in the DYZ19 region. However, there are several SNPs with multiple positive reads in SBT-A1. SBT-A1 is also positive (5G reads) for the terminal SNP for another individual in the FTDNA project. SBT-A1 is A1549- with 3G reads which is shown as the terminal SNP for another individual on the same branch at FTDNA. I don’t know all the novel SNPs from the two Big Y tests.

SBT-A1's branch isn't on the YFull tree, probably because it's a small group and neither the FGC YElite or the two Big Y tests have uploaded there. It would correspond to the FGC74521 branch on FTDNA's haplotree - SBT-A1 is FGC74521+ with 5 positive G reads. SBT-A1 also positive for BY46619 with 12 reads, which is on FTDNA’s haplotree with FGC74521, although it’s in the DYZ19 region, so I'd be a bit wary of that one. SBT-A1 is a no call for A1547 which is also on the same branch of FTDNA's haplotree. However, several positive reads on other SNPs on that branch I think we can be fairly confident on where SBT-A1 fits on the I-Z140 portion of the phylogenetic tree.

JMcB
10-06-2018, 02:33 PM
So that rules out a lot of the people in the project looking for a long distant Icelandic relative - sorry Spruithean and JMcB - he's quite far away from your branch

O well, you can’t win them all. ;-) Truthfully, I’m happy whenever any ancient I1 sample is found, anywhere! So F2642 is a major positive as far as I’m concerned! Nice work, Deadly! It’s a real plus having that extra information

Bollox79
10-06-2018, 02:56 PM
I decided to try and get my hands dirty with looking at some of these in more detail. I was most interested in SBT-A1 from the Science 2018 paper by Ebenesersdóttir et al. which reported the genomes of 27 ancient Icelanders. With a more recent paper, I thought the coverage might be more extensive and the paper listed SBT-A1 as I1a2a1a2, which would make him I-F2642/S2169. I'm I-Z140 but on a different branch down I-L338, and I figured some of my fellow Z140+ folks on here would be interested in SBT-A1 as well. :)

I downloaded the BAM file for SBT-A1, which is freely available, and I started looking at the data using the Broad Institute’s Integrated Genomics Viewer (IGV). The coverage of the Y chromosome looks to be a lot less that what we expect from looking at our own Big Y, YElite or WGS tests. Some areas of the Y chromosome are not well covered by whatever analysis method the researchers used and some portions are not covered at all. Please bear that in mind there are going to be a few holes from no calls and one read SNPs.

So, in checking for the SNP that we’re interested in, SBT-A1 is indeed F2642+, but it’s only one read for A. One-read SNPs can be false positives, so decided to check a few others – Z140+ (again 1 read), M253+ (4 positive reads). For the SNPs that are currently phyloequivalent for F2642, SBT-A1 is a no call for S2163, 1 read positive for S2155 and Z4725 plus some good positive reads for CTS3521 (12G) and CTS9191 (6T). So, despite the one read for F2642, I believe we can be reasonably confident from the other SNPs that SBT-A1 is F2642+.

What I really wanted to get into was looking at the subclades downstream of F2642. Started out with the most populated subclades – SBT-A1 is clearly CTS6772- (11C) and a no call for Y1966. SBT-A1 is also Y1884- (2C) and a no call for Y1843 and Y1854. SBT-A1 is also A1925- (2T). So that rules out a lot of the people in the project looking for a long distant Icelandic relative - sorry Spruithean and JMcB - he's quite far away from your branch:\

We do have a small group of six folks in the FTDNA Z140 project that are positive for Y1854 but negative for Y1843 or Y1884, so based on the no call for Y1854 in SBT-A1, I started looking around those. It looks like a couple of those have Big Y and one has FGC’s YElite. The FGC YElite results had a series of novel SNPs which I thought were worth looking for in SBT-A1’s BAM file, and quite a few of them match up with those. 15 of these SNPs are no calls, 10 SNPs are negative but for 12 of these SNPs SBT-A1 is positive, although some I would say are less confident as they are one read SNPs or in the DYZ19 region. However, there are several SNPs with multiple positive reads in SBT-A1. SBT-A1 is also positive (5G reads) for the terminal SNP for another individual in the FTDNA project. SBT-A1 is A1549- with 3G reads which is shown as the terminal SNP for another individual on the same branch at FTDNA. I don’t know all the novel SNPs from the two Big Y tests.

SBT-A1's branch isn't on the YFull tree, probably because it's a small group and neither the FGC YElite or the two Big Y tests have uploaded there. It would correspond to the FGC74521 branch on FTDNA's haplotree - SBT-A1 is FGC74521+ with 5 positive G reads. SBT-A1 also positive for BY46619 with 12 reads, which is on FTDNA’s haplotree with FGC74521, although it’s in the DYZ19 region, so I'd be a bit wary of that one. SBT-A1 is a no call for A1547 which is also on the same branch of FTDNA's haplotree. However, several positive reads on other SNPs on that branch I think we can be fairly confident on where SBT-A1 fits on the I-Z140 portion of the phylogenetic tree.

Great to see someone digging into the I ancient DNA ;-)! I try to follow a bit since I has been found with U106 in a couple papers etc!

deadly77
10-06-2018, 03:07 PM
O well, you can’t win them all. ;-) Truthfully, I’m happy whenever any ancient I1 sample is found, anywhere! So F2642 is a major positive as far as I’m concerned! Nice work, Deadly! It’s a real plus having that extra information

I figured - I said that more in jest than serious, but figured you'd get that. Yes, me too - especially with some of the ambiguous assignments on some of the samples from a different paper that were discussed earlier in this thread where one looked like he was I1 but with a terminal SNP from I2, or another one from the same paper that was positive for Z63 and L22... I think at least with SBT-A1 we can be reasonably confident as to where this one is. Still a lot of no calls in the data though, so maybe it's as good as it gets.

I sent an email to the guys at YFull - see if they say if the sample is good enough to put on the YFull tree.

:beerchug:

deadly77
10-06-2018, 03:11 PM
Great to see someone digging into the I ancient DNA ;-)! I try to follow a bit since I has been found with U106 in a couple papers etc!

Cheers - this was the first ancient one I looked at. The BAM file was available and I learned a fair bit about how to use the IGV. I would say it's good if you know what you're looking for - we're fortunate under I-Z140 to have a fairly decent population of testers which makes it easier to hunt and pick what I'm looking for. I'd be a bit less confident about doing the same thing with hunting for novel SNPs on data with this low coverage - some of the one reads not sure if they're real or not. But it worked well for tracking against the known Z140 tree.

spruithean
10-06-2018, 04:09 PM
Bummer that he isn't on our branch!

Thanks for digging into that one deadly77, I hope at some point we find some ancient L338 and ancient A13241. That field is still overwhelmingly R1b dominated.

Bollox79
10-06-2018, 05:00 PM
Cheers - this was the first ancient one I looked at. The BAM file was available and I learned a fair bit about how to use the IGV. I would say it's good if you know what you're looking for - we're fortunate under I-Z140 to have a fairly decent population of testers which makes it easier to hunt and pick what I'm looking for. I'd be a bit less confident about doing the same thing with hunting for novel SNPs on data with this low coverage - some of the one reads not sure if they're real or not. But it worked well for tracking against the known Z140 tree.

Certainly Cheers mate! For what it's worth (I realize this is a haplogroup I thread and try not to post TOO much U106 stuff here)... here is my current google doc that I keep on my group U106 and the samples that are so far U106+ and sub groups where possible. Several people including myself usually take a look at the Bam files or convert them from .fastq (I can look at Bams, but I can't convert - my crappy laptop is too slow hah). I usually ask Alex Williamson of Big Tree fame to run any sample I'm interested in through his process that calls SNP reads from the .fastq file. He is usually very helpful and sometimes, when time permits, adds them to his U106 Big Tree. His work is priceless ;-)! I record all U106+ samples (no matter if they are my sub group or not) and their burial and archeological and osteological data where possible, even if I have to translate it from another language (usually German and sometimes Czech for Unetice burial at Jinonice outside of Prague). Maybe you could start a similar one for haplogroup I? Google doc is very handy for this - I can just jump on and change stuff and it saves everything I do and I can post links and let people view. I turned off comments as I really only want comments from Alex or Dr. Iain McDonald - Dr. Iain and myself are the real reason I am keeping this list, but I like to share it with anyone who has an interest in aDNA. Here is the link: https://docs.google.com/document/d/1h6ZFaJe9gUtwl2r2Iu33B5_kCc6er5n9oEthCe25wV0/edit?usp=sharing

Cheers,
Charlie

Edit: on my doc the stuff at the beginning is a summary of the burials - Dr. Iain suggested I add that so when we get enough samples that he would use them in his dating programs etc... he can have a quick reference and not have to dig through the archeological stuff! Below that is all the other info under the main headings etc!

JonikW
10-06-2018, 05:35 PM
Great work from deadly77. We've got four papers coming up that potentially will have I1 ancient samples: on the Vikings, a Cambridgeshire Anglo-Saxon cemetery, the Goths and the Ostrogoths. The last two were flagged up recently on a Polish thread on this site.

spruithean
10-06-2018, 05:52 PM
I hope we get some new ancient I1. I hope we get at least a few individuals from those four papers. R1b should sit this one out :laugh:

Bollox79
10-06-2018, 07:19 PM
I hope we get some new ancient I1. I hope we get at least a few individuals from those four papers. R1b should sit this one out :laugh:

I am secretly hoping for a couple U106 along with plenty of I1 how's that? :-).

Edit: actually with House of Wettin's association with Saxony - if we just get one or two DF98ers in that Saxon cemetery that would enough for me!

JMcB
10-06-2018, 07:48 PM
Certainly Cheers mate! For what it's worth (I realize this is a haplogroup I thread and try not to post TOO much U106 stuff here)... here is my current google doc that I keep on my group U106 and the samples that are so far U106+ and sub groups where possible. Several people including myself usually take a look at the Bam files or convert them from .fastq (I can look at Bams, but I can't convert - my crappy laptop is too slow hah). I usually ask Alex Williamson of Big Tree fame to run any sample I'm interested in through his process that calls SNP reads from the .fastq file. He is usually very helpful and sometimes, when time permits, adds them to his U106 Big Tree. His work is priceless ;-)! I record all U106+ samples (no matter if they are my sub group or not) and their burial and archeological and osteological data where possible, even if I have to translate it from another language (usually German and sometimes Czech for Unetice burial at Jinonice outside of Prague). Maybe you could start a similar one for haplogroup I? Google doc is very handy for this - I can just jump on and change stuff and it saves everything I do and I can post links and let people view. I turned off comments as I really only want comments from Alex or Dr. Iain McDonald - Dr. Iain and myself are the real reason I am keeping this list, but I like to share it with anyone who has an interest in aDNA. Here is the link: https://docs.google.com/document/d/1h6ZFaJe9gUtwl2r2Iu33B5_kCc6er5n9oEthCe25wV0/edit?usp=sharing

Cheers,
Charlie

Edit: on my doc the stuff at the beginning is a summary of the burials - Dr. Iain suggested I add that so when we get enough samples that he would use them in his dating programs etc... he can have a quick reference and not have to dig through the archeological stuff! Below that is all the other info under the main headings etc!


Very nicely done, Charlie! That was nice to browse through.

JonikW
10-06-2018, 09:37 PM
I am secretly hoping for a couple U106 along with plenty of I1 how's that? :-).

Edit: actually with House of Wettin's association with Saxony - if we just get one or two DF98ers in that Saxon cemetery that would enough for me!

I hope we see more U106 soon too as well as I1. All we M253 guys are descended from one man who lived about 5,000 years ago so we're all brothers as far as I'm concerned. And we seem to be found wherever our U106 mates are.:)

oz
10-06-2018, 09:47 PM
I hope we see more U106 soon too as well as I1. All we M253 guys are descended from one man who lived about 5,000 years ago so we're all brothers as far as I'm concerned. And we seem to be found wherever our U106 mates are.:)

That's true right? The U106 and I1 seem to be the most interconnected. Besides Finland where it's N and I1 like 90%.

JonikW
10-06-2018, 10:25 PM
That's true right? The U106 and I1 seem to be the most interconnected. Besides Finland where it's N and I1 like 90%.

It seems as if they're the two main Germanic markers, with I1 being Nordic in origin and U106 Indo-European.

spruithean
10-06-2018, 11:06 PM
I am secretly hoping for a couple U106 along with plenty of I1 how's that? :-).

Edit: actually with House of Wettin's association with Saxony - if we just get one or two DF98ers in that Saxon cemetery that would enough for me!

Yeah, I always follow some U106 aDNA as my maternal grandmother's family has some U106 lineages (U198 too).


I hope we see more U106 soon too as well as I1. All we M253 guys are descended from one man who lived about 5,000 years ago so we're all brothers as far as I'm concerned. And we seem to be found wherever our U106 mates are.:)

That's what makes I1 intriguing to me. Something happened that bottlenecked the population and eventually M253 spread into different branches DF29, Z131, Z17925, Y19086. Obviously the vast majority of modern I1 falls under DF29 with (CTS6364, Z58 and Z63). Obviously with the lack of supporting material we can only imagine what lead to this.


That's true right? The U106 and I1 seem to be the most interconnected. Besides Finland where it's N and I1 like 90%.

It seems so, I1 populations obviously would have not been able to "avoid" R1b (or even R1a) populations, considering the proximity and likely syncretism.


It seems as if they're the two main Germanic markers, with I1 being Nordic in origin and U106 Indo-European.

I think this was covered to some degree in Carlos Quiles Indo-European paper. It seems there was almost a gradient or so between R1b-U106, I1-M253 and R1a-Z284. With generally West Germanic areas being dominated by R1b-U106 and the more North Germanic areas having "clans" of I1-M253 and R1a-Z284.

oz
10-07-2018, 09:53 AM
Yeah, I always follow some U106 aDNA as my maternal grandmother's family has some U106 lineages (U198 too).



That's what makes I1 intriguing to me. Something happened that bottlenecked the population and eventually M253 spread into different branches DF29, Z131, Z17925, Y19086. Obviously the vast majority of modern I1 falls under DF29 with (CTS6364, Z58 and Z63). Obviously with the lack of supporting material we can only imagine what lead to this.



It seems so, I1 populations obviously would have not been able to "avoid" R1b (or even R1a) populations, considering the proximity and likely syncretism.



I think this was covered to some degree in Carlos Quiles Indo-European paper. It seems there was almost a gradient or so between R1b-U106, I1-M253 and R1a-Z284. With generally West Germanic areas being dominated by R1b-U106 and the more North Germanic areas having "clans" of I1-M253 and R1a-Z284.

Yes but the question is which group was the original Germanic and who got assimilated? It's not possible that they both developed similar languages simultaneously if they're from completely different tribes. R1a merged with I1 before R1b? Then R1a is the one who Indo-Europeanized I1. If I1,I2,R1a and others didn't exist R1b-U106 would be speaking the same non-Germanic language as his R1b brothers no? Maybe the reason R1b is more common as you go south and southwest of Scandinavia is because they were an even bigger majority there before they got assimilated by the invading people coming from the North and were the earliest R1b that got Germanized.

spruithean
10-07-2018, 11:47 AM
So far the argument seems to be that R1b-L23 (upstream of European R1b) was "Indo-European", here (https://indo-european.eu/2018/05/the-r1b-l23-late-pie-expansions-and-the-r1a-indo-european-association/) are some posts by Carlos Quiles.

deadly77
10-07-2018, 12:30 PM
Bummer that he isn't on our branch!

Thanks for digging into that one deadly77, I hope at some point we find some ancient L338 and ancient A13241. That field is still overwhelmingly R1b dominated.

I know... it would be a nice find to identify some remains that are close matches - but as JonikW says in another reply on this thread, the relatively late TMRCA of the I1 haplogroup puts all of us pretty close together. Plus there isn't as many of us as the R1b guys.

I'm sure more ancient I1 will turn up in the future, but I think there is a bit of a lottery on several factors, including how thorough the sequencing is (this might actually be better from an I1 perspective that so few ancient I1 listed previously that ones discovered in the future will be analyzed by better technology), the quality of the ancient sample and if the DNA has degraded over time.

I'll bring up the second point as I was rereading the Ebenesersdóttir paper - it looks like they originally selected 35 ancient Icelanders, but out of those 27 samples passed quality control for the WGS.

I downloaded one of the other individuals from the paper - this one was DAV-A9, which the paper just listed as I1. It's a significantly smaller BAM file - DAV-A9's BAM file was only 1.72 GB, while SBT-A1 was 15.2 GB. Looking into DAV-A9, the Y chromosome coverage is significantly more sparse than SBT-A1. I tried looking for a lot of the more well known I1 SNPs in DAV-A9's file - no call for DF29, Z140, L338, F2642, Z60, Z58, L22, L813, Z74, etc. DAV-A9 is even a no call for M253 itself, so they must have assigned Y haplogroup based on one or more of the other >300 SNPs.

Assuming it's the same lab and analysis for both samples it may be that the difference is just what appreciable DNA they were able to extract and analyze. And bear in mind that SBT-A1 had a fair few gaps as well - sometimes it's just going to be luck of the draw. But it was worth seeing what SBT-A1's BAM file had to offer and we now have a fairly good idea where he fits on a phylogenetic tree.

Although I'm happy to take a look at some of the other ones - HSJ-A1 and SSJ-A2 in particular seem to have some downstream of I-L22. I may look at them next, unless anybody has any particular requests.

deadly77
10-07-2018, 12:38 PM
Certainly Cheers mate! For what it's worth (I realize this is a haplogroup I thread and try not to post TOO much U106 stuff here)... here is my current google doc that I keep on my group U106 and the samples that are so far U106+ and sub groups where possible. Several people including myself usually take a look at the Bam files or convert them from .fastq (I can look at Bams, but I can't convert - my crappy laptop is too slow hah). I usually ask Alex Williamson of Big Tree fame to run any sample I'm interested in through his process that calls SNP reads from the .fastq file. He is usually very helpful and sometimes, when time permits, adds them to his U106 Big Tree. His work is priceless ;-)! I record all U106+ samples (no matter if they are my sub group or not) and their burial and archeological and osteological data where possible, even if I have to translate it from another language (usually German and sometimes Czech for Unetice burial at Jinonice outside of Prague). Maybe you could start a similar one for haplogroup I? Google doc is very handy for this - I can just jump on and change stuff and it saves everything I do and I can post links and let people view. I turned off comments as I really only want comments from Alex or Dr. Iain McDonald - Dr. Iain and myself are the real reason I am keeping this list, but I like to share it with anyone who has an interest in aDNA. Here is the link: https://docs.google.com/document/d/1h6ZFaJe9gUtwl2r2Iu33B5_kCc6er5n9oEthCe25wV0/edit?usp=sharing

Cheers,
Charlie

Edit: on my doc the stuff at the beginning is a summary of the burials - Dr. Iain suggested I add that so when we get enough samples that he would use them in his dating programs etc... he can have a quick reference and not have to dig through the archeological stuff! Below that is all the other info under the main headings etc!

That's a pretty impressive list Charlie - thanks for sharing. I'm a little jealous of that list compared to the relative paucity of ancient I1 samples. I've taken a look at some of Alex Williamson's Big Tree - I don't have any known relatives on those branches, but I see it referenced a lot in forums so it's more of a curiousity from my perspective - it's a really fantastic piece of work. I've also found Dr Iain MacDonald's excellent primers and guides very useful for helping my own understanding of the Y chromosome, so I'm very grateful that they make most of their research available, open and easy to follow.

spruithean
10-07-2018, 01:59 PM
Yeah, the sample qualities in the Iceland study were of varying quality and I believe they mentioned this in the study. It's better than no data at all, so I'll take the I-M253 with no subclades predictions! I believe the ancient I1 list needs to be updated anyway to include a few additions.

That U106 list is impressive, it certainly makes the I1 list look rather... bleak. It's quite clear just going through Quiles Indo-European paper that I1 is rather sparse in aDNA lists, the maps in that work certainly show this and the information for I1 is only a few paragraphs compared to the pages of R1b and R1a data.

Oh well, we just have to keep our eyes peeled for new I1 results from the 4 studies JonikW mentioned. We have to run into more ancient I1 eventually.

Radboud
10-07-2018, 02:54 PM
It seems so, I1 populations obviously would have not been able to "avoid" R1b (or even R1a) populations, considering the proximity and likely syncretism.


Yeah, the I1 carriers were probably part of a SHG forager population before R1a and R1b showed up in Scandinavia. Although it's now safe to say that R1a Z284 and L664 were part of the Corded Ware populations, the question remains when R1b-U106 and some specific subclades of R1b-P312 like L238 arrived in Scandinavia. Corded Ware, Bell Beakers, Unetice and unknown Steppe derived are candidates at the moment for the source imo. We know that U106 was present before 2000 BC in Scandinavia, but it's uncertain which population this sample was part of.

Bollox79
10-07-2018, 06:15 PM
Yeah, the I1 carriers were probably part of a SHG forager population before R1a and R1b showed up in Scandinavia. Although it's now safe to say that R1a Z284 and L664 were part of the Corded Ware populations, the question remains when R1b-U106 and some specific subclades of R1b-P312 like L238 arrived in Scandinavia. Corded Ware, Bell Beakers, Unetice and unknown Steppe derived are candidates at the moment for the source imo. We know that U106 was present before 2000 BC in Scandinavia, but it's uncertain which population this sample was part of.

Yep sounds about right... my focus is on U106 naturally and considering what I know and looking at my google doc (so strictly based on known and established data) - we only have three samples that are from Bronze Age (or near enough):

c. 2275-2032 BC, Battle Axe (2800 - 2300 B.C.)/Nordic LN (2200 - 1800 B.C.), Lille Beddinge 56 - Grave 49, Lilla Bedinge, Sweden, RISE 98, U106 > Z2265+ > BY30097- (FGC36477+)

c. 2200-1700 BC, Early Unetice, Prague-Jinonice “Zahradnictví”, Prague 5 – Jinonice, Czech Republic, I7196, U106 > Z381 > Z156 > Z304 > DF98 > S1911 > S1894

c. 1881–1646 calBCE, Early Bronze Age, 1900-1700 B.C., De Tuithoorn, Oostwoud, Noord-Holland (West Frisia), I4070, U106 > Z381

My sub group of DF98 and S1911 > S1894 (I share that with Dr. Iain) would look to be Unetice and I suspect we moved to Northern Germany with the spread of Unetice (and descendant cultures) West and North... hence our association with House of Wettin via Thuringia (but really we need samples from that area to confirm even more).

The next is the Roman gladiators - and then a bunch of Germanic migration burials... so really we need many more middle to late BA and Iron Age (Jastorf or even just samples from Northern Germany from the late B.C. times) to sort this stuff out. As far as overall for U106 at least - Z18 and especially L48 are very Germanic (Dr. Iain already noted ans assumed that based on pre-aDNA data) and Z156 seems more Rhineland or Western/SW Germanic... once again we need more samples from those population centers along the Rhine - in this map you can see the spread of DF98 in modern testers... 26541

Bollox79
10-07-2018, 06:16 PM
Double post

deadly77
10-14-2018, 11:00 PM
Ok, after the analysis of SBT-A1's BAM file proved fruitful and we have a fairly good idea where he fits on the phylogenetic tree, I decided to take a look at one of the other I1 samples from the Ancient Icelandic Genomes paper.

The next one I looked at was SVK-A1 - he was listed as I1b in the Y-DNA column of their report. That looks like it corresponds to I-Z131 in terminology that I'm more comfortable with. The majority of I1 lineages are I1a/DF29+ (>99%) so thought this one might be interesting.

SVK-A1's BAM file is not as big as the one I downloaded for SBT-A1 (5GB vs. 15GB), and looking for the SNP Z131, yep SVK-A1 is positive for that one, although it's only one read for that location. Then I looked for some of the downstream SNPs below Z131 - lots of no calls, but also quite a few negatives for SNPs defining subclades downstream of I-Z131. Again, a fair few of these were one read SNPs but a few were two or three read negative, which I have a bit more confidence in.

So after getting nowhere with the I1b/Z131 SNPs, I decided to check and make sure that SVK-A1 was actually DF29-. He's a no call for DF29, but there are five other SNPs that are phyloequivalent to DF29 that no one has split off from the main branch yet. SVK-A1 is a no call for CTS9857, but then it lights up with positive results for the other SNPs - Z2892 (10G reads), Z2890 (6A reads), Z2893 (7A reads).

So I'm pretty sure that SVK-A1 is actually I1a rather than I1b and the one read result for Z131 (which probably led to SVK-A1 being listed as I1b) is a false positive.

I'll dig in a bit more into SVK-A1's BAM file and see if I can figure out where he is downstream of I-DF29.

deadly77
10-14-2018, 11:03 PM
Huh, not sure why 15 gigabytes got auto-corrected to a smiley with shades on, but oh well.. not by design...

deadly77
10-15-2018, 10:04 AM
Ok, I believe that SVK-A1 is down the pathway I1->I-DF29->I-Z2336->I-L22->I-P109->I-S10200->I-FGC21685.

He's positive with one read for the following SNPs: Y3549, S25633, P109, Y5840, Y5836, FGC21685. He's also positive with two reads for S10891 and S10200 on that branch pathway.

This puts SVK-A1 at I-FGC21682 on the YFull tree and the FTDNA haplotree. SVK-A1 is a no call for FGC21682 itself, but positive (albeit with one read) for the currently phyloequivalent SNP FGC21685, and a no call for Y20204. It's entirely possible that SVK-A1 is FGC21682- and would split up the phyloequivalent SNPs on the known tree. SVK-A1 is negative for downstream SNPs Y20203, FGC21687, FGC21690 (all one read) and Y20205 (10 reads).

Given the large number of one reads (and that Z131 was a one read false positive), I wouldn't say this is 100%, but with a large number of these SNPs pointing in the right direction and a couple of them with more than one read, I'm reasonably confident with putting SVK-A1 as for sure I-P109, I-S10200 and I-Y5834, and quite likely I-FGC21685.

JonikW
10-15-2018, 10:07 AM
Ok, I believe that SVK-A1 is down the pathway I1->I-DF29->I-Z2336->I-L22->I-P109->I-S10200->I-FGC21685.

He's positive with one read for the following SNPs: Y3549, S25633, P109, Y5840, Y5836, FGC21685. He's also positive with two reads for S10891 and S10200 on that branch pathway.

This puts SVK-A1 at I-FGC21682 on the YFull tree and the FTDNA haplotree. SVK-A1 is a no call for FGC21682 itself, but positive (albeit with one read) for the currently phyloequivalent SNP FGC21685, and a no call for Y20204. It's entirely possible that SVK-A1 is FGC21682- and would split up the phyloequivalent SNPs on the known tree. SVK-A1 is negative for downstream SNPs Y20203, FGC21687, FGC21690 (all one read) and Y20205 (10 reads).

Given the large number of one reads (and that Z131 was a one read false positive), I wouldn't say this is 100%, but with a large number of these SNPs pointing in the right direction and a couple of them with more than one read, I'm reasonably confident with putting SVK-A1 as for sure I-P109, I-S10200 and I-Y5834, and quite likely I-FGC21685.

Excellent work and it also confirms that we shouldn't take the assignments as fact in some studies. Well done.

deadly77
10-15-2018, 11:12 AM
Excellent work and it also confirms that we shouldn't take the assignments as fact in some studies. Well done.

Cheers - these are quite fun and I'll continue to work through the rest of the I1 samples. Although HSJ-A1's BAM file is a bit of a monster at 55.5GB and that is taking a while to download. The flip side of that is there may be quite a bit of good data associated with HSJ-A1.

Agreed - we shouldn't take summaries at face value. I can see why they did it though, with the one read result for Z131+. Not all one reads are wrong - the F2642+ in the earlier genome of SBT-A1 was also a one read, but there is additional corroboration in the reads of additional SNPs to have more confidence in that one, while there isn't in the Z131+ for SVK-A1.

deadly77
10-16-2018, 02:32 PM
There's also a fair bit of discussion in the Science 2018 paper about other data associated with the ancient Icelandic genomes. For example, they mention that the ratio of strontium isotopes measured from the dental enamel can be used to class the samples as migrants or non-migrants, with the latter described in the paper as individuals who spent their first six years of life in Iceland. Both SBT-A1 and SVK-A1 fall into this category of non-migrants.

However, since the archaeological date for the majority of the samples is described as <1000 CE (and 14C dating for SVK-A1 agrees with <1050 CE) and the settling of Iceland was between 870-930 CE, there can't have been a lot of generations between the birth of the non-migrants in Iceland (such as SBT-A1 ad SVK-A1) and the settling of their ancestors in Iceland from wherever they cam from. There is a fair bit of discussion of autosomal DNA in the Science 2018 paper - they categorise the samples into "Norse" and "Gaelic".

SVK-A1 is rather more on the "Norse" side compared to "Gaelic" in their interpretation (see Fig 2B and 2C in the paper) compared to most of the other samples, and seems close to contemporary Norway on the PCA in Fig 2A. While I don't want to fully tie autosomal DNA in with Y-DNA haplogroups, looking at the genetic neighbourhood of I-P109 that SVK-A1 would fall in, I-Y5834 and I-FGC21682 at YFull, the distribution is largely Norway among the modern testers, with a few Sweden and one Ireland.

SBT-A1 then trends closer to what they are describing as "Gaelic" than "Norse" in Fig 2B and 2C, and he seems to fit in rather well with their reference for contemporary England in the PCA in Fig 2A. The modern I-Z140+ testers in the FTDNA project the British Isles (and especially England) are by far the largest population, although that's more likely due to significant population growth once they arrived in the British Isles rather than originating there. Still, given the dating, I guess we can rule out the Normans as an origin for SBT-A1 ;)

deadly77
10-16-2018, 03:07 PM
Back to the Y-DNA... I went through the BAM file for another one of the ancient Icelanders, this time HSJ-A1. The BAM file for this one was significantly larger than any of the other I1 samples - it's 55GB, so that took a fairly long time to download to my computer (which is a bit old and not the fastest). These BAM files were taking up a fair bit of space on my hard drive, so started storing them on an external hard drive to free up some space.

Anyway, the bigger BAM file for HSJ-A1 lead to a lot of good reads on his genome, so the greatest confidence about these assignments out of any of the ancient Icelanders so far. The positive SNPs for this one are multi-read, often between 10 and 25 reads, and some as high as 37 with much better coverage and less no calls. This one could probably go on the YFull tree.

The Science 2018 paper has HSJ-A1 as I1a1b3b which would be I-L813. Analysis of the BAM file confirms that, with 10 positive reads for L813 itself, coupled with positive reads for most of the phyloequivalent SNPs for that branch - Z718+, CTS9346+, Z270+ while FGC9478 is a no call.

Moving on to the subclades, HSJ-A1 is I-Y5476+ (25A, as well as one read for phyloequivalent SNP FGC9465) -> I-Y5483+ (14T) -> I-Y13039+ (14G, as well as Y13504+ from 33G/1A).

I-Y13039 is as far as HSJ-A1 goes on the YFull tree - HSJ-A1 is negative for all of the downstream subclades on the YFull tree - M10140, Y30042, Y16704, Y8943.

On FTDNA's haplotree, there are some branches below I-Y13039 that are not on the YFull tree. HSJ-A1 is I-Y111864+ with 10C reads. FTDNA's haplotree has a phyloequivalent SNP Y83756 which HSJ-A1 is negative for Y83756 with 12A reads, so HSJ-A1 splits that branch up. HSJ-A1 is also negative for all the SNPs listed on the I-BY42253 branch downstream of I-Y111864 on FTDNA's haplotree.

So, HSJ-A1 is I-Y13039 on YFull tree, I-Y111864 on FTDNA's haplotree.

JMcB
10-16-2018, 03:09 PM
There's also a fair bit of discussion in the Science 2018 paper about other data associated with the ancient Icelandic genomes. For example, they mention that the ratio of strontium isotopes measured from the dental enamel can be used to class the samples as migrants or non-migrants, with the latter described in the paper as individuals who spent their first six years of life in Iceland. Both SBT-A1 and SVK-A1 fall into this category of non-migrants.

However, since the archaeological date for the majority of the samples is described as <1000 CE (and 14C dating for SVK-A1 agrees with <1050 CE) and the settling of Iceland was between 870-930 CE, there can't have been a lot of generations between the birth of the non-migrants in Iceland (such as SBT-A1 ad SVK-A1) and the settling of their ancestors in Iceland from wherever they cam from. There is a fair bit of discussion of autosomal DNA in the Science 2018 paper - they categorise the samples into "Norse" and "Gaelic".

SVK-A1 is rather more on the "Norse" side compared to "Gaelic" in their interpretation (see Fig 2B and 2C in the paper) compared to most of the other samples, and seems close to contemporary Norway on the PCA in Fig 2A. While I don't want to fully tie autosomal DNA in with Y-DNA haplogroups, looking at the genetic neighbourhood of I-P109 that SVK-A1 would fall in, I-Y5834 and I-FGC21682 at YFull, the distribution is largely Norway among the modern testers, with a few Sweden and one Ireland.

SBT-A1 then trends closer to what they are describing as "Gaelic" than "Norse" in Fig 2B and 2C, and he seems to fit in rather well with their reference for contemporary England in the PCA in Fig 2A. The modern I-Z140+ testers in the FTDNA project the British Isles (and especially England) are by far the largest population, although that's more likely due to significant population growth once they arrived in the British Isles rather than originating there. Still, given the dating, I guess we can rule out the Normans as an origin for SBT-A1 ;)

Hello Deadly77,

Great work as usual! From your experience looking into these matters, do you know if these Bam files are available?

AED249 > I1 L840
STR486 > I1 L840
STR241 > I1 L840

Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

Many modern European states trace their roots back to a period known as the Migration Period that spans from Late Antiquity to the early Middle Ages. We have conducted the first population-level analysis of people from this era, generating genomic data from 41 graves from archaeological sites in present-day Bavaria in southern Germany mostly dating to around 500 AD. While they are predominantly of northern/central European ancestry, we also find significant evidence for a nonlocal genetic provenance that is highly enriched among resident Early Medieval women, demonstrating artificial skull deformation. We infer that the most likely origin of the majority of these women was southeastern Europe, resolving a debate that has lasted for more than half a century.

http://www.pnas.org/content/early/2018/03/06/1719880115

deadly77
10-16-2018, 04:09 PM
Hello Deadly77,

Great work as usual! From your experience looking into these matters, do you know if these Bam files are available?

AED249 > I1 L840
STR486 > I1 L840
STR241 > I1 L840

Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

Many modern European states trace their roots back to a period known as the Migration Period that spans from Late Antiquity to the early Middle Ages. We have conducted the first population-level analysis of people from this era, generating genomic data from 41 graves from archaeological sites in present-day Bavaria in southern Germany mostly dating to around 500 AD. While they are predominantly of northern/central European ancestry, we also find significant evidence for a nonlocal genetic provenance that is highly enriched among resident Early Medieval women, demonstrating artificial skull deformation. We infer that the most likely origin of the majority of these women was southeastern Europe, resolving a debate that has lasted for more than half a century.

http://www.pnas.org/content/early/2018/03/06/1719880115

Cheers JMcB - these are quite fun to work through, although each one takes me a bit of time. It's easier if I know what I'm looking for or the coverage is decent. Although with some of these samples I think we pretty much have to take what we can get.

I had a look at the European Nucleotide Archive for the BAM files that you mentioned - that's where I have been getting the BAM files from the ancient Icelanders.

AE249 is there, the BAM says it's hg19 and 992MB, which is a little smaller than SVK-A1. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979363
STR486 is there, the BAM says it's hg19 and 1.5GB. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979393
STR241 is there, the BAM says it's hg19 and 633MB. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979382

JMcB
10-16-2018, 05:00 PM
Cheers JMcB - these are quite fun to work through, although each one takes me a bit of time. It's easier if I know what I'm looking for or the coverage is decent. Although with some of these samples I think we pretty much have to take what we can get.

I had a look at the European Nucleotide Archive for the BAM files that you mentioned - that's where I have been getting the BAM files from the ancient Icelanders.

AE249 is there, the BAM says it's hg19 and 992MB, which is a little smaller than SVK-A1. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979363
STR486 is there, the BAM says it's hg19 and 1.5GB. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979393
STR241 is there, the BAM says it's hg19 and 633MB. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979382

It’s nice to know they have a central data base for many of these files. To be honest, I wasn’t sure if their basic call of I1 (L840) was because of coverage issues or a lack of time & resources.

deadly77
10-17-2018, 09:26 AM
It’s nice to know they have a central data base for many of these files. To be honest, I wasn’t sure if their basic call of I1 (L840) was because of coverage issues or a lack of time & resources.

Earlier in the thread, Bollox79 said he asked Mike Williamson to take a look at those three Bavarian samples - he said "they are targeted capture sequencing, which only looks at specific locations, rather than the whole genome. There isn't much there." so I guess there would be a difference in these tests compared to the whole genome sequencing that was done on the ancient Icelanders. So in addition to missing regions of the Y chromosome due to sample quality,degredation, etc. the analysis just may not cover the regions of the Y chromosome because they were left out of the scanning.

Bollox79 said that Mike Williamson's look at the samples showed a two were likely I-DF29 (or phyloquivalent) and the other one was I1 but didn't find anything more than that, although they both said that they weren't that familiar with the haplogroup I phylogenetic tree. I'll take a second look when I have some time to get to it - I'm definitely nowhere near as knowledgeable as Alex Williamson but perhaps I know I1 a little better.

The smart money says I'll likely end up with the same conclusions due to the limited data captured in targeted screening.

deadly77
10-18-2018, 01:44 PM
Continuing to work through the remaining three I1 samples from the Science 2018 paper about the ancient Icelandic genomes. The remaining BAM files are significantly less data than the first three that I analyzed - the largest one is 1.72GB. Bear in mind this is autosomal as well as Y. For comparison, my 30x WGS from YSEQ is 59GB.

SSJ-A2 is listed in the paper as I1a3b, which would make him I-Z74. In the BAM file, SSJ-A2 is one read positive for Z74. I looked at SNPs that are in the tree downstream of I-Z74 and SSJ-A2 is a no call for most of them, and negative for CTS5476 (which is phyloequivalent for CTS2208). No call for most of the SNPs under I-L813 that I looked for and negative for Y30373, Y19670, BY3434, Y30042 below I-L813. Despite only the one read for Z74, SSJ-A2 also positive for Y2592 and Y2593 (both phyloequivalent with I-Z2336 branch) ans also positive for Y3549 and CTS6868 along the way, so that all matches up.

SSG-A3 is just listed as I1. I didn't manage to get much out of this one. It looks like he's at least I-DF29 (like most of I1) with a one read positive for Z2892 and later on he's a one read positive for CTS6868 but a no call for most of the downstream SNPs that I looked at.

DAV-A9 again just listed as I1. Again it looks like he's at least I-DF29 (like most of I1) with a one read positive for CTS9857 and two positive reads for Z2892. I followed his BAM while I was tracking along with SSJ-A2 and SSG-A3, but nothing positive down those I-Z2336 lines. A few negative SNPs Y44733, Y19670, Y19207, Y18234 along the way. No call for Z58, Z59, Z60, Z140.

deadly77
10-18-2018, 06:44 PM
I was happy to receive an email from Vladimir at YFull regarding the ancient Icelandic samples. He says that 10 of the samples from that paper have sufficient quality that they can be added to the YFull tree. Accordingly, SBT-A1, SVK-A1 and HSJ-A1 are now listed as "analysis in progress" (see attached screenshots).

267802678126782

JMcB
10-18-2018, 06:54 PM
I was happy to receive an email from Vladimir at YFull regarding the ancient Icelandic samples. He says that 10 of the samples from that paper have sufficient quality that they can be added to the YFull tree. Accordingly, SBT-A1, SVK-A1 and HSJ-A1 are now listed as "analysis in progress" (see attached screenshots).

267802678126782

Excellent news and nicely done!

JonikW
10-18-2018, 07:09 PM
I was happy to receive an email from Vladimir at YFull regarding the ancient Icelandic samples. He says that 10 of the samples from that paper have sufficient quality that they can be added to the YFull tree. Accordingly, SBT-A1, SVK-A1 and HSJ-A1 are now listed as "analysis in progress" (see attached screenshots).

267802678126782

Truly exciting stuff. These must be the first ancient I1 samples to get the YFull treatment. Let's hope there will be more soon.

deadly77
10-18-2018, 10:29 PM
Truly exciting stuff. These must be the first ancient I1 samples to get the YFull treatment. Let's hope there will be more soon.

You may be correct - I had a look at the other papers that they include samples from, and a lot of them were haplogroup or region specific. There are I1 samples at YFull from the 1000 Genomes project, the Simons Genome Diversity project and the Sardinians paper, but I think these are all from modern individuals.

deadly77
10-19-2018, 09:55 AM
Not confined to I1, but while trawling round the interwebs for other stuff, I found this map that some helpful person has compiled to show the locations of ancient DNA, colour coded by time period. Clicking on one of the coloured dots brings up a pop up window with reference and in some cases haplogroup data. Just wish it there was an option to filter by haplogroup as well, but it's pretty neat as is. https://umap.openstreetmap.fr/en/map/ancient-human-dna_41837#2/51.0/2.0

deadly77
10-19-2018, 02:32 PM
Next up, 84005 from the Nunnan cemetery in Sigtuna, Sweden, described recently as I1a1b3 (I-Z74) in the paper "Genomic and Strontium Isotope Variation
Reveal Immigration Patterns in a Viking Age Town" by Krzewinska et al in Current Biology 2018.

The BAM file at ENA is hg19 rather than the hg38 in the Icelandic samples. That's ok as IGV has options for using either. But important to bear in mind when looking at SNP psoitions.

Yes, I-Z74 looks right - 84005 is positive for all the phyloequivalent SNPs on that branch (Z74, Z75, CTS1793). Negative for the SNPs associated with I-L813 or I-M6003 branches. Looks positive for some of the SNPs associated with I-CTS2208 branch - there are 11 phyloequivalent SNPs on that branch at YFull. 84005 is positive for Y2562 with two reads, then one read positive for CTS2208, CTS4791, Y2565. 84005 is also negative for Y21369 (two reads) and Z135 (one read) so my feeling is that 84005 breaks up that branch under I-CTS2208. However, with these low reads, some of the results may be false. The other 5 SNPs on that branch are no call.

Had a look at the branches under that too. No call for I-FGC60542, negative or no call for the SNPs associated with I-CTS7676 or I-Y24701. It's a bit odd on the other branch - under I-Y20287. Negative with two reads for Y20594 and Y20595, positive with one read for Y20288, no call for the remaining four SNPs on that branch.

I'm inclined to say that 84005 is at the I-CTS2208 branch and breaks that up (four positive SNPS, two negative SNPs), and the Y20288+ is a false positive one read. But it's a problem to make conclusions without the full data.

deadly77
10-19-2018, 02:32 PM
Double post

deadly77
10-20-2018, 09:55 AM
NO3423 was reported in a Nature Communications 2016 paper by Martiniano et al titled "Genomic signals of migration and continuity in Britain before the Anglo-Saxons" and it includes nine ancient genomes from Northern Britain - seven from a Roman era York cemetery (six R1b, 1 J2), bookended by earlier Iron-Age (female) and later Anglo-Saxon burials. The latter sample (NO3423) the paper assigns as Y-DNA haplogroup "I-S107" and is from Norton Bishopmill, a Christian cemetery dating to 650-910 AD. They sampled three individuals from the burials of 100 skeletons and selected the best preserved sample, which was NO3423 for study.

The village of Norton is about 30 miles away from me, so was rather interested in checking this one out.

In the supplementary material, they say "Due to the low coverage of our samples, 1X was the minimum coverage accepted for polymorphisms to be considered and therefore caution is necessary when interpreting these results, since it is likely that some of the alleles identified result of aDNA damage". I think we're going to see a fair bit of this in ancient DNA analysis, so I we should bear that in mind with all other samples too.

The analysis that they report in Supplementary Table 10 looks like this - seems that they assigned IJK based on L16, I based on P212 and then I1 based on S107. Not sure what's going on here, but in the table it says the mutation is A->C and they report the sample as 1 G read.
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I looked at my own results at YFull - I'm I1 and I'm a G at that position, although they list S107 again as A to C, with Y1863/FGC2426 as T to G, and then list all three together in Y report. Seems like an odd criterion for assigning I1, but there you go.
26817

So, on to NO3423's BAM file, which is available at ENA. This one is 2.84 GB in size and it's a hg19 BAM file. Yes, he's a G for S107, as the paper says. While hunting through the BAM file, I also found a positive two reads for Z2790, which is one of the SNPs in the big block of SNPs defining I1.

Looking for things that are a bit more interesting, NO3423 is positive for DF29 (2 reads) and phyloequivalent SNP CTS9857, which makes him definitely I1. I can rule out some of the small subclades below DF29 - PH790, FGC155560, Y11205, Y11252 and also one of the larger subclades Z63. For the two other big subclades, NO3423 is a no call for Z58 and Z2336 (as well as phyloequivalent SNPs Y2592 and Y2593). I haven't found anything positive downstream of either Z2336 or Z58 - lots of no calls. However, I can say a few things that NO3423 is probably not.
Under Z2336, NO3423 negative for M227, Y3603. No call for S6742, L22, CTS11603, Y3603, Y3549, S4767, P109.
Under Z58, NO3423 negative for Z138, Y128537, Z2041, CTS7362. No call for Z59, Z60, CTS8647, Z62, Y12342, Y22033. No call for Z140, but negative for Z141. Also checked F2642 and L338 and negative for those - so no luck for myself, JonikW, JMcB or Spruithean.
I'll keep taking a look. I'm guessing that he's positive for something under Z2336 or Z58, but just haven't found it yet.

deadly77
10-20-2018, 10:01 AM
Double post - seems that a lot of things I'm posting on Anthrogenica recently are coming up duplicate.

JonikW
10-20-2018, 10:08 AM
NO3423 was reported in a Nature Communications 2016 paper by Martiniano et al titled "Genomic signals of migration and continuity in Britain before the Anglo-Saxons" and it includes nine ancient genomes from Northern Britain - seven from a Roman era York cemetery (six R1b, 1 J2), bookended by earlier Iron-Age (female) and later Anglo-Saxon burials. The latter sample (NO3423) the paper assigns as Y-DNA haplogroup "I-S107" and is from Norton Bishopmill, a Christian cemetery dating to 650-910 AD. They sampled three individuals from the burials of 100 skeletons and selected the best preserved sample, which was NO3423 for study.

The village of Norton is about 30 miles away from me, so was rather interested in checking this one out.

In the supplementary material, they say "Due to the low coverage of our samples, 1X was the minimum coverage accepted for polymorphisms to be considered and therefore caution is necessary when interpreting these results, since it is likely that some of the alleles identified result of aDNA damage". I think we're going to see a fair bit of this in ancient DNA analysis, so I we should bear that in mind with all other samples too.

The analysis that they report in Supplementary Table 10 looks like this - seems that they assigned IJK based on L16, I based on P212 and then I1 based on S107. Not sure what's going on here, but in the table it says the mutation is A->C and they report the sample as 1 G read.
26816
I looked at my own results at YFull - I'm I1 and I'm a G at that position, although they list S107 again as A to C, with Y1863/FGC2426 as T to G, and then list all three together in Y report. Seems like an odd criterion for assigning I1, but there you go.
26817

So, on to NO3423's BAM file, which is available at ENA. This one is 2.84 GB in size and it's a hg19 BAM file. Yes, he's a G for S107, as the paper says. While hunting through the BAM file, I also found a positive two reads for Z2790, which is one of the SNPs in the big block of SNPs defining I1.

Looking for things that are a bit more interesting, NO3423 is positive for DF29 (2 reads) and phyloequivalent SNP CTS9857, which makes him definitely I1. I can rule out some of the small subclades below DF29 - PH790, FGC155560, Y11205, Y11252 and also one of the larger subclades Z63. For the two other big subclades, NO3423 is a no call for Z58 and Z2336 (as well as phyloequivalent SNPs Y2592 and Y2593). I haven't found anything positive downstream of either Z2336 or Z58 - lots of no calls. However, I can say a few things that NO3423 is probably not.
Under Z2336, NO3423 negative for M227, Y3603. No call for S6742, L22, CTS11603, Y3603, Y3549, S4767, P109.
Under Z58, NO3423 negative for Z138, Y128537, Z2041, CTS7362. No call for Z59, Z60, CTS8647, Z62, Y12342, Y22033. No call for Z140, but negative for Z141. Also checked F2642 and L338 and negative for those - so no luck for myself, JonikW, JMcB or Spruithean.
I'll keep taking a look. I'm guessing that he's positive for something under Z2336 or Z58, but just haven't found it yet.

That's remarkable work. He's the only Anglo-Saxon Y that we have so far and I was frustrated that they only pegged him as I1. Now we know a lot more. Thanks!

deadly77
10-20-2018, 09:29 PM
I went through the BAM files I1 samples AED246, STR241 and STR486 from the Early Medieval Bavaria PNAS paper 2018 from by Veeramah et al. These were mentioned in another post earlier in this thread. My bet was that I wouldn't get much more out of them than Mike Williamson did when he looked at them.

AED246 I managed to find a one read positive call for DF29+ and a one read negative call for P109-. Everything else I looked for was a no call.
STR241 seemed to have the lowest coverage out of this set. Everything I looked for was a no call apart from P109-.
STR486 looked like it had the most out of this set, but still not a lot to report: Z2891+ and Z2892+ (these are both phyloequivalent with I-DF29), then Y11252-, M227-, Z138-, Z60-, F2642-. No call at a whole lot of other positions.

spruithean
11-03-2018, 09:11 PM
Fantastic work Deadly!

I really appreciate you doing this, it is definitely painting the picture of where the ancient I1 samples fit in in the big picture.

So far it seems the vast majority of them are I-DF29 indeed.

deadly77
11-06-2018, 11:49 PM
Fantastic work Deadly!

I really appreciate you doing this, it is definitely painting the picture of where the ancient I1 samples fit in in the big picture.

So far it seems the vast majority of them are I-DF29 indeed.

Thanks - glad to hear that you guys are interested. And hey, Anthrogenica is back after being down for a while :)

Agreed, I'd expect a lot of them to be I-DF29, since the DF29- lineages are pretty rare. Probably fair to say that when I1/I-M253 is discussed, it's mostly actually I-DF29. Estimated TMRCA is so close to I1, it's splitting hairs.

I actually have more confidence in the samples where I'm reliably able to call DF29 or phyloequivalent SNPs. My original thoughts before getting into this would be that ancient DNA would be a good way of figuring out some of the the 300+ SNPs that define I1 along with M253 among the ancient samples may help break up that block and figure some things out between the formation and TMRCA of I1. But having looked at some of these, I think it's going to be risky to make some determinations on low read or no call SNPs. One of the admins of the I-L22 group at YFull was kind enough to share with me the YReport from HSJ-A1, which saves me looking up all of those SNPs. HSJ-A1 had the best coverage of all the ancient I1's that I've seen so far. The YFull YReport shows HSJ-A1 is a no call for 13 of those SNPs - that's not bad at all. My FGC YElite has no call on 34 of those SNPs and 3 more are ambiguous. Then my 30x WGS reads all of them but two are ambiguous. The majority of ancient DNA samples are lower coverage than this. So I'm happy when I can find at least DF29 - lets me know the missing I1 SNPs can be considered presumed positive.

spruithean
11-24-2018, 05:39 PM
At least Haplogroup I (and more specifically I1) was mentioned in this blog post (https://indo-european.eu/2018/02/germanic-tribes-during-the-barbarian-migrations-show-mainly-r1b-also-i-lineages/) at Carlos Quiles blog.

Here's to finding more I-M253 in 2019.

deadly77
01-11-2019, 01:06 AM
Happy New Year fellow ancient I-M253 enthusiasts.

It's been a while since I posted anything on this thread. We've discussed earlier on this thread the two I1 samples CL63 and SZ45 from the "Understanding 6th-century barbarian social organization and migration through paleogenomics" paper that was published in Nature Communications in 2018 by Amorim et al. Link to the paper and supporting information since it's been a while (although I'm sure most people reading are familiar): https://www.nature.com/articles/s41467-018-06024-4#Sec23

Specifically regarding SZ45, which was one of the samples that had a WGS and was listed as I1a1b1 (I-L22) in Supplementary Table 2. Looking at Supplementary Data 3, there's an excel spreadsheet summarises the Y-SNP analysis. While they list a few of the I1 SNPs, and record a positive result for L22 (which agrees with I1a1b1), they also list a positive result for Z63. We've mentioned this before on this thread, and we know that one of them has to be wrong. They also list P109 in among the I2 SNPs, so I think we can agree that the raw data is worth looking into further to clear up some of these discrepancies and get to the bottom of this.

The BAM file for SZ45 is available from NCBI, so I downloaded the file and took a look using the Broad Institute's IGV. SZ45 is clearly negative for Z63 (11C reads in the BAM), and L22 has a single positive read. Single positives can be false positives, but we also have good multi-read results for Z2337+ (6A) and Y3549+ (5T) upstream and downstream which adds weight that L22+ is genuine. Working further down the tree and eliminating branches based on negative results and confirming based on positive, I'm able to find P109+ (6T) and S7660+ (5A).

I'm pretty confident that SZ45 would be at least I-Y14999 on the YFull tree https://www.yfull.com/tree/I-Y14999/ and I-Y15520 on the FTDNA public haplotree. There are a couple of SNPs that are ambiguous reads, namely FGC21822 (4C, 1T) and BY35337 (10G, 3T) and another one has only one positive read (FGC21805). However, nine phyloequivalent SNPs on that branch are all multi-read positive - these are Y15520+, Y14999+, FGC21824+, FGC21823+, FGC21813+, FGC21814+, FGC21807+, FGC21811+, FGC21802+. This all adds up pretty well for this branch.

I can rule out a couple of the known descendant subclades that are on the YFull tree and the FTDNA public haplotree. Well characterized calls for BY35334-, BY42214- and BY78500- on one branch; and for the other branch Y37415-, BY35335- (DYZ19 region), Y37108-, Y37417- and Y37416- on the other branch.

SZ45 may be part of the I-FGC21819 branch, and I think he probably is FGC21819+. However, I'm tagging that one as ambiguous based on the data available from his BAM file - he has 5G reads for the derived allele and 2A reads for the ancestral allele at that position. Unfortunately, there aren't currently any phyloequivalent or downstream SNPs for I-FGC21819, so I'm guessing that this is the last point of commonality for the three folks in the databases of modern testers.

I'll also suggest to YFull that they add SZ45 to their list of ancient DNA samples. Based on comparison with others I have suggested, I think SZ45 has a good chance of making it.

Here's to a good 2019 for ancient I-M253 DNA (and modern descendants).

JonikW
01-11-2019, 01:14 AM
That's quality detective work and much appreciated. I'd like to join you in wishing us a wonderful year for I1 discoveries. I hope our picture of ancient distribution patterns will be much improved by the year end.:beerchug:

spruithean
01-11-2019, 02:15 AM
Wow! Great work, and here's to a productive year for ancient I1! I'm hoping we find some ancient Z140 or perhaps something upstream or downstream.

deadly77
01-11-2019, 11:22 AM
I also took a look at CL63 from the same paper. This one is from the other cemetery, Collegno in Northern Italy. This was assigned as I1a3, but with last downstream SNP as Z79. As we've discussed on previous posts on this thread, Z79 is in I2 rather than I1.

Worth noting that unlike SZ45 (which was a WGS), for CL63 In-solution capture was performed, targeting ~1,237,207 SNPs (“1240K capture”) scattered across the nuclear genome. The enriched DNA was then sequenced on a NextSeq (75bp single-end run or 150 cycles paired-end run). So we shouldn't expect the coverage that we observed for SZ45, but worth a look to see what we can get.

For Z79, that position lights up but there are 2G reads for derived and 1A read for ancestral. I'd call this ambiguous.

Looking at the I-DF29 branch and phyloequivalent SNPs, also pretty ambiguous - DF29 itself is a single negative call, Z2891 is a single positive call, no calls for Z2890, Z2891, Z2893. Not really sure we can claim anything of significance here.

Checked a few of the SNPs that they report for I1, namely M253 (3T), L81 (3C), L840 (2G) and they all check out.

I checked Z63 for the I1a3 reported in Supplementary Table 3 - that lights up with 11 reads for C (derivative), so I'd say that this is one of the SNPs they were targetting. I tried some of the downstream SNPs under Z63 but didn't come up with much. No calls for BY151, BY3394, PH5281, Y5940, BY351, L849, S11545, Y8331, S2077, S2078, L1237, S10360, BY1933.

JonikW
01-11-2019, 10:29 PM
Please keep up the fantastic work. It's great to have someone with the skills and tools to do this for I1 aDNA as I've seen so much good work on our R1b U106 fellow northerners. I hope you'll have a few more samples to look at before the year is out, with much exciting discussion here.

deadly77
01-12-2019, 12:37 PM
Cheers folks. The tools are mostly free to access - the Broad Institute's IGV for viewing and indexing the BAM files; European Nucleotide Archive (ENA) and National Center for Biotechnology Information (NCBI) for hosting the raw data and making it available for download; phylogenetic trees: YFull tree and FTDNA public haplotree; looking up positions of SNPs on YBrowse, YFull database and Brad Larkin's Genetic Homeland site - the latter two are extremely helpful as they include positions on the hg19 reference as well as hg38 reference - the majority of these BAM files are in hg19 format. The YFull database requires a one-time fee for access but in my opinion very much worth the price but the rest are open access. The skills are largely self taught and involved a fair bit of amateur blundering along the way - proper practitioners of genetics and bioinformatics would likely be highly amused at some of the approaches I went down. So it's mostly down to interest and time availability. But it's been a good learning experience and I've had fun working through these. I appreciate the interest and encouragement from the comments.

By my count, I've been through 13 of the 15 post-CE I1 individuals mentioned in this thread (6 Iceland, 3 Bavaria, 1 Sweden, 1 England, 1 Hungary, 1 Italy), some of which I've been able to assess in greater detail than some others, depending on the quality of the raw data. Should probably put together a summary in case there's a future avalanche of ancient I1...

The two that I haven't got to yet are the two samples from Poland KO_55 and ME_7 reference from Zenczak 2017. Does anyone have a link to the paper? All I have been able to find is this link on Academia here https://www.academia.edu/33791135/2017_Zenczak_.....Piontek_..._Y-chromosome_haplogroup_assignment_through_next_gene ration_sequencing_of_enriched_ancient_DNA_librarie s - this appears to be an abstract to a presentation which lists eight I1 individuals including three I-L1237 and one I-Z59. Has anything with a bit more detail been published?

I also tried searching for KO_55 and ME_7 at the ENA. I was unable to find any samples with these names, but I was able to find data for "Kow_55" here https://www.ebi.ac.uk/ena/data/view/SRS1815340 and "Mar_7" here https://www.ebi.ac.uk/ena/data/view/SRS1815413 - does anyone know if these are the correct ones?

Unfortunately, there are no BAM files associated with either sample at ENA. They do have FASTQ files - I have tried downloading these and converting them to BAM files using Felix Immanuel's SRA/FASTQ to BAM kit. However, the resultant BAM file isn't readable using IGV so I'm assuming there was some error or corruption during the conversion. It looks from the website that the developer is focused on other pursuits and hasn't updated these tools for a while (and doesn't seem likely to do so in the future). Are there any alternatives for converting a FASTQ to a BAM? I have a laptop running Windows and no familiarity with Linux systems.

Pribislav
01-12-2019, 03:58 PM
The two that I haven't got to yet are the two samples from Poland KO_55 and ME_7 reference from Zenczak 2017. Does anyone have a link to the paper? All I have been able to find is this link on Academia here https://www.academia.edu/33791135/2017_Zenczak_.....Piontek_..._Y-chromosome_haplogroup_assignment_through_next_gene ration_sequencing_of_enriched_ancient_DNA_librarie s - this appears to be an abstract to a presentation which lists eight I1 individuals including three I-L1237 and one I-Z59. Has anything with a bit more detail been published?

I also tried searching for KO_55 and ME_7 at the ENA. I was unable to find any samples with these names, but I was able to find data for "Kow_55" here https://www.ebi.ac.uk/ena/data/view/SRS1815340 and "Mar_7" here https://www.ebi.ac.uk/ena/data/view/SRS1815413 - does anyone know if these are the correct ones?

Unfortunately, there are no BAM files associated with either sample at ENA. They do have FASTQ files - I have tried downloading these and converting them to BAM files using Felix Immanuel's SRA/FASTQ to BAM kit. However, the resultant BAM file isn't readable using IGV so I'm assuming there was some error or corruption during the conversion. It looks from the website that the developer is focused on other pursuits and hasn't updated these tools for a while (and doesn't seem likely to do so in the future). Are there any alternatives for converting a FASTQ to a BAM? I have a laptop running Windows and no familiarity with Linux systems.

The Zenczak study, with Y-DNA and autosomal data, is yet to be published, hopefully this year, since mt-DNA study has been published last year (Stolarek et al.). So I doubt BAM files are available. Thanks for looking all these samples more closely, maybe you could look Nordic LN/BA samples from Allentoft study next. They are poor quality, but shotgun sequenced nevertheless, so you could get lucky with some downstream SNPs. Here's a recap of what we have thus far:

28327

deadly77
01-12-2019, 04:34 PM
The Zenczak study, with Y-DNA and autosomal data, is yet to be published, hopefully this year, since mt-DNA study has been published last year (Stolarek et al.). So I doubt BAM files are available. Thanks for looking all these samples more closely, maybe you could look Nordic LN/BA samples from Allentoft study next. They are poor quality, but shotgun sequenced nevertheless, so you could get lucky with some downstream SNPs. Here's a recap of what we have thus far:

28327

I've had a brief look at the four RISE samples from the Allentoft but not systematically worked through them. I hadn't written about them because to be honest, there's not a lot to report. You're correct that they are poor quality and as a result there's no read at most of the positions that I've looked at. All I've found so far are a really small bunch of one read negatives among some of the downstream SNPs. Most SNPs are no call, including all of the SNPs phyloequivalent to DF29. In fact among the >300 SNPs that define the I1 block, the four RISE samples are no call for at least 41 SNPs (including M253 itself) and I haven't had the motivation to go back and look at the rest yet. I'm not sure that they are fully I1 (as in, post the TMRCA of modern descendants) and may more appropriately be called pre-I1, proto-I1, I*, extinct lineage or whatever. Given the poor quality of the coverage in the BAM files it may be impossible to say one way or another. At least with the majority of the post-CE individuals I've been able to assign DF29 or one of the phyloequivalent SNPs so don't have to worry about holes upstream in the I1 block.

mwauthy
01-13-2019, 11:15 PM
I've had a brief look at the four RISE samples from the Allentoft but not systematically worked through them. I hadn't written about them because to be honest, there's not a lot to report. You're correct that they are poor quality and as a result there's no read at most of the positions that I've looked at. All I've found so far are a really small bunch of one read negatives among some of the downstream SNPs. Most SNPs are no call, including all of the SNPs phyloequivalent to DF29. In fact among the >300 SNPs that define the I1 block, the four RISE samples are no call for at least 41 SNPs (including M253 itself) and I haven't had the motivation to go back and look at the rest yet. I'm not sure that they are fully I1 (as in, post the TMRCA of modern descendants) and may more appropriately be called pre-I1, proto-I1, I*, extinct lineage or whatever. Given the poor quality of the coverage in the BAM files it may be impossible to say one way or another. At least with the majority of the post-CE individuals I've been able to assign DF29 or one of the phyloequivalent SNPs so don't have to worry about holes upstream in the I1 block.

Interesting that the earliest evidence of DF29+ is only from the Common Era.

Considering that DF29 accounts for 99% of all I1 you would think that this SNP would have several reads for any ancient dna testing.

deadly77
01-14-2019, 12:05 AM
Interesting that the earliest evidence of DF29+ is only from the Common Era.

Considering that DF29 accounts for 99% of all I1 you would think that this SNP would have several reads for any ancient dna testing.

It's not that these pre-CE samples are DF29- (or the five phyloequivalent SNPs). It's that they are no call - there is no information to assess whether they are DF29+ or DF29-. In the BAM file at that position it's just blank, so it's a Schrodinger's cat situation. Some of the ancient DNA BAM files have pretty decent coverage - HSJ-A1 and SZ45 for example. Some have less where there's not a lot of information that you can reliably call from looking at the BAM file. The RISE samples are in that latter category. I looked at the RISE samples for a few more of the block of SNPs that make up I1 before it divides into descendant subclades. Out of the 70 SNPs looked at so far, there are only 4 SNPs read across the four samples, and they are all one-read. So that's 4/(4x70)=1.4% of just getting a read on SNPs looked at so far. And none of the four SNPs with a reading are showing up in more than one sample so far.

I think one major factor is when the analysis was conducted. If you look at the publication dates, all but one of the post-CE samples I've looked are from papers published in 2018. The only one that wasn't was published in 2016. All of the pre-CE samples are from papers published in 2015 or 2014. Probably a bit of difference in the technology of sequencing. Also, the ancient remains have had a lot more time to degrade before they were analyzed.

It may be that some of the RISE samples are not positive for some of the SNPs in the I1 block and may be an extinct lineage that doesn't have descendants that are alive today (or at least not in any database of modern testers that I'm aware of). In that case, wouldn't expect them to be DF29+. But if it's all no calls or one-read positives or negatives, it may be impossible to say with any certainty. We've seen above that CL63 has a single read negative call for DF29, which is clearly bogus due to a much stronger call for Z63 with 11 positive reads. And then SVK-A1 has a single false positive for Z131+ which saw SVK-A1 assigned as I1b in the paper, but when digging further into the data shows he's actually I-FGC21682 based on stronger SNP reads (and therefore must be Z131-). Isolated single read SNPs for derived or ancestral alleles may not be conclusive as we have examples of them turning up false, so we need to approach such calls with a bit of caution.

mwauthy
01-14-2019, 04:12 PM
It's not that these pre-CE samples are DF29- (or the five phyloequivalent SNPs). It's that they are no call - there is no information to assess whether they are DF29+ or DF29-. In the BAM file at that position it's just blank, so it's a Schrodinger's cat situation. Some of the ancient DNA BAM files have pretty decent coverage - HSJ-A1 and SZ45 for example. Some have less where there's not a lot of information that you can reliably call from looking at the BAM file. The RISE samples are in that latter category. I looked at the RISE samples for a few more of the block of SNPs that make up I1 before it divides into descendant subclades. Out of the 70 SNPs looked at so far, there are only 4 SNPs read across the four samples, and they are all one-read. So that's 4/(4x70)=1.4% of just getting a read on SNPs looked at so far. And none of the four SNPs with a reading are showing up in more than one sample so far.

I think one major factor is when the analysis was conducted. If you look at the publication dates, all but one of the post-CE samples I've looked are from papers published in 2018. The only one that wasn't was published in 2016. All of the pre-CE samples are from papers published in 2015 or 2014. Probably a bit of difference in the technology of sequencing. Also, the ancient remains have had a lot more time to degrade before they were analyzed.

It may be that some of the RISE samples are not positive for some of the SNPs in the I1 block and may be an extinct lineage that doesn't have descendants that are alive today (or at least not in any database of modern testers that I'm aware of). In that case, wouldn't expect them to be DF29+. But if it's all no calls or one-read positives or negatives, it may be impossible to say with any certainty. We've seen above that CL63 has a single read negative call for DF29, which is clearly bogus due to a much stronger call for Z63 with 11 positive reads. And then SVK-A1 has a single false positive for Z131+ which saw SVK-A1 assigned as I1b in the paper, but when digging further into the data shows he's actually I-FGC21682 based on stronger SNP reads (and therefore must be Z131-). Isolated single read SNPs for derived or ancestral alleles may not be conclusive as we have examples of them turning up false, so we need to approach such calls with a bit of caution.

Unless the dna samples are too degraded to run further testing there should be a way to rerun tests on these samples using the latest SNP database. The I1 project alone could fund this testing if cost is an issue. It’s not like there are hundreds of ancient I1 samples to choose from. There are only a handful so the most extensive testing should be performed to glean as much knowledge as possible.

deadly77
01-14-2019, 11:37 PM
Unless the dna samples are too degraded to run further testing there should be a way to rerun tests on these samples using the latest SNP database. The I1 project alone could fund this testing if cost is an issue. It’s not like there are hundreds of ancient I1 samples to choose from. There are only a handful so the most extensive testing should be performed to glean as much knowledge as possible.

I think degradation has to be a factor in some of them. This is quite clear in the Ebenesersdóttir 2018 paper where they mention that they selected 35 ancient Icelanders for WGS, but only 27 of those passed quality control. And it looks like they were all sequenced WGS by the same technique, but there's a world of difference in the data when looking at the BAM files for the six I1 samples, say between HSJ-A1 and DAV-A9 for example.

A lot of the papers look like they are different institutions and in that case there's going to be differences in DNA extraction and sequencing. Some specify that they are using SNP capture, some specify WGS (say CL63 versus SZ45 in the Longobard cemetery paper). And the read length, depth, etc. are probably going to be different from study to study. I'm sure that leads to some differences as well.

Across the eight publications, none of them have deep Y chromosome analysis as the primary focus of the manuscript. In most cases, it's simply an entry in a table or a mentioned in a few sentences in the text, if it's mentioned at all. Most of the discussion tends to be about something else - usually autosomal DNA, comparison with modern populations, archaeology or geographic analysis from strontium isotope ratios. Those subjects all get more discussion than Y-DNA haplogroup in these publications. So perhaps there isn't the motivation among the authors and researchers of these publications for the most extensive testing on the Y chromosome if they get the data that they are more interested in. Given some of the incorrect or ambiguous assignment of some of the reported Y-DNA, I would say it isn't high on their agenda. And I would guess that retesting is also not high on their agenda.

When you say "The I1 project alone could fund this testing if cost is an issue" are you referring to the I1 project at FTDNA? If so, I'm not aware of the FTDNA I1 project funding ancient DNA tests (or retests) in the past. I know there's a general project fund but I would assume that was for sponsoring DTC tests at FTDNA rather than funding ancient DNA research. Several of the project admins have commented and shown interest in the results when I've shared the analysis of the BAM file, but none of them have brought up retesting or funding that. Or perhaps you're referring to another I1 project? Or are you representing one which is offering funding?

mwauthy
01-15-2019, 01:26 AM
I think degradation has to be a factor in some of them. This is quite clear in the Ebenesersdóttir 2018 paper where they mention that they selected 35 ancient Icelanders for WGS, but only 27 of those passed quality control. And it looks like they were all sequenced WGS by the same technique, but there's a world of difference in the data when looking at the BAM files for the six I1 samples, say between HSJ-A1 and DAV-A9 for example.

A lot of the papers look like they are different institutions and in that case there's going to be differences in DNA extraction and sequencing. Some specify that they are using SNP capture, some specify WGS (say CL63 versus SZ45 in the Longobard cemetery paper). And the read length, depth, etc. are probably going to be different from study to study. I'm sure that leads to some differences as well.

Across the eight publications, none of them have deep Y chromosome analysis as the primary focus of the manuscript. In most cases, it's simply an entry in a table or a mentioned in a few sentences in the text, if it's mentioned at all. Most of the discussion tends to be about something else - usually autosomal DNA, comparison with modern populations, archaeology or geographic analysis from strontium isotope ratios. Those subjects all get more discussion than Y-DNA haplogroup in these publications. So perhaps there isn't the motivation among the authors and researchers of these publications for the most extensive testing on the Y chromosome if they get the data that they are more interested in. Given some of the incorrect or ambiguous assignment of some of the reported Y-DNA, I would say it isn't high on their agenda. And I would guess that retesting is also not high on their agenda.

When you say "The I1 project alone could fund this testing if cost is an issue" are you referring to the I1 project at FTDNA? If so, I'm not aware of the FTDNA I1 project funding ancient DNA tests (or retests) in the past. I know there's a general project fund but I would assume that was for sponsoring DTC tests at FTDNA rather than funding ancient DNA research. Several of the project admins have commented and shown interest in the results when I've shared the analysis of the BAM file, but none of them have brought up retesting or funding that. Or perhaps you're referring to another I1 project? Or are you representing one which is offering funding?

I was just speaking generally. If every I1 project member at Ftdna contributed $10 then that would be over $70,000. I’d be much more willing to contribute money towards ancient I1 dna analysis that applies to us all than to a general fund whereby I’m not sure what it’s exactly being used for or for whom.

There are only 6 BCE I1 samples. That would be over $10k available per sample.

deadly77
01-17-2019, 10:50 PM
Good news - I received an email back from the YFull team - they agree with my analysis and say they will add SZ45 to the YFull tree in the near future, SZ45 will form a new branch I-FGC21818 below I-FGC21819 with sample YF01673.

JonikW
01-17-2019, 11:16 PM
Good news - I received an email back from the YFull team - they agree with my analysis and say they will add SZ45 to the YFull tree in the near future, SZ45 will form a new branch I-FGC21818 below I-FGC21819 with sample YF01673.

That's great news. Nice work and a valuable contribution to the I1 tree. Thanks.

spruithean
01-17-2019, 11:59 PM
Awesome!

I'm also hoping that we find some I1 samples in Eastern Germanic studies. It'd be nice to know if there was any I1 amongst the Gepids, Goths, Vandals, etc.

JonikW
01-18-2019, 12:34 AM
Awesome!

I'm also hoping that we find some I1 samples in Eastern Germanic studies. It'd be nice to know if there was any I1 amongst the Gepids, Goths, Vandals, etc.

Yes, I'm expecting a lot more Scandinavian I1 aDNA next. Even the modern samples on our Z140 branch suggest as much if you take a close look at YFull. Watch this space...

JMcB
01-18-2019, 01:08 AM
Good news - I received an email back from the YFull team - they agree with my analysis and say they will add SZ45 to the YFull tree in the near future, SZ45 will form a new branch I-FGC21818 below I-FGC21819 with sample YF01673.

As they say on Time Team, brilliant!

Nice work!

deadly77
01-18-2019, 10:21 AM
I went through the BAM file for Stora Förvar 11 (SF11) and the four RISE samples. These are among some of the lowest coverage Y-DNA BAM files that I have looked at. SF11 is the oldest, and in various forums I often see that it's cited as the earliest example of I1 found in ancient DNA samples. Despite the age of this sample, it appears that SF11 has better coverage than the four RISE samples from the Allentoft study.

Looked at the 312 SNPs that YFull are using today to define the I1 haplogroup on their tree. Three of the SNPs I couldn't find hg19 position for, so I had to leave these out. All of the ancient DNA BAM files that I have looked at are mapped against hg19 reference. The exceptions are the ancient Icelandic samples which are mapped to hg38.

However, of these 309 SNPs, only 19 positions have a reading in SF11's BAM file and all but two are one read. SF11 is derived for Z2726(1G), Z2792 (1C), Z2802/CTS6221 (1T), Z2882/YSC0000301 (1C), FGC2433 (1A), Z2805/CTS6629 (1A), CTS1748/Z2749 (1G), Z2683 (1T), Z2731 (1A). SF11 is ancestral for Y1831/FGC2468 (1T), Z2714/FGC2425 (1T), CTS3268/Z7262 (1T), L121/S62 (1A), Z2825/CTS9258 (2G), Z2825/CTS9258 (1C), CTS9845 (1A), Z2804/CTS6547 (2C), Z2690 (1G), FGC7871/Y1906 (1G).

So that's 9 positive SNPs - all of which are one read- out of 309 (2.9%) and 10 negative SNPs out of 309 (3.2%) as the evidence for SF11 to be I1. Could be argued that SF11 isn't I1 at all - more appropriately described as I*, pre-I1, etc. Most likely an extinct lineage that doesn't have descendants alive today - at least none that have tested in any of the current database. It's impossible to say how far between I and I1 that SF11 sits, given that 94% of the 309 SNPs looked at have no call. Perhaps there's a case for putting some of these SNPs in the I1 block as older than some others, but given all the positive SNPs in this block are only one read, I wouldn't have a lot of confidence in saying that.

While scanning the BAM, also came across a few SNPs that aren't in any database that I looked at: 16377199 1T (right next to L121), 19100097 1A, 4282847 1T, 4282860 1T as well as a couple that are named as found in other haplogroups: F15054+ (P haplogroup), CTS1547/PF4687 (J haplogroup). The latter could be recurrent SNPs and the former could be private mutations associated with SF11's line. Or they could just be false positive one reads. My hunch is the latter.

deadly77
01-18-2019, 02:20 PM
BAB5 is pretty easy to cover as there is no BAM file - from looking at Szécsényi-Nagy's 2015 paper here https://royalsocietypublishing.org/doi/full/10.1098/rspb.2015.0339 and dissertation here [URL="https://publications.ub.uni-mainz.de/theses/frontdoor.ph it appears that the Y-DNA testing on BAB5 comprised of a small number of single Y-SNPs. The only ones reported for the I haplogroup in the supplementary information were positive results for M170 (I) and M253 (I1), then a negative result for M438 (I2):
28483
None of the >300 phyloequivalent SNPs that make up the I1 block were tested. Given the date assigned to BAB5, it's before the estimated TMRCA of modern I1 descendants and as is the case for SF11, probably not positive for all of the SNPs that define I1. But no data to analyze to verify.

deadly77
01-18-2019, 02:21 PM
The RISE samples from the Allentoft 2015 study gave a rather poor return when looking at 309 of the SNPs that define I1:

RISE175 was positive for CTS6140/Z2799 (1C), Z2698/FGC2435 (1C), V5190/Z2742 (1A), YSC0000259/Z2761 (1A), Z2745 (3T), Z2678/CTS40 (1T), Y1882/FGC2471 (1C), FGC2445/Z2688 (1T). 8/309=2.6%.
RISE179 was positive for CTS3506/Z2765 (1G), CTS313/Z2681 (1C). 2/309=0.6%
RISE207 was positive for S109/M450 (1A). 1/309=0.3%
RISE210 was positive for Z2711/FGC2439 (1A), CTS11036/Z2863 (1C), CTS1755/Z2750 (1T), CTS733/Z2703 (1C), Z2784/CTS5167 (1T), Z2775/CTS4400 (1C), Z2806/CTS6765 (1C). 7/309= 2.3%.

So, didn't find any of the I1 SNPs that were negative (as was the case for SF11). However, given that >97% of the I1 SNPs were no call, that doesn't really mean much. Also note that all but one of the derived SNPs is a one-read positive, and no derived SNP is observed in any of the other three samples. The only one that had more than one read was Z2745 (3T) - however, there appears to be some issue with that region of the Y chromsome in RISE175 - the position immediately adjacent at 13314435 has 2G reads (ancestral) and 1A read.

JonikW
01-18-2019, 03:13 PM
BAB5 is pretty easy to cover as there is no BAM file - from looking at Szécsényi-Nagy's 2015 paper here https://royalsocietypublishing.org/doi/full/10.1098/rspb.2015.0339 and dissertation here [URL="https://publications.ub.uni-mainz.de/theses/frontdoor.ph it appears that the Y-DNA testing on BAB5 comprised of a small number of single Y-SNPs. The only ones reported for the I haplogroup in the supplementary information were positive results for M170 (I) and M253 (I1), then a negative result for M438 (I2):
28483
None of the >300 phyloequivalent SNPs that make up the I1 block were tested. Given the date assigned to BAB5, it's before the estimated TMRCA of modern I1 descendants and as is the case for SF11, probably not positive for all of the SNPs that define I1. But no data to analyze to verify.

Thanks for all that. BAB5 would of course be a particularly interesting sample to have more data on, given possible implications for the I1 tree. It's frustrating not to know more.

spruithean
01-18-2019, 03:44 PM
Thanks for these analyses. I've always suspected SF11 and BAB5 to be I*(pre-I1). I'm not sure we can count BAB5 and SF11 in the ancient I1 list anymore.

mwauthy
01-18-2019, 07:26 PM
BAB5 is pretty easy to cover as there is no BAM file - from looking at Szécsényi-Nagy's 2015 paper here https://royalsocietypublishing.org/doi/full/10.1098/rspb.2015.0339 and dissertation here [URL="https://publications.ub.uni-mainz.de/theses/frontdoor.ph it appears that the Y-DNA testing on BAB5 comprised of a small number of single Y-SNPs. The only ones reported for the I haplogroup in the supplementary information were positive results for M170 (I) and M253 (I1), then a negative result for M438 (I2):
28483
None of the >300 phyloequivalent SNPs that make up the I1 block were tested. Given the date assigned to BAB5, it's before the estimated TMRCA of modern I1 descendants and as is the case for SF11, probably not positive for all of the SNPs that define I1. But no data to analyze to verify.

Nice work! Your analysis has confirmed my assumptions that it’s extremely misleading to label a sample as I1 simply because it’s positive for 1/312 SNPs such as I-M253. This is especially true if there is only 1 read.

I feel that I-DF29 is a better SNP for analysis since it represents 99% of all modern I1, only has 6 phyloequivalent SNPs, and has a close TMRCA to I1.

spruithean
01-18-2019, 09:44 PM
Thanks for all that. BAB5 would of course be a particularly interesting sample to have more data on, given possible implications for the I1 tree. It's frustrating not to know more.

Agreed. It's unfortunate that BAB5 wasn't analyzed more in-depth (unless it was a low-quality sample in which case, nothing can really be done). I was already fairly certain about SF11 being I* (pre-I1) but I suspect that BAB5 could be in that same area. Perhaps there was possibly another lineage that would have divided the to-be-I1 lineage into two different groups.

Back to future aDNA results that might turn up some I1. Obviously areas where Germanic tribes are known to have been is likely to be the best source of potential I1, I'm quite curious about the tribal confederations like the Gepids, who in all likelihood had some Hun admixture (this is supported by a few aDNA results IIRC). I wonder how many paternal Gepid lineages were I1 and how many may have been Hunnic? We know several East Germanic tribes adopted a lot of Hunnic cultural aspects, so I wonder how much intermarriage there was between them.

JonikW
01-18-2019, 11:07 PM
Agreed. It's unfortunate that BAB5 wasn't analyzed more in-depth (unless it was a low-quality sample in which case, nothing can really be done). I was already fairly certain about SF11 being I* (pre-I1) but I suspect that BAB5 could be in that same area. Perhaps there was possibly another lineage that would have divided the to-be-I1 lineage into two different groups.

Back to future aDNA results that might turn up some I1. Obviously areas where Germanic tribes are known to have been is likely to be the best source of potential I1, I'm quite curious about the tribal confederations like the Gepids, who in all likelihood had some Hun admixture (this is supported by a few aDNA results IIRC). I wonder how many paternal Gepid lineages were I1 and how many may have been Hunnic? We know several East Germanic tribes adopted a lot of Hunnic cultural aspects, so I wonder how much intermarriage there was between them.

I would love to see aDNA there too. Given that the eastern Germanic tribes were probably predominantly Scandinavian I think we'll see more ancient L22 for sure. As for Z140 I may well be wrong but my hunch is we'll find the Jutland peninsula as the focal point, stretching into southern Sweden. I'd really like some idea of how many men were Z140 and L22 etc 2,000 years ago. Are we talking a few thousand?

deadly77
01-19-2019, 10:22 AM
Nice work! Your analysis has confirmed my assumptions that it’s extremely misleading to label a sample as I1 simply because it’s positive for 1/312 SNPs such as I-M253. This is especially true if there is only 1 read.

I feel that I-DF29 is a better SNP for analysis since it represents 99% of all modern I1, only has 6 phyloequivalent SNPs, and has a close TMRCA to I1.

Yes, agreed - I think there is a lot of information that gets taken at face value and then repeated many times in some forums, which can lead to misleading conclusions - sometimes unintentional and sometimes intentional depending on the individual. If the opportunity is available to go back and look at the primary data, I think that's always a good course. Although sometimes the primary data is incomplete or flawed (as is the case here) and I think it's important to be transparent about the limitations of what we can say based on the data that we have.

Also agreed on I-DF29 - in the majority of the post-CE samples I've been able to at least verify DF29 or one of the phyloequivalent SNPs - which is to be expected given the dates of those samples and TMRCA. It also means I don't have to hunt around among a block of >300 SNPs, which is not the most fun way to spend time. Before engaging in the big block, I checked all of the SNPs on the I-DF29 branch and they all came up as no call for all of the RISE samples. I've been through some of the more common subclades below I-DF29 and again it's a lot of no calls and a very small number of negatives for the RISE samples. However, the low call rate among the >300 block of I1 SNPs is illustrative in whether we can realistically expect to find anything from the data.

deadly77
01-19-2019, 10:45 AM
Agreed. It's unfortunate that BAB5 wasn't analyzed more in-depth (unless it was a low-quality sample in which case, nothing can really be done). I was already fairly certain about SF11 being I* (pre-I1) but I suspect that BAB5 could be in that same area. Perhaps there was possibly another lineage that would have divided the to-be-I1 lineage into two different groups.

Back to future aDNA results that might turn up some I1. Obviously areas where Germanic tribes are known to have been is likely to be the best source of potential I1, I'm quite curious about the tribal confederations like the Gepids, who in all likelihood had some Hun admixture (this is supported by a few aDNA results IIRC). I wonder how many paternal Gepid lineages were I1 and how many may have been Hunnic? We know several East Germanic tribes adopted a lot of Hunnic cultural aspects, so I wonder how much intermarriage there was between them.

Although in most ancient genomes I'm sure that the quality of the sample is the major factor in determining the data that we can get from the analysis, in the case of BAB5 the design of the analysis appears to have been more of a factor in the limited data output. It looks that they just looked at a limited number of Y-SNPs by design. I'd say an analogy to the direct-to-consumer tests that we're more familiar with would be that the researchers on BAB5 did the equivalent of a small SNP pack or panel (or even something like a 23andme test) rather than a Big Y or WGS. Of course, sample quality could still be a factor as well - subjecting BAB5 to a WGS may not yield much more, but for sure the scope of the analysis limited the scope of what could be determined from this study.

Of course, one "glass half-full" view is that since there haven't been many ancient I1 samples discovered to date, perhaps the ones discovered from now on will have a more comprehensive analysis as the technology improves and the price of sequencing drops.

Sassoneg
01-19-2019, 11:05 PM
Thank you so much for this, deadly. I'm glad you resolved the Lombard sample questions.

I'm part of the Z63 project and so far we have but two old samples: KO55 and now CL63.

We have three members who are currently Z63* with zero common SNPs. These are relatively new results and not publicly available. I wonder if CL63 would have any of our reads? Is there a format I can provide to check CL63 against?

It would be amazing if we could grab even one shared SNP.

deadly77
01-20-2019, 02:10 AM
Thank you so much for this, deadly. I'm glad you resolved the Lombard sample questions.

I'm part of the Z63 project and so far we have but two old samples: KO55 and now CL63.

We have three members who are currently Z63* with zero common SNPs. These are relatively new results and not publicly available. I wonder if CL63 would have any of our reads? Is there a format I can provide to check CL63 against?

It would be amazing if we could grab even one shared SNP.

Absolutely - the Lombard samples were vexing me for a while, largely due to the conflicting information. One of the reasons I didn't get to them for a while was that I acquired most of the BAM files for the other samples from the European Nucleotide Archive - for SZ45 and CL63 the ENA had FASTQ files only and I struggled to convert those into a format that I can read. Lots of banging my head against a brick wall on that one. It wasn't until I checked NCBI that I was able to get a BAM file, and I was also able to only download the Y-DNA BAM aside from the other chromosomes. This cuts down significantly on the download times and space on my archaic computer.

One thing I want to make clear is that CL63 is not confirmed negative for the SNPs downstream of I-Z63 that I listed - the ones that I listed were no call, so no positive or negative information. CL63 could very well be positive for some of those.

I'm happy to take a look in CL63's BAM file for any SNPs that you're interested in. To be honest, I'm not especially familiar with the I-Z63 branch and largely picked the ones that I listed from looking at the publicly available phylogenetic trees from YFull and FTDNA. I'd welcome input from someone more familiar with I-Z63 on other SNPs that may be worth checking. With regard to the I-Z63* members, we can do that as well. The best way to do this would be to get me a list of the SNPs that you want checked with the following information: position on the Y chromosome against the Hg19 reference, ancestral allele and derived allele. All of the serious Y-DNA testing companies doing business today are using the hg38 reference (and rightly so) but CL63 is on the hg19 reference. I can try and convert between hg38/hg19 but in some regions it doesn't translate.

Obviously the individuals in your project are alive today, and while some of their SNPs at I-Z63* are a few thousand years ago, some of their SNPs may be a lot closer to the present. Accordingly, we shouldn't advertise them in a public forum, so I suggest that you send me a PM and we can figure it out from there. I'd also request that you get the permission from those individuals on sharing the data regarding their private SNPs.

Sassoneg
01-23-2019, 12:37 AM
I have mentioned it in the group and will send my personal SNP list as soon as I can figure out how to convert it.

deadly77
01-23-2019, 09:19 AM
I have mentioned it in the group and will send my personal SNP list as soon as I can figure out how to convert it.

From the list you sent me, mostly no call, a few has the ancestral allele and one SNP was ambiguous - a few weird bits in other positions close by to that one. Sent you a PM with more specific details.

CL63 is probably on one of the more established branches of I-Z63 rather than I-Z63*, but the no calls from the "SNP capture" don't give any strong leads to where.

spruithean
01-23-2019, 05:55 PM
Carlos Quiles in his newest revision of the Indo-European paper, now within a large file called "Game of Clans" (the title is longer than that I forget the rest and I am unable to look it up at the moment), he mentions an old I1-M253 sample in Gotland circa 6950 BC. Is that a legitimate sample?

Also he seems to say that the I-M170 samples in a certain timeframe are more likely to be M253+.

Perhaps I1-M253 was present in Scandinavia but due to degradation the sequencing only yields M170 SNPs?

oz
01-23-2019, 08:18 PM
Unrelated to ancient I1, but i just got my result from Ftdna after ordering the I1 SNP pack deal which was around $80 and i'm disappointed that they've only tested down to the I-PR683 (which is under I1-Z63). Now they're offering me the I-PR683 snp pack for $119 and I don't know if it's worth it and how deep that test would be. If they won't provide a much younger tmrca than Y6228 (which was provided to me by 23andme) then it would definitely be a waste of money. And I don't want to pay more than around a $100 for these tests at this time or in the near future.

Any useful advice would be helpful...

spruithean
01-23-2019, 09:22 PM
What terminal SNP do most of your matches fall under (if any do at all)?

Perhaps look at YSEQ?

oz
01-23-2019, 09:35 PM
What terminal SNP do most of your matches fall under (if any do at all)?

Perhaps look at YSEQ?

Most of my matches on the chart just have I-M253. And it's odd that nothing changed there because i imagined that match list would get filtered and narrowed down to only the pr683 level and downstream. I'll look into YSEQ or maybe ordering from ftdna only the y6228 snp test and whatever downstream from that they have to offer.

deadly77
01-24-2019, 09:01 AM
Carlos Quiles in his newest revision of the Indo-European paper, now within a large file called "Game of Clans" (the title is longer than that I forget the rest and I am unable to look it up at the moment), he mentions an old I1-M253 sample in Gotland circa 6950 BC. Is that a legitimate sample?

Also he seems to say that the I-M170 samples in a certain timeframe are more likely to be M253+.

Perhaps I1-M253 was present in Scandinavia but due to degradation the sequencing only yields M170 SNPs?

I had a quick look (not a full read) and was able to find this one "A Game of Clans and a Clash of Chiefs" (definitely a George R. R. Martin reference) at ResarchGate here https://www.researchgate.net/profile/Carlos_Quiles/publication/330039212_A_Game_of_Clans_A_Clash_of_Chiefs/links/5c2b390092851c22a35289e3/A-Game-of-Clans-A-Clash-of-Chiefs.pdf?origin=publication_detail

He does mention "The first sample of haplogroup I1-M253 is probably found in Gotland ca. 6950 BC, which points to the survival of these lineages in pockets of Scandinavia until
the formation of the Nordic Late Neolithic". Quick search for "Gotland I-M253 6950 BC" goes to this manuscript on biorxiv https://www.biorxiv.org/content/biorxiv/suppl/2017/07/30/164400.DC2/164400-1.pdf - scanning that one comes up with "The cave of Stora Förvar, situated on the small island of Stora Karlsö, off the west coast of Gotland in the Baltic Sea"

I believe he's referring to SF11, which we've discussed as not quite being I1.

When Carlos Quiles talks about "and another from Abbekĺs (ca. 1900 BC) of hg. I1-M253, proper of Neolithic Scandinavia" and "three samples from Skĺne showing hg. I-M170 (probably all I1-M253)", he references the Allentoft et al. 2015 study and must be thinking of the RISE samples that we've discussed earlier in the thread as having some of the I1 SNPs, but a lot of no calls.

Later on in Game of Clans he mentions again "Haplogroup I1-M253 was reported previously only in a hunter-gatherer (ca.7000 BC) from Gotland (Günther et al. 2017)" - searching for Günther 2017 finds this paper here https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2003703 - he must be referring to SF11 - table 1 lists 7 Scandinavian Hunter Gatherers, and of the four males, three are I2. SF11 is the other one although the paper itself says "Not enough genome coverage" for the Y haplogroup of SF11. The paper itself doesnt make any reference to I1 or I-M253.

Later on he mentions the ancient Icelandic samples from Ebenesersdóttir 2018, but he described "one of them I1b-Z131 (formed ca. 2400 BC, TMRCA ca. 2000 BC)" - he must be referring to SVK-A1, which we know has a false positive read for Z131 and is actually I-FGC21682 under I-P109 (and so must be Z131-).

JonikW
01-24-2019, 09:07 AM
Once again, you've shown we need to be extremely wary of taking haplogroups cited in studies at face value... Thanks.

spruithean
01-24-2019, 12:37 PM
He also briefly mentioned SBT-A1 as being I-Z62, that is quite a bit upstream of SBT-A1's placement at YFull.

deadly77
01-24-2019, 04:35 PM
He also briefly mentioned SBT-A1 as being I-Z62, that is quite a bit upstream of SBT-A1's placement at YFull.

I think that's because he's going off the longhand Y-DNA haplogroup designation for SBT-A1 which is in Table 1 of the Ebenesersdóttir et al 2018 Science paper. That lists SBT-A1 as I1a2a1a2. If you look that up on the current ISOGG tree (which isn't easy to navigate), that appears to correspond to I-S26062 and that appears to be a descendant of I1a2a1a, which is what he has listed SBT-A1 as in his "A Game of Clans". The ISOGG 2018/2019 tree has I1a2a1a as I-Z62.

So it looks like he's missed the last "2" off the longhand description by mistake. Or he deliberately moved up to a branch that has been "confirmed within haplogroup" at ISOGG for Z62, versus "investigational item" that S26062 is currently listed as.

If you read the supplementary information of the Ebenesersdóttir et al 2018 Science paper, they say that they used the ISOGG 2016 Y chromosome tree. On that version of the ISOGG tree, I1a2a1a2 corresponds to I-F2642 (which is closer to where SBT-A1 is - I-S26062 would put him on a different branch while I-Z62 covers both).

Ugh - another good reason that everyone needs to move on from the longhand subclade nomenclature...

deadly77
01-25-2019, 12:14 AM
Once again, you've shown we need to be extremely wary of taking haplogroups cited in studies at face value... Thanks.

Absolutely - there's definitely a few cases of secondary information is being presented or misinterpreted as fact - sometimes unintentionally and sometimes intentionally. In the primary literature, such as the Allentoft et al 2015 paper or supporting info, the Günther et al 2017 paper, I don't have the paper for Skoglund et al 2012 (but I have the supporting information) - I can't find any mention of SF11 or the RISE samples connected to I1 or I-M253. But some blogs and forum posts have reported these samples as I1 or I-M253, and from there people reference the blogs and forums (secondary information) that report these rather than the primary literature, it gets repeated again and again and again. It doesn't get questioned that the assignment of I1 or I-M253 isn't based on solid evidence - less than 3% of the I1 SNPs even read, the small number of positive reads are all one read SNPs except for one SNP across five samples, ancestral alleles for I1 in the case of SF11. But if I had a pound for every time there's been a mention of one of these samples as being definitely I1...

I was checking out an course earlier today "Genealogy: Researching Your Family Tree" from University of Strathcylde. I've been researching my paper trail for about the last nine and a half years and got interested in the genetic aspects of genealogy about two and a half years ago. I definitely don't consider myself a beginner but feel there's benefits for taking a refresher/review, picking up other ways of looking at things or stuff I hadn't even considered. The course is free, online and came recommended by some people that have taken it.

Anyway, in the early steps they spend a bit of time on the nature of documentary evidence, discussing the differences between primary sources, primary derived sources, secondary sources, the importance of knowing the history of a source, how much confidence that we have in the source. While in the course, they're referring to traditional paper trail genealogy (although the course says it covers some genetic genealogy as well) it made me think of some of the examples that we're discussing here and how that could be applied to haplogroup assignments and references to secondary sources.

Sassoneg
01-25-2019, 03:17 AM
I downloaded a BAM viewer (IGV) and obtained the CL63 BAM from NCBI. I looked at CL63.

Results: Z63+, S2077+, PR683+, L1237-

28608

Much thanks to deadly77!

deadly77
01-25-2019, 08:43 AM
I downloaded a BAM viewer (IGV) and obtained the CL63 BAM from NCBI. I looked at CL63.

Results: Z63+, S2077+, PR683+, L1237-

28608

Much thanks to deadly77!

Nice one! Good to see that you were able to sort out the issues with the BAM file. I had a look back on my notes - I had noted the one read for Y2245 (same SNP as PR683, but YFull doesn't have it by that name) but for some reason I didn't include it in the summary I put on here. Probably got fed up with all of the no calls - that's why it's great to have a second opinion for things I may have missed. I definitely didn't check for FGC9504, which is a good find because it adds more confidence to the one read of Y2245.

deadly77
01-25-2019, 09:04 AM
Another good example of checking the primary data rather than relying on a secondary analysis (including my own analysis in that category) :)

JonikW
01-26-2019, 12:38 AM
Another good example of checking the primary data rather than relying on a secondary analysis (including my own analysis in that category) :)

Excellent. Two good sets of eyes on everything is a golden rule as far as I'm concerned. It's great to be seeing all this progress on I1. I don't know if it's just me but the next paper seems a long time coming... I hope the recent, ridiculous anti Reich stuff won't scare off those who have custody of the samples in future.

spruithean
01-26-2019, 12:43 AM
Excellent. Two good sets of eyes on everything is a golden rule as far as I'm concerned. It's great to be seeing all this progress on I1. I don't know if it's just me but the next paper seems a long time coming... I hope the recent, ridiculous anti Reich stuff won't scare off those who have custody of the samples in future.

It does seem like it has been eons since the announcement of that study. Perhaps it's just our own impatience. Hoping to see our haplogroup represented a little bit more in aDNA. R1b, R1a, I2, G, J, etc have a rather large representation in aDNA so far. Perhaps envy...

deadly77
01-26-2019, 10:59 AM
Perhaps not an especially "ancient" example (died in 1266 CE), but the haplogroup of Birger Magnusson aka Birger Jarl has been reported as I1. There are a few historical figures that are reported to be I1, most often from DNA testing of descendants, but the example of Birger Magnusson is the only one that I'm aware of that involved lab testing his supposed remains from his tomb. Thought I'd take a look and see if there's anything more to be determined from the testing.

Haplogroup I1 for Birger Magnusson and his son Erik were reported by Malmström et al in a paper in Annals of Anatomy published in 2012. It's on academia.edu for those of you that have an account here https://www.academia.edu/17955057/Finding_the_founder_of_Stockholm_A_kinship_study_b ased_on_Y-chromosomal_autosomal_and_mitochondrial_DNA

From reading the paper, samples were taken from a tooth each of a older male, younger male and female - the putative Birger, Erik and Metchild - during the reopening of the grave in Varnhem Abbey in 2002. Since the paper was published in 2012, the DNA analysis must have taken place some time between 2002 and 2012, which will put the testing earlier than most of the other examples in this thread. Most of the analysis is on the mitochondrial DNA - most likely better understood at the time, and mitochondrial DNA is easier to extract than nuclear DNA - but they also tested one autosomal SNP and three Y-SNPs (TAT for N1c, M253 for I1, M269 for R1b1b2). So unfortunately there's nothing else to be learned unless there was further testing done that I'm not aware of.

Both males tested derived (positive) for M253, so the Y-DNA didn't disprove a paternal relationship. Can't say much more certain, but it appears that the osteological analyses and the historical knowledge matched very well for the three individuals, and the mitochondrial DNA showed that the female was not the younger male's mother, consistent with Metchild and Erik. The limited Y-DNA testing is likely due to the available technology and expense at the time, but they also make reference to "Due to restricted amounts of DNA extract, only the older male Birger, was typed for all three Y SNPs." so that was probably a factor as well.

At the end of the paper, they note that further validation of haplogroup I1 could be obtained from testing samples from the Magnus Ladulĺs grave in Riddarholmskyrkan in Stockholm, which supposedly contain two of Birger's sons Magnus and Valdemar, which should have the same Y-DNA haplogroup, and also the same mtDNA haplogroup as the younger male Erik. The paper says that the a request to open the second grave was granted and was due to begin in 2011. Presumably the research of the second grave would have the advantage that the DNA analysis would be more comprehensive.

I haven't managed to find much out about the Riddarholmskyrkan grave project. Some links are dead, one said that remains were extracted, but were unlikely to be Magnus or Valdemar because dating of the skeletons showed that these remains date significantly later than the burial of the historical individuals. Another link my antivirus flagged with a threat warning.

I've read about examples where original dates assigned to skeletons were revised after accounting for a seafood diet, such as Richard III or the Repton burials. However, I haven't been able to see if the same was applied to the skeletons at the Riddarholmskyrkan grave. Or if the DNA analysis was conducted (which would rule them out by haplogroup - Erik appears to be mtDNA Z1a, which I don't see too often) or if further excavation was carried out to find the correct individuals.

spruithean
01-29-2019, 04:27 PM
I honestly wouldn't be surprised if we saw most of the aDNA sources for I1 being not as ancient as we'd hope. I think perhaps most of the samples will be seen ranging from the Migration Period onward to the Viking Age and beyond, and so far it looks to be the case with the Northumbrian Anglo-Saxon sample, the Icelanders, Baiovarii, etc. I suspect that cremation in the rather ancient days of the areas under Germanic influence, especially before their conversion to Christianity will have a impact on the ancient I1 that we can find, combine that with the dominance of R1b in Europe and it is no surprise that ancient R1b casts a large shadow on ancient I1.

Helgenes50
01-29-2019, 04:31 PM
Is it true that the Tollund man is L22 ?

http://www.next1000.com/family/EC/DNA.history.html?fbclid=IwAR3y6BJ8O6xCy7F_ZXTeiv0s GQi-fudm9rCfhRT1S7wjUEeEDZzaha_eiTw

spruithean
01-29-2019, 04:42 PM
Is it true that the Tollund man is L22 ?

http://www.next1000.com/family/EC/DNA.history.html?fbclid=IwAR3y6BJ8O6xCy7F_ZXTeiv0s GQi-fudm9rCfhRT1S7wjUEeEDZzaha_eiTw

That is extremely unlikely. Due to the conditions of the bog he was found in it is quite likely that there is no more genetic material in the cells. One team extracted bone from his femur and failed to yield any DNA results. Apparently the next attempt will take dense bone from the base of the skull in hopes of getting a DNA sample. However I have my doubts considering the environment his body was left in for the last 2,400 years.

Helgenes50
01-29-2019, 04:58 PM
That is extremely unlikely. Due to the conditions of the bog he was found in it is quite likely that there is no more genetic material in the cells. One team extracted bone from his femur and failed to yield any DNA results. Apparently the next attempt will take dense bone from the base of the skull in hopes of getting a DNA sample. However I have my doubts considering the environment his body was left in for the last 2,400 years.

This would also surprised me, the Tollund man is a star in the Nordic history.
But i could have missed this

deadly77
01-29-2019, 05:19 PM
Is it true that the Tollund man is L22 ?

http://www.next1000.com/family/EC/DNA.history.html?fbclid=IwAR3y6BJ8O6xCy7F_ZXTeiv0s GQi-fudm9rCfhRT1S7wjUEeEDZzaha_eiTw

Reading the segment about Tollund Man from the ink that you shared, I don't think the author definitively says that Tollund Man is L22, more that he's found just North of the area postulated as the geographic origin of I-L22 from a map on an FTDNA project page. It's not clear if the author believes that Tollund Man is I-L22, but he doesn't include a reference there, while he does for a few other points.

As Spruithean says, previous attempts to extract reliable DNA from Tollund Man have not proved successful. It seems that the acids in these bogs that are great at preserving soft tissue tend to destroy DNA. Perhaps a future attempt may get something, but as far as I can tell there's no current DNA evidence to say Tollund Man is I-L22 (or anything else).

Helgenes50
01-30-2019, 06:31 AM
Reading the segment about Tollund Man from the ink that you shared, I don't think the author definitively says that Tollund Man is L22, more that he's found just North of the area postulated as the geographic origin of I-L22 from a map on an FTDNA project page. It's not clear if the author believes that Tollund Man is I-L22, but he doesn't include a reference there, while he does for a few other points.

As Spruithean says, previous attempts to extract reliable DNA from Tollund Man have not proved successful. It seems that the acids in these bogs that are great at preserving soft tissue tend to destroy DNA. Perhaps a future attempt may get something, but as far as I can tell there's no current DNA evidence to say Tollund Man is I-L22 (or anything else).

Thanks for your precisions. Yes indeed what is written about Tollund Man in the link is not really clear and can be misleading. Too bad, given his state of preservation, we could put a face on a distant parent.

deadly77
01-30-2019, 09:15 AM
Thanks for your precisions. Yes indeed what is written about Tollund Man in the link is not really clear and can be misleading. Too bad, given his state of preservation, we could put a face on a distant parent.

Oh, I agree - the way the article is written is rather misleading. Not sure if that's unintentional clumsiness or if the author believes there is a link (or wants there to be one). But don't give up hope - as Spruithean says there will be a further attempt to take dense bone from the base of the skull in hopes of getting a DNA sample. So we may know in future. Although that attempt isn't guaranteed to be successful, at least there will be an attempt.

deadly77
01-30-2019, 03:59 PM
Thanks to the YFull team, SZ45 is now on the YFull tree, with preliminary placement at I-Y14999, analysis in progress...
28706
https://www.yfull.com/tree/I-Y14999/

Pribislav
02-03-2019, 08:39 PM
deadly77, since there's nothing new these days, maybe you could check this sample from Scheib et al. 2018 (http://science.sciencemag.org/content/360/6392/1024):

US-14, 1655-1707 AD, Shohola Creek, Indian Cabin Ridge, PA, USA, Colonist, U4c1a, I1a-Z58>>>Z73 (https://www.yfull.com/tree/I-Z73/)

deadly77
02-04-2019, 01:04 PM
deadly77, since there's nothing new these days, maybe you could check this sample from Scheib et al. 2018 (http://science.sciencemag.org/content/360/6392/1024):

US-14, 1655-1707 AD, Shohola Creek, Indian Cabin Ridge, PA, USA, Colonist, U4c1a, I1a-Z58>>>Z73 (https://www.yfull.com/tree/I-Z73/)

Thanks for the head-up Pribislav. I've found the BAM file for US-14 at ENA and downloading it now. It looks a little on the small side at 694 MB, but I'll see what I can figure out and post it up here when I've taken a look.

JMcB
02-04-2019, 03:57 PM
deadly77, since there's nothing new these days, maybe you could check this sample from Scheib et al. 2018 (http://science.sciencemag.org/content/360/6392/1024):

US-14, 1655-1707 AD, Shohola Creek, Indian Cabin Ridge, PA, USA, Colonist, U4c1a, I1a-Z58>>>Z73 (https://www.yfull.com/tree/I-Z73/)


Hello Pribislav,

Can you give us a little context on who this fellow (US-14) was and how he came to be sampled?

By the way, I like your avatar!

deadly77
02-04-2019, 04:31 PM
Hello Pribislav,

Can you give us a little context on who this fellow (US-14) was and how he came to be sampled?

By the way, I like your avatar!

Pribislav is likely more familiar with the paper, but from what I've been able to gather so far, the majority of the 91 ancient samples in this paper belong to Native American haplogroups. US-14 is listed in a paragraph in the supplementary material as remains from the American Museum of Natural History:

"Culturally unidentifiable individuals were selected for destructive sampling based on geographical provenience and availability of loose teeth or disarticulated cranial remains. The context of the individuals is scarce and restricted to what was written in the catalogue available for viewing by request to the museum curator(s). Individual US-14 (DNA analysis showed this individual to be entirely of European descent) was found at Shohola Creek, Indian Cabin Ridge, Pennsylvania, and donated to the museum in the 1960s."

US-14 listed in Table S1 as a "colonist" and age from raw 14C dating 269 +/- 26 ybp. Calibrated date in Table S2 is 1634 - 1662 AD.

deadly77
02-04-2019, 04:48 PM
The raw data for US-14 is rather poor. It looks like the average read depth is 0.448x for US-14 - probably shouldn't expect many multi-read samples. Read length is also 75bp. The supplementary information also mentions in discussion of the autosomal analysis "Three samples (NC-C, 523-Ac, and US-14) showed a high percentage of windows with unreliable estimates (>10%) and were excluded."

US-14 listed in Table S1 as I1a-Z73 for Y-DNA haplogroup. I looked in the BAM and US-14 is a no call for Z73. Also looked at the 14 phyloequivalent SNPs on this branch that are listed on the YFull tree and the FTDNA public haplotree and they are all no call as well. Then started looking at the SNPs on the way to Z73 - CTS9352, CTS9477, Z2895, CTS7362, Z2903, FGC8667, Z60, Z61, CTS8647, Z62, Z59 and Z58 are no call.

On the I-DF29 block, US-14 is a one read positive for DF29 itself and no call for the six phyloqequivalent SNPs. So could say perhaps US-14 is I1a based on DF29+. But I'm hesitant to hang a haplogroup on single one-read SNP with no corroborating information. Not sure where they get the Z73 designation from. Perhaps they found a more downstream SNP and moved it up to a more "known" branch, but nothing I've seen in the BAM file so far gives any evidence for US-14 being I-Z73

spruithean
02-04-2019, 08:22 PM
Hello Pribislav,

Can you give us a little context on who this fellow (US-14) was and how he came to be sampled?

By the way, I like your avatar!

From Schleib's Science Supplementary materials:


Remains from the American Museum of Natural History
Culturally unidentifiable individuals were selected for destructive sampling based on
geographical provenience and availability of loose teeth or disarticulated cranial remains.
The context of the individuals is scarce and restricted to what was written in the
catalogue available for viewing by request to the museum curator(s). Individual US-14
(DNA analysis showed this individual to be entirely of European descent) was found at
Shohola Creek, Indian Cabin Ridge, Pennsylvania, and donated to the museum in the
1960s.

He looks to be of European origins and dated to around "1634 - 1662 AD". However that's with a 68% probability. So who knows exactly how old the individual is.

deadly77
02-05-2019, 12:21 PM
I was listening to the Insitome podcast in parts over yesterday and today. It doesn't concern ancient I-M253 samples, and the majority of the podcast is about the recent New York Times article on David Reich but I found it interesting as it there's also a fair bit of discussion around ancient DNA sample quality, strategies and approaches to testing ancient DNA and technology used to do so, topics that we have touched on from time to time in this thread, so I think it's worth a listen. Can be found on itunes, etc. or here: https://insitome.libsyn.com/the-new-york-times-takes-on-ancient-dna

deadly77
02-06-2019, 09:37 AM
While I was discussing SZ45 with YFull, I asked them if they would mind taking a look at NO3423, the Anglo-Saxon from Norton, Teeside. I'd been through this one previously in this thread and managed to place him at I-DF29, rule out some downstream subclades from negative calls, but hadn't found anything positive among a lot of no calls. YFull replied that the quality of this sample is really low, but they provided a list of calls against known SNPs on the I1 section of their tree. The majority SNPs in their report are negative - there are eight positive SNPs. However, I'm fairly sure that these are false positives from the low read - several of them are in conflict with each other, appearing on different branches of the I1 tree and also read negative for phyloequivalent (and more importantly upstream) SNPs. I guess we'll be leaving NO3423 at I-DF29 with more ideas about what he's not than what he is. His subclade lineage is either obscured by the no calls in the BAM file or his Y-chromosome lineage may have died out and he has no descendants that are around today (at least that have tested and in one of the databases).

spruithean
02-06-2019, 05:12 PM
While I was discussing SZ45 with YFull, I asked them if they would mind taking a look at NO3423, the Anglo-Saxon from Norton, Teeside. I'd been through this one previously in this thread and managed to place him at I-DF29, rule out some downstream subclades from negative calls, but hadn't found anything positive among a lot of no calls. YFull replied that the quality of this sample is really low, but they provided a list of calls against known SNPs on the I1 section of their tree. The majority SNPs in their report are negative - there are eight positive SNPs. However, I'm fairly sure that these are false positives from the low read - several of them are in conflict with each other, appearing on different branches of the I1 tree and also read negative for phyloequivalent (and more importantly upstream) SNPs. I guess we'll be leaving NO3423 at I-DF29 with more ideas about what he's not than what he is. His subclade lineage is either obscured by the no calls in the BAM file or his Y-chromosome lineage may have died out and he has no descendants that are around today (at least that have tested and in one of the databases).

Too bad, it would have been nice to have had a good quality and a somewhat in-depth branch of I1 for an Anglo-Saxon, especially one that might predate the Norse kings in Northumbria. Although NO3423's date range ends with him possibly being alive during the Norse era. Hopefully some new studies will feature some Anglo-Saxons and Danelaw people, and perhaps have some good Y-DNA samples.

I can't say I'm surprised that he is most likely I-DF29 though, that is the most common branch of I1. I guess we'll never know if he was of the more Scandinavian clusters of I1 or the more West Germanic clusters... Oh well.

deadly77
02-06-2019, 05:46 PM
Too bad, it would have been nice to have had a good quality and a somewhat in-depth branch of I1 for an Anglo-Saxon, especially one that might predate the Norse kings in Northumbria. Although NO3423's date range ends with him possibly being alive during the Norse era. Hopefully some new studies will feature some Anglo-Saxons and Danelaw people, and perhaps have some good Y-DNA samples.

I can't say I'm surprised that he is most likely I-DF29 though, that is the most common branch of I1. I guess we'll never know if he was of the more Scandinavian clusters of I1 or the more West Germanic clusters... Oh well.

May be worth keeping an eye out for results from the Repton skeletons. I was listening to this podcast recently https://play.acast.com/s/dansnowshistoryhit/thegreatvikingarmyatrepton-catjarman?autoplay where Cat Jarman says that they are currently doing some DNA analysis. She says "We haven’t got the results just yet, but I’m working with a team at the University of California, Santa Cruz and the Max Planck Institute in Jena." and also "We’re doing full genome-wide sequencing with the ancient DNA to get as much information as we can about ancestry and things like family relationships." - there's an edited transcript here https://www.historyhit.com/discovering-the-secrets-of-reptons-viking-remains/

So, definitely some positives there - sounds like whole genome sequencing and with almost 300 skeletons to choose from, there may be some good ones.

spruithean
02-06-2019, 05:54 PM
I'm really looking forward to the Repton results. It should be interesting stuff. I really do wonder how many of the ancient individuals were born in Britain and how many migrated from Scandinavia or elsewhere.

deadly77
02-06-2019, 06:19 PM
I'm really looking forward to the Repton results. It should be interesting stuff. I really do wonder how many of the ancient individuals were born in Britain and how many migrated from Scandinavia or elsewhere.

Perhaps a bigger discussion in a later paper will follow, with similar to what we saw from the Ancient Icelandic genomes paper with regard to autosomal DNA comparison to populations and the strontium isotope ratio in teeth to determine where they grew up, which will be interesting reading.

There is a short mention in Cat Jarman's paper in Antiquity (appears to be open access) https://www.cambridge.org/core/journals/antiquity/article/viking-great-army-in-england-new-dates-from-the-repton-charnel/30DFE4A0D5581DEBC8B43096A37985EE where it says:

"Strontium and oxygen isotope analysis of tooth enamel from these two individuals has demonstrated that they both grew up in a region commensurate with values expected from southern Scandinavia (Budd et al. 2004)." and there's also a bit of discussion in the Antiquity paper about grave goods (especially dated coins) while the main part of the paper is a recalibration of the original dataing estimate based on a marine diet.

deadly77
03-06-2019, 10:45 AM
Hunter Provyn has added a Ancient DNA viewer to his Mygrations/Phylogeographer website, so you can visualize the locations of some of the ancient DNA findings on a map. The I1 samples are here: https://phylogeographer.com/ancient-dna-viewer/?I1

It appears to include five of the ancient Iceland samples; the Anglo-Saxon NO3423 from Norton, Teeside, England; two of the Bavarian samples from the elongated skulls paper (AED246 and STR486) and the two Longobard cemetery samples CL63 at Collegno and SZ45 at Szólád. The latter is currently in the wrong position - the fault is mine. I had added several of the more confident ancient samples to the I1 supplemental spreadsheet. mistakenly used the same value for latitude and longitude (46.28333333) which puts the location as shown in Phylogeographer near the Capsian Sea while the correct value should be latitude 46.28333333 and longitude 17.85 at Szólád in the Somogy County in present day Hungary, about 5 km south of Lake Balaton. Should be corrected in the future.

claudefrancis
03-07-2019, 08:51 AM
Hi

I receive my results of Yfull but after some analyze (I am not an expert) but I am surprise of
some results:

I am A6397 but I am negative tested S6402 !

It's possible to be positive under a branch of S6402 but negative S6402 ?

Because I have some STR variants (private mutations) shared with *** and ** (mutation rate)
of S6402.

Other surprise STR distant match – about 29 matchs
But the most close distant match is downstream under S6402

position 1
495 tested – 31 diff ---------------- 0,063% - A6469 (Sweden) – under S6402

position 4
505 tested – 38 diff -------------------0,075% - Y18386 (Sweden) – under S6402

position 6
My same A6397 SNP is more far of STR distance match
495 tested – 37 diff ------------------0,075% - A6397

Between 1 to 6 position are Sweden, Denmark, Scotland, lsle of Man and Germany between
1425 – 1700 periode AD.

spruithean
03-07-2019, 02:48 PM
I-A6397 is upstream of S6402. You don't descend from the man who first had S6402.

https://www.yfull.com/tree/I-A6397/

claudefrancis
03-07-2019, 03:38 PM
Hi spruithean

Thanks for the answer but my question is how I can have the best close STR with someone under S6402, better as another A6397

Other surprise STR distant match – about 29 matchs
But the most close distant match is downstream under S6402

position 1
495 tested – 31 diff ---------------- 0,063% - A6469 (Sweden) – under S6402

position 4
505 tested – 38 diff -------------------0,075% - Y18386 (Sweden) – under S6402

position 6
My same A6397 SNP is more far of STR distance match
495 tested – 37 diff ------------------0,075% - A6397

spruithean
03-07-2019, 03:51 PM
Haplotype convergence, I have the same thing with people on I1 branches related to mine.

claudefrancis
03-07-2019, 04:30 PM
Hi spruithean

Thanks, this convengence can be confirmed by test SNP or if I am negative S6402 all under will be negative ?
Because A6469 STR as the best close as A6397 very strange !
Honestly I have 3 convergence under S6402.

2 with A6469 - position 1 and 3
1 with Y18386 - position 5

Very strange

deadly77
03-07-2019, 05:34 PM
Hi claudefrancis - could I politely ask you to continue your discussion of your own results in the thread that you created here https://anthrogenica.com/showthread.php?15310-Ancien-I1-M253-gt-Z58 rather than this thread so that we can keep the discussion in the current thread on topic with ancient I1? Thanks.

claudefrancis
03-07-2019, 06:02 PM
Sure sorry to create problem.

deadly77
03-12-2019, 02:46 PM
Not specifically about ancient I1, but a recent article discussing ancient DNA - some interesting statistics on the increased number of ancient sequenced samples over the last few years, the discovery that the inner ear is a rich source of ancient DNA: https://theconversation.com/ancient-dna-is-a-powerful-tool-for-studying-the-past-when-archaeologists-and-geneticists-work-together-111127?fbclid=IwAR3n9ubziNTymLBqxKeyCQVwcGtlx5fvOO zQedh1LsfHS_6cxvsYdblAndc

deadly77
03-14-2019, 05:22 PM
Anglesqueville posted about a new report in the Ancient DNA Forum that comes from Current Biology concerning "Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula" https://www.cell.com/current-biology/fulltext/S0960-9822(19)30145-9?rss=yes

Skimming to the section on Y and mt haplogroups, the report states "BAL0051 could be assigned to haplogroup I1" although they don't mention how they have arrived at this conclusion - I've found the BAM file at ENA and I've downloaded it. I'll see what I can find.

deadly77
03-14-2019, 06:08 PM
Looking more like pre-I1 or I* so far rather than I1. Gone through 50 of the >300 SNPs that define the I1 haplogroup - so far two derived SNPs, five ancestral, 43 no calls. Sample from 1240K SNP capture assay rather than WGS. I'll keep going and see where we get to, but may take some time.

spruithean
03-14-2019, 06:31 PM
Interesting. I think we might find a fair bit of pre-I1 or I1-esque samples from this period and up until the actual TMRCA of I-M253 and perhaps I-DF29 and sibling clades. We already know R1b likely swamped all the other European haplogroups.

deadly77
03-14-2019, 07:00 PM
Interesting. I think we might find a fair bit of pre-I1 or I1-esque samples from this period and up until the actual TMRCA of I-M253 and perhaps I-DF29 and sibling clades. We already know R1b likely swamped all the other European haplogroups.

Yep, the age of BAL051 listed in the supplementary data as 11095±195; 10195±255 for lab radiocarbon date, 11,384–10,733; 10,681–9,263 Cal BCE (2σ), 13,380–12,660; 12,830–10,990 Cal BP (2σ) which would put it a bit before the TMRCA of modern I1.

At 100 SNPs, 4 derived, 11 ancestral so far.

oz
03-14-2019, 09:07 PM
Wow, even if it's not DF29 positive or even confidently M253, this is still exciting. It's like finding a unicorn for ancient Dna especially when it's really ancient.

deadly77
03-14-2019, 09:47 PM
Wow, even if it's not DF29 positive or even confidently M253, this is still exciting. It's like finding a unicorn for ancient Dna especially when it's really ancient.

I wasn't expecting the I1 designation until I read it in the paper. Was expecting to debunk this as another misreported I1, but there's actually a reasonable amount of data in this sample despite the age and that it's a SNP capture. I still think it's better called pre-I1 or I* than I1, but this is definitely worth looking at. Looks like more information in this sample than any of the RISE samples from Allentoft 2015 or SF11.

Current count in the big I1 block is 12 derived, 16 ancestral out of 200 SNPs looked at so far.

JonikW
03-14-2019, 09:49 PM
Yep, the age of BAL051 listed in the supplementary data as 11095±195; 10195±255 for lab radiocarbon date, 11,384–10,733; 10,681–9,263 Cal BCE (2σ), 13,380–12,660; 12,830–10,990 Cal BP (2σ) which would put it a bit before the TMRCA of modern I1.

At 100 SNPs, 4 derived, 11 ancestral so far.

Thanks for that analysis. So possibly more distant in time from the I1 source than we are. Or am I mistaken? All very interesting and I look forward to more insights.

deadly77
03-14-2019, 10:03 PM
Thanks for that analysis. So possibly more distant in time from the I1 source than we are. Or am I mistaken? All very interesting and I look forward to more insights.

I'd say so - given that he's ancestral for quite a few of the I1 SNPs, he could be a bridge on the way from I whose descendants had those SNPs mutate from ancestral to derived in line with I1 or he could be a representative of a dead lineage that isn't an ancestor of modern I1. Difficult to say - still a lot of gaps in the coverage and quite a few one read results (like a lot of ancient samples) although BAL051 has a few in the 2-4 read range. If he was dated after the TMRCA of modern I1 or had SNPs that aren't part of modern I1, easier to call as dead lineage. But where he is dated right now, more difficult to say. A higher call rate on the I1 SNPs, may have been able to apply the YFull age estimate and see if it matched the calibrated radiocarbon dates - unfortunately not enough to make that call.

oz
03-14-2019, 10:07 PM
Yeah and it's in Iberia of all places. I appreciate that someone like you is here to investigate and explain the I1 stuff. Otherwise me being a layman with this technology I wouldn't know what to make of reports like this, I'd just assume and wonder about all kinds of things without any concrete knowledge and conclusion. So kudos to you!

My guess would also be that it's some kind of pre-M253 or just M253 (I1). Otherwise they'd probably label it as I1a or something downstream. Hopefully you'll be able to answer if it's pre-I1 or I1.

Pribislav
03-14-2019, 10:49 PM
Yeah and it's in Iberia of all places. I appreciate that someone like you is here to investigate and explain the I1 stuff. Otherwise me being a layman with this technology I wouldn't know what to make of reports like this, I'd just assume and wonder about all kinds of things without any concrete knowledge and conclusion. So kudos to you!

My guess would also be that it's some kind of pre-M253 or just M253 (I1). Otherwise they'd probably label it as I1a or something downstream. Hopefully you'll be able to answer if it's pre-I1 or I1.

Every ancient sample that has even one ancestral SNP in I1 block should be technically called pre-I1. Proper I1 should be derived for all SNPs in the I1 block, at least for those that have been covered. So this guy is pre-I1, and definitely represents a dead lineage.

deadly77
03-14-2019, 10:50 PM
Yeah and it's in Iberia of all places. I appreciate that someone like you is here to investigate and explain the I1 stuff. Otherwise me being a layman with this technology I wouldn't know what to make of reports like this, I'd just assume and wonder about all kinds of things without any concrete knowledge and conclusion. So kudos to you!

My guess would also be that it's some kind of pre-M253 or just M253 (I1). Otherwise they'd probably label it as I1a or something downstream. Hopefully you'll be able to answer if it's pre-I1 or I1.

Cheers.

I'm already labeling BAL051 as pre-I1 before the analysis is complete - on the calls so far he'd break up the block of the >300 SNPs that define I1 and he's before the bottleneck that all modern I1 are descended from (at least those that have been tested so far) . Not sure where M253 itself as an individual SNP would fit in a revised phylogenetic tree as BAL051 is no call/not read for M253 itself. M253 is just one of over 300 SNPs defining I1.

deadly77
03-14-2019, 11:46 PM
Okay, I've been through 311 SNPs that are in the big I1 block - BAL051 has reads for 33 of these SNPs, so there is a lot of no calls where the position has no reading. Some of that is going to be down to the methodology of the test (the 1240K SNP Capture) and some of it may be due to the age of the sample - it's older than any of the other ones we've discussed in this thread. However, those 33 SNPs (10.6% of the 311 I1 SNPs) have more read SNPs in BAL051 individually than the four RISE samples from Allentoft 2015 combined.

Derived calls for 13 SNPs: Z2699/FGC2430 (2C), Z2751/L841/YSC0000257, Z2885, Z2887, CTS7751/Z2813, Z2812/CTS7652, Z2860, L124/S64, CTS4532/Z2777, Z2724/V1771 (2G), FGC2441 (2G), CTS10140/Z2837.
Ancestral calls for 20 SNPs: Z2886, Z2679/CTS136, Z2727, Z2850, Y1962 (4T), P40, Z2747, FGC2422/Z2715, CTS3506/Z2765, FGC33327, CTS11534/Z2871, Y1863/S107/FGC2426, L848/Z2877 /YSC0000299 (2C), FGC2433, Y1950, FGC2427/Z2713, Y1932/S2007, Z2870/CTS11526, S22865/Z2845, Z2806/CTS6765.
All above one read unless otherwise noted.

oz
03-14-2019, 11:51 PM
Every ancient sample that has even one ancestral SNP in I1 block should be technically called pre-I1. Proper I1 should be derived for all SNPs in the I1 block, at least for those that have been covered. So this guy is pre-I1, and definitely represents a dead lineage.

Cool avatar Raiden Tesla nice!
But how do you know for sure that it's definitely a dead lineage. Isn't it possible hypothetically that some of those I* people could be direct living descendants?

ADW_1981
03-15-2019, 12:02 AM
Every ancient sample that has even one ancestral SNP in I1 block should be technically called pre-I1. Proper I1 should be derived for all SNPs in the I1 block, at least for those that have been covered. So this guy is pre-I1, and definitely represents a dead lineage.

Although this far west is interesting. It might lend support that a survivor moved into the north and succeeded to a culture like Ahrensburg and later to something like TRB.

oz
03-15-2019, 12:11 AM
Okay, I've been through 311 SNPs that are in the big I1 block - BAL051 has reads for 33 of these SNPs, so there is a lot of no calls where the position has no reading. Some of that is going to be down to the methodology of the test (the 1240K SNP Capture) and some of it may be due to the age of the sample - it's older than any of the other ones we've discussed in this thread. However, those 33 SNPs (10.6% of the 311 I1 SNPs) have more read SNPs in BAL051 individually than the four RISE samples from Allentoft 2015 combined.

Derived calls for 13 SNPs: Z2699/FGC2430 (2C), Z2751/L841/YSC0000257, Z2885, Z2887, CTS7751/Z2813, Z2812/CTS7652, Z2860, L124/S64, CTS4532/Z2777, Z2724/V1771 (2G), FGC2441 (2G), CTS10140/Z2837.
Ancestral calls for 20 SNPs: Z2886, Z2679/CTS136, Z2727, Z2850, Y1962 (4T), P40, Z2747, FGC2422/Z2715, CTS3506/Z2765, FGC33327, CTS11534/Z2871, Y1863/S107/FGC2426, L848/Z2877 /YSC0000299 (2C), FGC2433, Y1950, FGC2427/Z2713, Y1932/S2007, Z2870/CTS11526, S22865/Z2845, Z2806/CTS6765.
All above one read unless otherwise noted.

I'm not familiar with that Allentoft 2015, what kind of I1 are those identified as, and what is the age and location of those samples? If you don't mind me asking.

JonikW
03-15-2019, 12:14 AM
Although this far west is interesting. It might lend support that a survivor moved into the north and succeeded to a culture like Ahrensburg and later to something like TRB.

Somebody did, that's for sure, regardless of whether this man's line died out. Don't know if it's just me but I'm frustrated with the lack of ancient I1 progress recently. We need some meaningful samples in a good solid paper.

oz
03-15-2019, 12:33 AM
Although this far west is interesting. It might lend support that a survivor moved into the north and succeeded to a culture like Ahrensburg and later to something like TRB.

That could only lend support for a nice fictional story, maybe a plot of a good movie thriller. Because there's absolutely no concrete evidence for it.

Pribislav
03-15-2019, 12:34 AM
Cool avatar Raiden Tesla nice!
But how do you know for sure that it's definitely a dead lineage. Isn't it possible hypothetically that some of those I* people could be direct living descendants?

Hypothetically yes, but if such lineage indeed existed I think it would turn up somewhere by now.

ADW_1981
03-15-2019, 12:38 AM
That could only lend support for a nice fictional story, maybe a plot of a good movie thriller. Because there's absolutely no concrete evidence for it.

Not really. You think it's Bosnian I bet. That's even funnier. There's a lot of support that the I1 progenitor was among HG in Denmark and northern Germany.

deadly77
03-15-2019, 12:39 AM
I'm not familiar with that Allentoft 2015, what kind of I1 are those identified as, and what is the age and location of those samples? If you don't mind me asking.

It's a paper that was published in Nature a few years ago titled "Population genomics of Bronze Age Eurasia" and includes a lot of samples - paper is here https://www.nature.com/articles/nature14507 although I'm not sure if it it is public access but you can get some of the supplementary information there, although you can probably get the main paper from Research Gate at https://www.researchgate.net/publication/278327861_Population_genomics_of_Bronze_Age_Eurasi a

Four of the RISE samples from Sweden in this study are often quoted on various blogs and forum posts as being examples of the earliest I1 samples. I'm not so convinced because of the quality and coverage observed in these samples - the data is very poor. For example, RISE207 was positive for a single SNP in the I1 block (and a one-read positive call at that) and no call for all the rest of the 311 SNPs. All of the RISE samples from the Allentoft paper are no call for >97% of the SNPs that define the I1 haplogroup. This makes it difficult to say if they are ancestors of I1 men living today or an extinct lineage. Not enough data. At least with BAL051 and Stora Förvar 11 (SF11) we can call some of the I1 SNPs as ancestral and they're pre-I1 rather than I1. I went through the SNP analysis of the RISE samples in post #131 on this thread.

oz
03-15-2019, 01:24 AM
Not really. You think it's Bosnian I bet. That's even funnier. There's a lot of support that the I1 progenitor was among HG in Denmark and northern Germany.

Calm down there gambler lol now you're just being a clown. My point was simply that there is no smoking gun evidence to support yours or any type of theory for origins of I1 at this point. Learn to take a joke without resorting to ad homs and butthurtness. Since you brought up Bosnia and I never did even remotely, I'd like to ask are you an expert on Bosnian history and archeology by any chance?

oz
03-15-2019, 01:45 AM
It's a paper that was published in Nature a few years ago titled "Population genomics of Bronze Age Eurasia" and includes a lot of samples - paper is here https://www.nature.com/articles/nature14507 although I'm not sure if it it is public access but you can get some of the supplementary information there, although you can probably get the main paper from Research Gate at https://www.researchgate.net/publication/278327861_Population_genomics_of_Bronze_Age_Eurasi a

Four of the RISE samples from Sweden in this study are often quoted on various blogs and forum posts as being examples of the earliest I1 samples. I'm not so convinced because of the quality and coverage observed in these samples - the data is very poor. For example, RISE207 was positive for a single SNP in the I1 block (and a one-read positive call at that) and no call for all the rest of the 311 SNPs. All of the RISE samples from the Allentoft paper are no call for >97% of the SNPs that define the I1 haplogroup. This makes it difficult to say if they are ancestors of I1 men living today or an extinct lineage. Not enough data. At least with BAL051 and Stora Förvar 11 (SF11) we can call some of the I1 SNPs as ancestral and they're pre-I1 rather than I1. I went through the SNP analysis of the RISE samples in post #131 on this thread.

Oh that's what that is, yes I'm familiar with it. Thanks for the informative rundown, it was more than I asked for, much appreciated.

mwauthy
03-15-2019, 01:36 PM
I’m guessing that as millions of more I1 men get tested someone will break up that 312 SNP bottleneck.

Maybe this is a stupid question but if the current living I1 folks who are not positive for I-DF29 don’t have all 312 SNPs tested, isn’t it possible that one of them might split the bottleneck. How many of these 312 SNPs are actually tested in most next generation tests such as Big Y-500? Are we sure that all of the the
I-Z17954 folks are positive for all 312 SNPs? What about the two folks on Yfull that are negative for I-DF29 and
I-Z17954?

Lastly, in my opinion there needs to be new classifications for ancient samples like the ones mentioned in Iberia, Hungary, and Sweden. Labeling these samples as I* or I1 is misleading.

Thanks deadly77 for your hard work and expertise. I’m learning more about “I1” from you than from most academic blowhards or nextgen testing companies.

deadly77
03-15-2019, 02:50 PM
I’m guessing that as millions of more I1 men get tested someone will break up that 312 SNP bottleneck.

Maybe this is a stupid question but if the current living I1 folks who are not positive for I-DF29 don’t have all 312 SNPs tested, isn’t it possible that one of them might split the bottleneck. How many of these 312 SNPs are actually tested in most next generation tests such as Big Y-500? Are we sure that all of the the
I-Z17954 folks are positive for all 312 SNPs? What about the two folks on Yfull that are negative for I-DF29 and
I-Z17954?

Lastly, in my opinion there needs to be new classifications for ancient samples like the ones mentioned in Iberia, Hungary, and Sweden. Labeling these samples as I* or I1 is misleading.

Thanks deadly77 for your hard work and expertise. I’m learning more about “I1” from you than from most academic blowhards or nextgen testing companies.

Cheers - I try and follow the real data when I can - there's a fair bit of conjecture out there. Some is good, some not so good... Going back to the primary data such as BAM files is always worth doing if that's an available option.

As far as I'm aware, no one has yet broken up the I1 bottleneck yet. It's entirely possible that someone will at some point, but if they have and have tested, I'm not aware. There are a few individuals of rare lineages on the DF29- branches. There was some crowdfunding on the I1 Facebook page a couple of years ago for testing one of the individuals with a YElite that is now in the I-CTS12798 branch (DF29-, Z17954-) in the hope that he would break up the I1 block but he didn't show up as confirmed negative for any of them - he was positive for ~270 of them with the remainder being no calls.

But all possible - in the last couple of years within I-Z140 we had a couple of guys test Z140+/Z141- and then another broke up several of the phyloequivalent SNPs on the I-F2642/S2169 branch which caused a bit of a reordering of the tree. But I thought if someone would break up the I1 block, would have found them by now. Wait and see, I guess.

You can see how many in your own Big Y test are covered if you go to your YFull homepage and click on YReport on the left hand menu - it will open a new window and the SNPs will be colour-coded on the YReport - green for confirmed positive, red for negative, yellow for ambiguous, grey for no call (the grey is a little harder to read since it is not too diferent from the green colour). I don't have a Big Y myself to look at but I have a FGC YElite - this has three ambiguous calls and 38 no calls in the big I1 block. That's not too bad and comparable to the I-CTS12798 individual mentioned above. I also have a 30x WGS which gets almost everything - zero no calls in the big I1 block and two ambiguous calls. I'd expect that a Big Y Y500 would have less coverage than both of these and a Big Y Y700 to be similar to the YElite.

I know for sure there are several WGS of I1 folks down the I-DF29 branch. I assume that the ambiguous and no calls in the Y-enrichment tests like Big Y are inferred positive. I guess they could be verified for sure with a Sanger test at YSEQ. I have no idea about the I-Z17954 branch and I think the two folks at I-CTS12798 are a Big Y and a YElite. But most people probably don't look at that part of their results as they are more concerned with their terminal branch and novel variants.

I agree that the using the I1 label for ancient samples like this is rather misleading - unfortunately they have been quoted as such many, many times and most people reference the blog posts and secondary analysis rather than the primary data. For several of those samples, the lack of data makes it impossible to assign with certainty. I try calling them pre-I1 but I'm not sure if that's appropriate either as it implies that they are an ancestor of modern I1 while to me it's not clear if they are an intermediate or a dead lineage. Not enough data to confirm or disconfirm.

mwauthy
03-15-2019, 03:29 PM
Cheers - I try and follow the real data when I can - there's a fair bit of conjecture out there. Some is good, some not so good... Going back to the primary data such as BAM files is always worth doing if that's an available option.

As far as I'm aware, no one has yet broken up the I1 bottleneck yet. It's entirely possible that someone will at some point, but if they have and have tested, I'm not aware. There are a few individuals of rare lineages on the DF29- branches. There was some crowdfunding on the I1 Facebook page a couple of years ago for testing one of the individuals with a YElite that is now in the I-CTS12798 branch (DF29-, Z17954-) in the hope that he would break up the I1 block but he didn't show up as confirmed negative for any of them - he was positive for ~270 of them with the remainder being no calls.

But all possible - in the last couple of years within I-Z140 we had a couple of guys test Z140+/Z141- and then another broke up several of the phyloequivalent SNPs on the I-F2642/S2169 branch which caused a bit of a reordering of the tree. But I thought if someone would break up the I1 block, would have found them by now. Wait and see, I guess.

You can see how many in your own Big Y test are covered if you go to your YFull homepage and click on YReport on the left hand menu - it will open a new window and the SNPs will be colour-coded on the YReport - green for confirmed positive, red for negative, yellow for ambiguous, grey for no call (the grey is a little harder to read since it is not too diferent from the green colour). I don't have a Big Y myself to look at but I have a FGC YElite - this has three ambiguous calls and 38 no calls in the big I1 block. That's not too bad and comparable to the I-CTS12798 individual mentioned above. I also have a 30x WGS which gets almost everything - zero no calls in the big I1 block and two ambiguous calls. I'd expect that a Big Y Y500 would have less coverage than both of these and a Big Y Y700 to be similar to the YElite.

I know for sure there are several WGS of I1 folks down the I-DF29 branch. I assume that the ambiguous and no calls in the Y-enrichment tests like Big Y are inferred positive. I guess they could be verified for sure with a Sanger test at YSEQ. I have no idea about the I-Z17954 branch and I think the two folks at I-CTS12798 are a Big Y and a YElite. But most people probably don't look at that part of their results as they are more concerned with their terminal branch and novel variants.

I agree that the using the I1 label for ancient samples like this is rather misleading - unfortunately they have been quoted as such many, many times and most people reference the blog posts and secondary analysis rather than the primary data. For several of those samples, the lack of data makes it impossible to assign with certainty. I try calling them pre-I1 but I'm not sure if that's appropriate either as it implies that they are an ancestor of modern I1 while to me it's not clear if they are an intermediate or a dead lineage. Not enough data to confirm or disconfirm.

Thanks for the detail response. I checked out my YReport for my Big Y-500 test and upon an initial quick scanning I am positive for over 200 SNPs associated with I1 and am ambiguous for 4 SNPs. I agree with you now that enough SNPs are tested with the nextgen tests to confidently classify people as I1.

deadly77
03-15-2019, 06:40 PM
For the ancient samples where I'm reliably able to assign a subclade (even if it's only as far as I-DF29), I haven't dug too heavily into the big block of I1 SNPs as in those cases they're all inferred to be positive. The only bit of data that I have came from when I was having a chat with one of the admins of the I-L22 project a while ago - he was kind enough to share the YFull YReport for the highest quality Icelandic sample HSJ-A1. HSJ-A1 had 13 SNPs that were no call from the big I1 block. Although that's helped by the testing done on HSJ-A1 that was a WGS.

oz
03-15-2019, 11:25 PM
Deadly77 what do you think about this BAL051 finding pushing back the TMRCA of I1 would that make sense? Does it have enough positive reads or however that works. Currently it's estimated at around 5,000 ybp isn't it? While DF29 and his descendants should obviously remain estimated to be much younger.

deadly77
03-16-2019, 12:25 AM
I don't think it would push back the TMRCA of I1 per the YFull tree estimate since that's based on counting the SNPs of modern testers backwards to the common ancestor branch, albeit with a few qualifiers and correction factors - see https://www.yfull.com/faq/what-yfulls-age-estimation-methodology/ and https://www.yfull.com/faq/how-does-yfull-determine-formed-age-tmrca-and-ci/ for details and you can see the numbers that make up the calculation if you click on the white info button next to the I1 branch https://www.yfull.com/tree/I1/ - there's a range of age estimates based on samples on that branch and ages of downstream branches and they all get averaged to a current TMRCA 4600 years ago, although there is a 95% confidence interval for 4000-5100 years ago. I don't think the TMRCA of I1 gets pushed back unless a modern tester (or prefereably multiple testers) is shown to be definitively negative for some of the SNPs in the Big I1 block.

What I think that you're actually asking is that if you insert BAL051 into the I1 block, then there's a new branch point in between I and I1 - that would have it's own formed date and TMRCA for that branch. I think it's hard to calculate for BAL051 (and same for SF11) because there is a lot of no calls for BAL051 in the big I1 block. Someone on the I-Z140 facebook page has postulated a age estimation for the branch point at BAL051 at about 18500 years ago by applying the ratio of 20/33 (ancestral/total read SNPs) to the years between the formed date and TMRCA. I'm not sure if I agree - there's no guarantee that same ratio of ancestral and derived SNPs is consistent among the 279 SNPs that were not read, so that's a big assumption with a significant amount of error. Also, not all of the 312 SNPs on the I1 big block are used for age estimation (which is why I included references to the YFull FAQ regarding SNPs in the CombBED region, etc.) - on the YFull tree it looks like it ranges between 142 and 192 SNPs depending on sample, so there would need to be a correction factor for that as well. I think it's a bit more complicated so I'll think about it a bit more, but I think it's going to come down to not enough data to get a confident answer based on the no calls.

oz
03-16-2019, 12:51 AM
Right I figured your response would be this line of thinking. I just figured I'd bring up the question since I don't think anyone else has so far. And the reason I asked if it's possible to consider this as proof of the earliest I1-M253 because on some other threads and including this academic study they're labeling it as I1 when technically that's not what it is if there's not enough positive snps, not even close really and therein lies the confusion. It should be labeled as pre I1 or I* but they're still calling it I1.

Either way I wish it was positive for all the SNPs and resembled more the modern I1s. I kinda always felt weird that I belong to a haplogroup that seems to have appeared out of nowhere much more recently than all the other major HGs, that's just me. The fact that I1 has such a large number of defining SNPs is also pretty strange in itself. But I'm not any kind of expert on this science to be able to even hypothesize what that means.

spruithean
03-16-2019, 03:41 AM
Right I figured your response would be this line of thinking. I just figured I'd bring up the question since I don't think anyone else has so far. And the reason I asked if it's possible to consider this as proof of the earliest I1-M253 because on some other threads and including this academic study they're labeling it as I1 when technically that's not what it is if there's not enough positive snps, not even close really and therein lies the confusion. It should be labeled as pre I1 or I* but they're still calling it I1.

Either way I wish it was positive for all the SNPs and resembled more the modern I1s. I kinda always felt weird that I belong to a haplogroup that seems to have appeared out of nowhere much more recently than all the other major HGs, that's just me. The fact that I1 has such a large number of defining SNPs is also pretty strange in itself. But I'm not any kind of expert on this science to be able to even hypothesize what that means.

I share this sentiment. With the amount of people who belong to the I-M253 umbrella, there sure isn't a whole lot of ancient samples that are far removed from the eras of the current known ancient I1 individuals. That bottleneck must have been intense.

oz
03-16-2019, 06:29 AM
I share this sentiment. With the amount of people who belong to the I-M253 umbrella, there sure isn't a whole lot of ancient samples that are far removed from the eras of the current known ancient I1 individuals. That bottleneck must have been intense.

Well when for tens of thousands of years you're constantly inbreeding and hiding like Bigfoot I guess that's what happens.

That may sound like a joke but it's what the academics basically claim.

deadly77
03-16-2019, 09:06 AM
Right I figured your response would be this line of thinking. I just figured I'd bring up the question since I don't think anyone else has so far. And the reason I asked if it's possible to consider this as proof of the earliest I1-M253 because on some other threads and including this academic study they're labeling it as I1 when technically that's not what it is if there's not enough positive snps, not even close really and therein lies the confusion. It should be labeled as pre I1 or I* but they're still calling it I1.

Either way I wish it was positive for all the SNPs and resembled more the modern I1s. I kinda always felt weird that I belong to a haplogroup that seems to have appeared out of nowhere much more recently than all the other major HGs, that's just me. The fact that I1 has such a large number of defining SNPs is also pretty strange in itself. But I'm not any kind of expert on this science to be able to even hypothesize what that means.

In my opinion, I would not say that BAL051 should be considered the earliest example of I1. For me, the I1 haplogroup is defined by that big block of >300 SNPs and any sample that is ancestral for some of the SNPs in the big block isn't fully I1 but a proto lineage whose descendants may have evolved into fully I1, or they may be representatives of extinct lineages where the descendants died out and not found today in the modern population. Richard Miller made a chart which I think describes this nicely:
29401
I'd include SF11 in that category of not fully I1 due to the ancestral I1 SNPs found in that sample. Not unexpected as these two samples are dated prior to the modern I1 TMRCA. I'd also include the four RISE samples from Allentoft and BAB5 in this category of not fully I1 due to a lack of reinforcing positive evidence since those designations are made on a very small number of SNPs. For me, the data is too shaky to confirm these samples as fully I1. This is just my opinion, and I know for sure that it isn't shared by everyone. I agree that it does add to the confusion. It is interesting that the authors of the paper (I'll call it Haak since that's the corresponding author) refer to BAL051 as I1, while the other big recent paper on the Iberian peninsula by Olade et al has a fair few samples that are listed as I, with some confirmed as I(xI2a1,xI2a2,xI2c) in Table S4 but they don't designate any as I1. It'll be interesting to have a closer look at some of the samples in the Olade paper once the BAM files are uploaded to ENA. Looks like the BAM files from that study will be deposited here (nothing there yet): https://www.ebi.ac.uk/ena/data/view/PRJEB30874

Yeah, the large number of defining SNPs is down to an unbroken line of descent from about 27,500 years ago to about 4,600 years ago when we start to see expansion and diversity of subclades. As Spruithean says, the bottleneck must have been intense. It did remind me of a snippet I heard when I was listening to The Insight podcast (well worth listening to in my opinion) last year - went back and found it on their website here https://insitome.libsyn.com/y-chromosomal-stars - there's a few comments from Razib Khan about I1 starting about 36 and a half minutes into the podcasts where he theorizes that as the Steppe people moved into Europe, they assimilated some of the local indigenous Europeans, with I1 "hitching a ride" among a tribe that was mostly non-I1.

I think it's impressive that an I1 lineage survived so long in the midst of that competition without dying or daughtering out, long enough to survive to get to the end of the bottleneck and propagate and expand from there.

oz
03-16-2019, 09:06 PM
Indeed it is impressive when you look at it from the survival aspect. It was a very headstrong, resilient I* that managed to keep a small lineage going for so long before branching out not too long ago amongst so many other lines who weren't as lucky.

deadly77
03-17-2019, 06:02 PM
Trying to scrape the barrel on the low coverage pre-I1 samples and look for SNPs that are read in more than one sample. It's not an exhaustive list:

CTS3506/Z2765: BAL051 ancestral (1A), RISE179 derived (1G).
FGC2433: BAL051 ancestral (1G), SF11 derived (1A).
Z2806/CTS6765: BAL051 ancestral (1T), RISE210 derived (1C).

So at least no red flags that wouldn't be easily explainable such as a derived allele for the older BAL051 sample and a corresponding ancestral allele on the same SNP in one of the younger SF11 or RISE samples. But a really small dataset. Not really sure if this means anything.

oz
03-18-2019, 02:18 AM
Trying to scrape the barrel on the low coverage pre-I1 samples and look for SNPs that are read in more than one sample. It's not an exhaustive list:

CTS3506/Z2765: BAL051 ancestral (1A), RISE179 derived (1G).
FGC2433: BAL051 ancestral (1G), SF11 derived (1A).
Z2806/CTS6765: BAL051 ancestral (1T), RISE210 derived (1C).

So at least no red flags that wouldn't be easily explainable such as a derived allele for the older BAL051 sample and a corresponding ancestral allele on the same SNP in one of the younger SF11 or RISE samples. But a really small dataset. Not really sure if this means anything.

So the Bal sample doesn't show a clear sign of being an ancestor of the younger SF11 and RISE?

What do you think of this? Someone posted it in another thread showing that BAL003 is an IJ instead of C1a1 as the official study shows? https://docs.google.com/spreadsheets/d/1cVvp_vqIbnlIztk61UFwRlAflTHq3uo3HLMgduzh-4E/edit?usp=sharing

deadly77
03-18-2019, 08:10 AM
So the Bal sample doesn't show a clear sign of being an ancestor of the younger SF11 and RISE?

What do you think of this? Someone posted it in another thread showing that BAL003 is an IJ instead of C1a1 as the official study shows? https://docs.google.com/spreadsheets/d/1cVvp_vqIbnlIztk61UFwRlAflTHq3uo3HLMgduzh-4E/edit?usp=sharing

Opposite - it doesn't rule it out. If we had for example FGC2433 was derived in BAL051 and ancestral SF11, it would have then made it unlikely that BAL051 could be an ancestor of SF11. If that were the case could argue that one or both are dead lineages (and may still be). But looking at a single SNP out of 312 that is one read in both samples makes any conclusions debatable at best. If I were a betting man, I wouldn't be betting on this.

I haven't looked at BAL003, but from the supplementary information it has the lowest coverage of any of the samples in the paper. Likely to be a lot of holes leading to no calls. The spreadsheet that you showed had I-P37? in the final column which implies I2. Would make more sense than C1a1 being in that area (admittedly I had to look up C1a1) although I haven't looked at the BAM files.

deadly77
04-04-2019, 10:14 AM
Rozenfield shared a BioRxiv preprint titled "Y-chromosome haplogroups from Hun, Avar and conquering Hungarian period nomadic people of the Carpathian Basin" from Torok et al. in the Ancient DNA section of Anthrogenica. The preprint and supporting info can be found here: https://www.biorxiv.org/content/10.1101/597997v1

Interesting to us on this thread is that two of the samples in the paper are reported as I1:

SzO/540 in the Szegvár-Oromdűlő graveyard, dated to 600–650/660 early Avar period.
K2/26 in the Karos-Eperjesszög II graveyard, dated to 895- mid Xth c. Conqueror period.

The supporting information isn't very comprehensive from a Y-DNA analysis perspective. From the I1 SNPs, they only report three SNPs: L80, M253 (both above samples positive) from the I1 block and L22 from subclades (both above samples negative).

The preprint says "BAM files were deposited to the European Nucleotide Archive under accession no: PRJEB31764" although I've looked at ENA and don't see anything under that accession number. The preprint was only posted yesterday so it may be a while before any get uploaded or the BAM files may be uploaded once the paper gets officially published . If and when that happens, I'll take a look at the BAM files and see if there's anything more specific to determine from an I1 Y-DNA perspective.

oz
04-04-2019, 08:00 PM
Rozenfield shared a BioRxiv preprint titled "Y-chromosome haplogroups from Hun, Avar and conquering Hungarian period nomadic people of the Carpathian Basin" from Torok et al. in the Ancient DNA section of Anthrogenica. The preprint and supporting info can be found here: https://www.biorxiv.org/content/10.1101/597997v1

Interesting to us on this thread is that two of the samples in the paper are reported as I1:

SzO/540 in the Szegvár-Oromdűlő graveyard, dated to 600–650/660 early Avar period.
K2/26 in the Karos-Eperjesszög II graveyard, dated to 895- mid Xth c. Conqueror period.

The supporting information isn't very comprehensive from a Y-DNA analysis perspective. From the I1 SNPs, they only report three SNPs: L80, M253 (both above samples positive) from the I1 block and L22 from subclades (both above samples negative).

The preprint says "BAM files were deposited to the European Nucleotide Archive under accession no: PRJEB31764" although I've looked at ENA and don't see anything under that accession number. The preprint was only posted yesterday so it may be a while before any get uploaded or the BAM files may be uploaded once the paper gets officially published . If and when that happens, I'll take a look at the BAM files and see if there's anything more specific to determine from an I1 Y-DNA perspective.

Fun times ahead. I hope those samples can be analyzed and provide enough information to determine deep subclades. And finally one more interesting study that found two I1 and it's close to my homeland which makes it that much more exciting to me. If they turn out to be negative for Z63 and positive for other subclades I'll be disappointed, but great thing for I1 regardless.

Do you know any more details about these two samples other than location, age estimate and Hg?

JonikW
04-04-2019, 08:19 PM
Rozenfield shared a BioRxiv preprint titled "Y-chromosome haplogroups from Hun, Avar and conquering Hungarian period nomadic people of the Carpathian Basin" from Torok et al. in the Ancient DNA section of Anthrogenica. The preprint and supporting info can be found here: https://www.biorxiv.org/content/10.1101/597997v1

Interesting to us on this thread is that two of the samples in the paper are reported as I1:

SzO/540 in the Szegvár-Oromdűlő graveyard, dated to 600–650/660 early Avar period.
K2/26 in the Karos-Eperjesszög II graveyard, dated to 895- mid Xth c. Conqueror period.

The supporting information isn't very comprehensive from a Y-DNA analysis perspective. From the I1 SNPs, they only report three SNPs: L80, M253 (both above samples positive) from the I1 block and L22 from subclades (both above samples negative).

The preprint says "BAM files were deposited to the European Nucleotide Archive under accession no: PRJEB31764" although I've looked at ENA and don't see anything under that accession number. The preprint was only posted yesterday so it may be a while before any get uploaded or the BAM files may be uploaded once the paper gets officially published . If and when that happens, I'll take a look at the BAM files and see if there's anything more specific to determine from an I1 Y-DNA perspective.

I hope those BAM files come through soon. Wise of them to check for L22 as that might seem most likely given the probable movements from Scandinavia. I look forward to hearing what subclades they actually carry. Finally, some more ancient I1.:)

spruithean
04-04-2019, 11:38 PM
The Avar period for one of those I1 individuals? Hmm perhaps a surviving Gepid (I'm hoping Gepid) or Lombard? This could be really interesting.

It'd be nice to see which subclades these two individuals belong to.

deadly77
04-04-2019, 11:41 PM
Fun times ahead. I hope those samples can be analyzed and provide enough information to determine deep subclades. And finally one more interesting study that found two I1 and it's close to my homeland which makes it that much more exciting to me. If they turn out to be negative for Z63 and positive for other subclades I'll be disappointed, but great thing for I1 regardless.

Do you know any more details about these two samples other than location, age estimate and Hg?

Well, we'll see on what they are. The samples have already been analyzed, but I'm not sure about what kind of coverage that they have until I look into the BAM files. But if they're negative for L22, by process of elimination the chances of them being I-Z63 have relatively gone up (although it could be argued that the chances of I-Z58 have gone up as well on a statistical basis as well...) - anyway, will have a better idea if and when we get some real data to look at.

As for more details, anything that you're looking for specifically? It's a bit difficult to guess what you might be interested in. The link that Rozenfield shared that I copied into the above post should take you to the preprint (which isn't a full paper yet) and links to the supporting information which is often worth a perusal. There's also a related paper here https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205920 that came out last year which goes through the mtDNA but includes information on the context of the graveyard for Karos-Eperjesszög.

deadly77
04-04-2019, 11:46 PM
I hope those BAM files come through soon. Wise of them to check for L22 as that might seem most likely given the probable movements from Scandinavia. I look forward to hearing what subclades they actually carry. Finally, some more ancient I1.:)

Indeed - I think they may have gone for that for elimination purposes. The supplementary material lists a significant number of reads for each of the three SNPs that they mention. But a look at the BAM file will be the best to figure it out.

deadly77
04-05-2019, 12:44 AM
The Avar period for one of those I1 individuals? Hmm perhaps a surviving Gepid (I'm hoping Gepid) or Lombard? This could be really interesting.

It'd be nice to see which subclades these two individuals belong to.

To be honest, I'd not heard of two of those groups before. But that's okay as it gives me something to read up on :). However, I think what is becoming clear with a lot more of these ancient DNA studies is that haplogroups that originated several thousand years ago aren't necessarily indicative of cultural groups of more recent times (and I mean relatively recently by that). I think a lot of these cultural groups, tribes, etc. were significantly more diverse than the homogeneous haplogroups that have been assigned to them. I look forward to more real data.

oz
04-05-2019, 01:06 AM
Yeah when I said analyzed that's what I meant looking at the BAM files. Hopefully the samples will be good quality and the autosomal data as well.

oz
04-05-2019, 01:27 AM
To be honest, I'd not heard of two of those groups before. But that's okay as it gives me something to read up on :). However, I think what is becoming clear with a lot more of these ancient DNA studies is that haplogroups that originated several thousand years ago aren't necessarily indicative of cultural groups of more recent times (and I mean relatively recently by that). I think a lot of these cultural groups, tribes, etc. were significantly more diverse than the homogeneous haplogroups that have been assigned to them. I look forward to more real data.

Their autosomal make up should hopefully provide enough clues as to where they might have come from and who they were besides just the material culture, time and location.

alexfritz
04-05-2019, 01:41 AM
The Avar period for one of those I1 individuals? Hmm perhaps a surviving Gepid (I'm hoping Gepid) or Lombard? This could be really interesting.

It'd be nice to see which subclades these two individuals belong to.

high prob gepid(in german) note p33 wanderings/movements post 630ad gepids move to the area of koros(incl K2/26(though supp-tableS2 heavily east-asian admixed)
http://docplayer.org/69176675-Ethnische-gruppen-im-awarenreich-1.html

the other germanic people within the avar realm seem to be the suebi yet remained in the transdanubian area, SzO/81 600-650ad from an area ascribed to the bulgars yet most prob(closest to) gepid aswell; longobards are no longer found in pannonia post 568ad they actually had a contract with the avars(khan baian) to cede all the lands fully move out and never(incl attempt) to return;

spruithean
04-05-2019, 03:15 PM
Ah yes, I figured it was probably not likely to be Lombardic given their easy entrance into Italy I would imagine most of them picked up and left Pannonia.

I suppose it is possible that this I1 Avar era sample is of Gepid origins, or perhaps an Avar who had an ancestor from I1 populated areas.

I seem to recall some Gepids were found in graves with Avar-Turkic armour and other items. I would think with the Gepids living under Hunnic and later Avar rule they adopted some cultural aspects of those people. I recall the magister militum named Mundo was the son of Giesmus who is sometimes said to have been a Hun who married the daughter of the Gepid King Ardaric.

oz
04-06-2019, 03:14 AM
So that paper is suggesting that the Avars were more eastern Siberian like than the Conquerors/Magyars. The original Avars might've been Tungusic or Mongolic speaking?
The Magyars on their PCA are closest to Volga/Ural populations like Bashkirs so there's definitely some Turkic connection there.
After the Bashkirs the conquerors plot closest to modern Hungarians, Bosnians, Slovakians and Polish. Interestingly they're a little closer to BIH than to Croats and Serbs on that plot.
It also says that the most prestigious graves in Karos2 and Karos3 cemeteries belonged to I2a1 and were most likely related.
Most of them have alleles for brown eyes and dark brown/black hair, including both of the I1 samples and both of them are not lactase persistent. And interesting that the I1 Avar is from the same cemetery as the East Asian N1. I don't know what those EU/EA admixture columns mean they're confusing, they show different percentages. And it's pretty odd that the PV/72 East Asian C2-Hg guy is 100% EU.

https://www.biorxiv.org/content/biorxiv/early/2019/04/03/597997.full.pdf

oz
04-06-2019, 03:36 AM
Ah yes, I figured it was probably not likely to be Lombardic given their easy entrance into Italy I would imagine most of them picked up and left Pannonia.

I suppose it is possible that this I1 Avar era sample is of Gepid origins, or perhaps an Avar who had an ancestor from I1 populated areas.

I seem to recall some Gepids were found in graves with Avar-Turkic armour and other items. I would think with the Gepids living under Hunnic and later Avar rule they adopted some cultural aspects of those people. I recall the magister militum named Mundo was the son of Giesmus who is sometimes said to have been a Hun who married the daughter of the Gepid King Ardaric.

The Gepids/Goths also allegedly had a war with the Huns and broke up the alliance after Atila's death, which they won. But they also apparently had wars against the Goths too, according to Wikipedia.
But speaking of I1 and East Germanics the Vandals were also allegedly an East Germanic people that migrated through Eastern Europe before they migrated to SW Europe (like the Visigoths) and then North Africa and sacked Rome at some point, hence the term "vandalism". So it's very problematic to discern which specific tribes these people belonged to and what Hg's or subclades they propagated when they're all documented as basically the same type of tribes with the same or similar origins.

oz
04-06-2019, 03:36 AM
double post

deadly77
04-06-2019, 07:38 AM
Your mention of Bashkir reminded me that we have a section of 11 individuals in the I1-Z140 project at FTDNA that are listed as the Bashkir group, Mirzalar clan. They're negative for all of the major branches of I-Z141 (Z2535, F3642, A196, Y6231, etc.). Most of the written work I can see on that comes from Bulat Muratov - he has quite a few papers on Academia, although I struggle to understand the language https://independent.academia.edu/BulatMuratov - Google translate probably helpful for looking into some of these. Somebody one of the sections concerning Z140 through Google translate which was helpful - I can't find the original link so thanks to whoever did that and apologies for not giving appropriate credit: https://docs.google.com/document/d/e/2PACX-1vRMaxRqkNCjXTFBsrlQFEw23Q6OPCyXanKPnG0V0HLaTcizGU 4rpts1gkWWYHQ_-ow2SCYRnfGsDEjz/pub?fbclid=IwAR0u2mmZBwjmyP4k46MPxlY%E2%80%A6

deadly77
04-06-2019, 08:57 AM
It's been mentioned in a few threads on the Ancient DNA section of the forum, but I'll bring it up here as well. David Reich's group at Harvard have shared a downloadable dataset of "Downloadable genotypes of present-day and ancient DNA data (compiled from published papers)" which can be found here: https://reich.hms.harvard.edu/downloadable-genotypes-worlds-published-ancient-dna-data

The easiest way that I can think of to look at the data is to download the .anno file to your computer, then excel and use that to open the .anno file. Filtering through the I1 individuals, most are modern samples from the 1000 Genomes project and a few were mtDNA haplogroup I1.

On the included Y-DNA I1 ancients, the dataset has included NO3423, AED 249, US14 (as AMNH, 99.1/2270), 84005, CL63 and SZ45, all of which have been discussed in this thread. Also included are Stora Förvar 11 and the four RISE samples from the Allentoft 2015 paper. None of the latter five are listed as I1 (which I agree with) - SF11 and three of the RISE samples are assigned as just I, RISE207 doesn't have a haplogroup assignment, probably because that sample has the least data.

oz
04-06-2019, 09:57 PM
Hopefully more ancient I1 will get added to that list.

deadly77
04-06-2019, 10:50 PM
Hopefully more ancient I1 will get added to that list.

I think it's inevitable. Consider that last year (2018) there were more ancient I1 (12 samples) reported in papers than all years before that combined, in line with an uptick in the amount of ancient genomes sequenced and analyzed across all haplogroups. It also means that samples reported from now on will have better analysis than they may have in the past. All good things and it's a good time to see it happening.

spruithean
04-07-2019, 01:08 AM
Things could get really interesting in the future. Which is a nice change of pace from the overwhelming numbers of R1b. We'll probably see more I1 in areas of Germanic influence for sure, it's just whether we'll find enough individuals or samples with good quality.

deadly77
04-08-2019, 11:14 AM
BAM files for the "Y-chromosome haplogroups from Hun, Avar and conquering Hungarian period nomadic people of the Carpathian Basin" paper have been uploaded to ENA.

I've downloaded the BAM files for K2/26 and SzO/540 which the paper reported as I1 and had a look using IGV. I'm afraid that the coverage is very poor and we're not going to get a lot out of these BAM files.

First I checked to verify the SNPs reported in the paper. K2/26 is derived for M253 (1T), L80 (2G) and ancestral for L22 (3A). SzO/540 is likewise derived for M253 (14T), L80 (19G) and ancestral for L22 (8A). So we know we have the right samples from the study.

Then the not so good news. Most of the BAM file has no data for a lot of the positions that I looked at. Both samples have no reading for DF29 and any of the five phyloquivalent SNPs. I checked Z63 and 18 branch SNPs downstream of that and there was no reading for any of those except for low read calls for L1237- in both samples (K2/26 has 1A, SzO/540 has 2A). Checking for Z58 and 17 branch SNPs downstream of that also came up with all no reads. The only other things I found were SNPs like M258+ in the I block upstream from I1.

I reread the preprint and the results section reads "We selected 168 phylogenetically informative Y chromosome SNP-s 14 defining all major Hg-s and the most frequent Eurasian sub-Hg-s, as well as the following 61autosomal SNP-s: 25 HirisPlex markers suitable for eye and hair color prediction"... "DNA segments containing above SNP-s were enriched from the next generation sequencing (NGS) library of each sample with hybridization capture"

So it sounds like if the area of the Y-chromosome that you're interested in isn't very close to one of their selected 168 Y-SNPs, it gets missed by the enrichment procedure and there's no data. Kind of like a low budget version of the enrichment process that the older Big Y targets the CombBED regions but with much lower return.

Unforntunately, I1 xL22 looks like it's all we're going to get out of these two samples.

mwauthy
04-08-2019, 02:37 PM
BAM files for the "Y-chromosome haplogroups from Hun, Avar and conquering Hungarian period nomadic people of the Carpathian Basin" paper have been uploaded to ENA.

I've downloaded the BAM files for K2/26 and SzO/540 which the paper reported as I1 and had a look using IGV. I'm afraid that the coverage is very poor and we're not going to get a lot out of these BAM files.

First I checked to verify the SNPs reported in the paper. K2/26 is derived for M253 (1T), L80 (2G) and ancestral for L22 (3A). SzO/540 is likewise derived for M253 (14T), L80 (19G) and ancestral for L22 (8A). So we know we have the right samples from the study.

Then the not so good news. Most of the BAM file has no data for a lot of the positions that I looked at. Both samples have no reading for DF29 and any of the five phyloquivalent SNPs. I checked Z63 and 18 branch SNPs downstream of that and there was no reading for any of those except for low read calls for L1237- in both samples (K2/26 has 1A, SzO/540 has 2A). Checking for Z58 and 17 branch SNPs downstream of that also came up with all no reads. The only other things I found were SNPs like M258+ in the I block upstream from I1.

I reread the preprint and the results section reads "We selected 168 phylogenetically informative Y chromosome SNP-s 14 defining all major Hg-s and the most frequent Eurasian sub-Hg-s, as well as the following 61autosomal SNP-s: 25 HirisPlex markers suitable for eye and hair color prediction"... "DNA segments containing above SNP-s were enriched from the next generation sequencing (NGS) library of each sample with hybridization capture"

So it sounds like if the area of the Y-chromosome that you're interested in isn't very close to one of their selected 168 Y-SNPs, it gets missed by the enrichment procedure and there's no data. Kind of like a low budget version of the enrichment process that the older Big Y targets the CombBED regions but with much lower return.

Unforntunately, I1 xL22 looks like it's all we're going to get out of these two samples.

Thanks again for looking at those samples. Once again the academic studies seem to be lacking necessary information to make more complete conclusions. That’s why I personally dislike labeling I1 as I-M253.

mwauthy
04-08-2019, 02:41 PM
Is there a reason why M253 was chosen as the SNP to describe I1 or was it completely arbitrary and any other of the 312 defining SNPs could have been chosen to label I1?

deadly77
04-08-2019, 03:09 PM
Thanks again for looking at those samples. Once again the academic studies seem to be lacking necessary information to make more complete conclusions. That’s why I personally dislike labeling I1 as I-M253.

Yes, I've moved on to labeling the overall haplogroup as I1 rather than I-M253. I much prefer this type of shorthand notation for downstream subclades compared to the old longhand alphabet soup - say I think I-L338 is much easier than I1a2a1a1a1a1 for example.

But I think this nomenclature is less appropriate for the major haplogroups like I1, I2, R1b, etc. It doesn't save any time and it can be confusing for the chronologically older samples that are in between the branch-off of I1 from I and the TMRCA of I1. Picking out one SNP from 312 when we don't know where it fits closer to the branch or the TMRCA doesn't really make a lot of sense to me.

oz
04-08-2019, 03:28 PM
So you're saying these samples don't have enough data to confirm any solid amount of snps? Why is that low coverage, bad quality?
And you're saying it's positive for M253 and a little bit for Z63-L1237? You checked for all of the Z63 snps?
Damn that's confusing, more samples that can't have determined subclades.

deadly77
04-08-2019, 03:29 PM
Is there a reason why M253 was chosen as the SNP to describe I1 or was it completely arbitrary and any other of the 312 defining SNPs could have been chosen to label I1?

I think that the name of that SNP being more closely associated with the haplogroup than any others may have influenced their decision, but they also targeted L80 as well in case they didn't get data from M253 position. They also included M170 and M258 for I and L68 and M438 for I2 - could have inferred I1 from positive results for I SNPs and negative results for I2 SNPs in the case of missing both M253 and L80. It seems they went for a pretty broad brush as they say in the preprint "defining all major Hg-s and the most frequent Eurasian sub-Hg-s" - this is not too dissimilar to what 23andme, LivingDNA and Nat Geo do in their tests - aim to cast a wide net that's pretty much guaranteed to net a major haplogroup correctly without getting very deep into the haplotree.

But they could have used other SNPs - other publications do. For example, Martiniano et al 2015 assigns the Anglo-Saxon sample NO3423 as I1 based on a single SNP S107 according to their supporting information. Although when I looked at the BAM file, NO3423 is positive for DF29 and phyloequivalent SNP CTS9857, so definitely I1.

deadly77
04-08-2019, 03:41 PM
So you're saying these samples don't have enough data to confirm any solid amount of snps? Why is that low coverage, bad quality?
And you're saying it's positive for M253 and a little bit for Z63-L1237? You checked for all of the Z63 snps?
Damn that's confusing, more samples that can't have determined subclades.

I believe it's down to how the researchers designed their assay. They say in the preprint they targeted "168 phylogenetically informative Y chromosome SNP-s" and then they treated the sample with an enrichment procedure to make sure the regions that those SNPs are found in were covered while sacrificing other regions. This is probably a trade off for them in that there is less to sequence and analyze and they get the information that they want.

I did not check all of the Z63 SNPs - I checked 19 of them including Z63 and the negative result for L1237 is the only one that had a reading. 18 SNPs had no call (can't tell if it's positive or negative - there is no data). Neither sample is positive for L1237 - both are negative for L1237. I didn't see any point in looking further as I feel that they will all be no read.

Megalophias
04-08-2019, 04:39 PM
Is there a reason why M253 was chosen as the SNP to describe I1 or was it completely arbitrary and any other of the 312 defining SNPs could have been chosen to label I1?
It was the first I1 SNP to be discovered. The first paper distinguishing I1, if I'm not mistaken, was published in 2004. That was one year after the first human genome sequence was completed, at the cost of 3 billion dollars. You couldn't just find SNPs willy-nilly back then. So much has changed so fast!

spruithean
04-08-2019, 04:44 PM
To answer the question about low coverage it can be because of poor quality in the sample due to degradation from time and environment or the casting of a wide net, or maybe both.