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Bollox79
03-22-2018, 04:09 AM
According to BAM files of samples found in this paper: http://www.pnas.org/content/early/2018/03/06/1719880115 I figured I'd post about it here as a thread if case some of you guys don't troll the aDNA section as often as I do (all the time haha).

Currently sample AED 106 who clusters autosomally near Saxony in a K36 PCA is so far U106+. More importantly (at least to my group as I'm Z306+) is ALH1 who is U106+, Z381+, Z156+, and Z306+. He clusters autosomally between Friesland, Norway and Denmark. AED 106 was buried with the typical Germanic older adult male grave goods (he was listed as 60+ in age) with a Spatha, bag, belt, vessels, glass. ALH1 I assume was too, but his grave was disturbed/robbed - he was also an older adult male aged 50-60.

These remains generally date to about late 400s - early 500s AD.

The Z306+ result is important because it's the first Z156 found in Migration Era remains ;-). Also down stream of Z306 is the DF98 group - aka the House of Wettin group which splits into S1911 and S18823/Wettin side.

Cheers!

rms2
03-26-2018, 08:22 PM
Remember the results from the 7th century Frankish burial at Ergolding in Bavaria (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702742/) a few years ago?

Unfortunately, that was before ancient NGS testing. They got some y-dna STR's. The guys buried in one part of the cave with weapons and chain mail (I'm working from memory here) had U106-looking haplotypes. There were one or two weaponless burials in another part that looked like G2a, as I recall.

It would be nice if they could go back and NGS test those samples.

rms2
03-26-2018, 10:34 PM
Remember the results from the 7th century Frankish burial at Ergolding in Bavaria (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702742/) a few years ago?

Unfortunately, that was before ancient NGS testing. They got some y-dna STR's. The guys buried in one part of the cave with weapons and chain mail (I'm working from memory here) had U106-looking haplotypes. There were one or two weaponless burials in another part that looked like G2a, as I recall.

It would be nice if they could go back and NGS test those samples.

Okay, I went and looked back a little, without dragging out a magnifying glass. The men buried together in the wooden burial chamber labeled by the researchers as Grave 244 were the ones who were tested. Skeletons 244A, 244B, and 244C were all R1b (and possibly U106). They are the ones from the western part of the burial chamber, who had weapons, armor and spurs.

Skeletons 244D, 244E, and 244F did not have armor, weapons or spurs, but they came from the eastern end of the burial chamber, which appears to have been plundered at some time, so who knows what they might have had. 244D was R1b (possibly U106). 244E and F were both G2a.

Man! That paper came out in 2009! Seems like yesterday to me. Phew! Time flies when you're having fun!

spruithean
03-26-2018, 10:54 PM
So what is the Y-haplogroup breakdown of all the individuals in these graves? This is certainly fascinating! Seems there is a decent amount of ancient R-U106 lately.

rms2
03-26-2018, 10:59 PM
So what is the Y-haplogroup breakdown of all the individuals in these graves? This is certainly fascinating! Seems there is a decent amount of ancient R-U106 lately.

Well, at Ergolding, four were R1b (possibly U106), and three of them had weapons, armor and spurs. Two other skeletons were G2a.

I know there was also a paper recently on some Lombard burials in Italy and Hungary, and some of those skeletons were R1b-U106, which was confirmed by SNP testing.

Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics (https://www.biorxiv.org/content/early/2018/02/20/268250)

spruithean
03-26-2018, 11:55 PM
Well, at Ergolding, four were R1b (possibly U106), and three of them had weapons, armor and spurs. Two other skeletons were G2a.

I know there was also a paper recently on some Lombard burials in Italy and Hungary, and some of those skeletons were R1b-U106, which was confirmed by SNP testing.

Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics (https://www.biorxiv.org/content/early/2018/02/20/268250)

Ah, okay. I was curious as to whether the results from Bavaria and elsewhere from these same time periods was overwhelmingly R-U106 or if there were any Germanic-speaking associated haplogroups found in the sites.

Cofgene
03-27-2018, 12:08 AM
Remember the results from the 7th century Frankish burial at Ergolding in Bavaria (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702742/) a few years ago?

Unfortunately, that was before ancient NGS testing. They got some y-dna STR's. The guys buried in one part of the cave with weapons and chain mail (I'm working from memory here) had U106-looking haplotypes. There were one or two weaponless burials in another part that looked like G2a, as I recall.

It would be nice if they could go back and NGS test those samples.

Based upon the limited STRs the results pointed towards Z8 or Z326..... funding probably could be obtained to get better sequencing for the U106 guy if the original authors could consider updating their results in the context of current autosomal and y/mt haplogroup research.

rms2
03-27-2018, 12:09 AM
Ah, okay. I was curious as to whether the results from Bavaria and elsewhere from these same time periods was overwhelmingly R-U106 or if there were any Germanic-speaking associated haplogroups found in the sites.

There were other haplogroups among the Lombards apparently, but I haven't followed that closely.

ArmandoR1b
03-27-2018, 12:44 AM
Ah, okay. I was curious as to whether the results from Bavaria and elsewhere from these same time periods was overwhelmingly R-U106 or if there were any Germanic-speaking associated haplogroups found in the sites.
About 50% from Bavaria are U106 according to what Bollox posted here (https://anthrogenica.com/showthread.php?13793-Y-DNA-of-Roman-Soldier-FN2-buried-in-Germany&p=370358&viewfull=1#post370358).

Other haplogroups are I1, I2a, and G2a.

Once an expert analyzes the files then the most downstream SNP can be determined.

Bollox79
03-27-2018, 01:12 AM
About 50% from Bavaria are U106 according to what Bollox posted here (https://anthrogenica.com/showthread.php?13793-Y-DNA-of-Roman-Soldier-FN2-buried-in-Germany&p=370358&viewfull=1#post370358).

Other haplogroups are I1, I2a, and G2a.

Once an expert analyzes the files then the most downstream SNP can be determined.

Yep what Armando said! He and I have been converting/processing the BAMs for the Bavarian guys with BAM analysis kit and Armando compared some of the results to what Rocca has found etc... seems to be good for the upstream SNPs at least and around U106... and a few downstream perhaps. Also user 167273 has processed some of these BAM files!

I'll try to summarize the newer migration era U106 results here:

Bavarian remains

AED 106 - U106+, Z156+ and possibly Z306: 60+ aged male buried with spatha, belt, bag, vessel, glass dated to about 480 - 510 AD
AED 92 - U106+ (didn't find any downstream per the BAM AK) 20-30 aged male buried with spatha, seax, lance, shield, belt, bag. These two remains were at Alternerding cemetery and from what I read on the early phase 1 (these graves are in that phase - aed92 is mentioned in the paper - only guy to have that weapon set) these are "founder's" graves or early graves and aed106 and aed92 are most likely kin? as they tended to bury in defined groups of related (?) individuals.

ALH 1 - U106+, Z156+ and possibly Z305 - Altheim - 50-60 age male with disturbed/robbed grave - this is a high quality sample (bam file is 12.8 gb) so maybe Alex or someone can confirm the downstream SNPs or find more? This grave listed as non-dateable lack of grave goods but ALH 2 and 3 and 10 carbon dated in the 300s-400s maybe 510 AD.

STR 316 - U106+ - male aged 40-60 buried with belt, bag, vessel - dated to about 480-510 AD

STR 393 - U106+ male aged 40-55 buried with a spatha - dated to about 460-530 AD

I have only done some research on the Alternerding cemetery (samples AED) so I need to look up some stuff on the other cemeteries (ALH and STR).

Bollox79
03-27-2018, 01:14 AM
Remember the results from the 7th century Frankish burial at Ergolding in Bavaria (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702742/) a few years ago?

Unfortunately, that was before ancient NGS testing. They got some y-dna STR's. The guys buried in one part of the cave with weapons and chain mail (I'm working from memory here) had U106-looking haplotypes. There were one or two weaponless burials in another part that looked like G2a, as I recall.

It would be nice if they could go back and NGS test those samples.

Yes Rms2 I remember this and actually recently looked at it and concur the STRs at least look possibly U106... I would love to see some of the newer testing done on these guys looking for newer SNPs...

Bollox79
03-27-2018, 01:18 AM
For the Longobard samples - this is per Alex Williamson:

I've taken a look at the 3 U106 samples and one DF27 sample which had full WGS sequencing. They all have great coverage and it's easy to work with them. There's not much that can be done with the others that had only targeted sequencing.

SZ5 (SRR6703600) belongs here: R-M269>P312/S116>Z40481>ZZ11>DF27/S250>Z195/S355>Z198>ZS312>FGC39101>BY3195

SZ2 (SRR6703603) belongs here: R-M269>U106/S21>Z2265>Z381/S263>Z301/S499>L48>Z9>Z30/S271>Z2>Z7>Z8>ZZ58

SZ4 (SRR6703601) belongs here: R-M269>U106/S21>Z2265>Z18>Z372/S375

SZ11 (SRR6703599) belongs here: 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

SZ5 split the BY3195 block I had. SZ4 may actually be negative for Z373/S495 but because it's within DYZ19 I wasn't 100% convinced. For SZ11, I had to create a new block downstream of FGC13489 as he shares a variant with BigY kit Cemin (N23903).

Bollox79
03-27-2018, 01:22 AM
Samples at Szolad SZ16 and SZ23 were also U106+ and Z381+. Collegno cample CL84 was U106+ and Z381+ and kin to several northern European males who were only tested to the L151 or L52 (R1b M269?) level and could still be U106?

Interesting difference between the Longobard and Bavarian samples is that the Longobards are Z381 - but are L48 and Z18 while some of the Bavarians (mixture of tribes?) are Z381, but appear Z156+. In the overall group of U106 L48 and Z156 have different distributions in modern U106 populations ;-).

Bollox79
03-27-2018, 01:39 AM
For the Longobards autosomally SZ5 had some Southern European admixture? Listed 50-70% Northern European ancestry

For SZ2, 4, 11, 16, and 23 they were listed as Greater than 70% Northern European ancestry.

CL84 was listed as Greater than 70% NE ancestry along with his "kin" group. 22354

Bollox79
03-27-2018, 01:43 AM
Ah, okay. I was curious as to whether the results from Bavaria and elsewhere from these same time periods was overwhelmingly R-U106 or if there were any Germanic-speaking associated haplogroups found in the sites.

The Bavarian guys seem to be a mixture of U106 (5 samples) and I1 (3 samples) and I2a (1 sample).

AED249 is I1 L840
STR486 is I1 L840
STR241 is I1 L840

STR491 is I2a - YP207/FGC8111/S2663/AM01263

The Bim37 guy is G2a-S317/L497

Bollox79
03-27-2018, 01:51 AM
So similar to the Longobard cemeteries in the sense that it's U106 with haplogroup I guys - though the Longobard cemeteries had some different haplogroups among the more Southern European autosomal samples... etc.

All the Bavarian male samples seem to be very Northern European including the G2a guy - and in the graphic that displays their autosomal ancestry in the paper I think they mixed the sample STR491 and AED1119 up as it has AED1119 under the "male" label, but according to the grave lists AED1119 is a 30-45 year old female buried with Alamannic-Frankish grave goods and dated to 510-530 AD. I think it's meant to be STR491 for who we got a y-snp result for and he is listed in the grave list as a 60+ aged male.

rms2
03-27-2018, 01:17 PM
You're doing good work on this, Bollox79. Thanks.

Are you keeping a Google spreadsheet of ancient/medieval U106 results?

Bollox79
03-27-2018, 10:07 PM
You're doing good work on this, Bollox79. Thanks.

Are you keeping a Google spreadsheet of ancient/medieval U106 results?

Thanks! I have a rough draft saved to note pad, but I'd like to make it more official with a google spreadsheet or something akin to that ;-). I might get cracking on that over the weekend - I usually work night shift, but have shifted to 4 10 hour days during the week for CDL classes - so a big swing in scheduling! I certainly plan on following up on the U106 Bavarian guys - bug Rich or Alex to at least take a look at ALH 1 who has a 12.8 gb BAM - or teach me how to look through the Fastq file for downstream SNPs etc... I'd like to learn how to do it so I don't have to bug them... I am assuming they are using a slightly more involved process than just running the BAM analysis kit (which seems to do OK for U106)...

I'd like to come up with a spreadsheet that has info on the grave site, the samples and their SNPs, and their general descriptions (grave goods, age, etc). Also include their autosomal info - so eventually when we get more and more (hopefully as more papers come in!) we can keep track of it all and maybe some more patterns will emerge ;-).

Wing Genealogist
09-18-2019, 11:48 AM
You're doing good work on this, Bollox79. Thanks.

Are you keeping a Google spreadsheet of ancient/medieval U106 results?

I have developed a Google spreadsheet of Ancient/Medieval/Royal U106 results at: https://docs.google.com/spreadsheets/d/1rpJP0Bt4qUQb9wWBFA7i1tLPV75ie_qS0iplwvvlVmQ/edit?usp=sharing You need to go to the last tab "Ancient/Medieval/Royal DNA to find the info.

It is extensively hyperlinked to various papers & studies (including Bollox79's research).

Wing Genealogist
09-18-2019, 11:51 AM
FWIW: Alex Williamson has re-analyzed the U106+ samples in the Veeramah 2018 paper http://www.pnas.org/content/early/2018/03/06/1719880115

Most of the U106 samples used a capture technique, rather than shotgun, so much less (and spotty) coverage. However, one sample ALH_1 (believed to have been shotgun sequenced) yielded extensive SNP results. Alex was able to further refine his subclade to:
DF96>FGC13326>S22047>FGC46344>FGC13611>FGC13603

altvred
04-05-2021, 02:39 PM
https://www.ebi.ac.uk/ena/browser/view/PRJEB41353

HGH1429, individual from a Medieval period mass burial site in Lubeck. Ran into that accession on the ENA by pure chance, couldn't find a free link to the paper he was published in.

https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3762113

https://i.imgur.com/vqNv2Zj.png

Link to BAM

Here (https://www.dropbox.com/s/jamq6y5p9215y2y/HGH1429.chrY.bam?dl=1)

Wing Genealogist
04-05-2021, 04:21 PM
https://www.ebi.ac.uk/ena/browser/view/PRJEB41353

HGH1429, individual from a Medieval period mass burial site in Lubeck. Ran into that accession on the ENA by pure chance, couldn't find a free link to the paper he was published in.

https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3762113

https://i.imgur.com/vqNv2Zj.png

Link to BAM

Here (https://www.dropbox.com/s/jamq6y5p9215y2y/HGH1429.chrY.bam?dl=1)

What do the (?) and ($) symbolize after the SNPs. I understand (+) positive, (-) negative.

Which symbol is for a no call (?)? and does the symbol ($) indicate both positive and negative calls??

sheepslayer
04-05-2021, 04:28 PM
What do the (?) and ($) symbolize after the SNPs. I understand (+) positive, (-) negative.

Which symbol is for a no call (?)? and does the symbol ($) indicate both positive and negative calls??

$ means this SNP can be purchased at YSEQ. ? just means the provided data does not contain information about this SNP

altvred
04-06-2021, 07:57 AM
What do the (?) and ($) symbolize after the SNPs. I understand (+) positive, (-) negative.

Which symbol is for a no call (?)? and does the symbol ($) indicate both positive and negative calls??
Essentially all the ? and $ means that these SNPs aren't included in the coverage for that sample.