› Miscellanea › Population Genomics › All Ancient DNA Dataset
Tagged: ancient, ancient DNA, database, dataset, DNA, haplogroup, mtDNA, samples, SNP, spreadsheet, subclade, Y-chromosome, Y-DNA
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March 2, 2020 at 11:50 am #27555Carlos QuilesKeymaster
Announcements of changes to the compiled dataset of Y-DNA and mtDNA data for reported ancient samples, including analyses of BAM files, nomenclature, culture labelling, etc.
Official site for different formats is at
For direct download of the latest version published use https://haplogroup.info/
March 4, 2020 at 10:08 am #27627Carlos QuilesKeymaster
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Files updated to v. 1.89, including newly reported samples from Sardinia and the Mediterranean, as well as some not so recent ones I had missed – Mazovian prince, Early Poles – and some updated SNPs of samples from different published papers.March 7, 2020 at 9:33 pm #27825Carlos QuilesKeymaster
I have updated the file with SNP inferences of samples from Sirak et al. (2019).
Two very interesting new ones from Late Trypillia and Italy MBA!
I had to delete update dates and start anew, because the previous ones were all messed up, probably due to messing around with different formats (Excel, CSV, txt).March 8, 2020 at 6:29 pm #27888Carlos QuilesKeymaster
These are some curiously similar SNP inferences around Lake Baikal, apparently N1a1*(xN1a1a), but nevertheless with multiple positives for N1a-L1026 equivalents, showing that this specific lineage (whichever it was) was widespread on both sides of the lake during the Neolithic.
I14460 Eneolithic Russia (Fofonovo)
For some reason, this last one didn’t make its way into YFull.
EDIT: According to Pribislav, they are N1a-pre-B187, from Y24317, a rare sister clade of N1a-708. ISOGG 2019 is really far behind new SNPs compared to FTDNA and YFull, and the current nomenclature doesn’t make much sense…March 8, 2020 at 6:37 pm #27889Carlos QuilesKeymaster
The SNP calls for Villabruna show it is negative for V2219 and L389 subclades (although the L389 level is not covered). I’d say it was more likely of a basal subclade that hasn’t survived to this day.
Villabruna Palaeolithic Epigravettian
The question is thus if the associated Epigravettian WHG expansion in Western Europe consisted mainly of this subclade, and V2219-associated peoples expanded in a different (later?) wave into SE Europe, or if it was a common L754-rich migration of which we can only see the effects after regional bottlenecks.
Sadly, Iboussieres31-2 has a too small coverage to help support any option.March 12, 2020 at 8:57 pm #27936Carlos QuilesKeymaster
I have updated the dataset, including reported Neanderthal and Denisovan Y-DNA (ISOGG only).
I have also checked out some of the samples of hg. T. I can’t find Genetiker’s reported SNP for the Varna individual. The best I can do (like the original paper) is CT+.
It’s quite interesting that the R1a-Z93 from the Balkans shows SNP calls similar to the Glăvăneştii one, suggesting that it is an R1a-Z93* sample more closely related to Late Trypillian groups, and thus a potential resurgence event more than a Srubnaya-related migration:
I have also updated all maps of Y-DNA.March 13, 2020 at 9:52 am #27943Carlos QuilesKeymaster
Updated with Sicilian Epigravettian, Mesolithic, and Early Neolithic samples from van de Loosdrecht et al. bioRxiv (2020).March 16, 2020 at 10:54 am #27974Carlos QuilesKeymaster
1. I have tested all Baltic Neolithic samples reported as R1b-L754 or P297: all have enough coverage to show they are of basal subclades P297* (xM73, xM269).
2. I also tried using Skoglund et al. (2014) PMDtools with different thresholds to improve damaged samples:
Unsuccessful with the Balkan Chalcolithic outlier from Smyadovo: all positive SNPs except BT are excluded, so we are stuck with the more risky: P-, but R+, R1b+, R1b-M269+ results. For some reason (maybe a specific threshold??) the authors assumed that the R-P280 call was acceptable, though.
Successful with the Samara HG sample: a low threshold (=0.1) confirms one R1b-M73-equivalent SNP, with two negative R1b-M269-equivalent reads, so the most plausible haplogroup seems to be M73, until proven otherwise.
3. I added samples from Egypt, including two newly reported from the Kurchatov Institute (no clear date or location), also the dubious R1b-M269 from the KV 55 coffin and the mtDNA of Djehutynakht in Loreille et al. (2018).March 23, 2020 at 9:57 am #28188Carlos QuilesKeymaster
Changes into version 1.89.16 include:
1. Addition of mtDNA from Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans, by Ding et al. Proc R Soc B (2020).
2. Review of SNP inferences of Bronze Age R1b-Z2103 samples, including negative SNPs.
Now using Yleaf v. 2.2, but I didn’t see any marked differences with previous inferences made with Yleaf v.2.March 31, 2020 at 8:22 am #28724Carlos QuilesKeymaster
Updated to version 1.90, including the recent East Asian samples from Wang et al. (2020) and Jeong et al. (2020).
In version 1.90.1 I added changes proposed by Kovalev to culture and group classification of samples from Jeong et al. (2020).
I have left the samples labelled as C2a… according to what I could find in Japanese pages, which suggest they belong to ISOGG 2019 C2b, even though no recent ISOGG nomenclature included them in the past 5 years… These include C2a1a1, C2a1a2, but particularly C2a1a3, whose corresponding C2b1a3?? I couldn’t find anywhere.
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