Y-DNA of 129 high quality shotgun ancient samples

ftdna-shotgun-samples-map

The Reich Lab has recently pre-published high quality shotgun sequencing data from 216 ancient individuals within the framework of the Allen Ancient Genome Diversity Project / John Templeton Ancient DNA Atlas. Metadata for the 216 genomes are available here.

Their median coverage is 4.9x, and among them there are 50 high coverage genomes (17-36x), but there are also samples with a coverage similar to the previously published ones.

The FamilyTreeDNA Haplotree team formed by phylogeneticist Michael Sager and Göran Runfeldt from the R&D team has analyzed all 129 males for Y-SNP calls, using – and updating with them – … Read the rest “Y-DNA of 129 high quality shotgun ancient samples”

Another “Pre-Yamnaya” sample from the Northern Caucasus?

wang-caucasus-maykop

I have updated the Ancient DNA Dataset, including a lot of new information from – among other sources – the latest version of Reich Lab curated Dataset, now renamed Allen Ancient DNA Resource (AADR). This includes new columns:

  1. Object-ID: I am now using whenever possible the Master-ID; Version-ID for a quick identification of the ‘best’ sample to include in SmartPCA or ADMIXTURE runs; and Index as a key with a unique reference number for each sample. That should make for enough stable references for any external tool to use the data.
  2. mtDNA: Added mtDNA coverage
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IBD sharing between Corded Ware and Yamnaya-related populations

yamnaya-corded-ware

Oral communication Ancient DNA and the New Science of the Human Past by David Reich (March 3, 2021).

I noticed this interesting slide called “Caught red-handed”, at approximately 45m 17s, where David Reich asserts that sampled Corded Ware populations had many “close cousins” with Yamnaya-related populations “within generations”. The method could also be used, always according to Reich, to identify “who the Yamnaya mixed with to form groups like Corded Ware”.

NOTE. Notice also the the number of new sampled individuals from Khvalynsk, Ekaterinovka, and new Yamnaya groups from Chelyabinsk, Urals, Volga, Don, Moldova, and Romania.

This represents the … Read the rest “IBD sharing between Corded Ware and Yamnaya-related populations”

Proto-Indo-Europeans: A family business

khvalynsk-yamnaya-y-dna-bottleneck

I have been updating the Ancient DNA Dataset with date estimates published in the recent preprint by Sedig, Olalde, Patterson & Reich bioRxiv (2020), and it had a reference to some interesting new samples from Khvalynsk, showing tight family connections.

Information below is taken from the preprint and from the latest version of the Reich Lab’s Allen Ancient DNA Resource (AADR). Information about the three published Khvalynsk samples is taken from Mathieson et al. Nature (2015) supplementary materials, and each ID features a different font color in the text below for clarity’s sake.

Khvalynsk Family A

I0434, … Read the rest “Proto-Indo-Europeans: A family business”

On Fatyanovo and the survival of R1a-Z93* among Mari-Permians

fatyanovo-balanovo-corded-ware

The recent preprint on ancient DNA from Veretye, Lyalovo/Volosovo and Fatyanovo from Saag et al. (2020) has been published in Science Advances Vol. 7, no. 4, eabd6535, and with it the BAM files.

Here are the Y-SNP calls from the files, following the FTDNA Haplotree standard, with Fatyanovo individuals in alphabetical order:

  • Veretye PES001 from Peschanitsa (ca. 10785–10626 calBC), mtDNA U4a1, Y-DNA R1aM459YP1301(pre-YP1272?), with 2 SNPs derived – YP1306 (T-C, 5 reads) and Y12474 (T-A, 6 reads) – and 46 SNPs ancestral at the YP1272 level. A sample with 5× coverage that
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Recent Yamnaya-related intrusion in a Denmark Late Neolithic burial

denmark-single-grave-gjerrild

Open access Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark, by Egfjord et al. PLoS One (2021).

Relevant excerpts (emphasis mine, content under CC-BY):

Gjerrild stone cist

The Gjerrild stone cist in northern Djursland, eastern Jutland, is remarkable for containing the largest and best-preserved assemblage of SGC skeletons known from Denmark. From this follows a unique opportunity to obtain information on the genetic ancestry of people representing the SGC in Denmark. In the cultural history of Neolithic Denmark, northern Djursland is peculiar as this area lacks finds from the final TRB period but

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The complexities of 3rd millennium Steppe-related migrations

yamnaya-corded-ware-bell-beaker-furholt

Open access paper Mobility and Social Change: Understanding the European Neolithic Period after the Archaeogenetic Revolution, by Martin Furholt, J. Archaeol. Res. (2021).

Content under CC-BY license. Interesting excerpts (emphasis mine, stylistic changes for clarity):

This detailed picture of Caucasian population history shows that the initial assertion in the 2015 papers, namely of a one-way migration from east to west, was a simplification supported by a variant of admixture analyses that featured Yamnaya as one unified genetic element (e.g., Haak et al. 2015, fig. 3), which led to calculations of Corded Ware individuals showing 75% Yamnaya ancestry. This

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Proto-Uralic Homeland (VIII): Earliest External Contacts

bandtoepfer-donau

This post is part of a draft on palaeolinguistics and the Proto-Uralic homeland. See below for the color code of protoforms.

14. Earliest PU ~ PIE contacts

14.1. Indo-Uralic?

The most reliable correspondences to propose an Indo-Uralic phylum come from basic morphological comparisons. Some of the most frequently mentioned ones include (e.g. Čop 1975, Kortlandt 2002, Bjørn 2019, or Lubotsky 2019):

  • Nominal endings:
  • PU nom.sg. *-Ø ~ PIA nom.-acc.sg. *-Ø (in neuter athematic nouns).
  • PU acc.sg. *-m ~ PIA acc.sg. *-m.
  • PU dual *-ki(-) ~ PIA nom.-acc.du. *-h₁.
  • PU abl. *-tA ~
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Proto-Uralic Homeland (VI): Mythology & Metallurgy

bronze-smelting

This post is part of a draft on palaeolinguistics and the Proto-Uralic homeland. See below for the color code of protoforms.

10. Metallurgy

PU (Saa., Fi., Md., Ma., P, Ms.?, Kh., Smy.?) *wäśkä (*waśki?) ‘copper; ore, brass’ (UEW Nº 1123; Kallio 2006: 6). Irregular cognates suggest it might have been borrowed during the split-up of Proto-Uralic (cf. Aikio 2015: 42). However, compare potentially regular cognates from *wäskä in PFi. *vaski ‘ore, copper, bronze; brass’ (Kallio 2012: 167; Zhivlov 2014: 115), PSaa. *weśkä ‘copper; brass’, Md. Kazhlodka viśkä ‘chain’ (Häkkinen 2012: 18), and possibly Hu. … Read the rest “Proto-Uralic Homeland (VI): Mythology & Metallurgy”