Y-DNA of 129 high quality shotgun ancient samples

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”

Proto-Indo-Europeans: A family business

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

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

… Read the rest

The complexities of 3rd millennium Steppe-related migrations

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

… Read the rest

Proto-Uralic Homeland (VII): Kinship & Numerals

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

12. Kinship Terminology

12.1. Immediate Family

PU? (Saa.?, Fi.?, Md.?, Ma.?, Kh.?, Ms.?, Hu.?, Smy.?) *äććä?/*eć(ć)ä/*ić(ć)ä/*äjćä ‘father’ (UEW Nº 35). PSmy. was was borrowed into Yukaghir ečē ‘father’. Samoyedic form borrowed into Yukaghir ečē ‘father’ (Aikio 2014: 57)

NOTE. Pre-PSmy. *äjćä? could reflect an earlier Pre-PIIr. *eićo- or PIIr. *aića- ‘to control, to own’. An underlying Pre-PFi., Pre-PSaa. (based on PSaa. *e̮ćē from Skolt and Kildin Saami) and PMa. *ićä could reflect PIIr. … Read the rest “Proto-Uralic Homeland (VII): Kinship & Numerals”

Longobards from Scandinavia, and the “Ural-Altaic” Árpád lineage

The Family Tree DNA R&D team formed by Göran Runfeldt and Michael Sager has reported detailed Y-SNPs of sampled Longobards from the open access paper Understanding 6th-century barbarian social organization and migration through paleogenomics, by Amorim et al. Nat. Commun. (2020). From the abstract:

We obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized

… Read the rest

Online GIS maps of ancient Y-DNA, mtDNA and ADMIXTURE

The last few weeks have been very exciting in terms the amount, diversity and quality of newly reported ancient samples, which included new genotypes and also Y-DNA and mtDNA haplogroups.

As some of you already know, I had been preparing a tailored GIS map of ancient DNA using QGIS-server on Ubuntu and trying some of the available plugins for the task, and was ready to use my old broken PC as a web server. For that, I needed to prepare different files corresponding to the different conventional divisions of the Prehistory Atlas. The crazy number of recently reported papers … Read the rest “Online GIS maps of ancient Y-DNA, mtDNA and ADMIXTURE”

Visualizing phylogenetic trees of ancient DNA in a map

Yesterday the Eaton Lab at Columbia University announced on Twitter a nifty little tool by Carlos Alonso Maya-Lastra called TreeToM, which accepts Newick trees and CSV latitude/longitude data to explore phylogeny and geography interactively, with no coding required.

I thought it could complement nicely my All Ancient DNA Dataset, particularly for those newly described SNPs (FTDNA private variants, etc.) that have not been incorporated yet into SNP Tracker.

Here are two examples with snippets to copy&paste to the appropriate boxes in TreeToM. Feel free to add others in the comments:… Read the rest “Visualizing phylogenetic trees of ancient DNA in a map”

The expansion of Indo-Europeans in Y-chromosome haplogroups

I have compiled for two years now the reported Y-DNA and mtDNA haplogroups of ancient DNA samples published, including also SNPs from analysis of the BAM files by hobbyists.

Y-DNA timeline

Here is a video with a timeline of the evolution of Indo-European speakers, according to what is known today about reconstructed languages, prehistoric cultures and ancient DNA:

NOTE. The video is best viewed in HD 1080p (1920×1080) with a display that allows for this or greater video quality, and a screen big enough to see haplogroup symbols, i.e. tablet or greater. The YouTube link is here. The … Read the rest “The expansion of Indo-Europeans in Y-chromosome haplogroups”