Visualizing phylogenetic trees of ancient DNA in a map

haplogroup-r1b-v88-v2219-phylogenetic

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”

Early Uralic – Indo-European contacts within Europe

north-west-indo-european-uralic

One of the most interesting aspects for future linguistic research, boosted by the current knowledge in population genomics, is the influence of Uralic – most likely spread initially with Corded Ware peoples across northern Europe – on early Indo-European dialects.

Whereas studies on the potential Afroasiatic (or Semitic), Vasconic, Etruscan, or non-Indo-European in general abound for ancient and southern IE branches (see e.g. more on the NWIE substrate words), almost exclusively Uralicists have dealt with the long-term mutual influences between Indo-European and Uralic dialects, and often mostly from the Uralic side.… Read the rest “Early Uralic – Indo-European contacts within Europe”

Spread of Indo-European and Uralic speakers in ADMIXTURE

indo-european-uralic-admixture

The following are updated files for unsupervised ADMIXTURE of most available ancient Eurasian samples with K=7. For reference, see PCA of ancient and modern Eurasian samples.

NOTE. For a precise interpretation of ancestry evolution, be sure to first check the posts on the expansion of “Steppe ancestry”, on the spread of Yamnaya ancestry with Indo-Europeans, and on the evolution of Corded Ware ancestry typical of modern Uralic populations.

ADMIXTURE timeline

This is a YouTube video similar to the one on Indo-Europeans and Y-DNA evolution:

admixture-video-youtube

Some comments

  • I have tried running supervised ADMIXTURE models by selecting
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Intense but irregular NWIE and Indo-Iranian contacts show Uralic disintegrated in the West

chalcolithic-early-uralic-indo-european

Open access PhD thesis Indo-Iranian borrowings in Uralic: Critical overview of sound substitutions and distribution criterion, by Sampsa Holopainen, University of Helsinki (2019), under the supervision of Forsberg, Saarikivi, and Kallio.

Interesting excerpts (emphasis mine):

The gap between Russian and Western scholarship

Many scholars in the Soviet Union and later the Russian Federation also have researched this topic over the last five decades. Notably the eminent Eugene Helimski dealt with this topic in several articles: his 1992 article (republished in Helimski 2000) on the emergence of Uralic consonantal stems used Indo-Iranian and other Indo-European loans as key evidence, and

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Samoyedic shows Yeniseic substrate; both influenced Tocharian

chalcolithic-late-tocharian

Open access paper The deviant typological profile of the Tocharian branch of Indo-European may be due to Uralic substrate influence by Peyrot, Indo-European Linguistics (2019).

NOTE. This seems to be part of the master’s thesis by Abel Warries, but the paper is authored only by Peyrot.

Interesting excerpts (emphasis mine):

1. The stop system

The loss in Tocharian of the Proto-Indo-European obstruent distinctions conventionally noted as voice and aspiration is a very strong indication of foreign influence. Since Proto-Indo-European roots mostly have at least one stop, and often two, the merger of all three stop series into one must have

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The expansion of Indo-Europeans in Y-chromosome haplogroups

yamnaya-corded-ware-y-dna-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.

EDIT (2 FEB 2020): I have published the All Ancient DNA dataset and updated OpenLayers maps in this post, now also divided by ages.

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:

yamnaya-expansion

NOTE. The video is best viewed in HD 1080p (1920×1080) with a display that allows for this Read the rest “The expansion of Indo-Europeans in Y-chromosome haplogroups”

R1b-L23-rich Bell Beaker-derived Italic peoples from the West vs. Etruscans from the East

final-bronze-age-italy

New paper (behind paywall) Ancient Rome: A genetic crossroads of Europe and the Mediterranean, by Antonio et al. Science (2019).

The paper offers a lot of interesting data concerning the Roman Empire and more recent periods, but I will focus on Italic and Etruscan origins.

NOTE. I have updated prehistoric maps with Y-DNA and mtDNA data, and also the PCA of ancient Eurasian samples by period including the recently published samples, now with added sample names to find them easily by searching the PDFs.

Apennine homeland problem

The traditional question of Italic vs. Etruscan origins from a cultural-historical … Read the rest “R1b-L23-rich Bell Beaker-derived Italic peoples from the West vs. Etruscans from the East”

“Steppe ancestry” step by step (2019): Mesolithic to Early Bronze Age Eurasia

yamnaya-gac-maykop-corded-ware-bell-beaker

The recent update on the Indo-Anatolian homeland in the Middle Volga region and its evolution as the Indo-Tocharian homeland in the Don–Volga area as described in Anthony (2019) has, at last, a strong scientific foundation, as it relies on previous linguistic and archaeological theories, now coupled with ancient phylogeography and genomic ancestry.

There are still some inconsistencies in the interpretation of the so-called “Steppe ancestry”, though, despite the one and a half years that have passed since we first had access to the closest Pontic–Caspian steppe source populations. Even my post “Steppe ancestry” step by step from a year ago … Read the rest ““Steppe ancestry” step by step (2019): Mesolithic to Early Bronze Age Eurasia”