Tag: P312

Updates to ASoSaH: new maps, updated PCA, and added newest research papers

steppe-ancestry-cut

The title says it all. I have used some free time to update the series A Song of Sheep and Horses:

I basically added information from the latest papers published, which (luckily enough for me) haven’t been too … Read the rest “Updates to ASoSaH: new maps, updated PCA, and added newest research papers”

A very “Yamnaya-like” East Bell Beaker from France, probably R1b-L151

bell-beaker-expansion

Interesting report by Bernard Sécher on Anthrogenica, about the Ph.D. thesis of Samantha Brunel from Institut Jacques Monod, Paris, Paléogénomique des dynamiques des populations humaines sur le territoire Français entre 7000 et 2000 (2018).

NOTE. You can visit Bernard Sécher’s blog on genetic genealogy.

A summary from user Jool, who was there, translated into English by Sécher (slight changes to translation, and emphasis mine):

They have a good hundred samples from the North, Alsace and the Mediterranean coast, from the Mesolithic to the Iron Age.

There is no major surprise compared to the rest of Europe. On the PCA

… Read the rest “A very “Yamnaya-like” East Bell Beaker from France, probably R1b-L151”

R1a-Z280 lineages in Srubna; and first Palaeo-Balkan R1b-Z2103?

herodotus-world-map

Scythian samples from the North Pontic area are far more complex than what could be seen at first glance. From the new Y-SNP calls we have now thanks to the publications at Molgen (see the spreadsheet) and in Anthrogenica threads, I think this is the basis to work with:

NOTE. I understand that writing a paper requires a lot of work, and probably statistical methods are the main interest of authors, editors, and reviewers. But it is difficult to comprehend how any user of open source tools can instantly offer a more complex assessment of the samples’ Y-SNP … Read the rest “R1a-Z280 lineages in Srubna; and first Palaeo-Balkan R1b-Z2103?”

Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component

invasion-from-the-steppe-yamnaya

Good timing for the publication of two interesting papers, that a lot of people should read very carefully:

ADMIXTURE

Open access A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots, by Daniel J. Lawson, Lucy van Dorp & Daniel Falush, Nature Communications (2018).

Interesting excerpts (emphasis mine):

Experienced researchers, particularly those interested in population structure and historical inference, typically present STRUCTURE results alongside other methods that make different modelling assumptions. These include TreeMix, ADMIXTUREGRAPH, fineSTRUCTURE, GLOBETROTTER, f3 and D statistics, amongst many others. These models can be used both to probe whether assumptions of the model

… Read the rest “Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component”

Reproductive success among ancient Icelanders stratified by ancestry

iceland-pca

New paper (behind paywall), Ancient genomes from Iceland reveal the making of a human population, by Ebenesersdóttir et al. Science (2018) 360(6392):1028-1032.

Abstract and relevant excerpts (emphasis mine):

Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of

… Read the rest “Reproductive success among ancient Icelanders stratified by ancestry”

Post-Neolithic Y-chromosome bottleneck explained by cultural hitchhiking and competition between patrilineal clans

Open access study Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck, by Zeng, Aw, and Feldman, Nature Communications (2018).

Abstract (emphasis mine):

In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among

… Read the rest “Post-Neolithic Y-chromosome bottleneck explained by cultural hitchhiking and competition between patrilineal clans”

The R1b-L23/Late PIE expansions, and the ‘R1a – Indo-European’ association

indo-european-yamnaya-corded-ware

I wrote a series of posts at the end of 2017 / beginning of 2018, to answer the wrong assumptions I could read in forums and blogs since 2015.

I decided not to publish them then, seeing how many successive papers were confirming my Indo-European demic diffusion model in a (surprisingly) clear-cut way.

Nevertheless, because I keep reading the same comments no matter what gets published, even in mid-2018 – the latest ones in our Facebook page (“was haplogroup X Indo-European?”), and in this very blog (“I see it very difficult to link Bell Beaker with Balto-Slavic, when now Balto-Slavic … Read the rest “The R1b-L23/Late PIE expansions, and the ‘R1a – Indo-European’ association”

Eurasian steppe dominated by Iranian peoples, Indo-Iranian expanded from East Yamna

yamna-indo-iranian-expansion

The expected study of Eurasian samples is out (behind paywall): 137 ancient human genomes from across the Eurasian steppes, by de Barros Damgaard et al. Nature (2018).

Dicussion (emphasis mine):

Our findings fit well with current insights from the historical linguistics of this region (Supplementary Information section 2). The steppes were probably largely Iranian-speaking in the first and second millennia bc. This is supported by the split of the Indo-Iranian linguistic branch into Iranian and Indian33, the distribution of the Iranian languages, and the preservation of Old Iranian loanwords in Tocharian34. The wide distribution of

… Read the rest “Eurasian steppe dominated by Iranian peoples, Indo-Iranian expanded from East Yamna”

Yleaf: software for human Y-chromosomal haplogroup inference from next generation sequencing data

portugal-bronze-age-admixture

Brief communication (behind paywall) Yleaf: software for human Y-chromosomal haplogroup inference from next generation sequencing data, by Arwin Ralf, Diego Montiel González, Kaiyin Zhong, and Manfred Kayser, Mol Biol Evol (2018), msy032.

Abstract

Next generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data it now contains many thousands. The complexity of both, Y tree and NGS data

… Read the rest “Yleaf: software for human Y-chromosomal haplogroup inference from next generation sequencing data”