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”

qpAdm best practices and common pitfalls

The recently published preprint Assessing the Performance of qpAdm, by Harney, Patterson, Reich, & Wakeley at bioRxiv (2020) offers some interesting clues about what previous papers using qpAdm might have done right, and – more importantly – what they might have done wrong.

Since it doesn’t make much sense to repeat what this open access paper says within quotes, I will try to use short sentences or rework them to sum it up, illustrating best practices and common pitfalls with what I believe are corresponding examples with Steppe-related populations to date, with an emphasis on Bell Beakers. Most … Read the rest “qpAdm best practices and common pitfalls”

Ancient phylogeography: spread of haplogroups R1b, R1a and N

The previous post showed the potential use of TreeToM to visualize ancient DNA samples in maps together with their Y-DNA phylogenetic trees. I have written Newick trees for Y-chromosome haplogroups R1b-L388 (encompassing R-V1636 and R-P297, which in turn split into R-M73 and R-M269), R1a, and N.

I have reviewed some of the BAM files from my previous bulk analyses with YLeaf v.2, to add information that I had not previously included in the All Ancient DNA Dataset, and which might be relevant to the proper depiction of phylogenetic trees; in particular, positive and negative SNPs potentially distinguishing archaic… Read the rest “Ancient phylogeography: spread of haplogroups R1b, R1a and N”

On the Ukraine Eneolithic outlier I6561 from Alexandria

Over the past week or so, since the publication of new Corded Ware samples in Narasimhan, Patterson et al. (2019) and after finding out that the R1a-M417 star-like phylogeny may have started ca. 3000 BC, I have been ruminating the relevance of contradictory data about the Ukraine_Eneolithic_o sample from Alexandria, its potential wrong radiocarbon date, and its implications for the Indo-European question.

How many other similar ‘controversial’ samples are there which we haven’t even considered? And what mechanisms are in place to control that the case of Hajji_Firuz_CA I2327 is not repeated?

Ukraine Eneolithic outlier I6561

It was not … Read the rest “On the Ukraine Eneolithic outlier I6561 from Alexandria”

Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations

Open access Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations, by Wang, Lu, Chung, and Xu, Hereditas (2018) 155:19.

Abstract (emphasis mine):

Background
Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied.

Results
We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed

… Read the rest

Indo-European demic diffusion model, 3rd edition

I have just uploaded the working draft of the third version of the Indo-European demic diffusion model. Unlike the previous two versions, which were published as essays (fully developed papers), this new version adds more information on human admixture, and probably needs important corrections before a definitive edition can be published.

The third version is available right now on ResearchGate and Academia.edu. I will post the PDF at Academia Prisca, as soon as possible:

Read or download at Academia.edu
Read or download at ResearchGate
[EDIT 21 September 2017:] Download in PDF from indo-european.info

Feel free to … Read the rest “Indo-European demic diffusion model, 3rd edition”

Something is very wrong with models based on the so-called ‘steppe admixture’ – and archaeologists are catching up

Russian archaeologist Leo Klejn has published an article Discussion: Are the Origins of Indo-European Languages Explained by the Migration of the Yamnaya Culture to the West?, which includes the criticism received from Wolfgang Haak, Iosif Lazaridis, Nick Patterson, and David Reich (mainly on the genetic aspect), and from Kristian Kristiansen, Karl-Göran Sjögren, Morten Allentoft, Martin Sikora, and Eske Willerslev (mainly on the archaeological aspect).

I will not post details of Klejn’s model of North-South Proto-Indo-European expansion – which is explained in the article, and relies on the north-south cline of ‘steppe admixture’ in the modern European population -, since … Read the rest “Something is very wrong with models based on the so-called ‘steppe admixture’ – and archaeologists are catching up”