mtDNA, lactase persistence, and admixr for ADMIXTOOLS

lactase-persistence-timing-geography

The following are some recent developments and updates:

I. Ancient DNA Dataset version 2

I.1. Accurate mtDNA haplogroups

I was meaning to update the mtDNA part of the Ancient DNA Dataset, and finally found some time to review FTDNA and YFull nomenclature (including hyperlinks), as well as those SNP calls from published samples found in YFull’s MTree. So, if you are interested in studies of mtDNA phylogeography, I think the data is now accurate and much more useful.

Given the number of columns and the size of the files, I have decided to post shorter standard versions, by … Read the rest “mtDNA, lactase persistence, and admixr for ADMIXTOOLS”

qpAdm best practices and common pitfalls

olalde-2018-qpadm-bell-beaker

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”

Bell Beakers and Mycenaeans from Yamnaya; Corded Ware from the forest steppe

eba-yamnaya-ancestry-hungary

I have recently written about the spread of Pre-Yamnaya or Yamnaya ancestry and Corded Ware-related ancestry throughout Eurasia, using exclusively analyses published by professional geneticists, and filling in the gaps and contradictory data with the most reasonable interpretations. I did so consciously, to avoid any suspicion that I was interspersing my own data or cherry picking results.

Now I’m finished recapitulating the known public data, and the only way forward is the assessment of these populations using the available datasets and free tools.

Understanding the complexities of qpAdm is fairly difficult without a proper genetic and statistical background, which I … Read the rest “Bell Beakers and Mycenaeans from Yamnaya; Corded Ware from the forest steppe”

On the Ukraine Eneolithic outlier I6561 from Alexandria

sredni-stog-eneolithic-late

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”

Uralic speakers formed clines of Corded Ware ancestry with WHG:ANE populations

steppe-forest-tundra-biomes-uralic

The preprint by Jeong et al. (2018) has been published: The genetic history of admixture across inner Eurasia Nature Ecol. Evol. (2019).

Interesting excerpts, referring mainly to Uralic peoples (emphasis mine):

A model-based clustering analysis using ADMIXTURE shows a similar pattern (Fig. 2b and Supplementary Fig. 3). Overall, the proportions of ancestry components associated with Eastern or Western Eurasians are well correlated with longitude in inner Eurasians (Fig. 3). Notable outliers include known historical migrants such as Kalmyks, Nogais and Dungans. The Uralic- and Yeniseian-speaking populations, as well as Russians from multiple locations, derive most of their Eastern Eurasian ancestry

Read the rest “Uralic speakers formed clines of Corded Ware ancestry with WHG:ANE populations”