mtDNA, lactase persistence, and admixr for ADMIXTOOLS

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”

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”

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”

Indo-Europeans and Finno-Ugric peoples might have shared the love for weed

Funny and interesting read to help relax the trolling wave caused by the first early Hittite samples:

Cannabis is indigenous to Europe and cultivation began during the Copper or Bronze age: a probabilistic synthesis of fossil pollen studies, by McPartland, Guy, & Hegman, Vegetation History and Archaeobotany (2018).

Abstract (emphasis mine):

Conventional wisdom states Cannabis sativa originated in Asia and its dispersal to Europe depended upon human transport. Various Neolithic or Bronze age groups have been named as pioneer cultivators. These theses were tested by examining fossil pollen studies (FPSs), obtained from the European Pollen Database. Many FPSs

… Read the rest