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”

Online GIS maps of ancient Y-DNA, mtDNA and ADMIXTURE

arcgis-online-y-dna

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

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.

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”

North-West Indo-Europeans of Iberian Beaker descent and haplogroup R1b-P312

iron-age-early-mediterranean

The recent data on ancient DNA from Iberia published by Olalde et al. (2019) was interesting for many different reasons, but I still have the impression that the authors – and consequently many readers – focused on not-so-relevant information about more recent population movements, or even highlighted the least interesting details related to historical events.

I have already written about the relevance of its findings for the Indo-European question in an initial assessment, then in a more detailed post about its consequences, then about the arrival of Celtic languages with hg. R1b-M167, and later in combination with Read the rest “North-West Indo-Europeans of Iberian Beaker descent and haplogroup R1b-P312”

Vikings, Vikings, Vikings! “eastern” ancestry in the whole Baltic Iron Age

Featuredvikings-middle-age

Open access Population genomics of the Viking world, by Margaryan et al. bioRxiv (2019), with a huge new sampling from the Viking Age.

#EDIT (16 SEP 2020): The paper has been published in Nature.

Interesting excerpts (emphasis mine, modified for clarity):

To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was

Read the rest “Vikings, Vikings, Vikings! “eastern” ancestry in the whole Baltic Iron Age”

A Song of Sheep and Horses, revised edition, now available as printed books

cover-song-sheep-and-horses

As I said 6 months ago, 2019 is a tough year to write a blog, because this was going to be a complex regional election year and therefore a time of political promises, hence tenure offers too. Now the preliminary offers have been made, elections have passed, but the timing has slightly shifted toward 2020. So I may have the time, but not really any benefit of dedicating too much effort to the blog, and a lot of potential benefit of dedicating any time to evaluable scientific work.

On the other hand, I saw some potential benefit for … Read the rest “A Song of Sheep and Horses, revised edition, now available as printed books”

Arrival of steppe ancestry with R1b-P312 in the Mediterranean: Balearic Islands, Sicily, and Iron Age Sardinia

steppe-balearic-sicily-sardinia

New preprint The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean by Fernandes, Mittnik, Olalde et al. bioRxiv (2019)

Interesting excerpts (emphasis in bold; modified for clarity):

Balearic Islands: The expansion of Iberian speakers

Mallorca_EBA dates to the earliest period of permanent occupation of the islands at around 2400 BCE. We parsimoniously modeled Mallorca_EBA as deriving 36.9 ± 4.2% of her ancestry from a source related to Yamnaya_Samara; (…). We next used qpAdm to identify “proximal” sources for Mallorca_EBA’s ancestry that are more closely related to this individual in space and time, and found

Read the rest “Arrival of steppe ancestry with R1b-P312 in the Mediterranean: Balearic Islands, Sicily, and Iron Age Sardinia”

ASoSaH Reread (I): Y-DNA haplogroups among Indo-Europeans (apart from R1b-L23)

eneolithic-early-admixture-steppe-ancestry

Given my reduced free time in these months, I have decided to keep updating the text on Indo-European and Uralic migrations and/or this blog, simultaneously or alternatively, to make the most out of the time I can dedicate to this. I will add the different ‘A Song of Sheep and Horses (ASoSaH) reread’ posts to the original post announcing the books. I would be especially interested in comments and corrections to the book chapters rather than the posts, but any comments are welcome (including in the forum, where comments are more likely to stick).

This is mainly a Read the rest “ASoSaH Reread (I): Y-DNA haplogroups among Indo-Europeans (apart from R1b-L23)”