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Thursday, June 5, 2014

Coming soon: genome-wide data from more than forty 3-9K year-old humans from the ancient Russian steppe

This here is a presentation abstract from the upcoming SMBE 2014 conference. I simply can't wait to see the paper, which I'm guessing will be published very soon.

A central challenge in ancient DNA research is that for many bones that contain genuine DNA, the great majority of molecules in sequencing libraries are microbial. Thus, it has been impractical to carry out whole genome analyses of substantial numbers of ancient individuals. We report a strategy for in-solution capture of ancient DNA from approximately 390,000 single nucleotide polymorphism (SNP) targets, adapting a method of Fu et al. PNAS 2013 who enriched a 40,000 year old DNA sample for the entire chromosome 21. Of the SNPs targets, the vast majority overlap the Affymetrix Human Origins array, allowing us to compare the ancient samples to a database of more than 2,700 present-day humans from 250 groups.

We applied the SNP capture as well as mitochondrial genome enrichment to a series of 65 bones dating to between 3,000-9,000 years ago from the Samara district of Russia in the far east of Europe, a region that has been suggested to be part of the Proto-Indo-European homeland. We successfully extracted nuclear data from 10-90% of targeted SNPs for more than 40 of the samples, and for all of these samples also obtained complete mitochondrial genomes. We report three key findings:

- Samples from the Samara region possess Ancient North Eurasian (ANE) admixture related to a recently published 24,000 year old Upper Paleolithic Siberian genome. This contrasts with both European agriculturalists and with European hunter-gatherers from Luxembourg and Iberia who had little such ancestry (Lazaridis et al. 2013). This suggests that European steppe groups may be implicated in the dispersal of ANE ancestry across Europe where it is currently pervasive.

- The mtDNA composition of the steppe population is primarily West Eurasian, in contrast with northwest Russian samples of this period (Der Sarkissian et al. PLoS Genetics 2013) where an East Eurasian presence is evident.

- Samara experienced major population turnovers over time: early samples (>6000 years) belong primarily to mtDNA haplogroups U4 and U5, typical of European hunter-gatherers but later ones include haplogroups W, H, T, I, K, J.

We report modeling analyses showing how the steppe samples may relate to ancient and present-day DNA samples from the rest of Europe, the Caucasus, and South Asia, thereby clarifying the relationship of steppe groups to the genetic, archaeological and linguistic transformations of the late Neolithic and Bronze ages.

David Reich et al., Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppe, SMBE 2014 abstract.

The other really interesting abstract from this conference concerns the Ust-Ishim genome from Upper Paleolithic western Siberia (see here). I'm betting its Y-chromosome haplogroup will be P*, but that's pure speculation on my part.

Update 11/02/2015: Massive migration from the steppe is a source for Indo-European languages in Europe (Haak et al. 2015 preprint) .

Wednesday, June 4, 2014

R1a-Z93 from Bronze Age Mongolia

Four out of the eight Bronze Age Altaian Y-chromosomes in this FSI: Genetics paper belonged to haplogroup R1a-Z93 (frequency map here). Moreover, one of the R1a-Z93 samples carried markers for blue eyes and brown hair, and another for dark blond or brown hair. The single Copper Age (or Eneolithic) individual belonged to Y-chromosome haplogroup Q-M242 and was inferred to have dark hair and eyes.

Interestingly, one of the Bronze Age females belonged to an European-specific lineage within mitochondrial haplogroup H1b, with five modern matches in Poland and one in Portugal. But this isn't the first time that an ancient European-like population has been detected deep in Asia (see here and here). It's a pity that a full genome or two weren't featured in this study, but hopefully we won't have to wait long for that. Here's the paper abstract:

The Altai Mountains have been a long term boundary zone between the Eurasian Steppe populations and South and East Asian populations. To disentangle some of the historical population movements in this area, 14 ancient human specimens excavated in the westernmost part of the Mongolian Altai were studied. Thirteen of them were dated from the Middle to the End of the Bronze Age and one of them to the Eneolithic period. The environmental conditions encountered in this region led to the good preservation of DNA in the human remains. Therefore, a multi-markers approach was adopted for the genetic analysis of identity, ancestry and phenotype markers. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages. To go further in the search of the origin of these ancient specimens, phenotypical characters (ie: hair and eye colour) were determined. For this purpose, we adapted the HIrisPlex assay recently described to MALDI-TOF mass spectrometry. In addition, some ancestry informative markers were analyzed with this assay. The results revealed mixed phenotypes among this group confirming the probable admixed ancestry of the studied Altaian population at the Middle Bronze Age. The good results obtained from ancient DNA samples suggest that this approach might be relevant for forensic casework too.

Hollard et al., Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers, Forensic Science International: Genetics, published online 04 June 2014, doi:10.1016/j.fsigen.2014.05.012