Monday, July 17, 2017

Seven New Mesolithic Scandinavian Hunter-Gatherer Genomes

A new bioRXviv preprint analyzes ancient autosomal DNA from seven Mesolithic Scandinavian hunter-gatherers. 

Eurogenes does an excellent job of hitting the high points of the paper which model Mesolithic Scandinavian hunter-gatherers (SHG) as an admixture of Western hunter-gatherers and Eastern hunter-gatherers with some additional variation no longer present in Europe and strong selective effects associated with Northern latitudes. In three of his particularly notable bullet points (not all of which are highlighted in the abstract to the paper), he notes that:
- EHG probably dispersed across Scandinavia in a counter-clockwise direction via an ice-free route along the Atlantic coast in what is now Norway, because SHG samples from northern and western Scandinavia show more EHG ancestry than those from eastern and southern Scandinavia
- at least 17% of the SNPs that are common in SHG are not found in present-day Europeans, suggesting that a large part of European variation has been lost since the Mesolithic 
- although it's unlikely that SHG made a significant contribution to the present-day Northern European gene pool, some gene-variants common in SHG that appear to be associated with metabolic, cardiovascular, developmental and psychological traits are carried at high frequencies by present-day Northern Europeans, especially compared to present-day Southern Europeans, probably due to strong selective pressures specific to northern latitudes in Europe
The comments at that post also make some notable observations. For example:

AWood notes that while the EHG mix is unexpected that: "The WHG moved north-east from modern Germany/Poland to the Baltic/Gotland/Sweden as we've seen from other results."

MaxT notes that: "3 out 6 SHG carried alleles for EDAR gene - gene associated with "shovel-shaped teeth and hair thickness phenotype" in Asians. 

"For rs3827760, within the EDAR gene, the derived G allele is associated with shovel-shaped teeth and hair thickness phenotype in East Asians. In the novel SHGs in this study, only the ancestral A allele is present (SF12 is homozygote AA). The derived variant was reported in three of the six Motala SHGs which are younger than most other SHGs in this study. It is clear that the variant was present among SHGs, and it is possible that it has a continuous (but varying) distribution from Scandinavia to East Asia during the Mesolithic, and that the very low sample size of EHGs has failed to pick up the variant. It is also possible that the derived rs3827760 variant was brought to Scandinavia by migration in the Late Mesolithic, perhaps related to the specific Motala group."

Only population who could have brought this is EHG-like population coming from Russia, more sampling for EHG will solve this over time."

A tweeted quotes quantifies the atypical EHG ancestry distribution, 55% in the Northwest v. 35% in Eastern and South-Central Scandinavia.

There are indications in the data based upon an effective population size measure that these groups had a common source population ca. 50,000 to 70,000 years ago, in the early Upper Paleolithic era that coincides with a possible Out of Africa (or perhaps Out of Arabia) event (as the existing paradigm would predict).

The paper and its abstract are as follows (the paragraph breaking and emphasis is mine):
Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. 
We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. This result suggests that Scandinavia was initially colonized following two different routes: one from the south, the other from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These adaptations include high frequencies of low pigmentation variants and a gene-region associated with physical performance, which shows strong continuity into modern-day northern Europeans. 
Finally, we were able to compute a 3D facial reconstruction of a Mesolithic woman from her high-coverage genome, giving a glimpse into an individual's physical appearance in the Mesolithic.
Günther et al., Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation, bioRxiv (July 17, 2017), doi:

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