Population genomics of Mesolithic Scandinavia : Investigating early postglacial migration routes and high-latitude adaptation

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). 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. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, 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 potential 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

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). 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. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, 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 potential 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.Günther T., Malmström H., Svensson E.M., Omrak A., Sánchez-Quinto F, Kılınç G.M., Krzewinska M., Eriksson G., Fraser M., Edlund H., Munters A.R., Coutinho A., Simões L.G., Vicente M., Sjölander A., Sellevold B.J., Jørgensen R., Claes P., Shriver M.D., Valdiosera C., Netea M.G., Apel J., Lidén K., Skar B., Storå J., Götherström A., Jakobsson M., ''Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation'', PLoS Biology, vol. 16, no. 1, pp. e2003703, 22 pp., January 9, 2018.status: publishe

Adaptation to high-latitude environments.

<p>(A) Plot of similarity between Mesolithic allele frequency and FIN allele frequency in contrast to difference to TSI allele frequency using the statistic D_sel. The figure shows all positive Z scores representing the number of standard deviations each SNP deviates from the mean. The green-highlighted SNPs are all located in the <i>TMEM131</i> gene. The plot was made with qqman [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref049" target="_blank">49</a>]. (B) Derived allele frequencies for three pigmentation-associated SNPs (<i>SLC24A5</i>, <i>SLC45A2</i>, which are associated with skin pigmentation, and <i>OCA2/HERC2</i>, which is associated with eye pigmentation). The dashed line connecting EHG and WHG represents potential allele frequencies if SHG were a linear combination of admixture between EHG and WHG. The solid horizontal line represents the derived allele frequency in SHG. The blue symbols representing SHGs were set on the average genome-wide WHG and EHG mixture proportion (on x-axis) across all SHGs, and the thick black line represents the minimum and maximum admixture proportions across all SHGs. Dashed horizontal lines represent modern European populations (CEU). The <i>p</i>-values were estimated from simulations of SHG allele frequencies based on their genome-wide ancestry proportions (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s014" target="_blank">S9 Text</a>). Data shown in this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s015" target="_blank">S1 Data</a>. CEU, Utah residents with Central European ancestry; EHG, eastern hunter-gatherer; FIN, modern-day Finnish individual; SHG, Scandinavian hunter-gatherer; TSI, modern-day Tuscan individual; WHG, western hunter-gatherer.</p

Migration scenarios into postglacial Scandinavia.

<p>Maps showing potential migration routes into Scandinavia. Scenario (a) shows a migration related to the Ahrensburgian tradition from the south (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s006" target="_blank">S1 Text</a>). Scenarios (b), (c), and (d) show different possible routes into Scandinavia for the EHG ancestry. The scenarios are discussed in the text and the scenario most consistent with genetic data and stone tools is a combination of routes (a) and (b). All maps were plotted using the R package rworldmap [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref028" target="_blank">28</a>]. EHG, eastern hunter-gatherer.</p

Information on the seven SHGs investigated in this study, including cal BP (corrected for the marine reservoir effect, given as a range of two standard deviations), average genome coverage, average mt coverage, mt and Y chromosome haplogroups, and contamination estimates based on the mt, the X-chromosome for males and the autosomes.

<p>Information on the seven SHGs investigated in this study, including cal BP (corrected for the marine reservoir effect, given as a range of two standard deviations), average genome coverage, average mt coverage, mt and Y chromosome haplogroups, and contamination estimates based on the mt, the X-chromosome for males and the autosomes.</p

Genetic diversity in prehistoric Europe.

<p>(A) RoH for the six prehistoric humans that have been sequenced to >15× genome coverage, (Kotias is a hunter-gatherer from the Caucasus region [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref035" target="_blank">35</a>], NE1 is an early Neolithic individual from modern-day Hungary [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref027" target="_blank">27</a>], the other individuals are described in the text), compared to all modern-day non African individuals from the 1000 Genomes Project [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref032" target="_blank">32</a>]. (B) LD decay for five prehistoric populations each represented by two individuals (eastern SHGs: SF [SF9 and SF12], western SHGs: Hum [Hum1 and Hum2], CHGs [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref035" target="_blank">35</a>]: [Kotias and Satsurblia], WHGs [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref018" target="_blank">18</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref035" target="_blank">35</a>] [Loschbour and Bichon], and early Neolithic Hungarians [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref027" target="_blank">27</a>]: EN_Hungary [NE1 and NE6]). LD was scaled in each distance bin by using the LD for two modern populations [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref032" target="_blank">32</a>] as 0 (TSI) and as 1 (PEL). LD was calculated from the covariance of derived allele frequencies of two haploid individuals per population (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s012" target="_blank">S7 Text</a>). Error bars show two standard errors estimated during 100 bootstraps across SNP pairs. (C) Effective population size over time as inferred by PSMC’ [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref044" target="_blank">44</a>] for four prehistoric humans with high genome coverage. The dashed lines show the effective population sizes for selected modern-day populations. All curves for prehistoric individuals were shifted along the x-axis according to their radiocarbon date. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s005" target="_blank">S4 Fig</a>. shows 100 bootstrap replicates per individual. Data shown in this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s015" target="_blank">S1 Data</a>. BP, before present; CHG, Caucasus hunter-gatherer; LD, linkage disequilibrium; PEL, modern-day Peruvian individual; PSMC’, pairwise sequentially Markovian coalescent; RoH, runs of homozygosity; SHG, Scandinavian hunter-gatherer; TSI, modern-day Tuscan individual; WHG, western hunter-gatherer.</p