Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
Fig 3
Genetic diversity in prehistoric Europe.
(A) RoH for the six prehistoric humans that have been sequenced to >15× genome coverage, (Kotias is a hunter-gatherer from the Caucasus region [35], NE1 is an early Neolithic individual from modern-day Hungary [27], the other individuals are described in the text), compared to all modern-day non African individuals from the 1000 Genomes Project [32]. (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 [35]: [Kotias and Satsurblia], WHGs [18,35] [Loschbour and Bichon], and early Neolithic Hungarians [27]: EN_Hungary [NE1 and NE6]). LD was scaled in each distance bin by using the LD for two modern populations [32] as 0 (TSI) and as 1 (PEL). LD was calculated from the covariance of derived allele frequencies of two haploid individuals per population (S7 Text). Error bars show two standard errors estimated during 100 bootstraps across SNP pairs. (C) Effective population size over time as inferred by PSMC’ [44] 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. S4 Fig. shows 100 bootstrap replicates per individual. Data shown in this figure can be found in S1 Data. 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.
