Abstract
The evolutionary relationships between extinct and extant lineages provide important insight into species’ response to environmental change. The grey wolf is among the few Holarctic large carnivores that survived the Late Pleistocene megafaunal extinctions, responding to that period’s profound environmental changes with loss of distinct lineages and phylogeographic shifts, and undergoing domestication. We reconstructed global genome-wide phylogeographic patterns in modern wolves, including previously underrepresented Siberian wolves, and assessed their evolutionary relationships with a previously genotyped wolf from Taimyr, Siberia, dated at 35 Kya. The inferred phylogeographic structure was affected by admixture with dogs, coyotes and golden jackals, stressing the importance of accounting for this process in phylogeographic studies. The Taimyr lineage was distinct from modern Siberian wolves and constituted a sister lineage of modern Eurasian wolves and domestic dogs, with an ambiguous position relative to North American wolves. We detected gene flow from the Taimyr lineage to Arctic dog breeds, but population clustering methods indicated closer similarity of the Taimyr wolf to modern wolves than dogs, implying complex post-divergence relationships among these lineages. Our study shows that introgression from ecologically diverse con-specific and con-generic populations was common in wolves’ evolutionary history, and could have facilitated their adaptation to environmental change.
Highlights
The Late Pleistocene was a period of numerous extinctions of large mammals, resulting from the combined effect of climate change and human impact[1]
A recent analysis of mitochondrial genomes of ancient and modern wolves inferred that modern wolf populations can be traced back to a single expansion event originating about 25 Kya in Beringia[19]
We found that all Asian wolf populations had similar levels of genome-wide heterozygosity (Ho = 0.27), which were comparable to those in European populations and higher than in North American populations (Supplementary Table 2)
Summary
The Late Pleistocene was a period of numerous extinctions of large mammals, resulting from the combined effect of climate change and human impact[1]. Palaeogenomic studies revealed the presence of genomic fragments originating from extinct species in gene pools of their extant relatives[9,10,11] This may point out to genetic swamping as a contributing factor of these extinctions, some populations carry hybridisation-derived gene variants showing signatures of positive selection[9,12,13]. The nuclear genome of a wolf from the Taimyr Peninsula in Siberia, dated at 34.9 Kya, was phylogenetically distinct from genomes of extant wolves and dogs, implying that this individual represents an extinct divergent lineage[10]. In this study we reconstruct genome-wide phylogeographic patterns in modern grey wolf populations across their Holarctic distribution, based on an extensive sample set that includes previously underrepresented Siberian wolves (Fig. 1).
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