Global Phylogeographic and Admixture Patterns in Grey Wolves and Genetic Legacy of An Ancient Siberian Lineage

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.

Himalayan wolf distribution and admixture based on multiple genetic markers

“…In general agreement with other wolf phylogeographic studies (Ersmark et al, 2016;Fan et al, 2016;Meng, Zhang & Meng, Zhang, & Meng, 2009;Pilot et al, 2010;Rueness et al, 2011;Zhang et al, 2014) Gopalakrishnan et al, 2018;Loog et al, 2018;Pilot et al, 2019). In studies where high-altitude samples have been included, reconstructions based on mitochondrial sequences (Aggarwal et al, 2007;Koepfli et al, 2015;Sharma et al, 2004;Werhahn et al, 2018;Werhahn, Senn, et al, 2017) have generated different patterns of relationship from those based on nuclear genomes (Fan et al, 2016…”

“…Hybridization is ubiquitous in nature (Stanton et al, 2019). It occurs between wild animals and their domestic relatives and among related wild species (Adams, Kelly, & Waits, 2003;Pacheco et al, 2017;Randi, 2008), with the latter having an important role in the evolution of the canid family (Gopalakrishnan et al, 2018;Pilot et al, 2019 Historically, wolves were present in most of continental China (Wang et al, 2016) The width of an admixture zone is assumed to be a function of the distance travelled between the places of birth and first reproduction, and the degree of selection against admixed individuals (Barton & Hewitt, 1985, 1989Wayne, Geffen, & Vilà, 2004). Baker and Bradley (2006) proposed that two taxa represent different species when hybridization is restricted to a limited geographic area, while outside this area the taxa represent well-supported monophyletic clades in terms of mitochondrial and nuclear genetic variation.…”

Morphological evidence for early dog domestication in the European Pleistocene: New evidence from a randomization approach to group differences

“…All fossil and prehistoric sites from which large canids were examined in this contribution are situated in the large geographical range of the RNW group. We did not include recent North American wolves in this reference group since the North American wolf lineage separated before the lineages of modern Eurasian wolves and domestic dogs diverged (Fan et al, 2016; Pilot et al, 2019) and because none of the studied sites is located in North America.…”

Population genetic structure and dispersal patterns of grey wolfs (Canis lupus) and golden jackals (Canis aureus) in Georgia, the Caucasus

“…*Software used: ARLEQUIN v3.5 (N, OH, EH, Theta (H), GW); Fstat (AR, Fis, Hs, Ht); BayesAss 3.0 (CI); averages AE standard error shown for individual variables. **Regional differences between the conspecific populations are insignificant for all parameters, P > 0.05. haplotypes with sheep-guarding dogs (Kopaliani et al, 2014), which reflects a broad gene introgression between wolves and dogs all throughout the grey wolf range (Pilot et al, 2019). However, even wolf haplotypes that are not shared with the dogs are much more diverse than jackal haplotypes.…”