Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia

Abstract

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown.Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere.This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog. K E Y W O R D S

Genome-wide local ancestries discriminate homoploid hybrid speciation from secondary introgression in the red wolf (Canidae:Canis rufus)

“…large Pleistocene individuals and more contemporary counterparts that were comparatively 273 diminutive (Meachen et al 2014). Response of canids to dietary shifts, demographic instability at 274 the glacial-interglacial interface, and wide-spread shuffling of distributions (Pardi and Smith 275 2016;Loog et al 2019) may have promoted interspecific contact. We suggest this scenario has 276 plausibility, given the emerging adaptive role for hybridization now commonly evoked in diverse 277 taxa (Lewontin and Birch 2006;Meier et al 2017;Jones et al 2018), to include canids (Kays et 278 al.…”

Sometimes Hidden but Always There: Assumptions Behind Demographic Inference from Ancient DNA Data

“…samples from before, during and after the demographic event of interest) and explicit statistical modelling that accounts for the randomness of individual loci and allows to formally consider the likelihood of different alternative demographic scenarios (e.g. [15,16]). Although ancient DNA alone already provides additional resolution that often enable researchers to exclude less likely scenarios (e.g.…”

“…A common question that can be addressed with ancient DNA is whether a present population is directly ancestral to a past population or if the latter has experienced admixture from external One way to overcome this problem is to use inference methods that allow explicit modelling of gene flow (e.g. in [49,15,58,16]). External lines of evidence, such as archaeological, linguistic and geographic information could be used to inform on the expected levels of gene flow to build a more realistic null model for testing continuity.…”

“…Eriksson et al [61] used a global spatial model to link late Pleistocene human demography to climate, and this model was later used to test the hypothesis of whether Eskimo-Inuit populations in the Arctic derive from the same population as the original founders of Native American populations [68]. Loog et al [16] used a spatiotemporally explicit framework to reconstruct wolf demography in the last 50,000 years using mitochondrial genomes. In the past, researchers have relied on inhouse custom simulation code, difficult to adapt to different demographic models and/or data but powerful, easy to use simulation tools such as msprime [69] (for coalescent demographic modelling) & SLiM [70] (forward in time, and can accommodate very complicated demographic scenarios, including genetic selection, and ecological interactions) have been recently created and are now publicly available for researchers to use.…”

Illuminating the mysteries of wolf history

“…In this issue, Loog et al. (2020) undertake a more comprehensive mtDNA genome sequencing of 45 ancient wolves spanning the last 50,000 years and 95 modern wolves, worldwide. By testing 16 different spatially and temporally explicit demographic scenarios, the authors found support for an expansion from the geographic region spanning Beringia, Northeast of Siberia.…”