Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge

Abstract

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide‐ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present‐day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0–0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long‐range dispersals across the BLB ~875–625 and ~200–50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.

Grey wolf genomic history reveals a dual ancestry of dogs

“…This mirrors European wolf history, but, while some deep local European ancestry persists, no deep North American ancestry appears to persist to the present. The Bering land bridge probably allowed for an influx of Siberian wolves into Alaska intermittently between 70 and 11 ka 28 , 29 , but we found no evidence of gene flow in the other direction. All present-day North American wolves can be modelled as having 10–20% coyote ancestry and the remaining ancestry from Siberian wolves younger than ~23 ka, with no contribution from earlier North American wolves (Fig.…”

Seeing the whole picture: What molecular ecology is gaining from whole genomes

“…Several studies in this special issue draw inference from WGS data to gain new insights into demographic and evolutionary histories. For example, effective population size changes are inferred through time using variation in coalescent rates in individual genomes, and cross‐coalescence between genomes from canids, caribou, horses, killer whales and sea turtles (see Sarabia et al (2021); Taylor et al, (2021); Vershinina et al, (2021); Foote et al, 2021; Torres Vilaça et al, 2021 respectively). As noted by Vershinina et al, 2021, (and illustrated by Foote et al, 2021, Sarabia et al, 2021, Taylor et al, 2021 and Torres Vilaça et al, 2021), even just a few nuclear genomes can provide estimates of gene flow versus isolation, even within and among species with complex evolutionary histories.…”

Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches

“…The horse is one of the most well studied species genetically, with almost 300 genomes of ancient horses having been sequenced [282] dating back 700,000 years in time [283,284] (Figures 1 and 4). This has contributed significantly to studies on the evolutionary history of the wild horse (Equus ferus) (e.g., [283][284][285][286]) and to archaeological scenarios of domestication and human movements [282].…”