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

Citation

Vershinina, Alisa et al. (2021), Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge, Dryad, Dataset, https://doi.org/10.7291/D18W9G

Abstract

The Bering Land Bridge (BLB) last connected Eurasia and North America during the 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 bi-directional 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 likely occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographic 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.

Methods

  • BEAST XML files for phylogenetic and phylogeographic analysis.
  • Filter regions for G-PhoCS coalescent simulation analysis (.bed on EquCab2.0 reference).

Usage Notes

Beast files are ready to run.

For the G-PhoCS analysis, one would need scripts from this repo: https://github.com/avershinina/BLB_horses

Funding

National Science Foundation, Award: ARC-1417036

Gordon and Betty Moore Foundation, Award: 3804

Russian Foundation for Basic Research, Award: 18–04–00327

Marie-Curie Intra-European fellowship, Award: IEF-302617

Federal theme of Zoological Institute of the Russian Academy of Sciences, Award: АААА-А19-119032590102-7

Russian Foundation for Basic Research, Award: 19-05-00477

Svenska Forskningsrådet Formas, Award: 2018-01640

European Union’s Horizon 2020, Award: 681605