A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses

Abstract

The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski's horses. Unlike single-nucleotide polymorphism (SNP) typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered—two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117–0.186 Ma, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski's horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski's horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski's and domestic horse lineages diverged at least 0.117 Ma but since then have retained ancestral genetic polymorphism and/or experienced gene flow.

Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication

“…This finding is in agreement with the observation that virtually all Przewalski's horse control region haplotypes belong to haplogroup F, with one notable exception (AF055879) (23). Recently, four complete Przewalski mtDNAs were published (24). Although three mtDNAs belonged to haplogroup F, the fourth mtDNA shared the control region motif with the above-mentioned sample AF055879, radiating before the J'K node in our phylogeny (SI Appendix, Fig.…”

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

“…We first compared the 16 complete mitochondrial sequences characterized here (SI Appendix, section S5.1) with complete mitochondrial sequences from 27 ancient and 78 present-day horses (14,18,(23)(24)(25)(26)(27)(28). Maximum likelihood (ML) and Bayesian phylogenetic inference showed that the Yakutian mitochondrial haplotypes of specimens Yak1-Yak7, Yak9, and CGG101397 are closely related to the mitochondrial haplotypes of domesticated breeds (SI Appendix, Figs.…”

Mitochondrial DNA lineages of Italian Giara and Sarcidano horses

“…In addition, all the 150 complete mtDNA genome sequences available from literature [NC_001640 (Xu and Arnason, 1994); EF597512-14 (Xu et al, 2007); AP012267-70 (Goto et al, 2011); EU939445 (Jiang et al, 2011); HQ439441-500 (Lippold et al, 2011);and JN398377-457 (Achilli et al, 2012)] were used to obtain more reliable and informative HVS-I patterns of sites defining haplogroups.…”