Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse

Abstract

SUMMARY Przewalski’s horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [1]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [2–4]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878–1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ~45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ~110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations.

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

“…Nevertheless, using a large modern DNA dataset in combination with a number of ancient sequences, we were able to support a scenario with an initial domestication followed by consecutive introgression from wild populations echoing findings from other species (57), such as horses (25,44,45), cattle (16), and pigs (15). Interestingly, in dromedaries, this restocking occurred from an unsourced wild "ghost" population, a pattern thus far observed in only few other domestic species (e.g., pigs and dogs).…”

“…Because wild and early-domesticated dromedaries coexisted in the Arabian Peninsula for only a short time [probably less than 2,000 y (8)], the period of potential gene flow was rather short compared those for cattle (16), pigs (15), or horses (25,44,45). This short period for potential gene flow, together with the possible existence of genomic islands of domestication, as recently proposed in pigs (15), likely explains the maintenance of the domestic phenotype in dromedaries.…”

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

“…All other brown bears show F values lower than 0.29. Two points should be noted here: First, inbreeding coverage is known to be correlated with the inbreeding coefficient estimated with population genetics methods or from pedigrees (26), meaning that the F values estimated in the Apennine bears correspond to the value expected in a large population after six generations of full sib mating. Second, F values are not solely a consequence of the average variation levels.…”

Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

“…The reference panel consists of nine equine genomes, using alignments published in , (Jónsson et al, 2014) and (Der Sarkissian et al, 2015). These include the complete genomes of two caballine individuals (a Przewalski's horse, Equus przewalski, and a Franches-Montagnes horse, Equus caballus) as well as seven non-caballine individuals: a domestic donkey (Equus africanus asinus), an African wild ass (Equus africanus somaliensis), a Grant's zebra (Equus quagga boehmi), a Grevyi's zebra (Equus grevyi), a Hartmann's mountain zebra (Equus zebra hartmannae), an onager (Equus hemionus onager), and a Tibetan kiang (Equus kiang).…”

“…Samples were genotyped using PALEOMIX (Schubert et al, 2014) as described in (Jónsson et al (2014)), and bi-allelic sites called in all samples were collected, for a total of ∼36.5 million autosomal sites, representing ∼15,000 sites per Mb. We further constructed a multiple mtDNA alignment of all species included in the reference panel, using a selection of complete mitochondrial sequences made available for the same species by , and (Der Sarkissian et al, 2015) (GenBank Accession Numbers: JX312719, JX312722, JX312730, JX312732, KM881680, KM881681, KT368746.1, KX669267, and KX669268). The repetitive region covering positions 16,129 to 16,371 of the horse mitochondrial genome (NC_001640.1) was masked.…”