Dataset Information

Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.

ABSTRACT: 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.

SUBMITTER: Der Sarkissian C

PROVIDER: S-EPMC5104162 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

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Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.

Der Sarkissian Clio C Ermini Luca L Schubert Mikkel M Yang Melinda A MA Librado Pablo P Fumagalli Matteo M Jónsson Hákon H Bar-Gal Gila Kahila GK Albrechtsen Anders A Vieira Filipe G FG Petersen Bent B Ginolhac Aurélien A Seguin-Orlando Andaine A Magnussen Kim K Fages Antoine A Gamba Cristina C Lorente-Galdos Belen B Polani Sagi S Steiner Cynthia C Neuditschko Markus M Jagannathan Vidhya V Feh Claudia C Greenblatt Charles L CL Ludwig Arne A Abramson Natalia I NI Abramson Natalia I NI Zimmermann Waltraut W Schafberg Renate R Tikhonov Alexei A Sicheritz-Ponten Thomas T Willerslev Eske E Marques-Bonet Tomas T Ryder Oliver A OA McCue Molly M Rieder Stefan S Leeb Tosso T Slatkin Montgomery M Orlando Ludovic L

Current biology : CB 20150924 19

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 ...[more]

PMID: 26412128

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Project description:Captivity maybe the only choice for survival of many endangered vertebrates, and understanding its broad effects is important for animal management and conservation, including breeding endangered species for subsequent release. Extreme environmental changes during captivity may influence survival ability in the wild. Captivity decreases gut bacterial diversity in a wide range of animals. However, most studies directly compare animals living in captivity with those in the wild, and there is a lack of understanding of effects of gradient shift in lifestyle during species reintroduction based on the soft-release strategy, which involves a confinement period in a field enclosure. Here, we used 16S rRNA amplicon sequencing to analyze gut microbiomes of 11 captive and 12 semi-wild Przewalski's horses (PH; Equus ferus przewalskii) under the same captivity environment, using fecal samples. A subset of samples with abundant extracted DNA (including 3 captive and 3 semi-wild individuals) was selected for whole-genome shotgun sequencing. We found that community diversity did not differ between the semi-wild PH and captive PH, but the semi-wild PH had significantly higher bacterial richness than those in captivity. Relative abundances of all dominant phyla were similar across the semi-wild or captive horses, while those of the non-dominant phyla Tenericutes and Proteobacteria were significantly higher in semi-wild PH than in captive PH. Beta diversity results indicated that bacterial communities of captives and semi-wild horses were clearly separated distinct when considering only composition. Functional profiling of the microbiomes revealed that the semi-wild and captive gut microbiomes were largely similar. However, semi-wild horse microbiomes had higher abundance of bacterial genes related to core metabolic processes, such as carbohydrates, amino acids, and nucleic acid metabolism. The study revealed that semi-wild PH could retain specific non-dominant bacteria and harbor a more diverse microbiome than the captive counterpart, and thus have higher metabolic potential to utilize the complex plants efficiently. These results indicate that change in host lifestyle may play a role in microbiome differentiation in the process of reintroduction, suggesting that a short period of time in captivity is acceptable for PH from the perspective of maintaining the richness of intestinal bacterial flora to some extent.

Dataset Information

Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.

Publications

Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.

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