Dataset Information

Genomic legacy of the African cheetah, Acinonyx jubatus.

ABSTRACT: BACKGROUND:Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS:Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084-12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p<0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah's extremely high (>80 %) pleiomorphic sperm. CONCLUSIONS:The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species' natural history, physiological adaptations and unique reproductive disposition.

SUBMITTER: Dobrynin P

PROVIDER: S-EPMC4676127 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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Genomic legacy of the African cheetah, Acinonyx jubatus.

Dobrynin Pavel P Liu Shiping S Tamazian Gaik G Xiong Zijun Z Yurchenko Andrey A AA Krasheninnikova Ksenia K Kliver Sergey S Schmidt-Küntzel Anne A Koepfli Klaus-Peter KP Johnson Warren W Kuderna Lukas F K LF García-Pérez Raquel R Manuel Marc de Md Godinez Ricardo R Komissarov Aleksey A Makunin Alexey A Brukhin Vladimir V Qiu Weilin W Zhou Long L Li Fang F Yi Jian J Driscoll Carlos C Antunes Agostinho A Oleksyk Taras K TK Eizirik Eduardo E Perelman Polina P Roelke Melody M Wildt David D Diekhans Mark M Marques-Bonet Tomas T Marker Laurie L Bhak Jong J Wang Jun J Zhang Guojie G O'Brien Stephen J SJ

Genome biology 20151210

<h4>Background</h4>Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.<h4>Results</h4>Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga ...[more]

PMID: 26653294

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Project description:Assessing the numbers and distribution of threatened species is a central challenge in conservation, often made difficult because the species of concern are rare and elusive. For some predators, this may be compounded by their being sparsely distributed over large areas. Such is the case with the cheetah Acinonyx jubatus. The IUCN Red List process solicits comments, is democratic, transparent, widely-used, and has recently assessed the species. Here, we present additional methods to that process and provide quantitative approaches that may afford greater detail and a benchmark against which to compare future assessments. The cheetah poses challenges, but also affords unique opportunities. It is photogenic, allowing the compilation of thousands of crowd-sourced data. It is also persecuted for killing livestock, enabling estimation of local population densities from the numbers persecuted. Documented instances of persecution in areas with known human and livestock density mean that these data can provide an estimate of where the species may or may not occur in areas without observational data. Compilations of extensive telemetry data coupled with nearly 20,000 additional observations from 39 sources show that free-ranging cheetahs were present across approximately 789,700 km2 of Namibia, Botswana, South Africa, and Zimbabwe (56%, 22%, 12% and 10% respectively) from 2010 to 2016, with an estimated adult population of 3,577 animals. We identified a further 742,800 km2 of potential cheetah habitat within the study region with low human and livestock densities, where another ?3,250 cheetahs may occur. Unlike many previous estimates, we make the data available and provide explicit information on exactly where cheetahs occur, or are unlikely to occur. We stress the value of gathering data from public sources though these data were mostly from well-visited protected areas. There is a contiguous, transboundary population of cheetah in southern Africa, known to be the largest in the world. We suggest that this population is more threatened than believed due to the concentration of about 55% of free-ranging individuals in two ecoregions. This area overlaps with commercial farmland with high persecution risk; adult cheetahs were removed at the rate of 0.3 individuals per 100 km2 per year. Our population estimate for confirmed cheetah presence areas is 11% lower than the IUCN's current assessment for the same region, lending additional support to the recent call for the up-listing of this species from vulnerable to endangered status.

Dataset Information

Genomic legacy of the African cheetah, Acinonyx jubatus.

Publications

Genomic legacy of the African cheetah, Acinonyx jubatus.

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