Biology Faculty Articles
ORCID
0000-0001-7353-8301
ResearcherID
N-1726-2015
Document Type
Article
Publication Title
Genome Biology
ISSN
1474-760X
Publication Date
12-10-2015
Keywords
Genetic diversity, Conservation biology, Population biology
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.
Volume
16
Issue
277
First Page
1
Last Page
19
Additional Comments
Russian Ministry of Science grant #: 11.G34.31.0068; St. Petersburg State University grant #: 1.50.1623.2013; ICREA grant #: BFU2014-55090-P; EMBO YIP 2013 grant #: BFU2015- 7116-ERC; MICINN grant #: BFU2015-6215-ERC; GenBank accession #: LLWD01000000
NSUWorks Citation
Dobrynin, Pavel; Shiping Liu; Gaik Tamazian; Zijun Xiong; Andrey A. Yurchenko; Ksenia Krasheninnikova; Sergey Kliver; A. Schmidt-Kunzel; Klaus-Peter Koepfli; Warren E. Johnson; Lukas F. K. Kuderna; Raquel Garcia-Perez; Marc de Manuel; Ricardo Godinez; Aleksey Komissarov; Alexey Makunin; Vladimir Brukhin; Weilin Qiu; Long Zhou; Fang Li; Jian Yi; Carlos A. Driscoll; Agostinho Antunes; T. K. Oleksyk; Eduardo Eizirik; Polina Perelman; Melody E. Roelke; David E. Wildt; Mark Diekhans; Tomas Marques-Bonet; Laurie Marker; Jong Bhak; Jun Wang; Guojie Zhang; and Stephen J. O'Brien. 2015. "Genomic Legacy of the African Cheetah, Acinonyx jubatus." Genome Biology 16, (277): 1-19. https://nsuworks.nova.edu/cnso_bio_facarticles/733
Comments
© 2015 Dobrynin et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.