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      Conservation Genetics of the Cheetah: Lessons Learned and New Opportunities

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          Abstract

          The dwindling wildlife species of our planet have become a cause célèbre for conservation groups, governments, and concerned citizens throughout the world. The application of powerful new genetic technologies to surviving populations of threatened mammals has revolutionized our ability to recognize hidden perils that afflict them. We have learned new lessons of survival, adaptation, and evolution from viewing the natural history of genomes in hundreds of detailed studies. A single case history of one species, the African cheetah, Acinonyx jubatus, is here reviewed to reveal a long-term story of conservation challenges and action informed by genetic discoveries and insights. A synthesis of 3 decades of data, interpretation, and controversy, capped by whole genome sequence analysis of cheetahs, provides a compelling tale of conservation relevance and action to protect this species and other threatened wildlife.

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          Most cited references38

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          Directions in Conservation Biology

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            Conservation genetics.

            R Frankham (1995)
            Inbreeding depression, accumulation and loss of deleterious mutations, loss of genetic variation in small populations, genetic adaptation to captivity and its effect on reintroduction success, and outbreeding depression are reviewed. The impact of genetic factors in endangerment and extinction has been underestimated in some recent publications. Inbreeding depression in wildlife and in the field has been clearly established, while its impact has been greatly underestimated. The size of populations where genetic factors become important is higher than previously recognized, as Ne/N ratios average 0.11. Purging effects have been overestimated as a mechanism for eliminating deleterious alleles in small populations. The impact of loss of genetic variation in increasing the susceptibility of populations to environmental stochasticity and catastrophes has generally been ignored. Consequently, extinctions are often attributed to "nongenetic" factors when these may have interacted with genetic factors to cause extinction.
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              A genomic history of Aboriginal Australia.

              The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.
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                Author and article information

                Journal
                J Hered
                J. Hered
                jhered
                Journal of Heredity
                Oxford University Press (US )
                0022-1503
                1465-7333
                September 2017
                20 May 2017
                01 September 2018
                : 108
                : 6
                : 671-677
                Affiliations
                [1 ]From the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University , St. Petersburg, Russia (O’Brien and Dobrynin); Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University , Ft Lauderdale, FL (O’Brien); Smithsonian Conservation Biology Institute, National Zoological Park , Front Royal, VA (Johnson); Laboratory of Neurogenetics, NIAAA , Rockville, MD (Driscoll); and Cheetah Conservation Fund , Otjiwarongo, Namibia (Marker).
                Author notes

                Address correspondence to Stephen J. O’Brien, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004 St. Petersburg, Russia, or e-mail: lgdchief@ 123456gmail.com .

                Corresponding Editor: C. Scott Baker

                Article
                esx047
                10.1093/jhered/esx047
                5892392
                28821181
                03e56f24-3b20-4a3b-84e5-2216e905a6ee
                © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

                This article is made available via the PMC Open Access Subset for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing. Upon expiration of these permissions, PMC is granted a perpetual license to make this article available via PMC and Europe PMC, consistent with existing copyright protections.

                History
                : 26 February 2017
                : 02 May 2017
                : 01 April 2017
                Page count
                Pages: 7
                Funding
                Funded by: National Institutes of Health 10.13039/100000002
                Funded by: National Cancer Institute 10.13039/100000054
                Funded by: Russian Science Foundation 10.13039/501100006769
                Award ID: 17-14-01138
                Categories
                Perspective

                Genetics
                acinonyx jubatus,cheetah genome, indian cheetah,population bottleneck
                Genetics
                acinonyx jubatus, cheetah genome, indian cheetah, population bottleneck

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