دورية أكاديمية
أعرض في EDS

Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.

التفاصيل البيبلوغرافية
العنوان: Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.
المؤلفون: Saremi NF; Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA., Supple MA; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA., Byrne A; Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA., Cahill JA; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.; Laboratory of Neurogenetics of Language, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA., Coutinho LL; Laboratório de Biotecnologia Animal, Departamento de Zootecnia, ESALQ, Universidade de São Paulo, Caixa Postal 09, Piracicaba, SP, 13418-900, Brazil., Dalén L; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, Stockholm, 10405, Sweden., Figueiró HV; Escola de Ciências, Pontifical Catholic University of Rio Grande do Sul, Avenida Ipiranga, 6681-Partenon, Porto Alegre-RS, 90619-900, Brazil., Johnson WE; Smithsonian Conservation Biology Institute, Smithsonian Institution, 600 Maryland Avenue SW, Washington, DC, 20002, USA.; Walter Reed Biosystematics Unit, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD, 20746, USA., Milne HJ; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA., O'Brien SJ; Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41 Sredniy Prospekt, Saint Petersburg, 199004, Russia., O'Connell B; Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR, 97239-3098, USA., Onorato DP; Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, 298 Sabal Palm Road, Naples, FL, 34114, USA., Riley SPD; Santa Monica Mountains National Recreation Area, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA.; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095-1601, USA., Sikich JA; Santa Monica Mountains National Recreation Area, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA., Stahler DR; Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY, 82190, USA., Villela PMS; EcoMol Consultoria e Projetos, Avenida Limeira, 1131- Areiao, Piracicaba-SP, Brazil., Vollmers C; Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA., Wayne RK; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095-1601, USA., Eizirik E; Escola de Ciências, Pontifical Catholic University of Rio Grande do Sul, Avenida Ipiranga, 6681-Partenon, Porto Alegre-RS, 90619-900, Brazil., Corbett-Detig RB; Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA., Green RE; Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA., Wilmers CC; Environmental Studies Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA., Shapiro B; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA. beth.shapiro@gmail.com.; Howard Hughes Medical Institute, 400 Jones Bridge Road, Chevy Chase, MD, 20815, USA. beth.shapiro@gmail.com.
المصدر: Nature communications [Nat Commun] 2019 Oct 18; Vol. 10 (1), pp. 4769. Date of Electronic Publication: 2019 Oct 18.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Genome-Wide Association Study/*methods , Genomics/*methods , Inbreeding/*methods , Puma/*genetics, Animals ; Gene Flow ; Genetic Variation ; Genetics, Population ; Geography ; North America ; Phylogeny ; Puma/classification ; South America
مستخلص: Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.
التعليقات: Erratum in: Nat Commun. 2019 Nov 21;10(1):5276. (PMID: 31754100)
References: Van Valkenburgh, B., Grady, F. & Kurtén, B. The Plio-Pleistocene cheetah-like cat Miracinonyx inexpectatus of North America. J. Vert. Paleontol. 10, 434–454 (1990). (PMID: 10.1080/02724634.1990.10011827)
Martin, L. D., Gilbert, B. M. & Adams, D. B. A cheetah-like cat in the north american pleistocene. Science 195, 981–982 (1977). (PMID: 1773567310.1126/science.195.4282.981)
Johnson, W. E. et al. The late Miocene radiation of modern Felidae: a genetic assessment. Science 311, 73–77 (2006). (PMID: 1640014610.1126/science.1122277)
Barnett, R. et al. Evolution of the extinct Sabretooths and the American cheetah-like cat. Curr. Biol. 15, R589–R590 (2005). (PMID: 1608547710.1016/j.cub.2005.07.052)
Bell, C. J. et al. 7. The Blancan, Irvingtonian, and Rancholabrean Mammal Ages. In Late Cretaceous and Cenozoic Mammals of North America (Columbia University Press, 2004).
Froese, D. et al. Fossil and genomic evidence constrains the timing of bison arrival in North America. Proc. Natl Acad. Sci. USA 114, 3457–3462 (2017). (PMID: 2828922210.1073/pnas.16207541145380047)
Culver, M., Johnson, W. E., Pecon-Slattery, J. & O’Brien, S. J. Genomic ancestry of the American puma (Puma concolor). J. Hered. 91, 186–197 (2000). (PMID: 1083304310.1093/jhered/91.3.186)
Matte, E. M. et al. Molecular evidence for a recent demographic expansion in the puma (Puma concolor) (Mammalia, Felidae). Genet. Mol. Biol. 36, 586–597 (2013). (PMID: 24385863387319110.1590/S1415-47572013000400018)
Chimento, N. R. & Dondas, A. First record of Puma concolor (Mammalia, Felidae) in the early-middle pleistocene of South America. J. Mamm. Evol. 25, 381–389 (2017).
Sunquist, M. & Sunquist, F. Wild cats of the world (University of Chicago Press, 2017).
Nowell, K., Jackson, P. & IUCN/SSC Cat Specialist Group. Wild Cats: Status Survey and Conservation Action Plan (World Conservation Union, 1996).
Feldhamer, G. A., Thompson, B. C. & Chapman, J. A. Wild Mammals of North America: Biology, Management, and Conservation. (JHU Press, 2003).
Hornocker, M. & Negri, S. Cougar: Ecology and Conservation. (University of Chicago Press, 2009).
Vickers, T. W. et al. Survival and mortality of Pumas (Puma concolor) in a fragmented, urbanizing landscape. PLoS One 10, e0131490 (2015). (PMID: 26177290450364310.1371/journal.pone.0131490)
Riley, S. P. D. et al. Individual behaviors dominate the dynamics of an urban mountain lion population isolated by roads. Curr. Biol. 24, 1989–1994 (2014). (PMID: 2513167610.1016/j.cub.2014.07.029)
Johnson, W. E. et al. Genetic restoration of the Florida panther. Science 329, 1641–1645 (2010). (PMID: 2092984710.1126/science.11928916993177)
Barone, M. A. et al. Reproductive characteristics of male Florida Panthers: comparative studies from Florida, Texas, Colorado, Latin America, and North American Zoos. J. Mammal. 75, 150–162 (1994). (PMID: 10.2307/1382247)
Onorato, D. et al. The Biology and Conservation of Wild Felids. 453–470 (Oxford University Press, 2010).
van de Kerk, M., Onorato, D. P., Hostetler, J. A., Bolker, B. M. & Oli, M. K. Dynamics, persistence, and genetic management of the endangered florida panther population. Wildl. Monogr. 203, 3–35 (2019). (PMID: 10.1002/wmon.1041)
O’Brien, S. J. Tears of the Cheetah: the genetic secrets of our animal ancestors. (St. Martin’s Griffin, 2015).
O’Brien, S. J. et al. Genetic Introgression within the Florida Panther (Felis concolor coryi). Nat. Geogr. Res. 6, 484–494 (1990).
Frankham, R. Conservation genetics. Annu. Rev. Genet. 29, 305–327 (1995). (PMID: 882547710.1146/annurev.ge.29.120195.001513)
Hudson, R. R. Gene genealogies and the coalescent process. in Oxford Surveys in Evolutionary Biology (eds. Futuyma, D. & Antonovics, J.) Vol. 7, 1–44 (Oxford University Press, 1991).
Schraiber, J. G. & Akey, J. M. Methods and models for unravelling human evolutionary history. Nat. Rev. Genet. 16, 727–740 (2015). (PMID: 2655332910.1038/nrg4005)
Palamara, P. F., Lencz, T., Darvasi, A. & Pe’er, I. Length distributions of identity by descent reveal fine-scale demographic history. Am. J. Hum. Genet. 91, 809–822 (2012). (PMID: 23103233348713210.1016/j.ajhg.2012.08.030)
Kardos, M. et al. Genomic consequences of intensive inbreeding in an isolated wolf population. Nat. Ecol. Evol. 2, 124–131 (2018). (PMID: 2915855410.1038/s41559-017-0375-4)
Jain, M., Olsen, H. E., Paten, B. & Akeson, M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 17, 239 (2016). (PMID: 27887629512426010.1186/s13059-016-1103-0)
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). (PMID: 2605971710.1093/bioinformatics/btv351)
Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011). (PMID: 21753753315464510.1038/nature10231)
Mazet, O., Rodríguez, W., Grusea, S., Boitard, S. & Chikhi, L. On the importance of being structured: instantaneous coalescence rates and human evolution–lessons for ancestral population size inference? Heredity 116, 362–371 (2016). (PMID: 2664765310.1038/hdy.2015.104)
Cahill, J. A., Soares, A. E. R., Green, R. E. & Shapiro, B. Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data. Philos. Trans. R. Soc. Lond. B Biol. Sci. 371, 20150138 (2016). (PMID: 27325835492033910.1098/rstb.2015.0138)
Schwartz, M. K. & McKelvey, K. S. Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. Conserv. Genet. 10, 441–452 (2009). (PMID: 10.1007/s10592-008-9622-1)
Wright, S. Isolation by distance. Genetics 28, 114–138 (1943). (PMID: 17247074120919610.1093/genetics/28.2.114)
Ernest, H. B., Vickers, T. W., Morrison, S. A., Buchalski, M. R. & Boyce, W. M. Fractured genetic connectivity threatens a southern california puma (Puma concolor) population. PLoS One 9, e107985 (2014). (PMID: 25295530418995410.1371/journal.pone.0107985)
Riley, S. P. D. et al. A southern California freeway is a physical and social barrier to gene flow in carnivores. Mol. Ecol. 15, 1733–1741 (2006). (PMID: 1668989310.1111/j.1365-294X.2006.02907.x)
McRae, B. H., Beier, P., Dewald, L. E., Huynh, L. Y. & Keim, P. Habitat barriers limit gene flow and illuminate historical events in a wide-ranging carnivore, the American puma. Mol. Ecol. 14, 1965–1977 (2005). (PMID: 1591031910.1111/j.1365-294x.2005.02571.x)
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M. & Wilson, J. F. Runs of homozygosity: windows into population history and trait architecture. Nat. Rev. Genet. 19, 220–234 (2018). (PMID: 2933564410.1038/nrg.2017.109)
Pemberton, T. J. et al. Genomic patterns of homozygosity in worldwide human populations. Am. J. Hum. Genet. 91, 275–292 (2012). (PMID: 22883143341554310.1016/j.ajhg.2012.06.014)
Dumont, B. L. & Payseur, B. A. Evolution of the genomic rate of recombination in mammals. Evolution 62, 276–294 (2008). (PMID: 1806756710.1111/j.1558-5646.2007.00278.x)
Thompson, E. A. Identity by descent: variation in meiosis, across genomes, and in populations. Genetics 194, 301–326 (2013). (PMID: 23733848366484310.1534/genetics.112.148825)
Schaller, G. B. & Crawshaw, P. G. Movement patterns of Jaguar. Biotropica 12, 161 (1980). (PMID: 10.2307/2387967)
Elbroch, L. M. & Kusler, A. Are pumas subordinate carnivores, and does it matter? PeerJ 6, e4293 (2018). (PMID: 29379688578688010.7717/peerj.4293)
Dyke, A. S. et al. The Laurentide and Innuitian ice sheets during the last glacial maximum. Quat. Sci. Rev. 21, 9–31 (2002). (PMID: 10.1016/S0277-3791(01)00095-6)
Wang, Y., Allen, M. L. & Wilmers, C. C. Mesopredator spatial and temporal responses to large predators and human development in the Santa Cruz Mountains of California. Biol. Conserv. 190, 23–33 (2015). (PMID: 10.1016/j.biocon.2015.05.007)
Sweanor, L. L., Logan, K. A. & Hornocker, M. G. Cougar dispersal patterns, metapopulation dynamics, and conservation. Conserv. Biol. 14, 798–808 (2000). (PMID: 10.1046/j.1523-1739.2000.99079.x)
Gustafson, K. D., Winston Vickers, T., Boyce, W. M. & Ernest, H. B. A single migrant enhances the genetic diversity of an inbred puma population. Royal Soc. Open Sci. 4, 170115 (2017). (PMID: 10.1098/rsos.170115)
Beier, P. Dispersal of Juvenile Cougars in fragmented habitat. J. Wildl. Manag. 59, 228 (1995). (PMID: 10.2307/3808935)
Benson, J. F., Sikich, J. A. & Riley, S. P. D. Individual and population level resource selection patterns of Mountain Lions Preying on Mule Deer along an Urban-Wildland Gradient. PLoS One 11, e0158006 (2016). (PMID: 27411098494363910.1371/journal.pone.0158006)
Robinson, J. A. et al. Genomic flatlining in the endangered island Fox. Curr. Biol. 26, 1183–1189 (2016). (PMID: 2711229110.1016/j.cub.2016.02.062)
Putnam, N. H. et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26, 342–350 (2016). (PMID: 26848124477201610.1101/gr.193474.115)
Françoise, T.-N. P., Alexander, S. P., Terence, M. P. & Dicuccio M. & Kitts, P. Eukaryotic Genome Annotation Pipeline (National Center for Biotechnology Information (US), 2013).
Dobrynin, P. et al. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol. 16, 277 (2015). (PMID: 26653294467612710.1186/s13059-015-0837-4)
Lopez, J. V., Yuhki, N., Masuda, R., Modi, W. & O’Brien, S. J. Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J. Mol. Evol. 39, 174–190 (1994). (PMID: 7932781)
Green, R. E. et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134, 416–426 (2008). (PMID: 18692465260284410.1016/j.cell.2008.06.021)
Bernt, M. et al. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313–319 (2013). (PMID: 10.1016/j.ympev.2012.08.02322982435)
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014). (PMID: 24451623399814410.1093/bioinformatics/btu033)
Lopez, J. V., Culver, M., Stephens, J. C., Johnson, W. E. & O’Brien, S. J. Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. Mol. Biol. Evol. 14, 277–286 (1997). (PMID: 906679510.1093/oxfordjournals.molbev.a025763)
Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, (2015).
U.S. Geological Survey. Gap Analysis Project, 2017, Cougar (Puma concolor) mCOUGx_CONUS_2001v1 Habitat Map. https://doi.org/10.5066/F79885C6 (2017).
Nielsen, C., Thompson, D., Kelly, M. & Lopez-Gonzalez, C. A. Puma concolor (errata version published in 2016). https://doi.org/10.2305/IUCN.UK.2015-4.RLTS.T18868A50663436.en (2015).
Cho, Y. S. et al. The tiger genome and comparative analysis with lion and snow leopard genomes. Nat. Commun. 4, 2433 (2013).
Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).
Falush, D., Stephens, M. & Pritchard, J. K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567–1587 (2003).
Jakobsson, M. & Rosenberg, N. A. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806 (2007).
Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620 (2005).
معلومات مُعتمدة: R35 GM128932 United States GM NIGMS NIH HHS; T32 HG008345 United States HG NHGRI NIH HHS
تواريخ الأحداث: Date Created: 20191020 Date Completed: 20200124 Latest Revision: 20220421
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC6800433
DOI: 10.1038/s41467-019-12741-1
PMID: 31628318
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-019-12741-1