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

Nedda F. Saremi, Megan A. Supple, Ashley Byrne, James A. Cahill, Luiz Lehmann Coutinho, Love Dalén, Henrique V. Figueiró, Warren E. Johnson, Heather J. Milne, Stephen J. O’Brien, Brendan O’Connell, David P. Onorato, Seth P. D. Riley, Jeff A. Sikich, Daniel R. Stahler, Priscilla Marqui Schmidt Villela, Christopher Vollmers, Robert K. Wayne, Eduardo Eizirik, Russell B. Corbett-Detig, Richard E. Green, Christopher C. Wilmers and Beth Shapiro ()
Additional contact information
Nedda F. Saremi: University of California, Santa Cruz
Megan A. Supple: University of California, Santa Cruz
Ashley Byrne: University of California, Santa Cruz
James A. Cahill: University of California, Santa Cruz
Luiz Lehmann Coutinho: Universidade de São Paulo
Love Dalén: Swedish Museum of Natural History
Henrique V. Figueiró: Pontifical Catholic University of Rio Grande do Sul
Warren E. Johnson: Smithsonian Conservation Biology Institute, Smithsonian Institution
Heather J. Milne: University of California, Santa Cruz
Stephen J. O’Brien: Saint Petersburg State University
Brendan O’Connell: University of California, Santa Cruz
David P. Onorato: Florida Fish and Wildlife Conservation Commission
Seth P. D. Riley: Santa Monica Mountains National Recreation Area
Jeff A. Sikich: Santa Monica Mountains National Recreation Area
Daniel R. Stahler: Yellowstone Center for Resources
Priscilla Marqui Schmidt Villela: EcoMol Consultoria e Projetos, Avenida Limeira
Christopher Vollmers: University of California, Santa Cruz
Robert K. Wayne: University of California, Los Angeles
Eduardo Eizirik: Pontifical Catholic University of Rio Grande do Sul
Russell B. Corbett-Detig: University of California, Santa Cruz
Richard E. Green: University of California, Santa Cruz
Christopher C. Wilmers: University of California, Santa Cruz
Beth Shapiro: University of California, Santa Cruz

Nature Communications, 2019, vol. 10, issue 1, 1-10

Abstract: Abstract 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.

Date: 2019
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DOI: 10.1038/s41467-019-12741-1

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