Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations

Johanna Seth (), Nicolas Dussex (), David Díez-del-Molino, Tom Valk, Verena E. Kutschera, Marcin Kierczak, Cynthia C. Steiner, Shanlin Liu, M. Thomas P. Gilbert, Mikkel-Holger S. Sinding, Stefan Prost, Katerina Guschanski, Senthilvel K. S. S. Nathan, Selina Brace, Yvonne L. Chan, Christopher W. Wheat, Pontus Skoglund, Oliver A. Ryder, Benoit Goossens, Anders Götherström and Love Dalén ()
Additional contact information
Johanna Seth: Centre for Palaeogenetics
Nicolas Dussex: Centre for Palaeogenetics
David Díez-del-Molino: Centre for Palaeogenetics
Tom Valk: Centre for Palaeogenetics
Verena E. Kutschera: Stockholm University
Marcin Kierczak: Uppsala University
Cynthia C. Steiner: Beckman Center for Conservation Research
Shanlin Liu: University of Copenhagen
M. Thomas P. Gilbert: University of Copenhagen
Mikkel-Holger S. Sinding: University of Copenhagen
Stefan Prost: LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg
Katerina Guschanski: Uppsala University
Senthilvel K. S. S. Nathan: Sabah Wildlife Department
Selina Brace: Natural History Museum
Yvonne L. Chan: Centre for Palaeogenetics
Christopher W. Wheat: Stockholm University
Pontus Skoglund: Francis Crick Institute
Oliver A. Ryder: Beckman Center for Conservation Research
Benoit Goossens: Sabah Wildlife Department
Anders Götherström: Centre for Palaeogenetics
Love Dalén: Centre for Palaeogenetics

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: Abstract Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.

Date: 2021
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DOI: 10.1038/s41467-021-22386-8

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