Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

Webb Miller, Vanessa M. Hayes, Aakrosh Ratan, Desiree C. Petersen, Nicola E. Wittekindt, Jason Miller, Brian Walenz, James Knight, Ji Qi, Fangqing Zhao, Qingyu Wang, Oscar C. Bedoya-Reina, Neerja Katiyar, Lynn P. Tomsho, Lindsay Mc Clellan Kasson, Rae Anne Hardie, Paula Woodbridge, Elizabeth A. Tindall, Mads Frost Bertelsen, Dale DixonStephen Pyecroft, Kristofer M. Helgen, Arthur M. Lesk, Thomas H. Pringle, Nick Patterson, Yu Zhang, Alexandre Kreiss, Gregory M. Woods, Menna E. Jones, Stephan C. Schuster

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128 Scopus citations

Abstract

The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we report a whole-genome analysis of two animals originating from extreme northwest and southeast Tasmania, the maximal geographic spread, together with the genome from a tumor taken from one of them. A 3.3-Gb de novo assembly of the sequence data from two complementary next-generation sequencing platforms was used to identify 1 million polymorphic genomic positions, roughly one-quarter of the number observed between two genetically distant human genomes. Analysis of 14 complete mitochondrial genomes from current and museum specimens, as well as mitochondrial and nuclear SNP markers in 175 animals, suggests that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations.

Original languageEnglish (US)
Pages (from-to)12348-12353
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume108
Issue number30
DOIs
StatePublished - Jul 26 2011

All Science Journal Classification (ASJC) codes

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    Miller, W., Hayes, V. M., Ratan, A., Petersen, D. C., Wittekindt, N. E., Miller, J., Walenz, B., Knight, J., Qi, J., Zhao, F., Wang, Q., Bedoya-Reina, O. C., Katiyar, N., Tomsho, L. P., Kasson, L. M. C., Hardie, R. A., Woodbridge, P., Tindall, E. A., Bertelsen, M. F., ... Schuster, S. C. (2011). Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences of the United States of America, 108(30), 12348-12353. https://doi.org/10.1073/pnas.1102838108