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

Citation

Miller, W and Hayes, VM and Ratan, A and Peterson, DC and Wittekindt, NE and Miller, J and Walenz, B and Knight, J and Qi, J and Zhao, F and Wang, Q and Bedoya-Reina, OC and Katiyar, N and Tomsho, LP and McClellan Kasson, L and Hardie, R-A and Woodbridge, P and Tindall, EA and Frost Bertelsen, M and Dixon, D and Pyecroft, S and Helgen, KM and Lesk, AM and Pringle, TH and Patterson, N and Zhang, Y and Kreiss, A and Woods, GM and Jones, ME and Schuster, SC, Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil), National Academy of Sciences of The United States of America. Proceedings, 108, (30) pp. 12348-12353. ISSN 0027-8424 (2011) [Refereed Article]


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Copyright © 2011 by the National Academy of Sciences

DOI: doi:10.1073/pnas.1102838108

Abstract

The Tasmanian devil (Sarcophilus harrisii ) is threatened with ex- tinction because of a contagious cancer known as Devil Facial Tu- mor 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 complemen- tary 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 nu- clear SNP markers in 175 animals, suggests that the observed low genetic diversity in todayís population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a geneti- cally characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations. Cloning and sequencing of MHC antigens has suggested that low genetic diversity may be contributing to the devastating success of DFTD (6, 7). Because MHC antigens can be in common between each individual host and the tumor, which initially arose from Schwann cells in a long-deceased individual (8), the hostís immune system may be unable to recognize the tumor as "nonself." On the other hand, a recent study demon- strated a functional humoral immune response against horse red blood cells, although cytotoxic T-cell immunity has not been evaluated to date (9). An extensive effort is underway to maintain a captive pop- ulation of Tasmanian devils until DFTD has run its course in the wild population, whereupon animals can be returned to the spe- ciesí original home range. The strategy for selecting animals for the captive population follows traditional conservation principles (10), without the potential benefits of applying contemporary methods for measuring and using actual species diversity. In hopes of helping efforts to conserve this iconic species, we are making available a preliminary assembly of the Tasmanian devil genome, along with data concerning intraspecies diversity, in- cluding a large set of SNPs.

Item Details

Item Type:Refereed Article
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Population, Ecological and Evolutionary Genetics
Objective Division:Environment
Objective Group:Ecosystem Assessment and Management
Objective Field:Ecosystem Assessment and Management at Regional or Larger Scales
Author:Kreiss, A (Dr Alexandre Kreiss)
Author:Woods, GM (Professor Gregory Woods)
Author:Jones, ME (Associate Professor Menna Jones)
ID Code:72077
Year Published:2011
Web of Science® Times Cited:100
Deposited By:Zoology
Deposited On:2011-08-19
Last Modified:2012-04-30
Downloads:2 View Download Statistics

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