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

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 today’s 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 host’s 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- cies’ 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.