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]
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.
