title: Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).
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.
authors.affiliation: Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: Vanessa M
authors.initials: VM
authors.lastname: Hayes
authors.forename: Aakrosh
authors.initials: A
authors.lastname: Ratan
authors.forename: Desiree C
authors.initials: DC
authors.lastname: Petersen
authors.forename: Nicola E
authors.initials: NE
authors.lastname: Wittekindt
authors.forename: Jason
authors.initials: J
authors.lastname: Miller
authors.forename: Brian
authors.initials: B
authors.lastname: Walenz
authors.forename: James
authors.initials: J
authors.lastname: Knight
authors.forename: Ji
authors.initials: J
authors.lastname: Qi
authors.forename: Fangqing
authors.initials: F
authors.lastname: Zhao
authors.forename: Qingyu
authors.initials: Q
authors.lastname: Wang
authors.forename: Oscar C
authors.initials: OC
authors.lastname: Bedoya-Reina
authors.forename: Neerja
authors.initials: N
authors.lastname: Katiyar
authors.forename: Lynn P
authors.initials: LP
authors.lastname: Tomsho
authors.forename: Lindsay McClellan
authors.initials: LM
authors.lastname: Kasson
authors.forename: Rae-Anne
authors.initials: RA
authors.lastname: Hardie
authors.forename: Paula
authors.initials: P
authors.lastname: Woodbridge
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Tindall
authors.forename: Mads Frost
authors.initials: MF
authors.lastname: Bertelsen
authors.forename: Dale
authors.initials: D
authors.lastname: Dixon
authors.forename: Stephen
authors.initials: S
authors.lastname: Pyecroft
authors.forename: Kristofer M
authors.initials: KM
authors.lastname: Helgen
authors.forename: Arthur M
authors.initials: AM
authors.lastname: Lesk
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Pringle
authors.forename: Nick
authors.initials: N
authors.lastname: Patterson
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.forename: Alexandre
authors.initials: A
authors.lastname: Kreiss
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Woods
authors.forename: Menna E
authors.initials: ME
authors.lastname: Jones
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
mesh_terms: D000818:Animals; D001947:Breeding; D004272:DNA, Mitochondrial / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics; D053476:Extinction, Biological; D005153:Facial Neoplasms / Q000235:genetics / Q000662:veterinary; D014644:Genetic Variation; D005828:Genetics, Population; D054629:Genome, Mitochondrial; D006801:Humans; D008394:Marsupialia / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins / Q000737:chemistry / Q000235:genetics; D009369:Neoplasms / Q000235:genetics / Q000662:veterinary; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013648:Tasmania; D013997:Time Factors
chemical_list: D004272:DNA, Mitochondrial; D004273:DNA, Neoplasm; D009363:Neoplasm Proteins