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

Research output: Contribution to journalArticle

120 Citations (Scopus)

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

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Marsupialia
Population
Genome
Neoplasms
Tasmania
Museums
Mitochondrial Genome
Human Genome
Breeding
Single Nucleotide Polymorphism
Disease Outbreaks

All Science Journal Classification (ASJC) codes

  • General

Cite this

Miller, Webb ; Hayes, Vanessa M. ; Ratan, Aakrosh ; Petersen, Desiree C. ; Wittekindt, Nicola E. ; Miller, Jason ; Walenz, Brian ; Knight, James ; Qi, Ji ; Zhao, Fangqing ; Wang, Qingyu ; Bedoya-Reina, Oscar C. ; Katiyar, Neerja ; Tomsho, Lynn P. ; Kasson, Lindsay Mc Clellan ; Hardie, Rae Anne ; Woodbridge, Paula ; Tindall, Elizabeth A. ; Bertelsen, Mads Frost ; Dixon, Dale ; Pyecroft, Stephen ; Helgen, Kristofer M. ; Lesk, Arthur M. ; Pringle, Thomas H. ; Patterson, Nick ; Zhang, Yu ; Kreiss, Alexandre ; Woods, Gregory M. ; Jones, Menna E. ; Schuster, Stephan C. / Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). In: Proceedings of the National Academy of Sciences of the United States of America. 2011 ; Vol. 108, No. 30. pp. 12348-12353.
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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.",
author = "Webb Miller and Hayes, {Vanessa M.} and Aakrosh Ratan and Petersen, {Desiree C.} and Wittekindt, {Nicola E.} and Jason Miller and Brian Walenz and James Knight and Ji Qi and Fangqing Zhao and Qingyu Wang and Bedoya-Reina, {Oscar C.} and Neerja Katiyar and Tomsho, {Lynn P.} and Kasson, {Lindsay Mc Clellan} and Hardie, {Rae Anne} and Paula Woodbridge and Tindall, {Elizabeth A.} and Bertelsen, {Mads Frost} and Dale Dixon and Stephen Pyecroft and Helgen, {Kristofer M.} and Lesk, {Arthur M.} and Pringle, {Thomas H.} and Nick Patterson and Yu Zhang and Alexandre Kreiss and Woods, {Gregory M.} and Jones, {Menna E.} and Schuster, {Stephan C.}",
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Miller, W, Hayes, VM, Ratan, A, Petersen, DC, Wittekindt, NE, Miller, J, Walenz, B, Knight, J, Qi, J, Zhao, F, Wang, Q, Bedoya-Reina, OC, Katiyar, N, Tomsho, LP, Kasson, LMC, Hardie, RA, Woodbridge, P, Tindall, EA, Bertelsen, MF, Dixon, D, Pyecroft, S, Helgen, KM, Lesk, AM, Pringle, TH, Patterson, N, Zhang, Y, Kreiss, A, Woods, GM, Jones, ME & Schuster, SC 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, vol. 108, no. 30, pp. 12348-12353. https://doi.org/10.1073/pnas.1102838108

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). / Miller, Webb; Hayes, Vanessa M.; Ratan, Aakrosh; Petersen, Desiree C.; Wittekindt, Nicola E.; Miller, Jason; Walenz, Brian; Knight, James; Qi, Ji; Zhao, Fangqing; Wang, Qingyu; Bedoya-Reina, Oscar C.; Katiyar, Neerja; Tomsho, Lynn P.; Kasson, Lindsay Mc Clellan; Hardie, Rae Anne; Woodbridge, Paula; Tindall, Elizabeth A.; Bertelsen, Mads Frost; Dixon, Dale; Pyecroft, Stephen; Helgen, Kristofer M.; Lesk, Arthur M.; Pringle, Thomas H.; Patterson, Nick; Zhang, Yu; Kreiss, Alexandre; Woods, Gregory M.; Jones, Menna E.; Schuster, Stephan C.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 108, No. 30, 26.07.2011, p. 12348-12353.

Research output: Contribution to journalArticle

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T1 - Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

AU - Miller, Webb

AU - Hayes, Vanessa M.

AU - Ratan, Aakrosh

AU - Petersen, Desiree C.

AU - Wittekindt, Nicola E.

AU - Miller, Jason

AU - Walenz, Brian

AU - Knight, James

AU - Qi, Ji

AU - Zhao, Fangqing

AU - Wang, Qingyu

AU - Bedoya-Reina, Oscar C.

AU - Katiyar, Neerja

AU - Tomsho, Lynn P.

AU - Kasson, Lindsay Mc Clellan

AU - Hardie, Rae Anne

AU - Woodbridge, Paula

AU - Tindall, Elizabeth A.

AU - Bertelsen, Mads Frost

AU - Dixon, Dale

AU - Pyecroft, Stephen

AU - Helgen, Kristofer M.

AU - Lesk, Arthur M.

AU - Pringle, Thomas H.

AU - Patterson, Nick

AU - Zhang, Yu

AU - Kreiss, Alexandre

AU - Woods, Gregory M.

AU - Jones, Menna E.

AU - Schuster, Stephan C.

PY - 2011/7/26

Y1 - 2011/7/26

N2 - 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.

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JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

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