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 McClellan Kasson; Rae-Anne Hardie; Paula Woodbridge; Elizabeth A. Tindall; Mads Frost Bertelsen; Dale Dixon; Stephen 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

doi:10.1073/pnas.1102838108

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 McClellan 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

143 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 language	English
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	108
Issue number	30
Pages (from-to)	12348-12353
Number of pages	6
ISSN	0027-8424
DOIs	https://doi.org/10.1073/pnas.1102838108
Publication status	Published - 26 Jul 2011

Keywords

Animals
Breeding
DNA, Mitochondrial
DNA, Neoplasm
Extinction, Biological
Facial Neoplasms
Genetic Variation
Genetics, Population
Genome, Mitochondrial
Humans
Marsupialia
Models, Molecular
Neoplasm Proteins
Neoplasms
Phylogeny
Polymorphism, Single Nucleotide
Tasmania
Time Factors

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1073/pnas.1102838108

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Miller, W., Hayes, V. M., Ratan, A., Petersen, D. C., Wittekindt, N. E., Miller, J., Walenz, B., Knight, J., Qi, J., Zhao, F., Wang, Q., Bedoya-Reina, O. C., Katiyar, N., Tomsho, L. P., Kasson, L. M., Hardie, R-A., Woodbridge, P., Tindall, E. A., Bertelsen, M. F., ... Schuster, S. C. (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, 108(30), 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 et al.

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 journal › Journal article › Research › peer-review

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, LM, Hardie, R-A, 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

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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.",

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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 McClellan} and Rae-Anne Hardie 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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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 McClellan

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

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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.

AB - 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.

KW - Animals

KW - Breeding

KW - DNA, Mitochondrial

KW - DNA, Neoplasm

KW - Extinction, Biological

KW - Facial Neoplasms

KW - Genetic Variation

KW - Genetics, Population

KW - Genome, Mitochondrial

KW - Humans

KW - Marsupialia

KW - Models, Molecular

KW - Neoplasm Proteins

KW - Neoplasms

KW - Phylogeny

KW - Polymorphism, Single Nucleotide

KW - Tasmania

KW - Time Factors

KW - wildlife conservation

KW - ancient DNA

KW - populationgenetics

KW - semicondctor sequencing

KW - selective breding

U2 - 10.1073/pnas.1102838108

DO - 10.1073/pnas.1102838108

M3 - Journal article

C2 - 21709235

SN - 0027-8424

VL - 108

SP - 12348

EP - 12353

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

IS - 30

ER -

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

Abstract

Keywords

UN SDGs

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