Population genomics of grey wolves and wolf-like canids in North America

Mikkel Holger S. Sinding; Shyam Gopalakrishan; Filipe G. Vieira; Jose A. Samaniego Castruita; Katrine Raundrup; Mads Peter Heide Jørgensen; Morten Meldgaard; Bent Petersen; Thomas Sicheritz-Ponten; Johan Brus Mikkelsen; Ulf Marquard-Petersen; Rune Dietz; Christian Sonne; Love Dalén; Lutz Bachmann; Øystein Wiig; Anders J. Hansen; M. Thomas P. Gilbert

doi:10.1371/journal.pgen.1007745

Population genomics of grey wolves and wolf-like canids in North America

Mikkel Holger S. Sinding, Shyam Gopalakrishan, Filipe G. Vieira, Jose A. Samaniego Castruita, Katrine Raundrup, Mads Peter Heide Jørgensen, Morten Meldgaard, Bent Petersen, Thomas Sicheritz-Ponten, Johan Brus Mikkelsen, Ulf Marquard-Petersen, Rune Dietz, Christian Sonne, Love Dalén, Lutz Bachmann, Øystein Wiig, Anders J. Hansen, M. Thomas P. Gilbert

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Abstract

North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified “Polar wolf” population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.

Original language	English
Article number	e1007745
Journal	PLOS Genetics
Volume	14
Issue number	11
Number of pages	23
ISSN	1553-7390
DOIs	https://doi.org/10.1371/journal.pgen.1007745
Publication status	Published - Nov 2018

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Population genomics of grey wolves and wolf-like canids in North AmericaFinal published version, 1.23 MBLicence: CC BY

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Sinding, M. H. S., Gopalakrishan, S., Vieira, F. G., Samaniego Castruita, J. A., Raundrup, K., Heide Jørgensen, M. P., Meldgaard, M., Petersen, B., Sicheritz-Ponten, T., Mikkelsen, J. B., Marquard-Petersen, U., Dietz, R., Sonne, C., Dalén, L., Bachmann, L., Wiig, Ø., Hansen, A. J., & Gilbert, M. T. P. (2018). Population genomics of grey wolves and wolf-like canids in North America. PLOS Genetics, 14(11), [e1007745]. https://doi.org/10.1371/journal.pgen.1007745

Sinding, MHS, Gopalakrishan, S, Vieira, FG, Samaniego Castruita, JA, Raundrup, K, Heide Jørgensen, MP, Meldgaard, M , Petersen, B, Sicheritz-Ponten, T, Mikkelsen, JB, Marquard-Petersen, U, Dietz, R, Sonne, C, Dalén, L, Bachmann, L, Wiig, Ø, Hansen, AJ & Gilbert, MTP 2018, 'Population genomics of grey wolves and wolf-like canids in North America', PLOS Genetics, vol. 14, no. 11, e1007745. https://doi.org/10.1371/journal.pgen.1007745

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title = "Population genomics of grey wolves and wolf-like canids in North America",

abstract = "North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified “Polar wolf” population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.",

author = "Sinding, {Mikkel Holger S.} and Shyam Gopalakrishan and Vieira, {Filipe G.} and {Samaniego Castruita}, {Jose A.} and Katrine Raundrup and {Heide J{\o}rgensen}, {Mads Peter} and Morten Meldgaard and Bent Petersen and Thomas Sicheritz-Ponten and Mikkelsen, {Johan Brus} and Ulf Marquard-Petersen and Rune Dietz and Christian Sonne and Love Dal{\'e}n and Lutz Bachmann and {\O}ystein Wiig and Hansen, {Anders J.} and Gilbert, {M. Thomas P.}",

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AU - Sonne, Christian

AU - Dalén, Love

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AU - Gilbert, M. Thomas P.

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N2 - North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified “Polar wolf” population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.

AB - North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified “Polar wolf” population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.

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Population genomics of grey wolves and wolf-like canids in North America

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