Interspecific Gene Flow Shaped the Evolution of the Genus Canis

Shyam Gopalakrishnan; Mikkel Holger S. Sinding; Jazmín Ramos-Madrigal; Jonas Niemann; Jose A. Samaniego Castruita; Filipe G. Vieira; Christian Carøe; Marc de Manuel Montero; Lukas Kuderna; Aitor Serres; Víctor Manuel González-Basallote; Yan Hu Liu; Guo Dong Wang; Tomas Marques-Bonet; Siavash Mirarab; Carlos Fernandes; Philippe Gaubert; Klaus Peter Koepfli; Jane Budd; Eli Knispel Rueness; Mads Peter Heide-Jørgensen; Bent Petersen; Thomas Sicheritz-Ponten; Lutz Bachmann; Øystein Wiig; Anders J. Hansen; M. Thomas P. Gilbert

doi:10.1016/j.cub.2018.08.041

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

Shyam Gopalakrishnan^*, Mikkel Holger S. Sinding, Jazmín Ramos-Madrigal, Jonas Niemann, Jose A. Samaniego Castruita, Filipe G. Vieira, Christian Carøe, Marc de Manuel Montero, Lukas Kuderna, Aitor Serres, Víctor Manuel González-Basallote, Yan Hu Liu, Guo Dong Wang, Tomas Marques-Bonet, Siavash Mirarab, Carlos Fernandes, Philippe Gaubert, Klaus Peter Koepfli, Jane Budd, Eli Knispel RuenessMads Peter Heide-Jørgensen, Bent Petersen, Thomas Sicheritz-Ponten, Lutz Bachmann, Øystein Wiig, Anders J. Hansen, M. Thomas P. Gilbert

^*Corresponding author for this work

33 Citations (Scopus)

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Abstract

The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1–6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a “ghost” basal canid lineage. Gopalakrishnan et al. present evidence of pervasive gene flow among species of the genus Canis. In addition to previously known admixture events, they find evidence of gene flow from a “ghost” canid, related to the dhole, into the ancestor of the gray wolf and coyote. Further, they suggest that the African golden wolf is a species of hybrid origin.

Original language	English
Journal	Current Biology
Volume	28
Issue number	21
Pages (from-to)	3441-3449
ISSN	0960-9822
DOIs	https://doi.org/10.1016/j.cub.2018.08.041
Publication status	Published - 5 Nov 2018

Keywords

African golden wolf
African hunting dog
canid hybridization
canid phylogeography
Ethiopian wolf
gray wolf
phylogenomics

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PIIS0960982218311254Final published version, 1.88 MBLicence: CC BY-NC-ND

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Gopalakrishnan, S., Sinding, M. H. S., Ramos-Madrigal, J., Niemann, J., Samaniego Castruita, J. A., Vieira, F. G., Carøe, C., Montero, M. D. M., Kuderna, L., Serres, A., González-Basallote, V. M., Liu, Y. H., Wang, G. D., Marques-Bonet, T., Mirarab, S., Fernandes, C., Gaubert, P., Koepfli, K. P., Budd, J., ... Gilbert, M. T. P. (2018). Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Current Biology, 28(21), 3441-3449. https://doi.org/10.1016/j.cub.2018.08.041

Gopalakrishnan, S , Sinding, MHS , Ramos-Madrigal, J , Niemann, J, Samaniego Castruita, JA, Vieira, FG , Carøe, C, Montero, MDM, Kuderna, L, Serres, A, González-Basallote, VM, Liu, YH, Wang, GD, Marques-Bonet, T, Mirarab, S, Fernandes, C, Gaubert, P, Koepfli, KP, Budd, J, Rueness, EK, Heide-Jørgensen, MP, Petersen, B, Sicheritz-Ponten, T, Bachmann, L, Wiig, Ø, Hansen, AJ & Gilbert, MTP 2018, 'Interspecific Gene Flow Shaped the Evolution of the Genus Canis', Current Biology, vol. 28, no. 21, pp. 3441-3449. https://doi.org/10.1016/j.cub.2018.08.041

@article{10e52a24cac242c08231a75d7559ce7b,

title = "Interspecific Gene Flow Shaped the Evolution of the Genus Canis",

abstract = "The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1–6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a “ghost” basal canid lineage. Gopalakrishnan et al. present evidence of pervasive gene flow among species of the genus Canis. In addition to previously known admixture events, they find evidence of gene flow from a “ghost” canid, related to the dhole, into the ancestor of the gray wolf and coyote. Further, they suggest that the African golden wolf is a species of hybrid origin.",

keywords = "African golden wolf, African hunting dog, canid hybridization, canid phylogeography, Ethiopian wolf, gray wolf, phylogenomics",

author = "Shyam Gopalakrishnan and Sinding, {Mikkel Holger S.} and Jazm{\'i}n Ramos-Madrigal and Jonas Niemann and {Samaniego Castruita}, {Jose A.} and Vieira, {Filipe G.} and Christian Car{\o}e and Montero, {Marc de Manuel} and Lukas Kuderna and Aitor Serres and Gonz{\'a}lez-Basallote, {V{\'i}ctor Manuel} and Liu, {Yan Hu} and Wang, {Guo Dong} and Tomas Marques-Bonet and Siavash Mirarab and Carlos Fernandes and Philippe Gaubert and Koepfli, {Klaus Peter} and Jane Budd and Rueness, {Eli Knispel} and Heide-J{\o}rgensen, {Mads Peter} and Bent Petersen and Thomas Sicheritz-Ponten and Lutz Bachmann and {\O}ystein Wiig and Hansen, {Anders J.} and Gilbert, {M. Thomas P.}",

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AU - Ramos-Madrigal, Jazmín

AU - Niemann, Jonas

AU - Samaniego Castruita, Jose A.

AU - Vieira, Filipe G.

AU - Carøe, Christian

AU - Montero, Marc de Manuel

AU - Kuderna, Lukas

AU - Serres, Aitor

AU - González-Basallote, Víctor Manuel

AU - Liu, Yan Hu

AU - Wang, Guo Dong

AU - Marques-Bonet, Tomas

AU - Mirarab, Siavash

AU - Fernandes, Carlos

AU - Gaubert, Philippe

AU - Koepfli, Klaus Peter

AU - Budd, Jane

AU - Rueness, Eli Knispel

AU - Heide-Jørgensen, Mads Peter

AU - Petersen, Bent

AU - Sicheritz-Ponten, Thomas

AU - Bachmann, Lutz

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AU - Hansen, Anders J.

AU - Gilbert, M. Thomas P.

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N2 - The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1–6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a “ghost” basal canid lineage. Gopalakrishnan et al. present evidence of pervasive gene flow among species of the genus Canis. In addition to previously known admixture events, they find evidence of gene flow from a “ghost” canid, related to the dhole, into the ancestor of the gray wolf and coyote. Further, they suggest that the African golden wolf is a species of hybrid origin.

AB - The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1–6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a “ghost” basal canid lineage. Gopalakrishnan et al. present evidence of pervasive gene flow among species of the genus Canis. In addition to previously known admixture events, they find evidence of gene flow from a “ghost” canid, related to the dhole, into the ancestor of the gray wolf and coyote. Further, they suggest that the African golden wolf is a species of hybrid origin.

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KW - canid phylogeography

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VL - 28

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EP - 3449

JO - Current Biology

JF - Current Biology

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ER -

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

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Keywords

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