Evolutionary history of the genus Capra (Mammalia, Artiodactyla): Discordance between mitochondrial DNA and Y-chromosome phylogenies

Nathalie Pidancier; Steve Jordan; Gordon Luikart; Pierre Taberlet

doi:10.1016/j.ympev.2006.04.002

Evolutionary history of the genus Capra (Mammalia, Artiodactyla): Discordance between mitochondrial DNA and Y-chromosome phylogenies

Nathalie Pidancier
, Steve Jordan
, Gordon Luikart
, Pierre Taberlet

Flathead Lake Biological Station

Research output: Contribution to journal › Article › peer-review

116 Scopus citations

Abstract

The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytochrome b sequences. For the Y-chromosome phylogeny, we sequenced segments from the amelogenin (AMELY) and zinc finger (ZFY) genes from all of the eight wild taxa and from domestic goats (Capra hircus). Phylogenetic analysis of the Y-chromosome data revealed two well-defined clades. The domestic goat (C. hircus), the bezoar (Capra aegagrus), and the markhor (C. falconeri) belong to one clade (ML bootstrap value [BP]: 98%), suggesting that domestic goats originated from one or both of these wild species. The second clade (ML BP: 92%) is comprised of all the other wild species. Horn morphology is generally concordant with the Y-chromosome phylogeny. The mtDNA data also revealed two well-defined clades. However, the species in each clade are different from those inferred from the Y-chromosome data. To explain the discordance between Y-chromosome and mtDNA phylogenies, several hypotheses are considered. We suggest that a plausible scenario involves mtDNA introgression between ancestral taxa before the relatively recent colonization of Western Europe, the Caucasus Mountains, and East Africa by Capra populations.

Original language	English
Pages (from-to)	739-749
Number of pages	11
Journal	Molecular Phylogenetics and Evolution
Volume	40
Issue number	3
DOIs	https://doi.org/10.1016/j.ympev.2006.04.002
State	Published - Sep 2006

Funding

We thank the following who provided samples: N. Hasima, A. Virk, A. Ghaffar, O. Hanotte and the ILRI, E. Bedin, R. Soriguer, M.K. Sanyasi, L.O. Ngere, D. Zygoyiannis, A. Amcoff, M. Gough, P. Evans, V. Fet, H. Amaturado, I. Coroiu, I. Moglan, Y. Komarov, T.M. Correic, E. Zimba, S. Breznik, E. Eyporsdottir, W. Hamdine, J. Honmode, J.M. Villemot, V.I. Glazko, E. Martyniuk, Ferme du Pic Bois, C. Couturier, M. Dye, R. Del Olmo, T. Faure, and especially M. Abo-Shaheda, O. Ertugrul, Y. Zagdsuren, G. Ruff, G. Dolf, K. Scribner, and Z. Gurielidze. We offer sincere thanks to Paul Weinberg who provided critical samples, identifications, and guidance. ZFY primers were kindly provided by Lori Lawson. We also thank all anonymous referees for helpful suggestions on all versions of the manuscript, H. Fernandez and L. Gielly for help in the laboratory, and Julie Dlugos, who drew Fig. 1 . This work was funded by grants from the European Commission (No. BIO4CT 961189), the North Atlantic Treaty Organization (LST.CLG.977824), and the US National Science Foundation (No. 0107373).

Funders	Funder number
0107373
LST.CLG.977824
European Commission	BIO4CT 961189

Keywords

Capra
Caprinae
Goat domestication
Introgression
Y-chromosome evolution

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10.1016/j.ympev.2006.04.002

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@article{3d99c4670d1c45238b88ac50942286aa,

title = "Evolutionary history of the genus Capra (Mammalia, Artiodactyla): Discordance between mitochondrial DNA and Y-chromosome phylogenies",

abstract = "The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytochrome b sequences. For the Y-chromosome phylogeny, we sequenced segments from the amelogenin (AMELY) and zinc finger (ZFY) genes from all of the eight wild taxa and from domestic goats (Capra hircus). Phylogenetic analysis of the Y-chromosome data revealed two well-defined clades. The domestic goat (C. hircus), the bezoar (Capra aegagrus), and the markhor (C. falconeri) belong to one clade (ML bootstrap value [BP]: 98\%), suggesting that domestic goats originated from one or both of these wild species. The second clade (ML BP: 92\%) is comprised of all the other wild species. Horn morphology is generally concordant with the Y-chromosome phylogeny. The mtDNA data also revealed two well-defined clades. However, the species in each clade are different from those inferred from the Y-chromosome data. To explain the discordance between Y-chromosome and mtDNA phylogenies, several hypotheses are considered. We suggest that a plausible scenario involves mtDNA introgression between ancestral taxa before the relatively recent colonization of Western Europe, the Caucasus Mountains, and East Africa by Capra populations.",

keywords = "Capra, Caprinae, Goat domestication, Introgression, Y-chromosome evolution",

author = "Nathalie Pidancier and Steve Jordan and Gordon Luikart and Pierre Taberlet",

note = "Funding Information: We thank the following who provided samples: N. Hasima, A. Virk, A. Ghaffar, O. Hanotte and the ILRI, E. Bedin, R. Soriguer, M.K. Sanyasi, L.O. Ngere, D. Zygoyiannis, A. Amcoff, M. Gough, P. Evans, V. Fet, H. Amaturado, I. Coroiu, I. Moglan, Y. Komarov, T.M. Correic, E. Zimba, S. Breznik, E. Eyporsdottir, W. Hamdine, J. Honmode, J.M. Villemot, V.I. Glazko, E. Martyniuk, Ferme du Pic Bois, C. Couturier, M. Dye, R. Del Olmo, T. Faure, and especially M. Abo-Shaheda, O. Ertugrul, Y. Zagdsuren, G. Ruff, G. Dolf, K. Scribner, and Z. Gurielidze. We offer sincere thanks to Paul Weinberg who provided critical samples, identifications, and guidance. ZFY primers were kindly provided by Lori Lawson. We also thank all anonymous referees for helpful suggestions on all versions of the manuscript, H. Fernandez and L. Gielly for help in the laboratory, and Julie Dlugos, who drew Fig. 1 . This work was funded by grants from the European Commission (No. BIO4CT 961189), the North Atlantic Treaty Organization (LST.CLG.977824), and the US National Science Foundation (No. 0107373). ",

year = "2006",

month = sep,

doi = "10.1016/j.ympev.2006.04.002",

language = "English",

volume = "40",

pages = "739--749",

journal = "Molecular Phylogenetics and Evolution",

issn = "1055-7903",

publisher = "Academic Press Inc.",

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T1 - Evolutionary history of the genus Capra (Mammalia, Artiodactyla)

T2 - Discordance between mitochondrial DNA and Y-chromosome phylogenies

AU - Pidancier, Nathalie

AU - Jordan, Steve

AU - Luikart, Gordon

AU - Taberlet, Pierre

N1 - Funding Information: We thank the following who provided samples: N. Hasima, A. Virk, A. Ghaffar, O. Hanotte and the ILRI, E. Bedin, R. Soriguer, M.K. Sanyasi, L.O. Ngere, D. Zygoyiannis, A. Amcoff, M. Gough, P. Evans, V. Fet, H. Amaturado, I. Coroiu, I. Moglan, Y. Komarov, T.M. Correic, E. Zimba, S. Breznik, E. Eyporsdottir, W. Hamdine, J. Honmode, J.M. Villemot, V.I. Glazko, E. Martyniuk, Ferme du Pic Bois, C. Couturier, M. Dye, R. Del Olmo, T. Faure, and especially M. Abo-Shaheda, O. Ertugrul, Y. Zagdsuren, G. Ruff, G. Dolf, K. Scribner, and Z. Gurielidze. We offer sincere thanks to Paul Weinberg who provided critical samples, identifications, and guidance. ZFY primers were kindly provided by Lori Lawson. We also thank all anonymous referees for helpful suggestions on all versions of the manuscript, H. Fernandez and L. Gielly for help in the laboratory, and Julie Dlugos, who drew Fig. 1 . This work was funded by grants from the European Commission (No. BIO4CT 961189), the North Atlantic Treaty Organization (LST.CLG.977824), and the US National Science Foundation (No. 0107373).

PY - 2006/9

Y1 - 2006/9

N2 - The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytochrome b sequences. For the Y-chromosome phylogeny, we sequenced segments from the amelogenin (AMELY) and zinc finger (ZFY) genes from all of the eight wild taxa and from domestic goats (Capra hircus). Phylogenetic analysis of the Y-chromosome data revealed two well-defined clades. The domestic goat (C. hircus), the bezoar (Capra aegagrus), and the markhor (C. falconeri) belong to one clade (ML bootstrap value [BP]: 98%), suggesting that domestic goats originated from one or both of these wild species. The second clade (ML BP: 92%) is comprised of all the other wild species. Horn morphology is generally concordant with the Y-chromosome phylogeny. The mtDNA data also revealed two well-defined clades. However, the species in each clade are different from those inferred from the Y-chromosome data. To explain the discordance between Y-chromosome and mtDNA phylogenies, several hypotheses are considered. We suggest that a plausible scenario involves mtDNA introgression between ancestral taxa before the relatively recent colonization of Western Europe, the Caucasus Mountains, and East Africa by Capra populations.

AB - The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytochrome b sequences. For the Y-chromosome phylogeny, we sequenced segments from the amelogenin (AMELY) and zinc finger (ZFY) genes from all of the eight wild taxa and from domestic goats (Capra hircus). Phylogenetic analysis of the Y-chromosome data revealed two well-defined clades. The domestic goat (C. hircus), the bezoar (Capra aegagrus), and the markhor (C. falconeri) belong to one clade (ML bootstrap value [BP]: 98%), suggesting that domestic goats originated from one or both of these wild species. The second clade (ML BP: 92%) is comprised of all the other wild species. Horn morphology is generally concordant with the Y-chromosome phylogeny. The mtDNA data also revealed two well-defined clades. However, the species in each clade are different from those inferred from the Y-chromosome data. To explain the discordance between Y-chromosome and mtDNA phylogenies, several hypotheses are considered. We suggest that a plausible scenario involves mtDNA introgression between ancestral taxa before the relatively recent colonization of Western Europe, the Caucasus Mountains, and East Africa by Capra populations.

KW - Capra

KW - Caprinae

KW - Goat domestication

KW - Introgression

KW - Y-chromosome evolution

UR - https://www.scopus.com/pages/publications/33746921574

U2 - 10.1016/j.ympev.2006.04.002

DO - 10.1016/j.ympev.2006.04.002

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AN - SCOPUS:33746921574

SN - 1055-7903

VL - 40

SP - 739

EP - 749

JO - Molecular Phylogenetics and Evolution

JF - Molecular Phylogenetics and Evolution

IS - 3

ER -

Evolutionary history of the genus Capra (Mammalia, Artiodactyla): Discordance between mitochondrial DNA and Y-chromosome phylogenies

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Keywords

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