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Mitochondrial phylogenomics of modern and ancient Equids

Mitochondrial phylogenomics of modern and ancient Equids
Mitochondrial phylogenomics of modern and ancient Equids
The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).
1932-6203
1-12
Weinstock, J.
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Vilstrup, J.T.
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Seguin-Orlando, A.
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Stiller, M.
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Ginolhac, A.
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Raghavan, M.
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Nielsen, S.C.A.
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Froese, D.
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Vasiliev, S.K.
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Ovodov, N.D.
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Clary, J.
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Helgen, K.M.
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Fleischer, R.C.
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Copper, A.
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Shapiro, B.
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Orlando, L.
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Weinstock, J.
edcdb255-f6d0-4a66-8c47-28b70d79896e
Vilstrup, J.T.
403a6457-d38b-4fed-84ad-ef14a105e4b5
Seguin-Orlando, A.
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Stiller, M.
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Ginolhac, A.
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Raghavan, M.
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Nielsen, S.C.A.
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Froese, D.
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Vasiliev, S.K.
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Ovodov, N.D.
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Clary, J.
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Helgen, K.M.
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Fleischer, R.C.
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Copper, A.
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Shapiro, B.
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Orlando, L.
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Weinstock, J., Vilstrup, J.T., Seguin-Orlando, A., Stiller, M., Ginolhac, A., Raghavan, M., Nielsen, S.C.A., Froese, D., Vasiliev, S.K., Ovodov, N.D., Clary, J., Helgen, K.M., Fleischer, R.C., Copper, A., Shapiro, B. and Orlando, L. (2013) Mitochondrial phylogenomics of modern and ancient Equids. PLoS ONE, 8 (2), 1-12. (doi:10.1371/journal.pone.0055950). (PMID:23437078)

Record type: Article

Abstract

The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).

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Accepted/In Press date: 7 January 2013
Published date: 20 February 2013
Organisations: Archaeology

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Local EPrints ID: 395530
URI: http://eprints.soton.ac.uk/id/eprint/395530
ISSN: 1932-6203
PURE UUID: a9b5eaf3-aee4-4c81-bb49-7e4fb952489e

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Date deposited: 29 Jun 2016 16:02
Last modified: 16 Dec 2019 19:54

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Contributors

Author: J. Weinstock
Author: J.T. Vilstrup
Author: A. Seguin-Orlando
Author: M. Stiller
Author: A. Ginolhac
Author: M. Raghavan
Author: S.C.A. Nielsen
Author: D. Froese
Author: S.K. Vasiliev
Author: N.D. Ovodov
Author: J. Clary
Author: K.M. Helgen
Author: R.C. Fleischer
Author: A. Copper
Author: B. Shapiro
Author: L. Orlando

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