Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens

Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1–4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of...

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Autores: Barnett, Ross, Westbury, Michael V., Sandoval-Velasco, Marcela, Vieira, Filipe Garrett, Jeon, Sungwon, Zazula, Grant, Martin, Michael D., Ho, Simon Y.W., Mather, Niklas, Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, Manuel, Marc de, Zepeda-Mendoza, M. Lisandra, Antunes, Agostinho, Carmona Báez, Aldo, Cahsan, Binia de, Larson, Greger, O’Brien, Stephen J., Eizirik, Eduardo, Johnson, Warren E., Koepfli, Klaus-Peter, Wilting, Andreas, Fickel, Jörns, Dalén, Love, Lorenzen, Eline D., Marqués-Bonet, Tomàs, Hansen, Anders J., Zhang, Guojie, Bhak, Jong, Yamaguchi, Nobuyuki, Gilbert, M. Thomas P.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2020
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/236679
Acceso en línea:http://hdl.handle.net/10261/236679
Access Level:acceso abierto
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spelling Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidensBarnett, RossWestbury, Michael V.Sandoval-Velasco, MarcelaVieira, Filipe GarrettJeon, SungwonZazula, GrantMartin, Michael D.Ho, Simon Y.W.Mather, NiklasGopalakrishnan, ShyamRamos-Madrigal, JazmínManuel, Marc deZepeda-Mendoza, M. LisandraAntunes, AgostinhoCarmona Báez, AldoCahsan, Binia deLarson, GregerO’Brien, Stephen J.Eizirik, EduardoJohnson, Warren E.Koepfli, Klaus-PeterWilting, AndreasFickel, JörnsDalén, LoveLorenzen, Eline D.Marqués-Bonet, TomàsHansen, Anders J.Zhang, GuojieBhak, JongYamaguchi, NobuyukiGilbert, M. Thomas P.Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1–4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6–8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a 7x nuclear genome and a 38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11–14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.This project received funding from the European Union’s Seventh Framework Programme for Research, Technological Development, and Demonstration under grant agreement no. FP7-PEOPLE-2011-IEF-298820 and ERC Consolidator Award 681396—Extinction Genomics to M.T.P.G. Portions of this manuscript were prepared while W.E.J. held a National Research Council Research Associateship Award at the Walter Reed Army Institute of Research (WRAIR).Cell PressEuropean CommissionEuropean Research CouncilNational Research Council of CanadaWalter Reed Army Institute of ResearchConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2021202120202021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/236679reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/FP7/298820info:eu-repo/grantAgreement/EC/H2020/681396http://dx.doi.org/10.1016/j.cub.2020.09.051Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2366792026-05-22T06:33:51Z
dc.title.none.fl_str_mv Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
title Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
spellingShingle Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
Barnett, Ross
title_short Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
title_full Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
title_fullStr Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
title_full_unstemmed Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
title_sort Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
dc.creator.none.fl_str_mv Barnett, Ross
Westbury, Michael V.
Sandoval-Velasco, Marcela
Vieira, Filipe Garrett
Jeon, Sungwon
Zazula, Grant
Martin, Michael D.
Ho, Simon Y.W.
Mather, Niklas
Gopalakrishnan, Shyam
Ramos-Madrigal, Jazmín
Manuel, Marc de
Zepeda-Mendoza, M. Lisandra
Antunes, Agostinho
Carmona Báez, Aldo
Cahsan, Binia de
Larson, Greger
O’Brien, Stephen J.
Eizirik, Eduardo
Johnson, Warren E.
Koepfli, Klaus-Peter
Wilting, Andreas
Fickel, Jörns
Dalén, Love
Lorenzen, Eline D.
Marqués-Bonet, Tomàs
Hansen, Anders J.
Zhang, Guojie
Bhak, Jong
Yamaguchi, Nobuyuki
Gilbert, M. Thomas P.
author Barnett, Ross
author_facet Barnett, Ross
Westbury, Michael V.
Sandoval-Velasco, Marcela
Vieira, Filipe Garrett
Jeon, Sungwon
Zazula, Grant
Martin, Michael D.
Ho, Simon Y.W.
Mather, Niklas
Gopalakrishnan, Shyam
Ramos-Madrigal, Jazmín
Manuel, Marc de
Zepeda-Mendoza, M. Lisandra
Antunes, Agostinho
Carmona Báez, Aldo
Cahsan, Binia de
Larson, Greger
O’Brien, Stephen J.
Eizirik, Eduardo
Johnson, Warren E.
Koepfli, Klaus-Peter
Wilting, Andreas
Fickel, Jörns
Dalén, Love
Lorenzen, Eline D.
Marqués-Bonet, Tomàs
Hansen, Anders J.
Zhang, Guojie
Bhak, Jong
Yamaguchi, Nobuyuki
Gilbert, M. Thomas P.
author_role author
author2 Westbury, Michael V.
Sandoval-Velasco, Marcela
Vieira, Filipe Garrett
Jeon, Sungwon
Zazula, Grant
Martin, Michael D.
Ho, Simon Y.W.
Mather, Niklas
Gopalakrishnan, Shyam
Ramos-Madrigal, Jazmín
Manuel, Marc de
Zepeda-Mendoza, M. Lisandra
Antunes, Agostinho
Carmona Báez, Aldo
Cahsan, Binia de
Larson, Greger
O’Brien, Stephen J.
Eizirik, Eduardo
Johnson, Warren E.
Koepfli, Klaus-Peter
Wilting, Andreas
Fickel, Jörns
Dalén, Love
Lorenzen, Eline D.
Marqués-Bonet, Tomàs
Hansen, Anders J.
Zhang, Guojie
Bhak, Jong
Yamaguchi, Nobuyuki
Gilbert, M. Thomas P.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Commission
European Research Council
National Research Council of Canada
Walter Reed Army Institute of Research
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
description Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1–4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6–8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a 7x nuclear genome and a 38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11–14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.
publishDate 2020
dc.date.none.fl_str_mv 2020
2021
2021
2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/236679
url http://hdl.handle.net/10261/236679
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/FP7/298820
info:eu-repo/grantAgreement/EC/H2020/681396
http://dx.doi.org/10.1016/j.cub.2020.09.051
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Cell Press
publisher.none.fl_str_mv Cell Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
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collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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