Genome-wide signatures of complex introgression and adaptive evolution in the big cats
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1126/sciadv.1700299 http://hdl.handle.net/11449/159822 |
Resumo: | The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting similar to 19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages. |
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Genome-wide signatures of complex introgression and adaptive evolution in the big catsThe great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting similar to 19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAPERGS/BrazilFundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Morris Animal FoundationRussian Science FoundationRussian Ministry of SciencePontificial Catholic Univ Rio Grande Sul PUCRS, Lab Biol Genom & Mol, Fac Biociencias, Porto Alegre, RS, BrazilTexas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77843 USAFIOCRUZ Minas, Ctr Pesquisa Rene Rachou, Belo Horizonte, MG, BrazilUniv Coll Dublin, Sch Biol & Environm Sci, Dublin, IrelandSt Petersburg State Univ, Theodosius Dobzhansky Ctr Genome Bioinformat, St Petersburg, RussiaUniv Porto, Dept Biol, Fac Ciencias, Oporto, PortugalUniv Porto, CIIMAR CIMAR, Oporto, PortugalUniv Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USAUniv Calif Berkeley, Calif Inst Quantitat Biosci, Computat Genom Resource Lab, Berkeley, CA 94720 USAUniv Calif Berkeley, Museum Vertebrate Zool, Berkeley, CA 94720 USAInst Onca Pintada, Mineiros, Go, BrazilUniv Fed Sao Joao, Sao Joao Del Rei, MG, BrazilInst Pro Carnivoros, Atibaia, SP, BrazilInst Chico Mendes Conservacao Biodiversida, Brasilia, DF, BrazilInst Desenvolvimento Sustentavel Mamiraua, Tefe, Amazonas, BrazilUniv Sao Paulo, ESALQ, Piracicaba, SP, BrazilZool Municipal Sorocaba, Sorocaba, SP, BrazilUniv Estadual Paulista Botucatu, Programa Posgrad Anim Selvagens, Sao Paulo, BrazilCtr Genom Regulat CRG, Bioinformat & Genom Programme, Barcelona, SpainUniv Pompeu Fabra, Barcelona, SpainInst Biol & Med Expt, Buenos Aires, DF, ArgentinaICREA, Barcelona, SpainInst Tecnol Vale, Belem, Para, BrazilUniv Estadual Paulista Botucatu, Programa Posgrad Anim Selvagens, Sao Paulo, BrazilCNPq: 311327/2011-7CNPq: 487396/2012-0CNPq: 309312/2012-4FAPERGS/Brazil: 12/2236-0FAPEMIG: RED-00014-14Morris Animal Foundation: D12FE-019Morris Animal Foundation: D12FE-502Russian Science Foundation: 17-14-01138Russian Ministry of Science: 11.G34.31.0068Amer Assoc Advancement SciencePontificial Catholic Univ Rio Grande Sul PUCRSTexas A&M UnivFIOCRUZ MinasUniv Coll DublinSt Petersburg State UnivUniv PortoUniv Calif BerkeleyInst Onca PintadaUniv Fed Sao JoaoInst Pro CarnivorosInst Chico Mendes Conservacao BiodiversidaInst Desenvolvimento Sustentavel MamirauaUniversidade de São Paulo (USP)Zool Municipal SorocabaUniversidade Estadual Paulista (Unesp)Ctr Genom Regulat CRGUniv Pompeu FabraInst Biol & Med ExptICREAInst Tecnol ValeFigueiro, Henrique V.Li, GangTrindade, Fernanda J.Assis, JulianaPais, FabianoFernandes, GabrielSantos, Sarah H. D.Hughes, Graham M.Komissarov, AlekseyAntunes, AgostinhoTrinca, Cristine S.Rodrigues, Maira R.Linderoth, TylerBi, KeSilveira, LeandroAzevedo, Fernando C. C.Kantek, DanielRamalho, EmilianoBrassaloti, Ricardo A.Villela, Priscilla M. S.Nunes, Adauto L. V.Teixeira, Rodrigo H. F. [UNESP]Morato, Ronaldo G.Loska, DamianSaragueta, PatriciaGabaldon, ToniTeeling, Emma C.O'Brien, Stephen J.Nielsen, RasmusCoutinho, Luiz L.Oliveira, GuilhermeMurphy, William J.Eizirik, Eduardo2018-11-26T15:45:22Z2018-11-26T15:45:22Z2017-07-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article13application/pdfhttp://dx.doi.org/10.1126/sciadv.1700299Science Advances. Washington: Amer Assoc Advancement Science, v. 3, n. 7, 13 p., 2017.2375-2548http://hdl.handle.net/11449/15982210.1126/sciadv.1700299WOS:000411588000043WOS000411588000043.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengScience Advances5,817info:eu-repo/semantics/openAccess2023-11-22T06:16:47Zoai:repositorio.unesp.br:11449/159822Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T18:26:42.459996Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genome-wide signatures of complex introgression and adaptive evolution in the big cats |
title |
Genome-wide signatures of complex introgression and adaptive evolution in the big cats |
spellingShingle |
Genome-wide signatures of complex introgression and adaptive evolution in the big cats Figueiro, Henrique V. |
title_short |
Genome-wide signatures of complex introgression and adaptive evolution in the big cats |
title_full |
Genome-wide signatures of complex introgression and adaptive evolution in the big cats |
title_fullStr |
Genome-wide signatures of complex introgression and adaptive evolution in the big cats |
title_full_unstemmed |
Genome-wide signatures of complex introgression and adaptive evolution in the big cats |
title_sort |
Genome-wide signatures of complex introgression and adaptive evolution in the big cats |
author |
Figueiro, Henrique V. |
author_facet |
Figueiro, Henrique V. Li, Gang Trindade, Fernanda J. Assis, Juliana Pais, Fabiano Fernandes, Gabriel Santos, Sarah H. D. Hughes, Graham M. Komissarov, Aleksey Antunes, Agostinho Trinca, Cristine S. Rodrigues, Maira R. Linderoth, Tyler Bi, Ke Silveira, Leandro Azevedo, Fernando C. C. Kantek, Daniel Ramalho, Emiliano Brassaloti, Ricardo A. Villela, Priscilla M. S. Nunes, Adauto L. V. Teixeira, Rodrigo H. F. [UNESP] Morato, Ronaldo G. Loska, Damian Saragueta, Patricia Gabaldon, Toni Teeling, Emma C. O'Brien, Stephen J. Nielsen, Rasmus Coutinho, Luiz L. Oliveira, Guilherme Murphy, William J. Eizirik, Eduardo |
author_role |
author |
author2 |
Li, Gang Trindade, Fernanda J. Assis, Juliana Pais, Fabiano Fernandes, Gabriel Santos, Sarah H. D. Hughes, Graham M. Komissarov, Aleksey Antunes, Agostinho Trinca, Cristine S. Rodrigues, Maira R. Linderoth, Tyler Bi, Ke Silveira, Leandro Azevedo, Fernando C. C. Kantek, Daniel Ramalho, Emiliano Brassaloti, Ricardo A. Villela, Priscilla M. S. Nunes, Adauto L. V. Teixeira, Rodrigo H. F. [UNESP] Morato, Ronaldo G. Loska, Damian Saragueta, Patricia Gabaldon, Toni Teeling, Emma C. O'Brien, Stephen J. Nielsen, Rasmus Coutinho, Luiz L. Oliveira, Guilherme Murphy, William J. Eizirik, Eduardo |
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 author author |
dc.contributor.none.fl_str_mv |
Pontificial Catholic Univ Rio Grande Sul PUCRS Texas A&M Univ FIOCRUZ Minas Univ Coll Dublin St Petersburg State Univ Univ Porto Univ Calif Berkeley Inst Onca Pintada Univ Fed Sao Joao Inst Pro Carnivoros Inst Chico Mendes Conservacao Biodiversida Inst Desenvolvimento Sustentavel Mamiraua Universidade de São Paulo (USP) Zool Municipal Sorocaba Universidade Estadual Paulista (Unesp) Ctr Genom Regulat CRG Univ Pompeu Fabra Inst Biol & Med Expt ICREA Inst Tecnol Vale |
dc.contributor.author.fl_str_mv |
Figueiro, Henrique V. Li, Gang Trindade, Fernanda J. Assis, Juliana Pais, Fabiano Fernandes, Gabriel Santos, Sarah H. D. Hughes, Graham M. Komissarov, Aleksey Antunes, Agostinho Trinca, Cristine S. Rodrigues, Maira R. Linderoth, Tyler Bi, Ke Silveira, Leandro Azevedo, Fernando C. C. Kantek, Daniel Ramalho, Emiliano Brassaloti, Ricardo A. Villela, Priscilla M. S. Nunes, Adauto L. V. Teixeira, Rodrigo H. F. [UNESP] Morato, Ronaldo G. Loska, Damian Saragueta, Patricia Gabaldon, Toni Teeling, Emma C. O'Brien, Stephen J. Nielsen, Rasmus Coutinho, Luiz L. Oliveira, Guilherme Murphy, William J. Eizirik, Eduardo |
description |
The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting similar to 19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-07-01 2018-11-26T15:45:22Z 2018-11-26T15:45:22Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1126/sciadv.1700299 Science Advances. Washington: Amer Assoc Advancement Science, v. 3, n. 7, 13 p., 2017. 2375-2548 http://hdl.handle.net/11449/159822 10.1126/sciadv.1700299 WOS:000411588000043 WOS000411588000043.pdf |
url |
http://dx.doi.org/10.1126/sciadv.1700299 http://hdl.handle.net/11449/159822 |
identifier_str_mv |
Science Advances. Washington: Amer Assoc Advancement Science, v. 3, n. 7, 13 p., 2017. 2375-2548 10.1126/sciadv.1700299 WOS:000411588000043 WOS000411588000043.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Science Advances 5,817 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
13 application/pdf |
dc.publisher.none.fl_str_mv |
Amer Assoc Advancement Science |
publisher.none.fl_str_mv |
Amer Assoc Advancement Science |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1808128932944281600 |