Genome-wide signatures of complex introgression and adaptive evolution in the big cats

Detalhes bibliográficos
Autor(a) principal: Figueiro, Henrique V.
Data de Publicação: 2017
Outros Autores: 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
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.
id UNSP_89c9f1aceffdbaa7efb1c3d216f3308d
oai_identifier_str oai:repositorio.unesp.br:11449/159822
network_acronym_str UNSP
network_name_str Repositório Institucional da UNESP
repository_id_str 2946
spelling 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
_version_ 1808128932944281600