Please use this identifier to cite or link to this item: https://www.arca.fiocruz.br/handle/icict/25924

Type
Article
Copyright
Restricted access
Embargo date
2022-01-01
Collections
Share

Statistics
Metadata
Show full item record

GENOME-WIDE SIGNATURES OF COMPLEX INTROGRESSION AND ADAPTIVE EVOLUTION IN THE BIG CATS
Figueiró, Henrique Vieira et al. | Date Issued: 2017
Author
Figueiró, Henrique Vieira
Li, Gang
Trindade, Fernanda J.
Geraldo, Juliana Assis
Pais, Fabiano Sviatopolk Mirsky
Fernandes, Gabriel da Rocha
Santos, Sarah H. D.
Hughes, Graham M.
Komissarov, Aleksey
Antunes, Agostinho
Trinca, Cristine S.
Rodrigues, Maíra 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.
Morato, Ronaldo G.
Loska, Damian
Saragüeta, Patricia
Gabaldón, Toni
Teeling, Emma C.
O’Brien, Stephen J.
Nielsen, Rasmus
Coutinho, Luiz L.
Oliveira, Guilherme Corrêa de
Murphy, William J.
Eizirik, Eduardo
Affilliation
Faculdade de Biociências. Laboratório de Biologia Genômica e Molecular. Pontificia Universidade Catolica do Rio Grande do Sul. Porto Alegre, RS, Brazil.
Department of Veterinary Integrative Biosciences. Texas A&M University. College Station, TX, USA.
Faculdade de Biociências. Laboratório de Biologia Genômica e Molecular. Pontificia Universidade Catolica do Rio Grande do Sul. Porto Alegre, RS, Brazil.
Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.
Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.
Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.
Faculdade de Biociências. Laboratório de Biologia Genômica e Molecular. Pontificia Universidade Catolica do Rio Grande do Sul. Porto Alegre, RS, Brazil.
School of Biology and Environmental Science. University College Dublin. Dublin, Ireland.
Theodosius Dobzhansky Center for Genome Bioinformatics. Saint Petersburg State University. St. Petersburg, Russia.
Universidade do Porto. Faculdade de Ciências and CIIMAR/CIMAR. Departamento de Biologia. Porto, Portugal.
Faculdade de Biociências. Laboratório de Biologia Genômica e Molecular. Pontificia Universidade Catolica do Rio Grande do Sul. Porto Alegre, RS, Brazil.
Faculdade de Biociências. Laboratório de Biologia Genômica e Molecular. Pontificia Universidade Catolica do Rio Grande do Sul. Porto Alegre, RS, Brazil.
Department of Integrative Biology. University of California. Berkeley, Berkeley, CA, USA.
Computational Genomics Resource Laboratory. California Institute for Quantitative Biosciences and Museum of Vertebrate Zoology. University of California. Berkeley, Berkeley, CA, USA.
Instituto Onça Pintada. Mineiros, GO, Brazil.
Universidade Federal de São João Del Rey, São João Del Rey, Minas Gerais, Brazil/Instituto Pró-Carnívoros. Atibaia, SP, Brazil.
Faculdade de Biociências. Laboratório de Biologia Genômica e Molecular. Pontificia Universidade Catolica do Rio Grande do Sul. Porto Alegre, RS, Brazil/ Instituto Chico Mendes de Conservação da Biodiversidade. Brasília, DF, Brazil
Instituto Pró-Carnívoros. Atibaia, SP, Brazil/Instituto de Desenvolvimento Sustentável Mamirauá. Tefé, AM, Brazil.
Escola Superior de Agricultura Luiz de Queiroz. Piracicaba, São Paulo, Brazil.
Escola Superior de Agricultura Luiz de Queiroz. Piracicaba, São Paulo, Brazil.
Escola Superior de Agricultura Luiz de Queiroz. Piracicaba, São Paulo, Brazil.
Zoológico Municipal de Sorocaba. Sorocaba, SP, Brazil.
Zoológico Municipal de Sorocaba. Sorocaba, SP, Brazil/Universidade Estadual Paulista. Programa de Pós-Graduação em Animais Selvagens. Botucatu, SP, Brazil.
Instituto Pró-Carnívoros. Atibaia, SP, Brazil/Instituto Chico Mendes de Conservação da Biodiversidade. Brasília, DF, Brazil
Centre for Genomic Regulation. Bioinformatics and Genomics Programme. Barcelona, Spain/Universitat Pompeu Fabra. Barcelona, Spain
Instituto de Biología y Medicina Experimental. Buenos Aires, Argentina.
Centre for Genomic Regulation. Bioinformatics and Genomics Programme. Barcelona, Spain/Universitat Pompeu Fabra. Barcelona, Spain/Institució Catalana de Recerca i Estudis Avançats. Barcelona, Spain.
School of Biology and Environmental Science. University College Dublin. Dublin, Ireland.
Theodosius Dobzhansky Center for Genome Bioinformatics. Saint Petersburg State University. St. Petersburg, Russia.
Department of Integrative Biology. University of California. Berkeley, Berkeley, CA, USA.
Escola Superior de Agricultura Luiz de Queiroz. Piracicaba, São Paulo, Brazil.
Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil/Instituto Tecnológico Vale. Belém, Pará, Brazil.
Department of Veterinary Integrative Biosciences. Texas A&M University. College Station, TX, USA.
Faculdade de Biociências. Laboratório de Biologia Genômica e Molecular. Pontificia Universidade Catolica do Rio Grande do Sul. Porto Alegre, RS, Brazil/ Instituto Pró-Carnívoros. Atibaia, SP, Brazil.
Abstract
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 ~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.
Keywords in Portuguese
gatos
Keywords
cats
Publisher
American Association for the Advancement of Science
Citation
FIGUEIRÓ, Henrique Vieira et al. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Sci Adv., v. 3, n. 7, e1700299, 2017.
DOI
10.1126/sciadv.1700299
ISSN
2375-2548