Biology Faculty Articles


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


Henrique V. Figueiró, Pontifícia Universidade Católica do Rio Grande do Sul
Gang Li, Texas A&M College of Veterinary Medicine & Biomedical Sciences
Fernanda J. Trindade, Pontifícia Universidade Católica do Rio Grande do Sul
Juliana Assis, Fundacao Oswaldo Cruz
Fabiano Pais, Fundacao Oswaldo Cruz
Gabriel Fernandes, Fundacao Oswaldo Cruz
Sarah H.D. Santos, Pontifícia Universidade Católica do Rio Grande do Sul
Graham M. Hughes, University College Dublin
Aleksey Komissarov, Saint Petersburg State University
Agostinho Antunes, University of Porto, Interdisciplinary Centre of Marine and Environmental Research
Cristine S. Trinca, Pontifícia Universidade Católica do Rio Grande do Sul
Maíra R. Rodrigues, Pontifícia Universidade Católica do Rio Grande do Sul
Tyler Linderoth, University of California, Berkeley
Ke Bi, California Institute for Quantitative Biosciences
Leandro Silveira, Jaguar Conservation Fund/Instituto Onça-Pintada
Fernando C.C. Azevedo, Universidade Federal de São João del-Rey
Daniel Kantek, Pontifícia Universidade Católica do Rio Grande do Sul
Emiliano Ramalho, Instituto Pró-Carnívoros
Ricardo A. Brassaloti, Universidade de São Paulo
Priscilla M.S. Villela, Universidade de São Paulo
Adauto L.V. Nunes, Zoológico Municipal de Sorocaba
Rodrigo H.F. Teixeira, Zoológico Municipal de Sorocaba
Ronaldo G. Morato, Instituto Pró-Carnívoros
Damian Loska, Centro de Regulacion Genomica, Barcelona
Patricia Saragüeta, Instituto de Biologia y Medicina Experimental
Toni Gabaldón, Centro de Regulacion Genomica, Barcelona
Emma C. Teeling, University College Dublin
Stephen J. O'Brien, Saint Petersburg State UniversityFollow
Rasmus Nielsen, University of California, Berkeley

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Science Advances








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 phylogenywhile 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.