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

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• dc.contributor.author Figueiró, Henrique V.
• dc.contributor.author Loska, Damian
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
• dc.contributor.author Eizirik, Eduardo
• dc.date.accessioned 2023-12-19T06:57:06Z
• dc.date.available 2023-12-19T06:57:06Z
• dc.date.issued 2017
• dc.description.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.
• dc.format.mimetype application/pdf
• dc.identifier.citation Figueiró HV, Li G, Trindade FJ, Assis J, Pais F, Fernandes G, et al. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Sci Adv. 2017 Jul 7;3(7):e1700299. DOI: 10.1126/sciadv.1700299
• dc.identifier.doi http://dx.doi.org/10.1126/sciadv.1700299
• dc.identifier.issn 2375-2548
• dc.identifier.uri http://hdl.handle.net/10230/58580
• dc.language.iso eng
• dc.publisher American Association for the Advancement of Science (AAAS)
• dc.relation.ispartof Science Advances. 2017 Jul 7;3(7):e1700299
• dc.rights Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.other Gats
• dc.subject.other Evolució
• dc.subject.other Genètica animal
• dc.title Genome-wide signatures of complex introgression and adaptive evolution in the big cats
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion