Genomes reveal marked differences in the adaptive evolution between orangutan species

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• dc.contributor.author Mattle-Greminger, Maja P.
• dc.contributor.author Bilgin Sonay, Tugce
• dc.contributor.author Nater, Alexander
• dc.contributor.author Pybus Oliveras, Marc, 1985-
• dc.contributor.author Desai, Tariq
• dc.contributor.author de Valles-Ibáñez, Guillem
• dc.contributor.author Casals López, Ferran
• dc.contributor.author Scally, Aylwyn
• dc.contributor.author Bertranpetit, Jaume, 1952-
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-
• dc.contributor.author Van Schaik, Carel P.
• dc.contributor.author Anisimova, Maria
• dc.contributor.author Krützen, Michael
• dc.date.accessioned 2019-01-28T17:31:07Z
• dc.date.available 2019-01-28T17:31:07Z
• dc.date.issued 2018
• dc.description.abstract Background: Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. Here, we used whole-genome sequencing data from critically endangered orangutans from North Sumatra (Pongo abelii) and Borneo (P. pygmaeus) to investigate adaptive responses of each species to environmental differences during the Pleistocene. Results: Taking into account the markedly disparate demographic histories of each species after their split ~ 1 Ma ago, we show that persistent environmental differences on each island had a strong impact on the adaptive evolution of the genus Pongo. Across a range of tests for positive selection, we find a consistent pattern of between-island and species differences. In the more productive Sumatran environment, the most notable signals of positive selection involve genes linked to brain and neuronal development, learning, and glucose metabolism. On Borneo, however, positive selection comprised genes involved in lipid metabolism, as well as cardiac and muscle activities. Conclusions: We find strikingly different sets of genes appearing to have evolved under strong positive selection in each species. In Sumatran orangutans, selection patterns were congruent with well-documented cognitive and behavioral differences between the species, such as a larger and more complex cultural repertoire and higher degrees of sociality. However, in Bornean orangutans, selective responses to fluctuating environmental conditions appear to have produced physiological adaptations to generally lower and temporally more unpredictable food supplies.
• dc.description.sponsorship This work was financially supported by University of Zurich Forschungskredit grants FK-10 (MPMG), FK-15-103 (AN), and FK-14-094 (TBS), Swiss National Science Foundation grants 3100A-116848 (MK, CvS) and P300PA_177852 (AN), Leakey Foundation (MPMG), UZH Research Priority Program “Evolution in Action” (MK), MINECO/FEDER UE BFU2017-86471-P (TMB), U01 MH106874 (TMB), Howard Hughes International Early Career (TMB), Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (TMB), Julius–Klaus Foundation (MK), Ministerio de Economía y Competitividad grant BFU2013-43726-P (JB, MP), Gates Cambridge Trust (TD), A.H. Schultz Foundation grants (MK, MPMG), and the Department of Anthropology at the University of Zurich.
• dc.format.mimetype application/pdf
• dc.identifier.citation Mattle-Greminger MP, Bilgin Sonay T, Nater A, Pybus M, Desai T, de Valles G et al. Genomes reveal marked differences in the adaptive evolution between orangutan species. Genome Biol. 2018;19(1):193. DOI 10.1186/s13059-018-1562-6
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-018-1562-6
• dc.identifier.issn 1474-7596
• dc.identifier.uri http://hdl.handle.net/10230/36447
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof Genome Biology. 2018;19(1):193
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2013-43726-P
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2017-86471-P
• dc.rights © The Author(s). 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Local adaptation
• dc.subject.keyword Great apes
• dc.subject.keyword Demographic history
• dc.subject.keyword Cognitive evolution
• dc.subject.keyword Pongo
• dc.subject.keyword Pleistocene glaciations
• dc.title Genomes reveal marked differences in the adaptive evolution between orangutan species
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion