Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Abascal, Federico; Corvelo, André; Cruz, Fernando; Villanueva Cañas, José Luis, 1984-; Vlasova, Anna; Marcet Houben, Marina; Prieto Barja, Pablo, 1986-; Quilez Oliete, Javier; Frias, Leonor; Ribeca, Paolo; Capella Gutiérrez, Salvador Jesús, 1985-; Câmara Ferreira, Francisco; Lowy Gallego, Ernesto; Cozzuto, Luca; Erb, Ionas; Rodríguez Ales, José Luis; Ruiz Orera, Jorge, 1988-; Reverter, Ferran; Derdak, Sophia; Blanc, Julie; Gut, Marta; Lorente-Galdós, Belén, 1981-; Gut, Ivo Glynne; Guigó Serra, Roderic; Gabaldón Estevan, Juan Antonio, 1973-; Godoy, José A.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

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dc.contributor.author Abascal, Federicoca
dc.contributor.author Corvelo, Andréca
dc.contributor.author Cruz, Fernandoca
dc.contributor.author Villanueva Cañas, José Luis, 1984-ca
dc.contributor.author Vlasova, Annaca
dc.contributor.author Marcet Houben, Marinaca
dc.contributor.author Prieto Barja, Pablo, 1986-ca
dc.contributor.author Quilez Oliete, Javierca
dc.contributor.author Frias, Leonorca
dc.contributor.author Ribeca, Paoloca
dc.contributor.author Capella Gutiérrez, Salvador Jesús, 1985-ca
dc.contributor.author Câmara Ferreira, Franciscoca
dc.contributor.author Lowy Gallego, Ernestoca
dc.contributor.author Cozzuto, Lucaca
dc.contributor.author Erb, Ionasca
dc.contributor.author Rodríguez Ales, José Luisca
dc.contributor.author Ruiz Orera, Jorge, 1988-ca
dc.contributor.author Reverter, Ferranca
dc.contributor.author Derdak, Sophiaca
dc.contributor.author Blanc, Julieca
dc.contributor.author Gut, Martaca
dc.contributor.author Lorente-Galdós, Belén, 1981-ca
dc.contributor.author Gut, Ivo Glynneca
dc.contributor.author Guigó Serra, Rodericca
dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
dc.contributor.author Godoy, José A.ca
dc.date.accessioned 2017-03-06T13:51:46Z
dc.date.available 2017-03-06T13:51:46Z
dc.date.issued 2016
dc.description.abstract Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. Results: We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. Conclusions: The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.
dc.description.sponsorship The financial support for this work was provided by Banco de Santander, CSIC, and Fundación General CSIC through a “Proyectos Cero” grant. FC and BM-C were hired under the EcoGenes project funded by the European FP7 program (264125-FP7-REGPOT-2010-1) and AVl and FCa under the INB Project PT13/0001/0021 (ISCIII - Subdirección General de Evaluación y Fomento de la Investigación/FEDER “Una Manera de hacer Europa”). EBD-CSIC and CRG received support from the Spanish Ministry of Economy and Competitiveness under the “Centro de Excelencia Severo Ochoa 2013-2017” program, grants SEV-2012-0262 and SEV-2012-0208.
dc.format.mimetype application/pdfca
dc.identifier.citation Abascal F, Corvelo A, Cruz F, Villanueva Cañas JL, Vlasova A, Marcet-Houben M et. al. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lyn. Genome Biology. 2016;17:251. DOI: 10.1186/s13059-016-1090-1
dc.identifier.doi http://dx.doi.org/10.1186/s13059-016-1090-1
dc.identifier.issn 1474-760X
dc.identifier.uri http://hdl.handle.net/10230/28171
dc.language.iso eng
dc.publisher BioMed Centralca
dc.relation.ispartof Genome Biology. 2016;17:251
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/264125
dc.rights © The Author(s). 2016. Open Access. 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.
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.keyword Conservation genomics
dc.subject.keyword Genetic diversity
dc.subject.keyword Inbreeding
dc.subject.keyword Genetic drift
dc.subject.keyword Lynx
dc.title Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynxca
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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