Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
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...
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2016 |
| País: | España |
| Recursos: | Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
| Repositorio: | Recercat. Dipósit de la Recerca de Catalunya |
| OAI Identifier: | oai:recercat.cat:10230/28171 |
| Acesso em linha: | http://hdl.handle.net/10230/28171 http://dx.doi.org/10.1186/s13059-016-1090-1 |
| Access Level: | acceso abierto |
| Palavra-chave: | Conservation genomics Genetic diversity Inbreeding Genetic drift Lynx |
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Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynxAbascal, FedericoCorvelo, AndréCruz, FernandoVillanueva Cañas, José Luis, 1984-Vlasova, AnnaMarcet Houben, MarinaPrieto Barja, Pablo, 1986-Quilez Oliete, JavierFrias, LeonorRibeca, PaoloCapella Gutiérrez, Salvador Jesús, 1985-Câmara Ferreira, FranciscoLowy Gallego, ErnestoCozzuto, LucaErb, IonasRodríguez Ales, José LuisRuiz Orera, Jorge, 1988-Reverter Comes, FerranDerdak, SophiaBlanc, JulieGut, MartaLorente-Galdós, Belén, 1981-Gut, Ivo GlynneGuigó Serra, RodericGabaldón Estevan, Juan Antonio, 1973-Godoy, José A.Conservation genomicsGenetic diversityInbreedingGenetic driftLynxBackground: 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.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.BioMed Central201720172016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/28171http://dx.doi.org/10.1186/s13059-016-1090-1reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésGenome Biology. 2016;17:251info:eu-repo/grantAgreement/EC/FP7/264125© 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.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/281712026-05-29T05:05:01Z |
| dc.title.none.fl_str_mv |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx |
| title |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx |
| spellingShingle |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx Abascal, Federico Conservation genomics Genetic diversity Inbreeding Genetic drift Lynx |
| title_short |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx |
| title_full |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx |
| title_fullStr |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx |
| title_full_unstemmed |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx |
| title_sort |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx |
| dc.creator.none.fl_str_mv |
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 Comes, 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. |
| author |
Abascal, Federico |
| author_facet |
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 Comes, 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. |
| author_role |
author |
| author2 |
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 Comes, 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. |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Conservation genomics Genetic diversity Inbreeding Genetic drift Lynx |
| topic |
Conservation genomics Genetic diversity Inbreeding Genetic drift Lynx |
| description |
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. |
| publishDate |
2016 |
| dc.date.none.fl_str_mv |
2016 2017 2017 |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10230/28171 http://dx.doi.org/10.1186/s13059-016-1090-1 |
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http://hdl.handle.net/10230/28171 http://dx.doi.org/10.1186/s13059-016-1090-1 |
| dc.language.none.fl_str_mv |
Inglés |
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Inglés |
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Genome Biology. 2016;17:251 info:eu-repo/grantAgreement/EC/FP7/264125 |
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http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf application/pdf |
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BioMed Central |
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BioMed Central |
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