Genetic load of loss-of-function polymorphic variants in great apes
Loss of function (LoF) genetic variants are predicted to disrupt gene function, and are therefore expected to substantially reduce individual's viability. Knowing the genetic burden of LoF variants in endangered species is of interest for a better understanding of the effects of declining p...
| Autores: | , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2016 |
| País: | España |
| Institución: | 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:10230/26284 |
| Acceso en línea: | http://hdl.handle.net/10230/26284 http://dx.doi.org/10.1093/gbe/evw040 |
| Access Level: | acceso abierto |
| Palabra clave: | Goril·les Genètica animal Great apes diversity Comparative genomics Genetic load Loss of function |
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Genetic load of loss-of-function polymorphic variants in great apesde Valles-Ibáñez, GuillemHernández Rodríguez, Jéssica, 1983-Prado Martínez, Javier, 1987-Luisi, Pierre, 1985-Marquès i Bonet, Tomàs, 1975-Casals López, FerranGoril·lesGenètica animalGreat apes diversityComparative genomicsGenetic loadLoss of functionLoss of function (LoF) genetic variants are predicted to disrupt gene function, and are therefore expected to substantially reduce individual's viability. Knowing the genetic burden of LoF variants in endangered species is of interest for a better understanding of the effects of declining population sizes on species viability. In this study, we have estimated the number of LoF polymorphic variants in six great ape populations, based on whole-genome sequencing data in 79 individuals. Our results show that although the number of functional variants per individual is conditioned by the effective population size, the number of variants with a drastic phenotypic effect is very similar across species. We hypothesize that for those variants with high selection coefficients, differences in effective population size are not important enough to affect the efficiency of natural selection to remove them. We also describe that mostly CpG LoF mutations are shared across species, and an accumulation of LoF variants at olfactory receptor genes in agreement with its pseudogenization in humans and other primate species.The authors thank funding to F.C. by grant SAF2012-35025 from the Ministerio de Economía y Competitividad (Spain) and FEDER and by Direcció General de Recerca, Generalitat de Catalunya (2014SGR-866). T.M.B. is supported by EMBO YIP 2013, MINECO BFU2011-28549, BFU2014-55090-P (FEDER), BFU2015-7116-ERC and BFU2015-6215-ERC (www.mecd.gob.es), NIH U01 MH106874 grant and Fundació Zoo Barcelona.Oxford University Press201620162016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/26284http://dx.doi.org/10.1093/gbe/evw040reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésGenome biology and evolution. 2016; 2(1): 871-877info:eu-repo/grantAgreement/ES/3PN/BFU2011-28549info:eu-repo/grantAgreement/ES/1PE/BFU2014-55090-Pinfo:eu-repo/grantAgreement/ES/1PE/BFU2015-7116-ERC© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution./nThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/262842026-05-29T05:05:01Z |
| dc.title.none.fl_str_mv |
Genetic load of loss-of-function polymorphic variants in great apes |
| title |
Genetic load of loss-of-function polymorphic variants in great apes |
| spellingShingle |
Genetic load of loss-of-function polymorphic variants in great apes de Valles-Ibáñez, Guillem Goril·les Genètica animal Great apes diversity Comparative genomics Genetic load Loss of function |
| title_short |
Genetic load of loss-of-function polymorphic variants in great apes |
| title_full |
Genetic load of loss-of-function polymorphic variants in great apes |
| title_fullStr |
Genetic load of loss-of-function polymorphic variants in great apes |
| title_full_unstemmed |
Genetic load of loss-of-function polymorphic variants in great apes |
| title_sort |
Genetic load of loss-of-function polymorphic variants in great apes |
| dc.creator.none.fl_str_mv |
de Valles-Ibáñez, Guillem Hernández Rodríguez, Jéssica, 1983- Prado Martínez, Javier, 1987- Luisi, Pierre, 1985- Marquès i Bonet, Tomàs, 1975- Casals López, Ferran |
| author |
de Valles-Ibáñez, Guillem |
| author_facet |
de Valles-Ibáñez, Guillem Hernández Rodríguez, Jéssica, 1983- Prado Martínez, Javier, 1987- Luisi, Pierre, 1985- Marquès i Bonet, Tomàs, 1975- Casals López, Ferran |
| author_role |
author |
| author2 |
Hernández Rodríguez, Jéssica, 1983- Prado Martínez, Javier, 1987- Luisi, Pierre, 1985- Marquès i Bonet, Tomàs, 1975- Casals López, Ferran |
| author2_role |
author author author author author |
| dc.subject.none.fl_str_mv |
Goril·les Genètica animal Great apes diversity Comparative genomics Genetic load Loss of function |
| topic |
Goril·les Genètica animal Great apes diversity Comparative genomics Genetic load Loss of function |
| description |
Loss of function (LoF) genetic variants are predicted to disrupt gene function, and are therefore expected to substantially reduce individual's viability. Knowing the genetic burden of LoF variants in endangered species is of interest for a better understanding of the effects of declining population sizes on species viability. In this study, we have estimated the number of LoF polymorphic variants in six great ape populations, based on whole-genome sequencing data in 79 individuals. Our results show that although the number of functional variants per individual is conditioned by the effective population size, the number of variants with a drastic phenotypic effect is very similar across species. We hypothesize that for those variants with high selection coefficients, differences in effective population size are not important enough to affect the efficiency of natural selection to remove them. We also describe that mostly CpG LoF mutations are shared across species, and an accumulation of LoF variants at olfactory receptor genes in agreement with its pseudogenization in humans and other primate species. |
| publishDate |
2016 |
| dc.date.none.fl_str_mv |
2016 2016 2016 |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10230/26284 http://dx.doi.org/10.1093/gbe/evw040 |
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http://hdl.handle.net/10230/26284 http://dx.doi.org/10.1093/gbe/evw040 |
| dc.language.none.fl_str_mv |
Inglés |
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Inglés |
| dc.relation.none.fl_str_mv |
Genome biology and evolution. 2016; 2(1): 871-877 info:eu-repo/grantAgreement/ES/3PN/BFU2011-28549 info:eu-repo/grantAgreement/ES/1PE/BFU2014-55090-P info:eu-repo/grantAgreement/ES/1PE/BFU2015-7116-ERC |
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http://creativecommons.org/licenses/by-nc/4.0/ info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by-nc/4.0/ |
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openAccess |
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application/pdf application/pdf |
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Oxford University Press |
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Oxford University Press |
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Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
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