Evolutionary signals of selection on cognition from the great tit genome and methylome
[EN] For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important t...
| Autores: | , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2016 |
| País: | España |
| Institución: | Universitat Politècnica de València (UPV) |
| Repositorio: | RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia |
| Idioma: | inglés |
| OAI Identifier: | oai:riunet.upv.es:10251/62805 |
| Acceso en línea: | https://riunet.upv.es/handle/10251/62805 |
| Access Level: | acceso abierto |
| Palabra clave: | Wild bird population Sequencing data Phenotypic plasticity Parus major Clutch size Alignment Generation History Memory Animal life ZOOLOGIA |
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Evolutionary signals of selection on cognition from the great tit genome and methylome |
| title |
Evolutionary signals of selection on cognition from the great tit genome and methylome |
| spellingShingle |
Evolutionary signals of selection on cognition from the great tit genome and methylome Laine, Veronika N. Wild bird population Sequencing data Phenotypic plasticity Parus major Clutch size Alignment Generation History Memory Animal life ZOOLOGIA |
| title_short |
Evolutionary signals of selection on cognition from the great tit genome and methylome |
| title_full |
Evolutionary signals of selection on cognition from the great tit genome and methylome |
| title_fullStr |
Evolutionary signals of selection on cognition from the great tit genome and methylome |
| title_full_unstemmed |
Evolutionary signals of selection on cognition from the great tit genome and methylome |
| title_sort |
Evolutionary signals of selection on cognition from the great tit genome and methylome |
| dc.creator.none.fl_str_mv |
Laine, Veronika N. Gossmann, Toni I. Schachtschneider, Kyle M. Garroway, Colin J. Madsen, Ole Verhoeven, Koen J. F. de Jager, Victor Megens, Hendrik-Jan Warren, Wesley C. Minx, Patrick Crooijmans, Richard P. M. A. Corcoran, Padraic Great Tit HapMap Consortium Sheldon, Ben C. Slate, Jon |
| author |
Laine, Veronika N. |
| author_facet |
Laine, Veronika N. Gossmann, Toni I. Schachtschneider, Kyle M. Garroway, Colin J. Madsen, Ole Verhoeven, Koen J. F. de Jager, Victor Megens, Hendrik-Jan Warren, Wesley C. Minx, Patrick Crooijmans, Richard P. M. A. Corcoran, Padraic Great Tit HapMap Consortium Sheldon, Ben C. Slate, Jon |
| author_role |
author |
| author2 |
Gossmann, Toni I. Schachtschneider, Kyle M. Garroway, Colin J. Madsen, Ole Verhoeven, Koen J. F. de Jager, Victor Megens, Hendrik-Jan Warren, Wesley C. Minx, Patrick Crooijmans, Richard P. M. A. Corcoran, Padraic Great Tit HapMap Consortium Sheldon, Ben C. Slate, Jon |
| author2_role |
author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
European Research Council Biotechnology and Biological Sciences Research Council, Reino Unido UK Research and Innovation Netherlands Organization for Scientific Research International HapMap Project Rural Development Administration, Corea del Sur Repositorio Institucional de la Universitat Politècnica de València Riunet |
| dc.subject.none.fl_str_mv |
Wild bird population Sequencing data Phenotypic plasticity Parus major Clutch size Alignment Generation History Memory Animal life ZOOLOGIA |
| topic |
Wild bird population Sequencing data Phenotypic plasticity Parus major Clutch size Alignment Generation History Memory Animal life ZOOLOGIA |
| description |
[EN] For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory-and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species. |
| publishDate |
2016 |
| dc.date.none.fl_str_mv |
2016 2016-01-01 |
| dc.type.none.fl_str_mv |
journal article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
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article |
| dc.identifier.none.fl_str_mv |
https://riunet.upv.es/handle/10251/62805 |
| url |
https://riunet.upv.es/handle/10251/62805 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.relation.none.fl_str_mv |
UK Research and Innovation https://doi.org/10.13039/100014013 NE%2FK01126X%2FK1 Spatial ecological genomics of free-ranging Great tits UK Research and Innovation https://doi.org/10.13039/100014013 NE%2FJ012599%2FK1 Spatial ecological genomics of free-ranging Great tits UK Research and Innovation https://doi.org/10.13039/100014013 NE%2FL005328%2F1 GB Netherlands Organization for Scientific Research https://doi.org/10.13039/501100003246 2300162398 UK Research and Innovation https://doi.org/10.13039/100014013 BB%2FK000209%2F1 The effects of natural selection on genome-wide patterns of genetic variation European Commission https://doi.org/10.13039/501100000780 FP7 250164 Evolutionary Social Ecology in Wild Populations European Commission https://doi.org/10.13039/501100000780 FP7 202487 Evolutionary genetics in a ‘classical’ avian study system by high throughput transcriptome sequencing and SNP genotyping European Commission https://doi.org/10.13039/501100000780 FP7 339092 Evolutionary responses to a warming world: physiological genomics of seasonal timing Rural Development Administration, Corea del Sur https://doi.org/10.13039/501100003627 PJ009103 Netherlands Organization for Scientific Research https://doi.org/10.13039/501100003246 864.10.008 |
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open access http://purl.org/coar/access_right/c_abf2 Reconocimiento (by) http://creativecommons.org/licenses/by/4.0/ |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 Reconocimiento (by) http://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf |
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Nature Publishing Group: Nature Communications |
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Nature Publishing Group: Nature Communications |
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reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia instname:Universitat Politècnica de València (UPV) |
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Universitat Politècnica de València (UPV) |
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RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia |
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RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia |
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1869404364658966528 |
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Evolutionary signals of selection on cognition from the great tit genome and methylomeLaine, Veronika N.Gossmann, Toni I.Schachtschneider, Kyle M.Garroway, Colin J.Madsen, OleVerhoeven, Koen J. F.de Jager, VictorMegens, Hendrik-JanWarren, Wesley C.Minx, PatrickCrooijmans, Richard P. M. A.Corcoran, PadraicGreat Tit HapMap ConsortiumSheldon, Ben C.Slate, JonWild bird populationSequencing dataPhenotypic plasticityParus majorClutch sizeAlignmentGenerationHistoryMemoryAnimal lifeZOOLOGIA[EN] For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory-and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species.We thank Eveline Verhulst for help with the methylome data, Christa Mateman for lab assistance, Martijn Derks for calculating the sliding windows, Tieshan Xu for the help with the Trinity assembly, Louise Dittmar for the help in dN/dS and diversity analysis, Christian Huber for help on the sweep analysis and Jun-Mo Kim who designed the SNP chip. K.M.S. was supported by a grant from the Cooperative Research Program for Agriculture Science & Technology Development (PJ009103) of the Rural Development Administration, Republic of Korea. T.I.G., P.C. and K.Z. were supported by a BBSRC grant (BB/K000209/1) and a NERC grant (NE/L005328/1) awarded to K.Z., C.J.G. was funded by Natural Environment Research Council (NERC) (NE/K01126X/1). K.J.F.V. was funded by the Dutch Organisation for Scientific Research, NWO VIDI grant (864.10.008). B.C.S. was funded by ERC Advanced Grant (250164) and by a Wolfson Merit Award from the Royal Society. J.S. was funded by a European Research Council (ERC) Starting grant, Avian EGG (202487) and a Natural Environment Research Council (NERC), The Great Tit HapMap Project (NE/J012599/1). M.E.V. was supported by the Netherlands Organisation for Scientific Research (NWO-VICI grant) and the European Research Council (ERC-2013-AdG 339092).Nature Publishing Group: Nature CommunicationsEuropean Research CouncilBiotechnology and Biological Sciences Research Council, Reino UnidoUK Research and InnovationNetherlands Organization for Scientific ResearchInternational HapMap ProjectRural Development Administration, Corea del SurRepositorio Institucional de la Universitat Politècnica de València Riunet20162016-01-01journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://riunet.upv.es/handle/10251/62805reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valénciainstname:Universitat Politècnica de València (UPV)InglésengUK Research and Innovation https://doi.org/10.13039/100014013 NE%2FK01126X%2FK1 Spatial ecological genomics of free-ranging Great titsUK Research and Innovation https://doi.org/10.13039/100014013 NE%2FJ012599%2FK1 Spatial ecological genomics of free-ranging Great titsUK Research and Innovation https://doi.org/10.13039/100014013 NE%2FL005328%2F1 GBNetherlands Organization for Scientific Research https://doi.org/10.13039/501100003246 2300162398UK Research and Innovation https://doi.org/10.13039/100014013 BB%2FK000209%2F1 The effects of natural selection on genome-wide patterns of genetic variationEuropean Commission https://doi.org/10.13039/501100000780 FP7 250164 Evolutionary Social Ecology in Wild PopulationsEuropean Commission https://doi.org/10.13039/501100000780 FP7 202487 Evolutionary genetics in a ‘classical’ avian study system by high throughput transcriptome sequencing and SNP genotypingEuropean Commission https://doi.org/10.13039/501100000780 FP7 339092 Evolutionary responses to a warming world: physiological genomics of seasonal timingRural Development Administration, Corea del Sur https://doi.org/10.13039/501100003627 PJ009103Netherlands Organization for Scientific Research https://doi.org/10.13039/501100003246 864.10.008open accesshttp://purl.org/coar/access_right/c_abf2Reconocimiento (by)http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:riunet.upv.es:10251/628052026-06-13T07:49:27Z |
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15,300719 |