Evolutionary signals of selection on cognition from the great tit genome and methylome

V.N. Laine, T.I. Gossmann, K.M. Schachtschneider, C.J. Garroway, Ole Madsen, K.J.F. Verhoeven, Victor De Jager, Hendrik Jan Megens, W.C. Warren, Patrick Minx, R.P.M.A. Crooijmans, Pádraic Corcoran, Frank Adriaensen, Eduardo Belda, Andrey Bushuev, Mariusz Cichon, Anne Charmantier, Niels Dingemanse, Blandine Doligez, Tapio Eeva & 26 others Kjell Einar Erikstad, Slava Fedorov, Michaela Hau, Sabine Hille, Camilla Hinde, Bart Kempenaers, Anvar Kerimov, Milos Krist, Raivo Mand, Erik Matthysen, Reudi Nager, Claudia Norte, Markku Orell, Heinz Richner, Tore Slagsvold, Vallo Tilgar, Joost Tinbergen, Janos Torok, Barbara Tschirren, Tera Yuta, B.C. Sheldon, Jon Slate, Kai Zeng, Kees Van Oers, M.E. Visser, M.A.M. Groenen

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

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.

LanguageEnglish
Article number10474
JournalNature Communications
Volume7
DOIs
Publication statusPublished - 2016

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cognition
genome
Cognition
learning
methylation
Genes
Learning
Genome
Methylation
Behavioral Research
mammals
Behavioral research
Epigenomics
plastic properties
genes
Mammals
assembly
Plasticity
Research
Data storage equipment

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Laine, V.N. ; Gossmann, T.I. ; Schachtschneider, K.M. ; Garroway, C.J. ; Madsen, Ole ; Verhoeven, K.J.F. ; De Jager, Victor ; Megens, Hendrik Jan ; Warren, W.C. ; Minx, Patrick ; Crooijmans, R.P.M.A. ; Corcoran, Pádraic ; Adriaensen, Frank ; Belda, Eduardo ; Bushuev, Andrey ; Cichon, Mariusz ; Charmantier, Anne ; Dingemanse, Niels ; Doligez, Blandine ; Eeva, Tapio ; Erikstad, Kjell Einar ; Fedorov, Slava ; Hau, Michaela ; Hille, Sabine ; Hinde, Camilla ; Kempenaers, Bart ; Kerimov, Anvar ; Krist, Milos ; Mand, Raivo ; Matthysen, Erik ; Nager, Reudi ; Norte, Claudia ; Orell, Markku ; Richner, Heinz ; Slagsvold, Tore ; Tilgar, Vallo ; Tinbergen, Joost ; Torok, Janos ; Tschirren, Barbara ; Yuta, Tera ; Sheldon, B.C. ; Slate, Jon ; Zeng, Kai ; Van Oers, Kees ; Visser, M.E. ; Groenen, M.A.M. / Evolutionary signals of selection on cognition from the great tit genome and methylome. In: Nature Communications. 2016 ; Vol. 7.
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title = "Evolutionary signals of selection on cognition from the great tit genome and methylome",
abstract = "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.",
author = "V.N. Laine and T.I. Gossmann and K.M. Schachtschneider and C.J. Garroway and Ole Madsen and K.J.F. Verhoeven and {De Jager}, Victor and Megens, {Hendrik Jan} and W.C. Warren and Patrick Minx and R.P.M.A. Crooijmans and P{\'a}draic Corcoran and Frank Adriaensen and Eduardo Belda and Andrey Bushuev and Mariusz Cichon and Anne Charmantier and Niels Dingemanse and Blandine Doligez and Tapio Eeva and Erikstad, {Kjell Einar} and Slava Fedorov and Michaela Hau and Sabine Hille and Camilla Hinde and Bart Kempenaers and Anvar Kerimov and Milos Krist and Raivo Mand and Erik Matthysen and Reudi Nager and Claudia Norte and Markku Orell and Heinz Richner and Tore Slagsvold and Vallo Tilgar and Joost Tinbergen and Janos Torok and Barbara Tschirren and Tera Yuta and B.C. Sheldon and Jon Slate and Kai Zeng and {Van Oers}, Kees and M.E. Visser and M.A.M. Groenen",
year = "2016",
doi = "10.1038/ncomms10474",
language = "English",
volume = "7",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",

}

Laine, VN, Gossmann, TI, Schachtschneider, KM, Garroway, CJ, Madsen, O, Verhoeven, KJF, De Jager, V, Megens, HJ, Warren, WC, Minx, P, Crooijmans, RPMA, Corcoran, P, Adriaensen, F, Belda, E, Bushuev, A, Cichon, M, Charmantier, A, Dingemanse, N, Doligez, B, Eeva, T, Erikstad, KE, Fedorov, S, Hau, M, Hille, S, Hinde, C, Kempenaers, B, Kerimov, A, Krist, M, Mand, R, Matthysen, E, Nager, R, Norte, C, Orell, M, Richner, H, Slagsvold, T, Tilgar, V, Tinbergen, J, Torok, J, Tschirren, B, Yuta, T, Sheldon, BC, Slate, J, Zeng, K, Van Oers, K, Visser, ME & Groenen, MAM 2016, 'Evolutionary signals of selection on cognition from the great tit genome and methylome', Nature Communications, vol. 7, 10474. https://doi.org/10.1038/ncomms10474

Evolutionary signals of selection on cognition from the great tit genome and methylome. / Laine, V.N.; Gossmann, T.I.; Schachtschneider, K.M.; Garroway, C.J.; Madsen, Ole; Verhoeven, K.J.F.; De Jager, Victor; Megens, Hendrik Jan; Warren, W.C.; Minx, Patrick; Crooijmans, R.P.M.A.; Corcoran, Pádraic; Adriaensen, Frank; Belda, Eduardo; Bushuev, Andrey; Cichon, Mariusz; Charmantier, Anne; Dingemanse, Niels; Doligez, Blandine; Eeva, Tapio; Erikstad, Kjell Einar; Fedorov, Slava; Hau, Michaela; Hille, Sabine; Hinde, Camilla; Kempenaers, Bart; Kerimov, Anvar; Krist, Milos; Mand, Raivo; Matthysen, Erik; Nager, Reudi; Norte, Claudia; Orell, Markku; Richner, Heinz; Slagsvold, Tore; Tilgar, Vallo; Tinbergen, Joost; Torok, Janos; Tschirren, Barbara; Yuta, Tera; Sheldon, B.C.; Slate, Jon; Zeng, Kai; Van Oers, Kees; Visser, M.E.; Groenen, M.A.M.

In: Nature Communications, Vol. 7, 10474, 2016.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Evolutionary signals of selection on cognition from the great tit genome and methylome

AU - Laine, V.N.

AU - Gossmann, T.I.

AU - Schachtschneider, K.M.

AU - Garroway, C.J.

AU - Madsen, Ole

AU - Verhoeven, K.J.F.

AU - De Jager, Victor

AU - Megens, Hendrik Jan

AU - Warren, W.C.

AU - Minx, Patrick

AU - Crooijmans, R.P.M.A.

AU - Corcoran, Pádraic

AU - Adriaensen, Frank

AU - Belda, Eduardo

AU - Bushuev, Andrey

AU - Cichon, Mariusz

AU - Charmantier, Anne

AU - Dingemanse, Niels

AU - Doligez, Blandine

AU - Eeva, Tapio

AU - Erikstad, Kjell Einar

AU - Fedorov, Slava

AU - Hau, Michaela

AU - Hille, Sabine

AU - Hinde, Camilla

AU - Kempenaers, Bart

AU - Kerimov, Anvar

AU - Krist, Milos

AU - Mand, Raivo

AU - Matthysen, Erik

AU - Nager, Reudi

AU - Norte, Claudia

AU - Orell, Markku

AU - Richner, Heinz

AU - Slagsvold, Tore

AU - Tilgar, Vallo

AU - Tinbergen, Joost

AU - Torok, Janos

AU - Tschirren, Barbara

AU - Yuta, Tera

AU - Sheldon, B.C.

AU - Slate, Jon

AU - Zeng, Kai

AU - Van Oers, Kees

AU - Visser, M.E.

AU - Groenen, M.A.M.

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

U2 - 10.1038/ncomms10474

DO - 10.1038/ncomms10474

M3 - Article

VL - 7

JO - Nature Communications

T2 - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 10474

ER -