Epigenetics and the city: Non‐parallel DNA methylation modifications across pairs of urban‐forest Great tit populations
In: ISSN: 1752-4563, 2022
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academicJournal
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DNA sequences: RAD-seq GenBank accessions SRR17125662- SRR17125721, RRBS-seq GenBank accessions SRR17145241-SRR17145300; NCBI project PRJNA786007. Scripts: Github repository https://github.com/AudeCaizergues/Epigenetics_and_the_city. ; International audience ; Identifying the molecular mechanisms involved in rapid adaptation to novel environments and determining their predictability are central questions in evolutionary biology and pressing issues due to rapid global changes. Complementary to genetic responses to selection, faster epigenetic variations such as modifications of DNA methylation may play a substantial role in rapid adaptation. In the context of rampant urbanization, joint examinations of genomic and epigenomic mechanisms are still lacking. Here, we investigated genomic (SNP) and epigenomic (CpG methylation) responses to urban life in a passerine bird, the Great tit (Parus major). To test whether urban evolution is predictable (i.e. parallel) or involves mostly nonparallel molecular processes among cities, we analysed both SNP and CpG methylation variations across three distinct pairs of city and forest Great tit populations in Europe. Our analyses reveal a polygenic response to urban life, with both many genes putatively under weak divergent selection and multiple differentially methylated regions (DMRs) between forest and city great tits. DMRs mainly overlapped transcription start sites and promotor regions, suggesting their importance in modulating gene expression. Both genomic and epigenomic outliers were found in genomic regions enriched for genes with biological functions related to the nervous system, immunity, or behavioural, hormonal and stress responses. Interestingly, comparisons across the three pairs of city-forest populations suggested little parallelism in both genetic and epigenetic responses. Our results confirm, at both the genetic and epigenetic levels, hypotheses of polygenic and largely nonparallel mechanisms of rapid adaptation in novel environments such as urbanized areas.
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Epigenetics and the city: Non‐parallel DNA methylation modifications across pairs of urban‐forest Great tit populations
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Autor/in / Beteiligte Person: | Caizergues, Aude, E. ; Le Luyer, Jeremy ; Grégoire, Arnaud ; Szulkin, Marta ; Senar, Juan-Carlos ; Charmantier, Anne ; Perrier, Charles ; Centre d’Ecologie Fonctionnelle et Evolutive (CEFE) ; Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE) ; Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM) ; Ecosystèmes Insulaires Océaniens (UMR 241) (EIO) ; Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé Papeete (ILM) ; Institut de Recherche pour le Développement (IRD) ; University of Warsaw (UW) ; Centre of New Technologies ; Museu de Ciències Naturals de Barcelona ; Centre de Biologie pour la Gestion des Populations (UMR CBGP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier ; European Research Council: Starting grant ERC-2013-StG-337365-SHE (AC) ; OSU-OREME ; Polish National Science Centre grants Sonata BIS 2014/14/E/NZ8/00386 and Opus 2016/21/B/NZ8/03082 (MS) ; Ministry of Economy and Competitivity, Spanish Research Council grant CGL--2016-79568--C3--3--P (JCS). ; European Project: 337365,EC:FP7:ERC,ERC-2013-StG,SHE(2014) |
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Zeitschrift: | ISSN: 1752-4563, 2022 |
Veröffentlichung: | HAL CCSD ; Blackwell, 2022 |
Medientyp: | academicJournal |
DOI: | 10.1111/eva.13334 |
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