The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird
dc.contributor.author | Spurgin, LG | |
dc.contributor.author | Bosse, M | |
dc.contributor.author | Adriaensen, F | |
dc.contributor.author | Albayrak, T | |
dc.contributor.author | Barboutis, C | |
dc.contributor.author | Belda, E | |
dc.contributor.author | Bushuev, A | |
dc.contributor.author | Cecere, JG | |
dc.contributor.author | Charmantier, A | |
dc.contributor.author | Cichon, M | |
dc.contributor.author | Dingemanse, NJ | |
dc.contributor.author | Doligez, B | |
dc.contributor.author | Eeva, T | |
dc.contributor.author | Erikstad, KE | |
dc.contributor.author | Fedorov, V | |
dc.contributor.author | Griggio, M | |
dc.contributor.author | Heylen, D | |
dc.contributor.author | Hille, S | |
dc.contributor.author | Hinde, CA | |
dc.contributor.author | Ivankina, E | |
dc.contributor.author | Kempenaers, B | |
dc.contributor.author | Kerimov, A | |
dc.contributor.author | Krist, M | |
dc.contributor.author | Kvist, L | |
dc.contributor.author | Laine, VN | |
dc.contributor.author | Mänd, R | |
dc.contributor.author | Matthysen, E | |
dc.contributor.author | Nager, R | |
dc.contributor.author | Nikolov, BP | |
dc.contributor.author | Norte, AC | |
dc.contributor.author | Orell, M | |
dc.contributor.author | Ouyang, J | |
dc.contributor.author | Petrova‐Dinkova, G | |
dc.contributor.author | Richner, H | |
dc.contributor.author | Rubolini, D | |
dc.contributor.author | Slagsvold, T | |
dc.contributor.author | Tilgar, V | |
dc.contributor.author | Török, J | |
dc.contributor.author | Tschirren, B | |
dc.contributor.author | Vágási, CI | |
dc.contributor.author | Yuta, T | |
dc.contributor.author | Groenen, MAM | |
dc.contributor.author | Visser, ME | |
dc.contributor.author | van Oers, K | |
dc.contributor.author | Sheldon, BC | |
dc.contributor.author | Slate, J | |
dc.date.accessioned | 2024-05-23T12:24:46Z | |
dc.date.issued | 2024-05-15 | |
dc.date.updated | 2024-05-23T10:44:29Z | |
dc.description.abstract | A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude – almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear ‘islands of differentiation’, even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics. | en_GB |
dc.description.sponsorship | Natural Environment Research Council (NERC) | en_GB |
dc.description.sponsorship | European Research Council (ERC) | en_GB |
dc.description.sponsorship | Biotechnology and Biological Sciences Research Council (BBSRC) | en_GB |
dc.identifier.citation | Article e13969 | en_GB |
dc.identifier.doi | https://doi.org/10.1111/1755-0998.13969 | |
dc.identifier.grantnumber | NE/J012599/1 | en_GB |
dc.identifier.grantnumber | 202487 | en_GB |
dc.identifier.grantnumber | 339092 | en_GB |
dc.identifier.grantnumber | BB/N011759/1 | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/136020 | |
dc.identifier | ORCID: 0000-0003-4806-4102 (Tschirren, Barbara) | |
dc.identifier | ScopusID: 57207545347 | 6701813286 (Tschirren, Barbara) | |
dc.identifier | ResearcherID: F-8202-2011 (Tschirren, Barbara) | |
dc.language.iso | en | en_GB |
dc.publisher | Wiley | en_GB |
dc.relation.url | https://github.com/lgs85/SpurginBosse_Hapmap | en_GB |
dc.relation.url | https://doi.org/10.5061/dryad.w3r2280z5 | en_GB |
dc.rights | © 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. | en_GB |
dc.subject | adaptation | en_GB |
dc.subject | birds | en_GB |
dc.subject | ecological genetics | en_GB |
dc.subject | genomics/proteomics | en_GB |
dc.subject | molecular evolution | en_GB |
dc.subject | population genetics – empirical | en_GB |
dc.title | The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2024-05-23T12:24:46Z | |
dc.identifier.issn | 1755-098X | |
dc.description | This is the final version. Available on open access from Wiley via the DOI in this record | en_GB |
dc.description | Data availability statement: The code to reproduce the results is available on Github: https://github.com/lgs85/SpurginBosse_Hapmap. The data, including the Plink-formatted genotype files from all populations, and the downstream outputs are on Dryad: https://doi.org/10.5061/dryad.w3r2280z5. | en_GB |
dc.identifier.eissn | 1755-0998 | |
dc.identifier.journal | Molecular Ecology Resources | en_GB |
dc.relation.ispartof | Molecular Ecology Resources | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2024-04-29 | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2024-05-15 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2024-05-23T12:21:43Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2024-05-23T12:26:00Z | |
refterms.panel | A | en_GB |
refterms.dateFirstOnline | 2024-05-15 |
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Except where otherwise noted, this item's licence is described as © 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.