A1 Refereed original research article in a scientific journal
The great tit HapMap project : A continental-scale analysis of genomic variation in a songbird
Authors: Spurgin Lewis G., Bosse Mirte, Adriaensen Frank, Albayrak Tamer, Barboutis Christos, Belda Eduardo, Bushuev Andrey, Cecere Jacopo G., Charmantier Anne, Cichon Mariusz, Dingemanse Niels J., Doligez Blandine, Eeva Tapio, Erikstad Kjell Einar, Fedorov Vyacheslav, Griggio Matteo, Heylen Dieter, Hille Sabine, Hinde Camilla A., Ivankina Elena, Kempenaers Bart, Kerimov Anvar, Krist Milos, Kvist Laura, Laine Veronika N., Mänd Raivo, Matthysen Erik, Nager Ruedi, Nikolov Boris P., Norte Ana Claudia, Orell Markku, Ouyang Jenny, Petrova-Dinkova Gergana, Richner Heinz, Rubolini Diego, Slagsvold Tore, Tilgar Vallo, Török János, Tschirren Barbara, Vágási Csongor I., Yuta Teru, Groenen Martien A. M., Visser Marcel E., van Oers Kees, Sheldon Ben C., Slate Jon
Publisher: Wiley-Blackwell
Publication year: 2024
Journal: Molecular Ecology Resources
Journal name in source: Molecular ecology resources
Journal acronym: Mol Ecol Resour
Article number: e13969
Volume: 24
Issue: 5
ISSN: 1755-098X
eISSN: 1755-0998
DOI: https://doi.org/10.1111/1755-0998.13969
Web address : https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13969
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/404702894
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.
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Funding information in the publication:
Natural Environment Research Council, Grant/Award Number: NE/J012599/1; European Research Council, Grant/ Award Number: 202487 and 339092; Biotechnology and Biological Sciences Research Council, Grant/Award Number: BB/N011759/1
