The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird
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 (2024-05-15)
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
John Wiley & Sons
15.05.2024
Spurgin, L. G., Bosse, M., Adriaensen, F., Albayrak, T., Barboutis, C., Belda, E., Bushuev, A., Cecere, J. G., Charmantier, A., Cichon, M., Dingemanse, N. J., Doligez, B., Eeva, T., Erikstad, K. E., Fedorov, V., Griggio, M., Heylen, D., Hille, S., Hinde, C. A., … Slate, J. (2024). The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird. Molecular Ecology Resources, 24, e13969. https://doi.org/10.1111/1755-0998.13969
https://creativecommons.org/licenses/by/4.0/
© 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.
https://creativecommons.org/licenses/by/4.0/
© 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.
https://creativecommons.org/licenses/by/4.0/
Julkaisun pysyvä osoite on
https://urn.fi/URN:NBN:fi:oulu-202405203705
https://urn.fi/URN:NBN:fi:oulu-202405203705
Tiivistelmä
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.
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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