The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird
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 geograph...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Wiley
2024
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| _version_ | 1811140356849270784 |
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| author | Spurgin, LG Bosse, M Adriaensen, F Albayrak, T Barboutis, C Belda, E Bushuev, A Cecere, JG Charmantier, A Cichon, M Dingemanse, NJ Doligez, B Eeva, T Einar Erikstad, K Fedorov, V Griggio, M Heylen, D Hille, S Hinde, CA Ivankina, E Kempenaers, B Kerimov, A Krist, M Kvist, L Laine, VN Mänd, R Matthysen, E Nager, R Nikolov, B Norte, AC Orell, M Ouyang, J Petrova-Dinkova, G Richner, H Rubolini, D Slagsvold, T Tilgar, V Török, J Tschirren, B Vágási, CI Yuta, T Groenen, MAM Visser, ME van Oers, K Sheldon, B Slate, J |
| author_facet | Spurgin, LG Bosse, M Adriaensen, F Albayrak, T Barboutis, C Belda, E Bushuev, A Cecere, JG Charmantier, A Cichon, M Dingemanse, NJ Doligez, B Eeva, T Einar Erikstad, K Fedorov, V Griggio, M Heylen, D Hille, S Hinde, CA Ivankina, E Kempenaers, B Kerimov, A Krist, M Kvist, L Laine, VN Mänd, R Matthysen, E Nager, R Nikolov, B Norte, AC Orell, M Ouyang, J Petrova-Dinkova, G Richner, H Rubolini, D Slagsvold, T Tilgar, V Török, J Tschirren, B Vágási, CI Yuta, T Groenen, MAM Visser, ME van Oers, K Sheldon, B Slate, J |
| author_sort | Spurgin, LG |
| collection | OXFORD |
| description | 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 geographic range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugiam, 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. |
| first_indexed | 2024-09-25T04:20:41Z |
| format | Journal article |
| id | oxford-uuid:8872cde7-5f05-476a-ac3a-b9977e32ca2b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-09-25T04:20:41Z |
| publishDate | 2024 |
| publisher | Wiley |
| record_format | dspace |
| spelling | oxford-uuid:8872cde7-5f05-476a-ac3a-b9977e32ca2b2024-08-01T14:56:15ZThe great tit HapMap project: a continental-scale analysis of genomic variation in a songbirdJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:8872cde7-5f05-476a-ac3a-b9977e32ca2bEnglishSymplectic ElementsWiley2024Spurgin, LGBosse, MAdriaensen, FAlbayrak, TBarboutis, CBelda, EBushuev, ACecere, JGCharmantier, ACichon, MDingemanse, NJDoligez, BEeva, TEinar Erikstad, KFedorov, VGriggio, MHeylen, DHille, SHinde, CAIvankina, EKempenaers, BKerimov, AKrist, MKvist, LLaine, VNMänd, RMatthysen, ENager, RNikolov, BNorte, ACOrell, MOuyang, JPetrova-Dinkova, GRichner, HRubolini, DSlagsvold, TTilgar, VTörök, JTschirren, BVágási, CIYuta, TGroenen, MAMVisser, MEvan Oers, KSheldon, BSlate, JA 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 geographic range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugiam, 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. |
| spellingShingle | Spurgin, LG Bosse, M Adriaensen, F Albayrak, T Barboutis, C Belda, E Bushuev, A Cecere, JG Charmantier, A Cichon, M Dingemanse, NJ Doligez, B Eeva, T Einar Erikstad, K Fedorov, V Griggio, M Heylen, D Hille, S Hinde, CA Ivankina, E Kempenaers, B Kerimov, A Krist, M Kvist, L Laine, VN Mänd, R Matthysen, E Nager, R Nikolov, B Norte, AC Orell, M Ouyang, J Petrova-Dinkova, G Richner, H Rubolini, D Slagsvold, T Tilgar, V Török, J Tschirren, B Vágási, CI Yuta, T Groenen, MAM Visser, ME van Oers, K Sheldon, B Slate, J The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird |
| title | The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird |
| title_full | The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird |
| title_fullStr | The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird |
| title_full_unstemmed | The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird |
| title_short | The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird |
| title_sort | great tit hapmap project a continental scale analysis of genomic variation in a songbird |
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