The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird
Author:
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 A. 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 JonORCID
Abstract
AbstractA major aim of evolutionary biology is to understand why patterns of genomic diversity vary among populations and species. Large-scale genomic studies of widespread species are useful for studying how the environment and demographic history shape patterns of genomic divergence, and with the continually decreasing cost of sequencing and genotyping, such studies are now becoming feasible. Here, we carry out 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 almost the entire geographic range of the European great tit subspecies. We found that genome-wide variation was consistent with a recent colonisation across Europe from a single refugium in South-East Europe, 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 rate in the genome was 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 is a key driver of highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, most likely as a result of recent directional selection at the range edges of this species. Haplotype-based measures of selection were also related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. These regions under positive selection contained candidate genes associated with morphology, thermal adaptation and colouration, providing promising avenues for future investigation. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into evolution.
Publisher
Cold Spring Harbor Laboratory
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