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.

Animal Breeding and Genomics Wageningen University and Research Wageningen The Netherlands

Area Avifauna Migratrice Istituto Superiore per la Protezione e la Ricerca Ambientale Ozzano Emilia Italy

Behavioural Ecology Faculty of Biology LMU München Planegg Martinsried Germany

Behavioural Ecology Group Department of Life Sciences Anglia Ruskin University Cambridgeshire UK

Behavioural Ecology Group Department of Systematic Zoology and Ecology ELTE Eötvös Loránd University Budapest Hungary

Biology Education Buca Faculty of Education Mathematics and Science Education Dokuz Eylül University İzmir Turkey

Bulgarian Ornithological Centre Institute of Biodiversity and Ecosystem Research Bulgarian Academy of Sciences Sofia Bulgaria

CEFE Univ Montpellier CNRS EPHE IRD Montpellier France

Centre for Ecological and Evolutionary Synthesis Department of Biosciences University of Oslo Oslo Norway

Centre for Ecology and Conservation University of Exeter Penryn UK

Department of Animal Ecology Netherlands Institute of Ecology Wageningen The Netherlands

Department of Biology Edward Grey Institute University of Oxford Oxford UK

Department of Biology Science and art Faculty Mehmet Akif Ersoy University Istiklal Yerleskesi Burdur Turkey

Department of Biology University of Padova Padova Italy

Department of Biology University of Turku Turku Finland

Department of Ecological Science Animal Ecology Group Vrije Universiteit Amsterdam Amsterdam The Netherlands

Department of Ecology and Evolution Animal Ecology Evolutionary Biology Centre Uppsala University Uppsala Sweden

Department of Ecology and Genetics University of Oulu Oulu Finland

Department of Ornithology Max Planck Institute for Biological Intelligence Seewiesen Germany

Department of Zoology Faculty of Science Palacký University Olomouc Czech Republic

Department of Zoology University of Tartu Tartu Estonia

Dipartimento di Scienze e Politiche Ambientali Università Degli Studi di Milano Milan Italy

Evolutionary Ecology Group Department of Biology University of Antwerp Antwerp Belgium

Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeș Bolyai University Cluj Napoca Romania

Evolutionary Ecology Lab Institute of Ecology and Evolution University of Bern Bern Switzerland

Faculty of Biology Lomonosov Moscow State University Moscow Russia

Faculty of Biology Zvenigorod Biological Station Lomonosov Moscow State University Moscow Russia

Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen the Netherlands

Hellenic Ornithological Society BirdLife Greece Athens Greece

Institut d'Investigació per a la Gestió Integrada de Zones Costaneres Campus de Gandia Universitat Politècnica de València València Spain

Institute of Environmental Sciences Jagiellonian University Kraków Poland

Institute of Wildlife Biology and Game Management University of Natural Resources and Life Science Vienna Austria

Interuniversity Institute for Biostatistics and Statistical Bioinformatics Hasselt University Diepenbeek Belgium

MARE Marine and Environmental Sciences Centre Department of Life Sciences Faculty of Sciences and Technology University of Coimbra Coimbra Portugal

Norwegian Institute for Nature Research FRAM High North Research Centre for Climate and the Environment Tromsø Norway

School of Biodiversity One Health and Veterinary Medicine University of Glasgow Glasgow UK

School of Biological Sciences Norwich Research Park University of East Anglia Norwich UK

School of Biosciences University of Sheffield Sheffield UK

UMR CNRS 5558 LBBE Biométrie et Biologie Évolutive Villeurbanne France

University of Nevada Reno Nevada USA

Yamashina Institute for Ornithology Abiko Japan

Zoology Unit Finnish Museum of Natural History University of Helsinki Helsinki Finland

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Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub