The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird

Author:

Spurgin Lewis G.12,Bosse Mirte345,Adriaensen Frank6,Albayrak Tamer78,Barboutis Christos9,Belda Eduardo10,Bushuev Andrey11,Cecere Jacopo G.12,Charmantier Anne13,Cichon Mariusz14,Dingemanse Niels J.15,Doligez Blandine1617,Eeva Tapio18,Erikstad Kjell Einar19,Fedorov Vyacheslav11,Griggio Matteo20ORCID,Heylen Dieter2621,Hille Sabine22,Hinde Camilla A.23,Ivankina Elena24,Kempenaers Bart25ORCID,Kerimov Anvar11,Krist Milos26ORCID,Kvist Laura27,Laine Veronika N.328ORCID,Mänd Raivo29,Matthysen Erik6,Nager Ruedi30,Nikolov Boris P.31,Norte Ana Claudia32,Orell Markku27,Ouyang Jenny33,Petrova‐Dinkova Gergana31,Richner Heinz34,Rubolini Diego35,Slagsvold Tore36,Tilgar Vallo29,Török János37,Tschirren Barbara38ORCID,Vágási Csongor I.39,Yuta Teru40,Groenen Martien A. M.4ORCID,Visser Marcel E.3441,van Oers Kees3ORCID,Sheldon Ben C.2,Slate Jon42ORCID

Affiliation:

1. School of Biological Sciences Norwich Research Park, University of East Anglia Norwich UK

2. Department of Biology, Edward Grey Institute University of Oxford Oxford UK

3. Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands

4. Animal Breeding and Genomics Wageningen University and Research Wageningen The Netherlands

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

6. Evolutionary Ecology Group, Department of Biology University of Antwerp Antwerp Belgium

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

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

9. Hellenic Ornithological Society/BirdLife Greece Athens Greece

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

11. Faculty of Biology Lomonosov Moscow State University Moscow Russia

12. Area Avifauna Migratrice Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) Ozzano Emilia Italy

13. CEFE, Univ. Montpellier, CNRS, EPHE, IRD Montpellier France

14. Institute of Environmental Sciences Jagiellonian University Kraków Poland

15. Behavioural Ecology, Faculty of Biology LMU München Planegg‐Martinsried Germany

16. UMR CNRS 5558—LBBE, Biométrie et Biologie Évolutive Villeurbanne France

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

18. Department of Biology University of Turku Turku Finland

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

20. Department of Biology University of Padova Padova Italy

21. Interuniversity Institute for Biostatistics and Statistical Bioinformatics Hasselt University Diepenbeek Belgium

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

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

24. Faculty of Biology, Zvenigorod Biological Station Lomonosov Moscow State University Moscow Russia

25. Department of Ornithology Max Planck Institute for Biological Intelligence Seewiesen Germany

26. Department of Zoology, Faculty of Science Palacký University Olomouc Czech Republic

27. Department of Ecology and Genetics University of Oulu Oulu Finland

28. Zoology Unit, Finnish Museum of Natural History University of Helsinki Helsinki Finland

29. Department of Zoology University of Tartu Tartu Estonia

30. School of Biodiversity, One Health and Veterinary Medicine University of Glasgow Glasgow UK

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

32. MARE – Marine and Environmental Sciences Centre, Department of Life Sciences, Faculty of Sciences and Technology University of Coimbra Coimbra Portugal

33. University of Nevada Reno Nevada USA

34. Evolutionary Ecology Lab, Institute of Ecology and Evolution University of Bern Bern Switzerland

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

36. Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences University of Oslo Oslo Norway

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

38. Centre for Ecology and Conservation University of Exeter Penryn UK

39. Evolutionary Ecology Group, Hungarian Department of Biology and Ecology Babeș‐Bolyai University Cluj‐Napoca Romania

40. Yamashina Institute for Ornithology Abiko Japan

41. Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen the Netherlands

42. School of Biosciences University of Sheffield Sheffield UK

Abstract

AbstractA 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.

Funder

Natural Environment Research Council

European Research Council

Biotechnology and Biological Sciences Research Council

Publisher

Wiley

Cited by 1 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. Great Tit (Parus major);Birds of the World;2024-07-05

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3