Great Tit HapMap Project

 

Welcome to the homepage of the Great Tit (Parus major) HapMap Project

The project aims to understand the phylogeography and evolutionary history of great tits, one of the most widely studied vertebrates in evolutionary ecology. The consortium involves over 30 members, with great tit samples coming from across the species’ distribution. The project is coordinated by Jon Slate (j.slate@sheffield.ac.uk).

If you are interested in getting involved, providing samples or contributing in some other way then please do get in touch. We are especially keen to type additional birds from The Balkans, Italy and other ‘gaps’ on the map.

SampleLocations

Approximately 2000 individual great tits have been genotyped with a 500K Affymetrix SNP chip. We are using the data from the chip to measure population structure and levels of genetic diversity, to estimate effective population size, and to identify regions of the genome that have undergone selection. We hope to establish how adaptations to different environmental conditions have occurred. Great tits are a very good system for studying selection and evolution because they have a large effective population size, and plenty of gene flow between populations. The genome is sequenced and well annotated and linkage maps are available. Finally, there are a number of long-term individual-based studies of great tit populations spanning many decades (e.g. at Wytham Woods in Oxford, Hoge Veluwe in the Netherlands and Vleiland in the Netherlands), which means it might be possible to establish whether genes that affect fitness variation in contemporary populations have played a role in adaptation to different environments.

 

HapMap Consortium Publications

The first paper involving the HapMap Consortium is a description of the great tit genome. A bird from the Netherlands was sequenced at very high coverage to make the genome and a further 29 birds from across the species range were resequenced to identify regions under selection.

1) VN Laine, TI Gossmann, KM Schachtschneider, CJ Garroway, O Madsen, KJF Verhoeven, V de Jager,H-J Megens, WC Warren, P Minx, RPMA Crooijmans, P Corcoran, The Great Tit HapMap Consortium, BC Sheldon, J Slate , K Zeng, K van Oers, ME Visser & MAMG Groenen (2016) Evolutionary signals of selection on cognition from the great tit genome and methylome Nature Communications 7:10474
doi:10.1038/ncomms10474
http://www.nature.com/ncomms/2016/160125/ncomms10474/full/ncomms10474.html

The genome is available here and at NCBI/EMBL/DDBJ here
Reads from the resequenced birds are here

 

 

Contributors to the Project

Frank Adriaensen: Evolutionary Ecology Group, Department of Biology, University of Antwerp, B-2020 Antwerp, Belgium frank.adriaensen@uantwerpen.be
Eduardo Jorge Belda Pérez: Departamento de Ciencia Animal, IGIC, Universidad Politécnica de Valencia, C/Paranimf nº 1, E-46730, Gandía (Valencia), España ebelda@dca.upv.es
Mirte Bosse: Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, Wageningen 6700 AB, The Netherlands m.bosse@nioo.knaw.nl
Andrey Bushuev: Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia a_bushuev@mail.ru
Mariusz Cichon: Inst. of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland mariusz.cichon@uj.edu.pl
Anne Charmantier: CEFE-CNRS, UMR 5175, 1919, route de Mende, F34293 Montpellier Cedex 5, France anne.charmantier@cefe.cnrs.fr
Niels Dingemanse: Max Planck Institute for Ornithology, Department of Behavioural Ecology & Evolutionary Genetics, Eberhard-Gwinner-Straße, House 5, 82319 Seewiesen (Starnberg), Germany ndingemanse@orn.mpg.de
Blandine Doligez: UMR CNRS 5558 – LBBE, Biométrie et Biologie Évolutive, UCB Lyon 1 – Bât. Grégor Mendel, 43 bd du 11 novembre 1918, 69622 VILLEURBANNE cedex, France blandine.doligez@univ-lyon1.fr
Tapio Eeva: Section of Ecology, Department of Biology, 20014 University of Turku, Turku, Finland tapio.eeva@utu.fi
Kjell Einar Erikstad: Norwegian Institute for Nature Research, FRAM-High North Research Centre for Climate and the Environment, 9296 Tromsø, Norway kjell.e.erikstad@nina.no
Slava Fedorov: Department of Vertebrate Zoology, Moscow State University, Moscow, 119899 Russia fedorovslava@mail.ru
Toni Gossmann: Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK t.gossmann@sheffield.ac.uk
Martien Groenen: Animal Breeding and Genomics Centre, Wageningen University, 6708 WD, Wageningen, The Netherlands Martien.Groenen@wur.nl
Michaela Hau: Max Planck Institute for Ornithology, Department of Behavioural Ecology & Evolutionary Genetics, Eberhard-Gwinner-Straße, House 5, 82319 Seewiesen (Starnberg), Germany mhau@orn.mpg.de
Dieter Heylen: Evolutionary Ecology Group, Department of Biology, University of Antwerp, B-2020 Antwerp, Belgium dieter.heylen@uantwerpen.be
Sabine Hille: Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Science, A-1180 Vienna, Austria sabine.hille@boku.ac.at
Camilla Hinde: Behavioural Ecology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands camilla.hinde@wur.nl
Bart Kempenaers: Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany b.kempenaers@orn.mpg.de
Anvar Kerimov: Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia anvar_kerimov@mail.ru
Miloš Krist: Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacký University, Olomouc, Czech Republic milos.krist@upol.cz
Veronika Laine: Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, Wageningen 6700 AB, The Netherlands v.laine@nioo.knaw.nl
Raivo Mänd: Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu 51014, Estonia raivo.mand@ut.ee
Erik Matthysen: Evolutionary Ecology Group, University of Antwerp, Antwerp 2020, Belgium erik.matthysen@uantwerpen.be
Reudi Nager: Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK Ruedi.Nager@glasgow.ac.uk
Ana Cláudia Norte: Department of Life Sciences, Institute of Marine Research IMAR/CMA, University of Coimbra, Coimbra, Portugal acgnorte@ci.uc.pt
Kees van Oers: Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, Wageningen 6700 AB, The Netherlands K.vanOers@nioo.knaw.nl
Markku Orell: Department of Biology, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland Markku.Orell@Oulu.Fi
Heinz Richner: Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland heinz.richner@iee.unibe.ch
Ben Sheldon: The Edward Grey Institute, Department of Zoology, Tinbergen Building, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK ben.sheldon@zoo.ox.ac.uk
Tore Slagsvold: Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway tore.slagsvold@ibv.uio.no
Jon Slate: Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK j.slate@sheffield.ac.uk
Lewis Spurgin: Edward Grey Institute, Department of Zoology, Tinbergen Building, University of Oxford, South Parks Road, Oxford, OX1 3PS,  UK lewis.spurgin@zoo.ox.ac.uk
Vallo Tilgar: Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu 51014, Estonia vallo.tilgar@ut.ee
Joost Tinbergen: Centre for Ecological and Evolutionary Studies (CEES), Univ. of Groningen, PO Box 11103, NL-9700 CC Groningen, The Netherlands j.m.tinbergen@rug.nl
Janos Torok: Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary yeti01@elte.hu
Barbara Tschirren: Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich barbara.tschirren@ieu.uzh.ch
Marcel Visser: Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, Wageningen 6700 AB, The Netherlands M.Visser@nioo.knaw.nl
Teru Yuta: Graduate School of Environmental Science, Hokkaido University, N10 W5 Sapporo, Hokkaido 060-0810, Japan tyuta@fsc.hokudai.ac.jp
Kai Zeng: Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK k.zeng@sheffield.ac.uk