title: Genomics and the origin of species.
abstract: Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.
authors.affiliation: Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
authors.forename: Ole
authors.initials: O
authors.lastname: Seehausen
authors.affiliation: Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK; and the Sven Lovén Centre - Tjärnö, University of Gothenburg, S-452 96 Strömstad, Sweden.
authors.forename: Roger K
authors.initials: RK
authors.lastname: Butlin
authors.affiliation: Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and the Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland.
authors.forename: Irene
authors.initials: I
authors.lastname: Keller
authors.affiliation: Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
authors.forename: Catherine E
authors.initials: CE
authors.lastname: Wagner
authors.affiliation: Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Department of Zoology; Ecology, Evolutionary Biology and Behavior Program; BEACON Center, Michigan State University, 203 Natural Sciences, East Lansing, Michigan 48824, USA.
authors.forename: Janette W
authors.initials: JW
authors.lastname: Boughman
authors.affiliation: Department of Biological Sciences, Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844-3051, USA.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Hohenlohe
authors.affiliation: Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Catherine L
authors.initials: CL
authors.lastname: Peichel
authors.affiliation: Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway.
authors.forename: Glenn-Peter
authors.initials: GP
authors.lastname: Saetre
authors.affiliation: School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Claudia
authors.initials: C
authors.lastname: Bank
authors.affiliation: Integrated Science Laboratory and the Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden.
authors.forename: Ake
authors.initials: A
authors.lastname: Brännström
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Alan
authors.initials: A
authors.lastname: Brelsford
authors.affiliation: Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK.
authors.forename: Chris S
authors.initials: CS
authors.lastname: Clarkson
authors.affiliation: Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Eroukhmanoff
authors.affiliation: Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556-0369 USA.
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Feder
authors.affiliation: Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland.
authors.forename: Martin C
authors.initials: MC
authors.lastname: Fischer
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. Present address: the Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Foote
authors.affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
authors.forename: Paolo
authors.initials: P
authors.lastname: Franchini
authors.affiliation: Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
authors.forename: Chris D
authors.initials: CD
authors.lastname: Jiggins
authors.affiliation: Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany.
authors.forename: Felicity C
authors.initials: FC
authors.lastname: Jones
authors.affiliation: Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland.
authors.forename: Anna K
authors.initials: AK
authors.lastname: Lindholm
authors.affiliation: Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
authors.forename: Kay
authors.initials: K
authors.lastname: Lucek
authors.affiliation: Behavioural Biology Group, Centre for Behaviour and Neurosciences, University of Groningen, PO BOX 11103, 9700 CC Groningen, The Netherlands.
authors.forename: Martine E
authors.initials: ME
authors.lastname: Maan
authors.affiliation: Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
authors.forename: David A
authors.initials: DA
authors.lastname: Marques
authors.affiliation: Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
authors.forename: Simon H
authors.initials: SH
authors.lastname: Martin
authors.affiliation: Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland.
authors.forename: Blake
authors.initials: B
authors.lastname: Matthews
authors.affiliation: Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
authors.forename: Joana I
authors.initials: JI
authors.lastname: Meier
authors.affiliation: Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK; and the Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland.
authors.forename: Markus
authors.initials: M
authors.lastname: Möst
authors.affiliation: Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720-3160, USA.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Nachman
authors.affiliation: Integrated Science Laboratory and Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden.
authors.forename: Etsuko
authors.initials: E
authors.lastname: Nonaka
authors.affiliation: Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Diana J
authors.initials: DJ
authors.lastname: Rennison
authors.affiliation: Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Schwarzer
authors.affiliation: Department of Biology, The University of Texas at Arlington, 76010-0498 Texas, USA.
authors.forename: Eric T
authors.initials: ET
authors.lastname: Watson
authors.affiliation: Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK.
authors.forename: Anja M
authors.initials: AM
authors.lastname: Westram
authors.affiliation: Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland.
authors.forename: Alex
authors.initials: A
authors.lastname: Widmer
mesh_terms: D044822:Biodiversity; D023281:Genomics; D008957:Models, Genetic