title: Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
abstract: The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.
authors.affiliation: CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.
authors.forename: Miguel
authors.initials: M
authors.lastname: Carneiro
authors.affiliation: Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Carl-Johan
authors.initials: CJ
authors.lastname: Rubin
authors.affiliation: Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.|Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK.
authors.forename: Federica
authors.initials: F
authors.lastname: Di Palma
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Frank W
authors.initials: FW
authors.lastname: Albert
authors.affiliation: Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Alföldi
authors.affiliation: Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Alvaro
authors.initials: A
authors.lastname: Martinez Barrio
authors.affiliation: Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Gerli
authors.initials: G
authors.lastname: Pielberg
authors.affiliation: Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Nima
authors.initials: N
authors.lastname: Rafati
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Shumaila
authors.initials: S
authors.lastname: Sayyab
authors.affiliation: Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Turner-Maier
authors.affiliation: Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.|Department of Animal Production, Ain Shams University, Shoubra El-Kheima, Cairo, Egypt.
authors.forename: Shady
authors.initials: S
authors.lastname: Younis
authors.affiliation: CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.
authors.forename: Sandra
authors.initials: S
authors.lastname: Afonso
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.|European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Bronwen
authors.initials: B
authors.lastname: Aken
authors.affiliation: CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.|Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
authors.forename: Joel M
authors.initials: JM
authors.lastname: Alves
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.|European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Daniel
authors.initials: D
authors.lastname: Barrell
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326 Castanet-Tolosan, France.
authors.forename: Gerard
authors.initials: G
authors.lastname: Bolet
authors.affiliation: Labovet Conseil, Les Herbiers Cedex, France.
authors.forename: Samuel
authors.initials: S
authors.lastname: Boucher
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Hernán A
authors.initials: HA
authors.lastname: Burbano
authors.affiliation: CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.
authors.forename: Rita
authors.initials: R
authors.lastname: Campos
authors.affiliation: Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Jean L
authors.initials: JL
authors.lastname: Chang
authors.affiliation: INRA, UMR1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
authors.forename: Veronique
authors.initials: V
authors.lastname: Duranthon
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Fontanesi
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326 Castanet-Tolosan, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Garreau
authors.affiliation: Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: David
authors.initials: D
authors.lastname: Heiman
authors.affiliation: Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Johnson
authors.affiliation: Laboratory of Immunology, NIAID, NIH, Bethesda, MD, 20892, USA.
authors.forename: Rose G
authors.initials: RG
authors.lastname: Mage
authors.affiliation: DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598.
authors.forename: Ze
authors.initials: Z
authors.lastname: Peng
authors.affiliation: ANTAGENE, Animal Genomics Laboratory, Lyon, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Queney
authors.affiliation: INRA, UMR1313 Génétique Animale et Biologie Intégrative, F- 78350, Jouy-en-Josas, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Rogel-Gaillard
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.|European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Magali
authors.initials: M
authors.lastname: Ruffier
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Steve
authors.initials: S
authors.lastname: Searle
authors.affiliation: Instituto de Estudios Sociales Avanzados, (IESA-CSIC) Campo Santo de los Mártires 7, Córdoba Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Villafuerte
authors.affiliation: Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
authors.forename: Anqi
authors.initials: A
authors.lastname: Xiong
authors.affiliation: Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Young
authors.affiliation: Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
authors.forename: Karin
authors.initials: K
authors.lastname: Forsberg-Nilsson
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.|Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Good
authors.affiliation: Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.affiliation: CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.|Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n. 4169-007 Porto, Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Ferrand
authors.affiliation: Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.|Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.affiliation: Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.|Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.|Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, USA.
authors.forename: Leif
authors.initials: L
authors.lastname: Andersson
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000033:anatomy & histology / Q000235:genetics* / Q000523:psychology; D000835:Animals, Wild / Q000033:anatomy & histology / Q000235:genetics* / Q000523:psychology; D001483:Base Sequence; D001522:Behavior, Animal; D001947:Breeding; D019143:Evolution, Molecular; D005787:Gene Frequency; D056426:Genetic Loci; D016678:Genome / Q000235:genetics; D008969:Molecular Sequence Data; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011817:Rabbits / Q000033:anatomy & histology / Q000235:genetics* / Q000523:psychology; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA