title: Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits.
abstract: Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the FST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.
authors.affiliation: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.|Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
authors.forename: Joel M
authors.initials: JM
authors.lastname: Alves
authors.affiliation: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal.|Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
authors.forename: Miguel
authors.initials: M
authors.lastname: Carneiro
authors.affiliation: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal.
authors.forename: Sandra
authors.initials: S
authors.lastname: Afonso
authors.affiliation: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal.
authors.forename: Susana
authors.initials: S
authors.lastname: Lopes
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Garreau
authors.affiliation: Labovet Conseil (réseau Cristal), Les Herbiers, France.
authors.forename: Samuel
authors.initials: S
authors.lastname: Boucher
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.
authors.forename: Daniel
authors.initials: D
authors.lastname: Allain
authors.affiliation: ANTAGENE, Wildlife Genetics Laboratory, Limonest (Lyon), France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Queney
authors.affiliation: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal.|CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal.
authors.forename: Pedro J
authors.initials: PJ
authors.lastname: Esteves
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.
authors.forename: Gerard
authors.initials: G
authors.lastname: Bolet
authors.affiliation: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal.|Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Ferrand
mesh_terms: D000818:Animals; D001947:Breeding; D005260:Female; D014644:Genetic Variation; D008297:Male; D018895:Microsatellite Repeats; D011817:Rabbits