title: How do introgression events shape the partitioning of diversity among breeds: a case study in sheep.
abstract: BACKGROUND
  From domestication to the current pattern of differentiation, domestic species have been influenced by reticulate evolution with multiple events of migration, introgression, and isolation; this has resulted in a very large number of breeds. In order to manage these breeds and their genetic diversity, one must know the current genetic structure of the populations and the relationships among these. This paper presents the results of a genetic diversity analysis on an almost exhaustive sample of the sheep breeds reared in France. Molecular characterization was performed with a set of 21 microsatellite markers on a collection of 49 breeds that include five breed types: meat, hardy meat, dairy, high prolificacy and patrimonial breeds.
  
  
  RESULTS
  Values of expected heterozygosity ranged from 0.48 to 0.76 depending on the breed, with specialized meat breeds exhibiting the lowest values. Neighbor-Net, multidimensional analysis or clustering approaches revealed a clear differentiation of the meat breeds compared to the other breed types. Moreover, the group that clustered meat breeds included all the breeds that originated from the United Kingdom (UK) and those that originated from crossbreeding between UK breeds and French local breeds. We also highlighted old genetic introgression events that were related to the diffusion of Merino rams to improve wool production. As a result of these introgression events, especially that regarding the UK breeds, the breeds that were clustered in the 'meat type cluster' exhibited the lowest contribution to total diversity. That means that similar allelic combinations could be observed in different breeds of this group.
  
  
  CONCLUSIONS
  The genetic differentiation pattern of the sheep breeds reared in France results from a combination of factors, i.e. geographical origin, historic gene flow, and breed use. The Merino influence is weaker than that of UK breeds, which is consistent with how sheep use changed radically at the end of 19(th) century when wool-producing animals (Merino-like) were replaced by meat-producing breeds. These results are highly relevant to monitor and manage the genetic diversity of sheep and can be used to set priorities in conservation programs when needed.
authors.affiliation: AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, F-75231, Paris 05, France. gregoire.leroy@agroparistech.fr.|INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352, Jouy-en-Josas, France. gregoire.leroy@agroparistech.fr.
authors.forename: Grégoire
authors.initials: G
authors.lastname: Leroy
authors.affiliation: Institut de l'Élevage, F-75595, Paris 12, France. coralie.danchin@idele.fr.
authors.forename: Coralie
authors.initials: C
authors.lastname: Danchin-Burge
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31326, Castanet-Tolosan, France. isabelle.palhiere@toulouse.inra.fr.|Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31076, Toulouse, France. isabelle.palhiere@toulouse.inra.fr.|Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31326, Castanet-Tolosan, France. isabelle.palhiere@toulouse.inra.fr.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Palhière
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31326, Castanet-Tolosan, France. magali.san-cristobal@toulouse.inra.fr.|Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31076, Toulouse, France. magali.san-cristobal@toulouse.inra.fr.|Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31326, Castanet-Tolosan, France. magali.san-cristobal@toulouse.inra.fr.
authors.forename: Magali
authors.initials: M
authors.lastname: SanCristobal
authors.affiliation: AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, F-75231, Paris 05, France. ynedelec@jeunes-agriculteurs.fr.|INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352, Jouy-en-Josas, France. ynedelec@jeunes-agriculteurs.fr.
authors.forename: Yann
authors.initials: Y
authors.lastname: Nédélec
authors.affiliation: AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, F-75231, Paris 05, France. etienne.verrier@agroparistech.fr.|INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352, Jouy-en-Josas, France. etienne.verrier@agroparistech.fr.
authors.forename: Etienne
authors.initials: E
authors.lastname: Verrier
authors.affiliation: AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, F-75231, Paris 05, France. xavier.rognon@agroparistech.fr.|INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352, Jouy-en-Josas, France. xavier.rognon@agroparistech.fr.
authors.forename: Xavier
authors.initials: X
authors.lastname: Rognon
mesh_terms: D000818:Animals; D005602:France; D014644:Genetic Variation; D060005:Genotyping Techniques; D018895:Microsatellite Repeats; D058974:Phylogeography; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D000068618:Selective Breeding / Q000235:genetics*; D012756:Sheep / Q000235:genetics*; D006113:United Kingdom