title: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle.
abstract: The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Jared E
authors.initials: JE
authors.lastname: Decker
authors.affiliation: Department of Animal Science, The University of Vermont, Burlington, Vermont, United States of America.
authors.forename: Stephanie D
authors.initials: SD
authors.lastname: McKay
authors.affiliation: Department of Animal Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America.
authors.forename: Megan M
authors.initials: MM
authors.lastname: Rolf
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Jaewoo
authors.initials: J
authors.lastname: Kim
authors.affiliation: Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Molina Alcalá
authors.affiliation: USDA-ARS Bovine Functional Genomics Lab, Beltsville, Maryland, United States of America.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Medicine & Health Sciences, The University of Nottingham, Nottingham, United Kingdom.
authors.forename: Olivier
authors.initials: O
authors.lastname: Hanotte
authors.affiliation: Evolutionary Biology Centre, Uppsala Universitet, Uppsala, Sweden.
authors.forename: Anders
authors.initials: A
authors.lastname: Götherström
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Seabury
authors.affiliation: Indonesian Research Institute for Animal Production, Ciawi, Bogor, Indonesia.
authors.forename: Lisa
authors.initials: L
authors.lastname: Praharani
authors.affiliation: Institute of Biochemistry & Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
authors.forename: Masroor Ellahi
authors.initials: ME
authors.lastname: Babar
authors.affiliation: Animal Molecular Genetics, Embrapa Pecuaria Sudeste, Sao Carlos, Sao Paulo, Brasil.
authors.forename: Luciana
authors.initials: L
authors.lastname: Correia de Almeida Regitano
authors.affiliation: Animal Science, Biometry and Genetics, Ankara University, Diskapi, Ankara, Turkey.
authors.forename: Mehmet Ali
authors.initials: MA
authors.lastname: Yildiz
authors.affiliation: USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Heaton
authors.affiliation: Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, United States of America.
authors.forename: Wan-Sheng
authors.initials: WS
authors.lastname: Liu
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Chu-Zhao
authors.initials: CZ
authors.lastname: Lei
authors.affiliation: Department of Animal Science, Iowa State University, Ames, Iowa, United States of America.
authors.forename: James M
authors.initials: JM
authors.lastname: Reecy
authors.affiliation: Department of Animal Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Saif-Ur-Rehman
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Schnabel
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Jeremy F
authors.initials: JF
authors.lastname: Taylor
mesh_terms: D000483:Alleles; D000818:Animals; D000829:Animals, Domestic / Q000235:genetics*; D001947:Breeding; D002417:Cattle; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D006801:Humans; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide