Dryad
Published February 14, 2015 | Version v1
Dataset Open

Data from: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

Creators

  • 1. University of Missouri
  • 2. University of Vermont
  • 3. Oklahoma State University
  • 4. University of Córdoba
  • 5. United States Department of Agriculture
  • 6. University of Nottingham
  • 7. Uppsala University
  • 8. Texas A&M University
  • 9. Indonesian Research Institute for Animal Production, Ciawi, Bogor, Indonesia*
  • 10. University of Veterinary and Animal Sciences
  • 11. Animal Molecular Genetics, Embrapa Pecuaria Sudeste, Sao Carlos, Sao Paulo, Brasil*
  • 12. Ankara University
  • 13. Pennsylvania State University
  • 14. North West Agriculture and Forestry University
  • 15. Iowa State University
  • 16. University of Agriculture

Description

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds 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 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 are shown to be of Iberian, and not African, decent. 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.

Notes

Genotypes, SNP information, and sample information for 1,543 cattle from 134 breeds
This file contains the genotypes from 43,043 SNP markers scored in 1,543 cattle. Samples were genotyped with the Illumina BovineSNP50 BeadChip. Genotypes were called using GenomeStudio.
WorldWideCattleDryad.zip

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README_for_WorldWideCattleDryad.txt

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Additional details

Related works

Is cited by
10.1371/journal.pgen.1004254 (DOI)