Cited by 529Genetic and phenotypic traits in livestockGenetic diversity and population structureForensic and Genetic Research

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Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

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Decker, Jared E., McKay, Stephanie D., Rolf, Megan M., Kim, JaeWoo, Molina Alcalá, Antonio, Sonstegard, Tad S., Hanotte, Olivier, Götherström, Anders, Seabury, Christopher M., Praharani, Lisa, Babar, Masroor Ellahi, Correia de Almeida Regitano, Luciana, Yildiz, Mehmet Ali, Heaton, Michael P., Liu, Wan-Sheng, Lei, Chu-Zhao, Reecy, James M., Saif-Ur-Rehman, Muhammad, Schnabel, Robert D., Taylor, Jeremy F.·2014·PLoS Genetics

DOI 10.1371/journal.pgen.1004254PMC PMC3967955

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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.

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Additional file 16 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 4 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 26 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 25 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 2 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
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Additional file 3 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
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Additional file 15 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 1 of Whole-genome sequencing reveals genomic diversity and selection signatures in Xia’nan cattle
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Additional file 22 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 6 of Genetic diversity and effective population sizes of thirteen Indian cattle breeds
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Additional file 23 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 4 of Whole-genome sequencing reveals genomic diversity and selection signatures in Xia’nan cattle
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Additional file 21 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 2 of Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data
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Additional file 14 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 7 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
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Additional file 12 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
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Additional file 1 of Variants at the ASIP locus contribute to coat color darkening in Nellore cattle
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Additional file 6 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
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Additional file 3 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
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Additional file 3 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411471
Additional file 13 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411423
Additional file 11 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411417
Additional file 3 of Whole-genome sequencing reveals genomic diversity and selection signatures in Xia’nan cattle
Song, X., Yao, Z., Zhang, Z., Lyv, S., Chen, N., Qi, X., Liu, X., Ma, W., Wang, W., Lei, C., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26729875
Self-citation
Additional file 8 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411486
Additional file 5 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411477
Additional file 9 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411489
Additional file 10 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Senczuk, G., Mastrangelo, S., Ajmone-Marsan, P., Becskei, Z., Colangelo, P., Colli, L., Ferretti, L., Karslı, T., Lancioni, H., Lasagna, E., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14722011
Additional file 2 of Whole-genome sequencing reveals genomic diversity and selection signatures in Xia’nan cattle
Song, X., Yao, Z., Zhang, Z., Lyv, S., Chen, N., Qi, X., Liu, X., Ma, W., Wang, W., Lei, C., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26729872
Self-citation
Additional file 18 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411438
Additional file 1 of Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data
Zhang, S., Yao, Z., Li, X., Zhang, Z., Liu, X., Yang, P., Chen, N., Xia, X., Lyv, S., Shi, Q., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20113946
Self-citation
Additional file 20 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411447
Additional file 2 of Genetic diversity and effective population sizes of thirteen Indian cattle breeds
Strucken, E. M., Gebrehiwot, N. Z., Swaminathan, M., Joshi, S., Kalaldeh, M. A., & Gibson, J. P. (2021) · Figshare · doi:10.6084/m9.figshare.14715190
Additional file 6 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411480
Additional file 1 of Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data
Xia, X., Zhang, S., Zhang, H., Zhang, Z., Chen, N., Li, Z., HongXia, S., Liu, X., Lyv, S., Wang, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13551045
Self-citation
Additional file 10 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411414
Additional file 4 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
Schmidtmann, C., Schönherz, A. A., Guldbrandtsen, B., Marjanovic, J., Calus, M., Hinrichs, D., & Thaller, G. (2021) · Figshare · doi:10.6084/m9.figshare.14176198
Additional file 17 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411435
Additional file 19 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411441
Additional file 2 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411468
Additional file 24 of Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Jiang, F., Lin, R., Xiao, C., Xie, T., Jiang, Y., Chen, J., Ni, P., Sung, W.-K., Han, J., Du, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14411459
Additional file 3 of SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle
Gebrehiwot, N. Z., Strucken, E. M., Marshall, K., Aliloo, H., & Gibson, J. P. (2021) · Figshare · doi:10.6084/m9.figshare.14151034

Authors: Decker, J. E., McKay, S. D., Rolf, M. M., Kim, J., Molina Alcalá, A., Sonstegard, T. S., Hanotte, O., Götherström, A., Seabury, C. M., Praharani, L., Babar, M. E., Correia de Almeida Regitano, L., Yildiz, M. A., Heaton, M. P., Liu, W.-S., Lei, C.-Z., Reecy, J. M., Saif-Ur-Rehman, M., Schnabel, R. D., & Taylor, J. F.
Affiliations: University of Missouri (US)
University of Vermont (US)
Oklahoma State University (US)
Agricultural Research Service (US)
University of Nottingham (GB)
Uppsala University (SE)
Texas A&M University (US)
University of Veterinary and Animal Sciences (PK)
Roman L. Hruska U.S. Meat Animal Research Center (US)
Pennsylvania State University (US)
Iowa State University (US)
Corresponding author: Decker, Jared E.
Taylor, Jeremy F.
ORCID: Decker, Jared E.
McKay, Stephanie D.
Rolf, Megan M.
Sonstegard, Tad S.
Hanotte, Olivier
Götherström, Anders
Seabury, Christopher M.
Praharani, Lisa
Babar, Masroor Ellahi
Heaton, Michael P.
Reecy, James M.
Schnabel, Robert D.
Taylor, Jeremy F.
Venue: PLoS Genetics
Publisher: Public Library of Science (PLoS)
Published: 2014-03-27
Volume: 10
Issue: 3
Pages: e1004254
ISSN: 1553-7390 (ISSN-L)
1553-7404
DOI: 10.1371/journal.pgen.1004254
PMC: PMC3967955
OpenAlex: W2177259980
Cited by: 521
References: 59
Citations by year: 2026: 33 · 2025: 29 · 2024: 34 · 2023: 36 · 2022: 45 · 2021: 93 · 2020: 40 · 2019: 35 · 2018: 64 · 2017: 34 · 2016: 29 · 2015: 34 · 2014: 13
FWCI: 24.02
Type: journal article
Language: en
Open access: gold
doi.org
Licence: public-domain
creativecommons.org/publicdomain/zero/1.0/ (unspecified)
Locations: PLoS Genetics (publishedVersion, public-domain)
Europe PMC (PubMed Central) (publishedVersion, public-domain)
PubMed Central (publishedVersion, public-domain)
PubMed (publishedVersion)
LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (publishedVersion, other-oa)
arXiv (Cornell University) (submittedVersion)
Iowa State University Digital Repository (Iowa State University) (submittedVersion)
KTH Publication Database DiVA (KTH Royal Institute of Technology) (submittedVersion, other-oa)
RePEc: Research Papers in Economics (submittedVersion)
LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by-nc-nd)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Universidad de Córdoba Insitutional Repository (Universidad de Córdoba) (submittedVersion, cc-by-nc-nd)
OakTrust (Texas A&M University Libraries) (submittedVersion)
arXiv (Cornell University)
Greater South Information System
Funders: U.S. Department of Agriculture (#2011-68004-30367, 2013-68004-20364, 2013-68004, 2011-68004-30214)
National Institute of Food and Agriculture (2013-68004, 2011-68004-30214, 2011-68004-30367, 2013-68004-20364, 2009-65205-05635)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Keywords: cattle breeds, population structure, admixture, hybridization, Bos indicus, taurine cattle, introgression, Shorthorn cattle, Criollo cattle, Iberian cattle, European cattle breeds, cattle, phylogenetic networks
MeSH terms: Alleles, Animals, Animals, Domestic, Breeding, Cattle, Gene Frequency, Genetics, Population, Humans, Phylogeny, Genetic Variation, Polymorphism, Single Nucleotide

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Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

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