The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data
Open accessAbstract
Background: Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods: Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus,and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results: The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus.The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61%Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor.Ne estimates based on r2and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion: African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus.This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.
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Zebu cattle spread westward from the Abyssinian region across the continent and penetrated south to Zambia, forming two major hybrid zones of taurine and zebu cattle in West and Southern Africa.
“Zebu cattle spread westward from the Abyssinian region across the continent and penetrated south to Zambia, forming two major hybrid zones of taurine and zebu cattle in West and Southern Africa [48,49,50].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [48]
The Discussion (Genetic diversity and relationships; page unavailable) reports taurine–indicine admixture in West and Southern African cattle, supporting the claim’s broad geographic admixture point. It does not describe a westward spread from Abyssinia, penetration south to Zambia, or two major hybrid zones. (LLM, conf=0.86)
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The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution
Liu, Y., Dao, W., Gao, R., Fan, X., Yang, R., & Miao, Y. (2026) · Animals · doi:10.3390/ani16050776 · Cited by 1 · see citing works
- Authors
- Gebrehiwot, N. Z., Strucken, E. M., Aliloo, H., Marshall, K., & Gibson, J. P.
- Affiliations
- University of New England (AU)
- International Livestock Research Institute (KE)
- Corresponding author
- Gebrehiwot, N. Z.
- Gibson, J. P.
- Venue
- BMC Genomics
- Published
- 2020-12
- Volume
- 21
- Issue
- 1
- Pages
- 869-869
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC7720612
- OpenAlex
- W3112781676
- Cited by
- 50
- References
- 72
- Citations by year
- 2026: 7 · 2025: 9 · 2024: 11 · 2023: 5 · 2022: 7 · 2021: 11
- FWCI
- 3.35
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RUNE (Research UNE) (submittedVersion, cc-by)
- CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Department for International Development, UK Government (OPP1127286)
- 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 › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- African cattle breeds, cattle, Bos indicus, admixture, indigenous cattle, population structure, genetic diversity, effective population size, linkage disequilibrium, ancestry, cattle conservation, domestication
- MeSH terms
- Africa, Animals, Cattle, Genetics, Population, Genetic Variation, Genome, Polymorphism, Single Nucleotide
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