Legacies of Domestication, Trade and Herder Mobility Shape Extant Male Zebu Cattle Diversity in South Asia and Africa
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Abstract All tropically adapted humped cattle ( Bos indicus or “zebu”), descend from a domestication process that took place >8,000 years ago in South Asia. Here we present an intercontinental survey of Y-chromosome diversity and a comprehensive reconstruction of male-lineage zebu cattle history and diversity patterns. Phylogenetic analysis revealed that all the zebu Y-chromosome haplotypes in our dataset group within three different lineages: Y3 A , the most predominant and cosmopolitan lineage; Y3 B , only observed in West Africa; and Y3 C , predominant in South and Northeast India. The divergence times estimated for these three Zebu-specific lineages predate domestication. Coalescent demographic models support either de novo domestication of genetically divergent paternal lineages or more complex process including gene flow between wild and domestic animals. Our data suggest export of varied zebu lineages from domestication centres through time. The almost exclusive presence of Y3 A haplotypes in East Africa is consistent with recent cattle restocking in this area. The cryptic presence of Y3 B haplotypes in West Africa, found nowhere else, suggests that these haplotypes might represent the oldest zebu lineage introduced to Africa ca. 3,000 B.P. and subsequently replaced in most of the world. The informative ability of Interspersed Multilocus Microsatellites and Y-specific microsatellites to identify genetic structuring in cattle populations is confirmed.
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Significant influxes occurred during the Arab expansion (~700 AD), introducing male zebu cattle with the Y3b and Y3c sub-haplogroups, and again in the late 19th century, when cattle of the Y3a sub-haplogroup were introduced to restock herds devastated by the Rinderpest pandemic.
“Significant influxes occurred during the Arab expansion (~700 AD), introducing male zebu cattle with the Y3b and Y3c sub-haplogroups, and again in the late 19th century, when cattle of the Y3a sub-haplogroup were introduced to restock herds devastated by the Rinderpest pandemic [36].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [36]
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Experimental — accuracy not yet measuredThe mtDNA I1 haplogroup and Y3b sub-haplogroup are widely distributed in India and other parts of the world, while Y3a sub-haplogroup predominates in southern China and Southeast Asia.
“The mtDNA I1 haplogroup and Y3b sub-haplogroup are widely distributed in India and other parts of the world, while Y3a sub-haplogroup predominates in southern China and Southeast Asia [6,9,36,37].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [36]
The Introduction reports that mtDNA I1 may have spread through South Asia and beyond, and identifies Y3b mainly with Indian sires. The Results identify Y3b-compatible lineages in India and Africa and say Y3a was mainly identified in Chinese sires. Neither passage establishes that Y3a predominates specifically in southern China and Southeast Asia; the paper also identifies Y3a-compatible samples in India. Page numbers were not available in our copy. (LLM, conf=0.85)
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- Authors
- Pérez-Pardal, L., Sánchez-Gracia, A., Álvarez, I., Traoré, A., Ferraz, J. B. S., Fernández, I., Costa, V., Chen, S., Tapio, M., Cantet, R. J. C., Patel, A., Meadow, R. H., Marshall, F. B., Beja-Pereira, A., & Goyache, F.
- Affiliations
- Universidade do Porto (PT)
- Servicio Regional de Investigación y Desarrollo Agroalimentario (ES)
- Institut de l'Environnement et Recherches Agricoles (BF)
- Universidade de São Paulo (BR)
- Yunnan University (CN)
- Natural Resources Institute Finland (FI)
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- Harvard University (US)
- Washington University in St. Louis (US)
- Corresponding author
- Goyache, Félix
- ORCID
- Venue
- Scientific Reports
- Published
- 2018-12-21
- Volume
- 8
- Issue
- 1
- Pages
- 18027-18027
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC6303292
- OpenAlex
- W2904400044
- Cited by
- 45
- References
- 50
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 4 · 2023: 3 · 2022: 9 · 2021: 10 · 2020: 5 · 2019: 1
- FWCI
- 2.45
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Dipòsit Digital de la Universitat de Barcelona (Universitat de Barcelona) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Jukuri (Natural Resources Institute Finland (Luke)) (submittedVersion)
- Greater South Information System
- Funders
- National Natural Science Foundation of China (31460281)
- Fundação para a Ciência e a Tecnologia (COMPETE, SFRH/BPD/94518/2013, PTDC/CVT/117851/2010, SFRH/BD/88129/2012, FCOMP-01-0124-FEDER)
- 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
- Bos indicus, cattle domestication, Y-chromosome haplotypes, trade, genetic structure, microsatellite markers, South Asia, Africa
- MeSH terms
- Domestication, Farms, Africa, Agriculture, Animals, Animals, Domestic, Asia, Cattle, Commerce, Haplotypes, Male, Phylogeny, Population Dynamics, Genetic Variation, Y Chromosome, Microsatellite Repeats, Animal Migration
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