Deciphering the Patterns of Genetic Admixture and Diversity in Southern European Cattle Using Genome-Wide SNPs
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) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non-European cattle ancestry in these cattle breeds.
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African cattle (mtDNA T1, mixed with zebu lineage) were once introduced to the European Mediterranean region.
“As previously mentioned, African cattle (mtDNA T1, mixed with zebu lineage) were once introduced to the European Mediterranean region [26,52,53].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [53]
The Introduction and Discussion (pages not provided) report African taurine ancestry in Iberian cattle and both African taurine and zebu-like ancestry in some Italian and Balkan breeds. They do not identify an mtDNA T1 lineage or establish that African cattle already mixed with zebu were introduced into the Mediterranean region; the origin of the dual ancestry remains uncertain. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIn the 15th century, southern European herds carrying African indicine ancestry were introduced to the Americas.
“Subsequently, in the 15th century, southern European herds carrying African indicine ancestry were introduced to the Americas [52,53].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [53]
The Results section (page unavailable) finds both African and indicine ancestry in several Balkan and Italian cattle breeds, supporting the ancestry portion of the claim. It does not say those herds were introduced to the Americas in the 15th century, and it describes African and indicine ancestry as distinct components rather than establishing an African origin for the indicine component. (LLM, conf=0.86)
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Bos taurus haplotypes segregating in Nellore (Bos indicus) cattle
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Association of PCSK1 gene polymorphisms with abdominal fat content in broilers
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Exploring genetic diversity and genomic inbreeding across local beef cattle breeds
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IBD sharing patterns as intra-breed admixture indicators in small ruminants
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Whole genome sequencing reveals signals of adaptive admixture in Creole cattlePreprint
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The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution
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EVALUATION OF GENETIC DIVERSITY IN SELECTED BEEF BREEDS
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Self-citationUnveiling the genetic structure of Costa Rican bovines through genetic admixture models
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- Authors
- Upadhyay, M., Bortoluzzi, C., Barbato, M., Ajmone‐Marsan, P., Colli, L., Ginja, C., Sonstegard, T. S., Bosse, M., Lenstra, J. A., Groenen, M. A. M., & Crooijmans, R. P. M. A.
- Affiliations
- Swedish University of Agricultural Sciences (SE)
- Wageningen University & Research (NL)
- Università Cattolica del Sacro Cuore (IT)
- Universidade do Porto (PT)
- Recombinetics (United States) (US)
- Utrecht University (NL)
- Corresponding author
- Upadhyay, Maulik
- ORCID
- Venue
- Evolutionary Applications
- Publisher
- Wiley
- Published
- 2019-02-08
- Volume
- 12
- Issue
- 5
- Pages
- 951-963
- ISSN
- 1752-4563 (ISSN-L)
- 1752-4571
- PMC
- PMC6503822
- OpenAlex
- W2910573735
- Cited by
- 45
- References
- 61
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 3 · 2023: 5 · 2022: 6 · 2021: 10 · 2020: 11 · 2019: 2
- FWCI
- 4.36
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Evolutionary Applications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- Funders
- European Commission
- Fundação para a Ciência e a Tecnologia (IF/00866/2014, PTDC/CVTLIV/2827/2014)
- 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
- linkage disequilibrium decay, population bottleneck, founder populations, Iberian cattle, nucleotide diversity, demographic history
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