The Enigmatic Origin of Bovine mtDNA Haplogroup R: Sporadic Interbreeding or an Independent Event of Bos primigenius Domestication in Italy?
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BACKGROUND: When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. METHODOLOGY: The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. These mtDNAs were then integrated in a phylogenetic tree encompassing all available P, Q and R complete mtDNA sequences. CONCLUSIONS: Phylogenetic analyses of 28 mitochondrial genomes belonging to haplogroups P (N = 2), Q (N = 16) and R (N = 10) together with an extensive survey of all previously published mtDNA datasets revealed major similarities between haplogroups Q and T. Therefore, Q most likely represents an additional minor lineage domesticated in the Near East together with the founders of the T subhaplogroups. Whereas, haplogroup R is found, at least for the moment, only in Italy and nowhere else, either in modern or ancient samples, thus supporting an origin from European aurochsen. Haplogroup R could have been acquired through sporadic interbreeding of wild and domestic animals, but our data do not rule out the possibility of a local and secondary event of B. primigenius domestication in Italy.
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The P, Q, and R haplogroups represent ancient branches parallel to the T lineage, indicating secondary introgression of European aurochs genes during the expansion of cattle populations into Europe.
“The P, Q, and R haplogroups represent ancient branches parallel to the T lineage, indicating secondary introgression of European aurochs genes during the expansion of cattle populations into Europe [5,39,40].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [39]
The Introduction identifies P, Q and R as ancient non-T mitochondrial branches. But the Discussion describes Q as a lineage likely domesticated in the Near East and spread with human migrations; it considers European-aurochs interbreeding only as one possible explanation for R in Italian cattle. The paper therefore does not support attributing secondary European-aurochs introgression to all three haplogroups during cattle’s expansion into Europe. (LLM, conf=0.88)
Experimental — accuracy not yet measuredIn southern European populations, such as Italian cattle, small amounts of mitochondrial Q and R haplogroups are present.
“In southern European populations, such as Italian cattle, small amounts of mitochondrial Q and R haplogroups are present [39,40].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [39]
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Mitochondrial DNA-based genetic evaluation of autochthonous cattle breeds in Croatia
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Mitochondrial DNA diversity of the Sardinian local cattle stock
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Mitogenome Diversity and Evolution of Bos indicus Cattle in India
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- Authors
- Bonfiglio, S., Achilli, A., Olivieri, A., Negrini, R., Colli, L., Liotta, L., Ajmone-Marsan, P., Torroni, A., & Ferretti, L.
- Affiliations
- University of Pavia (IT)
- Università Cattolica del Sacro Cuore (IT)
- University of Messina (IT)
- Corresponding author
- Ferretti, Luca
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-12-28
- Volume
- 5
- Issue
- 12
- Pages
- e15760
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3011016
- OpenAlex
- W2120661540
- Cited by
- 113
- References
- 39
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 6 · 2023: 10 · 2022: 7 · 2021: 15 · 2020: 4 · 2019: 4 · 2018: 7 · 2017: 2 · 2016: 8 · 2015: 17 · 2014: 10 · 2013: 4 · 2012: 7
- FWCI
- 2.52
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- PubliCatt (Università Cattolica del Sacro Cuore) (submittedVersion, other-oa)
- Funders
- Ministero delle Politiche Agricole Alimentari e Forestali
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- Bos primigenius, aurochs, cattle domestication, mitochondrial genome, European cattle breeds
- MeSH terms
- Animals, Animals, Domestic, Cattle, Crosses, Genetic, DNA, Mitochondrial, Haplotypes, Italy, Models, Genetic, Phylogeny, Ruminants, Genetic Variation, Likelihood Functions, Polymerase Chain Reaction, Evolution, Molecular, Genome, Mitochondrial
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