The enigmatic origin of bovine mtDNA haplogroup R: sporadic interbreeding or an independent event of Bos primigenius domestication in Italy?

Abstract

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.

Figure 1. Most-parsimonious tree of bovine complete MtDNA sequences.

The tree is drawn to scale. Phylogeny construction was performed by hand following a parsimony approach, while the evolutionary distances were computed using the Maximum Likelihood (ML) method. The exact values for clades and subclades are available in Table 3 together with averaged distance (rho) of the haplotypes of a clade to the respective root haplotype. Sixteen of the sequences (#1–3, #5, #9–13, #16, #22–26, #28) are new, while the others were previously published: Bos taurus Reference Sequence (BRS) (GenBank accession number V00654) # 14–15, #17 ; #4, #6–8, #19–21, #27 ; #18 . Taking into account that sequence #18 is from an ancient British aurochs radiocarbon dated to 6,738±68 calibrated years BP, the divergence of the haplogroup P node is underestimated. Additional information regarding each mtDNA sequence, including GenBank accession numbers, is provided in Table 2. An additional branch, named E, placed between P and R has been reported previously , but was not included in the tree since it is not a complete mitochrondrial genome sequence.

Figure 2. Tree of complete bovine mtDNA sequences.

This tree, built and rooted as previously described by Achilli et al. 2008 illustrates the relationships between the common haplogroup T represented by BRS and the rare mtDNAs belonging to haplogroups P, Q and R. Shown divergence times are those obtained using ML as reported in Table 3. Mutations are shown on the branches and are numbered according to the BRS; they are transitions unless a base is explicitly indicated; suffixes indicate transversions (to A, G, C, or T) or indels (+, d) and should be read as if the BRS was an artificial root. Recurrent mutations are underlined, and true back mutations with respect to evolutionary direction are prefixed with the superscript β (beta) in addition (which is thus in alternation with prefix @ on the path between the overall root and BRS). Note that the reconstruction of recurrent mutations in the control region is ambiguous in a number of cases. Heteroplasmy is marked with a suffix (h). The numbering of sequences is the same as in Figure 1.

Figure 3. Spatial frequency distribution (%) of haplogroup R.

The dots indicate the geographical location of the populations included in the survey. Population samples and corresponding frequency values are listed in Table S2. This frequency map was obtained using Surfer version 6.04 (Golden Software, Inc.), with the Kriging procedure, and estimates at each grid node were inferred by considering the entire data set.