Origin and Spread of Bos taurus: New Clues from Mitochondrial Genomes Belonging to Haplogroup T1

Abstract

BackgroundMost genetic studies on modern cattle have established a common origin for all taurine breeds in the Near East, during the Neolithic transition about 10 thousand years (ka) ago. Yet, the possibility of independent and/or secondary domestication events is still debated and is fostered by the finding of rare mitochondrial DNA (mtDNA) haplogroups like P, Q and R. Haplogroup T1, because of its geographic distribution, has been the subject of several investigations pointing to a possible independent domestication event in Africa and suggesting a genetic contribution of African cattle to the formation of Iberian and Creole cattle. Whole mitochondrial genome sequence analysis, with its proven effectiveness in improving the resolution of phylogeographic studies, is the most appropriate tool to investigate the origin and structure of haplogroup T1.MethodologyA survey of >2200 bovine mtDNA control regions representing 28 breeds (15 European, 10 African, 3 American) identified 281 subjects belonging to haplogroup T1. Fifty-four were selected for whole mtDNA genome sequencing, and combined with ten T1 complete sequences from previous studies into the most detailed T1 phylogenetic tree available to date.ConclusionsPhylogenetic analysis of the 64 T1 mitochondrial complete genomes revealed six distinct sub-haplogroups (T1a–T1f). Our data support the overall scenario of a Near Eastern origin of the T1 sub-haplogroups from as much as eight founding T1 haplotypes. However, the possibility that one sub-haplogroup (T1d) arose in North Africa, in domesticated stocks, shortly after their arrival from the Near East, can not be ruled out. Finally, the previously identified “African-derived American" (AA) haplotype turned out to be a sub-clade of T1c (T1c1a1). This haplotype was found here for the first time in Africa (Egypt), indicating that it probably originated in North Africa, reached the Iberian Peninsula and sailed to America, with the first European settlers.

Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

“…In Africa, haplotypes from haplogroups other than T1 have been found only in Egypt (combined frequency 38.5%) and Northwest Africa (less than 2%) and are completely absent in the rest of the continent. A recent comprehensive study of whole mtDNA of the T1 haplogroup identified eight haplotypes as founders of the African T1 population [11]. Estimates of coalescence times for the T1 sub-haplogroups (6,200 to 12,900 BP) and their current geographic distributions are compatible with a Southwest-Asian origin for most T1 sub-haplogroups, which for sub-haplogroup T1c1 has been confirmed by it discovery in Iraq [14].…”

“…As shown for haplogroup T1 in Africa [11,44], whole-mtDNA sequencing may detect additional sub-haplogroups informative for movements of cattle between or within continents and expansion of populations. Ancient DNA studies contribute essentially to the historic reconstructions by providing geographic and historic anchor points for specific haplotypes.…”

“…Five taurine (T) and two indicine (I) haplogroups account for the vast majority of mtDNA haplotypes [6][7][8][9]. Complete mtDNA sequences have established an accurate phylogeny and indicated a Southwest-Asian origin for all major T haplogroups, including the African T1 and East-Asian T4 [10,11]. These and other studies also identified the rare haplogroups P, Q and R, with P and R most likely derived from European aurochs [12][13][14].…”

The characterization of goat genetic diversity: Towards a genomic approach

“…Recent evidence, both in livestock and wildlife, showed that molecular phylogenies based on a short and fastevolving portion of mtDNA, such as the control region, can be heavily affected by the effects of NUMTs (NUclear Mitochondrial Transpositions, also called pseudogenes; Hassanin et al, 2010;Moyle et al, 2013) and homoplasy (McCracken and Sorenson, 2005;Bonfiglio et al, 2012), which may mask the actual extent of divergence/similarity between mitochondrial lineages. mtDNA control region analysis in cattle proved to be inadequate for a thorough characterization of maternal lineages, and a far more precise picture has been obtained from complete sequences of mitochondrial genomes (Achilli et al, 2008;Bonfiglio et al, 2010Bonfiglio et al, , 2012.…”

“…mtDNA control region analysis in cattle proved to be inadequate for a thorough characterization of maternal lineages, and a far more precise picture has been obtained from complete sequences of mitochondrial genomes (Achilli et al, 2008;Bonfiglio et al, 2010Bonfiglio et al, , 2012. Next generation sequencing technologies now permit the high throughput/low cost analysis of entire mitochondrial genomes at the maximum resolution, and have become the common standard for the investigation of the human maternal lineages.…”