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

Abstract

Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role.

Interrogation of modern and ancient genomes reveals the complex domestic history of cattle

“…Lineages would then be lost through successive colonization events, resulting in reduced diversity in derived populations at a distance from the source. The geographical distribution of taurine mtDNA haplogroups, whereby European diversity is a subsample of the diversity encountered in the Near East, supports the hypothesis that European cattle are a derivative of the Near Eastern Neolithic complex (Troy et al, 2001;Lenstra et al, 2014). This is supported by archaeological evidence and indicates that B. taurus domesticates migrated from the Near East with nomadic pastoralists into central and northern Europe following the Danubian route, finally reaching western Europe and Britain around 6,000 cal.…”

“…Haplogroup T1 almost exclusively describes African mtDNA diversity and is found only at low frequencies elsewhere; in Africa, non-T1 haplogroups have been reported only in Egyptian and northwest African populations (Troy et al, 2001;Lenstra et al, 2014). The over-representation of the T1 haplogroup in Africa has been cited as evidence for the separate domestication of the founding populations of the African continent, as previously proposed by archaeological data (Stock and Gifford-Gonzalez, 2013).…”

“…This has allowed these phylogeographical exceptions to be securely identified as secondary introductions, which is most likely a legacy of the westward introduction of zebu cattle and subsequent mating with native taurine populations (Troy et al, 2001;Edwards et al, 2007a). With some symmetry, the modern zebu breeds of northern India have been shown to possess a minority component of taurine mtDNA ancestry (Magee et al, 2007;Lenstra et al, 2014). Reciprocal migrations of zebu and taurine cattle from their respective geographic centers of origin, and subsequent mating with native populations elsewhere, were presumably a consequence of the extensive ancient trading routes across southwest Asia, which would have provided an opportunity for genetic exchange between the two taxa (Zeuner, 1963;Naik, 1978;Misra, 2001).…”

“…This is particularly evident in Africa, where analysis of nuclear genetic markers has shown that modern African zebu populations possess autosomal genomes more similar to Indian B. indicus despite all sampled modern African cattle having mtDNA sequences that are clearly B. taurus in origin (MacHugh et al, 1997;Hanotte et al, 2002;Bovine HapMap Consortium, 2009;Lenstra et al, 2014). This finding is further supported by the use of autosomal and Y chromosomal zebu-specific markers (that is, markers that are present at high frequencies in Indian B. indicus populations compared with B. taurus populations), where a cline of east-west zebu-derived alleles running in an east-west direction across the continent and a north-south direction in West Africa is evident (Bradley et al, 1994;MacHugh et al, 1997;Free- Freeman et al, 2006).…”

“…Despite the availability of a large set of modern data, the information content of cattle mitochondrial haplotypes limits their use for ancient DNA studies; while valuable for global phylogeography, current western European cattle populations display little mitochondrial population genetic structure (Lenstra et al, 2014). On the other hand, nuclear DNA data have been shown to provide a breed-level genetic resolution within modern cattle and thus a more nuanced picture of genetic variation across Europe (Bovine HapMap Consortium, 2009;Gautier et al, 2010;Edwards et al, 2011).…”