Evidence for independent domestication of sheep mtDNA lineage A in India and introduction of lineage B through Arabian sea route

Abstract

India ranks the second in the world in terms of its sheep population with approximately 74.26 million represented by 44 well-described breeds in addition to several non-descript populations. Genetic diversity and phylogeography of Indian sheep breeds remain poorly understood, particularly for south Indian breeds. To have a comprehensive view of the domestication history of Indian sheep, we sequenced the mitochondrial DNA (mtDNA) control region (D-loop) and cytochrome b gene (CYTB) of 16 Indian domestic sheep breeds, most of them (13) from the south India. We analysed these sequences along with published data of domestic and wild sheep from different countries, including India. The haplotype diversity was relatively high in Indian sheep, which were classified into the three known mtDNA lineages, namely A, B and C. Lineage A was predominant among Indian sheep whereas lineages B and C were observed at low frequencies but C was restricted to the breeds of north and east India. The median joining network showed five major expanding haplogroups of lineage A (A1–A5). Out of which, A2, A4 and A5 were more frequent in Indian sheep in contrast to breeds from other parts of the world. Among the 27 Indian sheep breeds analysed, Mandya and Sonadi breeds were significantly different from other Indian breeds in the MDS analyses. This was explained by a very high contribution of lineage B into these two breeds. The Approximate Bayesian Computation (ABC) provided evidence for the domestication of lineage A sheep in the Indian subcontinent. Contrary to the current knowledge, we also found strong support for the introduction of lineage B into Indian subcontinent through sea route rather than from the Mongolian Plateau. The neighbour-joining tree of domestic and wild sheep revealed the close genetic relationship of Indian domestic sheep with Pakistani wild sheep O. vignei blanfordi. Based on our analyses and archaeological evidences, we suggest the Indian subcontinent as one of the domestication centres of the lineage A sheep, while lineage B sheep might have arrived into India from elsewhere via Arabian sea route. To the best of our knowledge, this is the first comprehensive study on Indian sheep where we have analysed more than 740 animals belonging to 27 sheep breeds raised in various regions of India. Our study provides insight into the understanding of the origin and migratory history of Indian sheep.

Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep ( Ovis aries )

“…The phylogeographic structure that we observed in modern mitochondrial sheep haplogroups, where haplogroup B predominates in western populations and haplogroup A does so in eastern populations, is consistent with various reports [e.g., (33,(41)(42)(43)]. Such structure has been explained by means of multiple domestication origins (33,(44)(45)(46)(47), the domestication of different wild populations or species (33), introgression (41), and lineage sorting-and-gene drift (33). Although multiple domestication origins are still being invoked to explain haplogroup structure (44)(45)(46)(47), its popularity was most certainly influenced a few decades ago by the discovery of multiple domestication origins in pigs and cattle (33).…”

“…Such structure has been explained by means of multiple domestication origins (33,(44)(45)(46)(47), the domestication of different wild populations or species (33), introgression (41), and lineage sorting-and-gene drift (33). Although multiple domestication origins are still being invoked to explain haplogroup structure (44)(45)(46)(47), its popularity was most certainly influenced a few decades ago by the discovery of multiple domestication origins in pigs and cattle (33). However, sheep domestication centers outside southwest Asia have never been identified (48).…”

Phylogeographic Patterns of the Greater Cane Rat (Thryonomys Swinderianus) Populations from Eastern, Western and Southern Africa and Implications for Wildlife Conservation

“…Mt-DNA has been used to assess haplogroup histories, maternal lineages and the genetic affinities of many vertebrates, including mammals (Guo et al, 2005; Kamalakkannan et al, 2021), birds (Di Lorenzo et al, 2015), reptiles (Candan et al, 2021) and amphibians (Wang et al, 2021). Mt-DNA was deemed valuable for characterizing populations of cane rats occurring in distant localities by considering sequences of the hypervariable D-loop region (Excoffier et al, 1992).…”

Phylogenetic Analysis of Russian Native Sheep Breeds Based on mtDNA Sequences

“…In this regard, mtDNA polymorphism analysis is widely used to investigate phylogenetic links and genetic structure of various livestock species [ 21 , 22 , 23 , 24 , 25 ]. Numerous studies including tracing the maternal lineage, and establishing phylogenetic relationships, structure, and diversity of the population have been carried out based on the D-loop mtDNA region and the CytB gene [ 26 , 27 ].…”