Legacies of domestication, trade and herder mobility shape extant male zebu cattle diversity in South Asia and Africa

Abstract

All tropically adapted humped cattle (Bos indicus or “zebu”), descend from a domestication process that took place >8,000 years ago in South Asia. Here we present an intercontinental survey of Y-chromosome diversity and a comprehensive reconstruction of male-lineage zebu cattle history and diversity patterns. Phylogenetic analysis revealed that all the zebu Y-chromosome haplotypes in our dataset group within three different lineages: Y3A, the most predominant and cosmopolitan lineage; Y3B, only observed in West Africa; and Y3C, predominant in South and Northeast India. The divergence times estimated for these three Zebu-specific lineages predate domestication. Coalescent demographic models support either de novo domestication of genetically divergent paternal lineages or more complex process including gene flow between wild and domestic animals. Our data suggest export of varied zebu lineages from domestication centres through time. The almost exclusive presence of Y3A haplotypes in East Africa is consistent with recent cattle restocking in this area. The cryptic presence of Y3B haplotypes in West Africa, found nowhere else, suggests that these haplotypes might represent the oldest zebu lineage introduced to Africa ca. 3,000 B.P. and subsequently replaced in most of the world. The informative ability of Interspersed Multilocus Microsatellites and Y-specific microsatellites to identify genetic structuring in cattle populations is confirmed.

Evolution and domestication of the Bovini species

“…On the basis of microsatellites, an African–south Asian Y3 A , an African Y3 B and a south Asian Y3 C were futher suggested (Pérez‐Pardal et al . 2018).…”

A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

“…Cattle are among the most important livestock species worldwide, with almost~1.5 billion individuals in 2012, of which almost a quarter were present in India and China [2]. Two main cattle domestication events have been described, the first~10,000 YA in the Fertile Crescent, which gave rise to taurine cattle (Bos taurus), and the second~2,000 years later in the Indus Valley, giving rise to indicine cattle (Bos indicus) [14,15]. After domestication, cattle were spread across the world following human migration and trade.…”

Y-chromosome genetic diversity of Bos indicus cattle in close proximity to the centre of domestication

“…The identification of five single nucleotide polymorphisms (SNPs) has permitted the classification of worldwide extant cattle breeds into three Y-chromosome haplogroups, named Y1, Y2 and Y3 7. The Y chromosome diversity found in indicus cattle is represented by a single haplogroup (Y3) and variability within this haplogroup makes it possible to differentiate paternal lineages between Indian and Chinese cattle 8 and to recognize the presence of Y3b haplotype family of Indian origin exclusively in West African Zebu animal 9 . The Y-specific microsatellite loci have been studied in several cattle breeds from different geographical areas [10][11][12][13] or local breeds such as Ethiopian cattle 14 , Portuguese cattle 15 , Spanish cattle 16 and Polish cattle 17 .…”