Genomic analyses of Asiatic Mouflon in Iran provide insights into the domestication and evolution of sheep

Background Asiatic mouflon ( O. gmelini ) consists of several subspecies mainly distributed in Armenia, southern Azerbaijan, Cyprus, northern, southern, and western regions of Iran, and eastern and central regions of Turkey nowadays. Genome analyses of Asiatic mouflon in Iran revealed that they could have diverged from the direct ancestor of domestic sheep, and showed genetic introgression into domestic sheep after domestication. However, the impact of the Asiatic mouflon subspecies in Iran on sheep domestication remains unclear. Results Here, we conducted a comprehensive population genomics analysis of Asiatic mouflons in Iran with 780 whole-genome sequences, 767 whole mitogenomes, and 239 Y chromosomes. Whole-genome sequence analyses revealed two subpopulations of the Asiatic mouflons in Iran: O. gmelini _2 limited in Kabudan and O. gmelini _1 over a wide geographic area. Phylogenetic analyses of the Asiatic mouflons in Iran based on uniparental variants revealed a monophyletic lineage with the mitochondrial haplogroups C+E, and clustered into a monophyletic with Y-chromosomal lineage HY2 of sheep. Additionally, introgression tests detected significant signals of genetic introgression from O. gmelini _2 to four sheep populations (e.g., Garut, Garole, Bangladeshi, and Sumatra) in South and Southeast Asia. In the four sheep populations, selective tests and introgression signals revealed that the wild introgression could have contributed to their small body size and local adaptation to the hot and humid environments in the Indian Peninsula. Conclusions Our results suggested that the maternal haplogroups C+E and paternal lineage HY2 could have originated from the Asiatic mouflon in Iran. Also, our findings provide new insights into sheep domestication and subsequent introgressions from wild ancestors to domestic populations.