Maternal and paternal lineage analysis of Island Southeast Asian goats reveals continental propagation routes and introgression through the Indian ocean

The Philippines and Indonesia, located at the crossroads of historical human migrations in the Asia-Pacific region, lie in the southeasternmost part of Mainland Southeast Asia. Both countries are recognized as mega-diverse nations, hosting a wide variety of species. However, the history of goat propagation in Island Southeast Asia remains unclear due to limited molecular studies and the absence of archaeological evidence in this region. This study conducted phylogeographic analyses of mtDNA hypervariable region 1 and SRY 3'UTR sequences of goats from the Philippines and Indonesia, comparing them with Old World domestic goats. Philippine goat mtDNA haplotypes were classified into haplogroups B (152/206, 73.8%) and A (54/206, 26.2%), whereas all Indonesian goat mtDNA haplotypes belonged to haplogroup B (72/72, 100%). The distribution of mtDNA haplogroup B and regional differences suggest two propagation routes: one from China/Taiwan to the Philippines and another from Mainland Southeast Asia to Indonesia. The distribution of five SRY haplotypes demonstrated that haplotype Y2A, absent in Mainland Southeast Asia, was present in Island Southeast Asia, indicating gene introgression through the Indian Ocean from the African continent and/or southern Europe. This introgression may have been driven by human activities, such as European migrations between the 16th and 19th centuries.