Genetic evidence for the proto-Austronesian homeland in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes

Previous studies of mtDNA variation in indigenous Taiwanese populations hav e suggested that they held an ancestral position in the spread of mtDNAs th roughout Southeast Asia and Oceania (Melton et al. 1995; Sykes et al. 1995) , but the question of an absolute proto-Austronesian homeland remains. To s earch for Asian roots for indigenous Taiwanese populations, 28 mtDNAs repre sentative of variation in four tribal groups (Ami, Atayal, Bunun, and Paiwa n) were sequenced and were compared with each other and with mtDNAs from 25 other populations from Asia and Oceania. In addition, eight polymorphic Al u insertion loci were analyzed, to determine if the pattern of mtDNA variat ion is concordant with nuclear DNA variation. Tribal groups shared consider able mtDNA sequence identity (P > .90), where gene flow is believed to have been low, arguing for a common source or sources for the tribes. mtDNAs wi th a 9-bp deletion have considerable mainland-Asian diversity and have spre ad to Southeast Asia and Oceania through a Taiwanese bottleneck. Only four Taiwanese mtDNA haplotypes without the 9-bp deletion were shared with any o ther populations, but these shared types were widely dispersed geographical ly throughout mainland Asia. Phylogenetic and principal-component analyses of Alu loci were concordant with conclusions from the mtDNA analyses; overa ll, the results suggest that the Taiwanese have temporally deep roots, prob ably in central or south China, and have been isolated from other Asian pop ulations in recent history.