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The origin of modern Polynesians, the route of their expansion into the Pacific Ocean, and the timing of their movements all remain contentious topics in modern anthropology. Numerous studies have used molecular data to elucidate settlement patterns in the Indo-Pacific region, but the same evidence is often interpreted in opposing ways by different researchers. Above all, mitochondrial DNA (mtDNA) diversity has been used to discriminate between competing migration models and has narrowed the probable source of proto-Polynesian peoples to southern China and Taiwan or eastern Indonesia. Richards et al. (1998) used a dating method employing the ρ statistic to argue for an origin of Polynesian peoples in eastern Indonesia during the Pleistocene (>10,000 years ago). Here, the time to the most recent common ancestor (TMRCA) is recalculated for a new series of Indonesian mtDNA sequences with Polynesian affinities. These data, which incorporate additional sequences published after 1998, produce dates that cannot rule out the possibility of a common ancestor for these sequences during the Holocene (<10,000 years ago). This implies that previous estimates of TMRCA dates for Indonesian sequences lacked the statistical robustness necessary for replicability. The extant mtDNA evidence can no longer be viewed as favoring a Polynesian origin in eastern Indonesia, but instead remains consistent with an origin of proto-Polynesian peoples in southern China and Taiwan.