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"Early results from studies using mtDNA to explore this question were conflicting or inconclusive; however, recent research by Trejaut et al. has shed more light on the subject. Trejaut et al. analyzed DNA from people in China, Southeast Asia, Polynesia, and Taiwan. The authors focused specifically on the aboriginal populations of Taiwan, thought to be ancestors of today's Polynesians, and looked for unique genetic markers that occurred in the aboriginal people. They then compared these markers to those found in mainland Chinese, Taiwanese, and other Southeast Asian peoples, and asked: do the aboriginal people of Taiwan have a common ancestor in mainland China, and if yes, how long ago? And do the aboriginal Taiwanese share a common ancestry with the Polynesians?
Although Taiwan is currently inhabited mainly by migrants of recent Chinese origin, this has not always been the case. Today, roughly 2% of the inhabitants are direct descendents of the island's indigenous people and have a unique culture, language, and genetic makeup. And while the Chinese immigrants colonized Taiwan a mere 400 years ago, archeological records show that Taiwan may have been inhabited for the last 15,000 years.
Trejaut et al. found that the indigenous Taiwanese, Melanesian, and Polynesian populations share three specific mutations in their mtDNA that do not occur in mainland east Asian populations. Furthermore, they showed that there were enough different mtDNA mutations between the mainland Chinese population and the aboriginal Taiwanese to support the archeological findings suggesting a long period of habitation.
Taken together, these results suggest that Taiwanese aboriginal populations have genetically been isolated from mainland Chinese for 10,000 to 20,000 years, though the whereabouts of their origin in the Asian region is still unclear. Additionally, these results demonstrate that Polynesian migration most likely originated from people identical to the aboriginal Taiwanese. These findings provide the first direct evidence for the common ancestry of Polynesians and indigenous Taiwanese, and suggest that Taiwan genetically belongs to that region of insular Southeast Asia that might have been the point from where Polynesians started their migration across the Pacific, followed by later cultures that developed from their descendents in east Indonesia and Melanesia. Further research will be necessary to accurately determine the origins of the aboriginal Taiwanese; however, these results are a step towards clarifying the origins of Polynesians."

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Source(s):
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166355/

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