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Recent work on autosomal DNA genetic variation across Southeast Asia suggests that genetic diversity largely reflects Pleistocene colonization by modern humans, and was not influenced to any significant degree by major cultural and linguistic changes during the mid to late Holocene (roughly, from ~5,000 years ago to the present). These results seemingly show that the spread of Austronesian languages across Island Southeast Asia was not associated with population movements that were significant enough to affect the overall phylogeny of the autosomal DNA tree. Consequently, the spread of genes is not significantly linked to the spread of languages in Island Southeast Asia; each represents different processes of different antiquity.
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Donohue et al. (2011) studied this question.
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