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Genetic studies

Genetic studies have been conducted on Austronesian peoples. Haplogroup O1a, marked by the M119 SNP, is frequently detected in Native Taiwanese and people of the northern Philippines as well as some people in Indonesia, Malaysia, and non-Austronesian populations in southern China. A 2007 analysis of the DNA recovered from human remains in archaeological sites of prehistoric peoples along the Yangtze River in China also shows high frequencies of Haplogroup O1 in the Neolithic Liangzhu culture, linking them to Austronesian and Tai-Kadai peoples. The Liangzhu culture existed in coastal areas around the mouth of the Yangtze. Haplogroup O1 was absent in other archaeological sites inland. The authors of the study suggest that this may be evidence of two different human migration routes during the peopling of Eastern Asia; one coastal and the other inland, with little gene flow between them.

An important breakthrough in studies in Austronesian genetics was the identification of the "Polynesian motif" (haplogroup B4a1a1) in 1989, a specific nine-base-pair deletion mutation in mitochondrial DNA. Several studies have shown that it is shared by Polynesians and Island Southeast Asians, with a sub-branch also identified in Madagascar, indicating shared maternal ancestry among Austronesians. Austronesian-speaking regions also have high-to-moderate frequencies of Haplogroup O1 of the Y-DNA (including Madagascar), indicating shared paternal ancestry, with the exception of Polynesia where the Papuan -derived Haplogroup C2a1 predominates (although lower frequencies of Austronesian Haplogroup O-M122 also exist). This indicates that the Lapita people, the direct ancestors of Polynesians, were likely matrilocal, assimilating Papuan men from outside the community by marriage in Near Oceania, prior to the Polynesian expansion into Remote Oceania.

Moodley et al. (2009) identified two distinct populations of the gut bacteria Helicobacter pylori that accompanied human migrations into Island Southeast Asia and Oceania, called hpSahul and hspMāori. The study sampled Native Australians, Native Taiwanese, highlanders in New Guinea, and Melanesians and Polynesians in New Caledonia, which were then compared with other H. pylori haplotypes from Europeans, Asians, Pacific Islanders, and others. They found that hpSahul diverged from mainland Asian H. pylori populations approximately 31,000 to 37,000 years ago and have remained isolated for 23,000 to 32,000 years, confirming the Australo-Melanesian substratum in Island Southeast Asia and New Guinea. hspMāori, on the other hand, is a subpopulation of hpEastAsia, previously isolated from Polynesians (Māori, Tongans, Samoans) in New Zealand, and three individuals from the Philippines and Japan. The study found hspMāori from Native Taiwanese, Melanesians, Polynesians, and two inhabitants from the Torres Strait Islands, all of which are Austronesian sources. As expected, hspMāori showed greatest genetic diversity in Taiwan, while all non-Taiwanese hspMāori populations belonged to a single lineage they called the "Pacific clade". They also calculated the isolation-with-migration model (IMa), which showed that the divergence of the Pacific clade of hspMāori was unidirectional from Taiwan to the Pacific. This is consistent with the Out-of-Taiwan model of Austronesian expansion.

On 16 January 2020, the personal genomics company 23andMe added the category "Filipino & Austronesian" after customers with no known Filipino ancestors were getting false positives for 5% or more "Filipino" ancestry in their ancestry composition report (the proportion was as high as 75% in Samoa, 71% in Tonga, 68% in Guam, 18% in Hawaii, and 34% in Madagascar). The company's scientists surmised that this was due to the shared Austronesian genetic heritage being incorrectly identified as Filipino ancestry.

A study about the ancestral composition of modern ethnic groups in the Philippines from 2021 similarly suggests that distinctive Basal-East Asian (East-Eurasian) ancestry originated in Mainland Southeast Asia at ~50,000 BCE and expanded through multiple migration waves southwards and northwards, respectively. Basal-East Asian ancestry as well as later Austroasiatic ancestry from Mainland Southeast Asia, arrived into the Philippines prior to the Austronesian expansion. Austronesian speakers themselves are suggested to have arrived in Taiwan and the northern Philippines between 10,000 BCE to 7,000 BCE from coastal Fujian. The authors concluded that the Austronesian expansion into Island Southeast Asia and Polynesia was outgoing from the Philippines rather than Taiwan and that modern Austronesian-speaking people mostly have ancestry from the earliest Basal-East Asians, Austroasiatic migrants from Mainland Southeast Asia, and Austronesian-speaking seafarers from the Philippines.