Genetic studies on Filipinos

[5] A 2008 genetic study by Leeds University and published in Molecular Biology and Evolution, showed that mitochondrial DNA lineages have been evolving within Maritime Southeast Asia since modern humans arrived approximately 50,000 years ago.

[6] However, these have been repudiated by a 2014 study published by Nature using whole genome sequencing (instead of only mtDNA) which has found that all ISEA populations had genes originating from the aboriginal Taiwanese.

[7][5] A 2021 study states that the Philippines faced five migratory waves, with the first being led by Northern and Southern Negritos, who were distantly related to Australian and Papuan groups.

[10] In a study by Delfin et al. (2011), 21.1% (8/38) of a sample of highlanders of northern Luzon (17 Bugkalot, 12 Kalanguya, 6 Kankanaey, 2 Ibaloi, and 1 Ifugao) were found to belong to haplogroup O2a2a1a2-M7, which is outside of the O2a2b-P164 clade and is uncommon among Austronesian-speaking populations, being rather frequently observed among speakers of Hmong-Mien, Katuic, and Bahnaric languages in southwestern China and eastern Mainland Southeast Asia.

[12]) Haplogroup O1a-M119 is also commonly found among Filipinos (25/146 = 17.1% O1a-M119(xO1a1a-P203, O1a2-M50), 20/146 = 13.7% O1a1a-P203, 17/146 = 11.6% O1a2-M50, 62/146 = 42.5% O1a-M119 total according to Trejaut et al. 2014) and is shared with other Austronesian-speaking populations, especially those in Taiwan, western Indonesia, and Madagascar.

[14][15][16] According to another genetic study done by the Kaiser Permanente (KP) Research Program on Genes, Environment, and Health (RPGEH), substantial number of Californian residents self-identifying as Filipinos sampled have "modest" amounts of European ancestry consistent with older admixture.

[21] The integration of Southeast Asia into Indian Ocean trading networks around 2,000 years ago also shows some impact, with South Asian genetic signals that are present in the Indonesian archipelago also extending into the Philippines among the Sama-Bajau communities.

[19] A recent genetic study found 10-20% of Cebuano ancestry is attributable to South Asian (Indian) descent,[22] dated to a time when Precolonial Cebu practiced Hinduism.

Chronological map of the Austronesian expansion [ 2 ]
Distribution of Y haplogroup O lineages in East Asia
The most common Y-DNA Haplogroup type is O, which Filipinos share with Chinese and fellow Southeast Asians. The South Asian Y-DNA H1a indicate the presence of Indians while the 13% frequency of European Y-DNA R1b is evidence of Spanish immigration. [ 14 ] [ 15 ] [ 16 ]