The Filipino genetic makeup is largely to exclusively of East-Eurasian origin, with the great majority being made up by the East/Southeast Asians lineage (ESEA) at ~90% (specifically Fujian ancestry associated with Austronesians). Minor influences come from the Australasian lineage (AA), such as from Papuan-related groups. Often referred Spanish/European admixture is largely neglectable and range from 0–5%. In this regard, Filipinos are most closely related to Native Taiwanese and other Austronesian-speaking Southeast Asian groups.

A study by Larena et al.

[1]

about the ancestral composition of modern ethnic groups in the Philippines from 2021 concluded that the ancestral source of East Asian ancestry originated in Mainland Southeast Asia at ~50,000BC, and expanded through multiple migration waves southwards and northwards respectively.

The Philippines were populated first by a deep East-Eurasian lineage which diverged from Australo-Melanesians ~45,000 years ago and settled the Philippines approximately 35,000 years ago.

Early Basal-East Asian ancestry, as well as later Austroasiatic-associated ancestry, from Mainland Southeast Asia, arrived into the Philippines, through the Sunda region, prior to the Austronesian expansion, sometimes before 12,000 years ago (perhaps ~25,000 years ago) and between 12,000 to 8,000 years ago respectively.

Austronesian-speakers themself are suggested to have arrived on Taiwan and the northern Philippines sometime at 7,000BC from coastal southern China (Fujian). The authors concluded that the later Austronesian expansion into Insular Southeast Asia and Polynesia was outgoing from the Philippines rather than Taiwan, and that modern Austronesian-speaking people have largely ancestry from the earliest Basal-East Asians, Austroasiatic migrants from Mainland Southeast Asia, and Austronesian-speaking seafarers from the Philippines.

There was also a later westward expansion of people from Papua New Guinea to the Philippines as evidenced by Papuan admixture in Blaan and Sangir peoples of Mindanao, as well as minor immigration from Southern India, as detected in the genetics of the Sama-Dilaut people.

The results of a DNA study conducted by the National Geographic's, "The Genographic Project", based on genetic testings of 80,000 Filipino people by the National Geographic in 2008–2009, found that the average Filipino's genes are around 53% Southeast Asia and Oceania, 36% East Asian, 5% Southern European, 3% South Asian and 2% Native American.

A comprehensive genetic study by Olivera et al. published in 09 June 2022 by the Nature Journal, found that East Asians and Southeast Asians cluster nearly completelly together, without much external admixture.

PCA of publicly available whole-genome data merged with the Affymetrix Human Origins and Affymetrix 6.0 genotype data, including samples from East Asia, Mainland Southeast Asia, Insular Southeast Asia and Oceania:

If we look carefully, we see that the majority population of East Asia, Mainland Southeast Asia and Insular Southeast Asia cluster tightly together in a single coherent cluster:

The Fujian sub-lineage of the ESEA source lineage makes up slightly more than 90% among Filipinos, and can be associated with early Austronesians:

By looking at the ethnic minority groups, such as the Australasian Negritos (Aeta, Agta, Aita), these are characterized by strong Austronesian admixture and positioned within a cline between Australasians and East/Southeast Asians. While there is no strong shift towards West-Eurasians, West-Eurasians themselves are shifted towards East-Eurasians in a modest manner.

East/Southeast Asians generally display extrem genetic similarity, compared to other populations, such as Australasians, which display stronger heterogeneity, but are still on the East-Eurasian branch.

It is therefore misleading to differentiate between East Asians and Southeast Asians. We are literally one single cluster within the wider East-Eurasian meta-population. Therefore population genomics have adopted the term “East/Southeast Asian” or the “ESEA lineage”.

This does not mean that the various ethnic groups are identical, no, but it shows the high genetic continuity and population structure.

The Y-chromosome frequency of Filipinos:

They are characterized by mostly East/Southeast Asian clades, as well as some Australasian clades. European clades (specifically R1b) is found at a very low frequency. Surprisingly, the P clades (P*, P1, and P2, are found at very low frequency, more commonly among Agta) are indirectly ancestral to R1b, through the northwards expansion of P1 into Siberia.

Overall, Filipinos are largely to exclusively of Austronesian descent (harboring primarily Fujian ancestry from the ESEA source population).

For a summary of the genetic history of East-Eurasians, please see:

Overview and summary about the genetic history of East Asians and closely related populations

Thank you for reading!

Footnotes