Genetic and anthropology studies on Filipinos

Various genetic and anthropology studies have been performed on Filipinos to analyze the population genetics of the various ethnic groups in the Philippines.
The results of a DNA study conducted by the National Geographic's "The Genographic Project", based on genetic testings of Filipino people by the National Geographic in 2008–2009, found that the Philippines is made up of around 53% Southeast Asia and Oceania, 36% East Asian, 5% Southern European, 3% South Asian and 2% Native American genes.
The first Austronesians reached the Philippines at around 2200 BC, settling the Batanes Islands and northern Luzon. From there, they rapidly spread downwards to the rest of the islands of the Philippines and Southeast Asia, as well as voyaging further east to reach the Northern Mariana Islands by around 1500 BC. They assimilated the older Negrito groups which arrived during the Paleolithic, resulting in the modern Filipino ethnic groups which all display various ratios of genetic admixture between Austronesian and Negrito groups.
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. The authors concluded that it was proof that Austronesians evolved within Island Southeast Asia and did not come from Taiwan (the "Out-of-Sundaland" hypothesis). Population dispersals occurred at the same time as sea levels rose, which resulted in migrations from the Philippine Islands into Taiwan within the last 10,000 years.
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. Contrary to the claim of a south-to-north migration in the "Out-of-Sundaland" hypothesis, the new whole genome analysis strongly confirms the north-to-south dispersal of the Austronesian peoples in the prevailing "Out-of-Taiwan" hypothesis. The researchers further pointed out that while humans have been living in Sundaland for at least 40,000 years, the Austronesian people were recent arrivals. The results of the 2008 study failed to take into account admixture with the more ancient but unrelated Negrito and Papuan populations.
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. The next wave was led by Manobo and Sama, who populated the southern Philippines. The Sama show high genetic affinities with Austroasiatic-speaking groups in Mainland Southeast Asia such as Mlabri and Htin and diverged from a common East Asian branch before Han, Dai, and Kinh split from Amis, Atayal, or Cordillerans. The latest wave was led by the Cordillerans, who settled in the Cordilleran mountain range of north-central Luzon. They mixed with the older Negrito populations although Southern Negritos received additional Papuan-related ancestry. However, central Cordillerans show no admixture with Negritos despite extensive interaction with their neighbors. The study also found evidence of Northeast Asian ancestry, originating from the coastal China/Taiwan area, being dispersed into the Batanes Islands and coastal regions of Luzon. Overall, all Filipino ethnic groups share more alleles with Cordillerans than with Austronesians like Ami or Atayal, who display some admixture with Austroasiatic-related and Northeast Asian-related groups. Also included is haplogroup H1a, that came from South Asian sources.
In addition, there is evidence of low-lying European ancestry in individuals from Bolinao, Cebuano, Ibaloi, Itabayaten, Ilocano, Ivatan, Kapampangan, Pangasinan, and Yogad groups, dating back to the Spanish colonial period. Nonetheless, Filipino demography remains relatively unaffected by Spanish colonialism compared to other colonies.
The most frequently occurring Y-DNA haplogroups among modern Filipinos are haplogroup O1a-M119, which has been found with maximal frequency among the indigenous peoples of Nias, the Mentawai Islands, northern Luzon, the Batanes, and Taiwan, and Haplogroup O2-M122, which is found with high frequency in many populations of East Asia, Southeast Asia, and Polynesia.
In particular, the type of O2-M122 that is found frequently among Filipinos in general, O-P164(xM134), is also found frequently in other Austronesian populations, including Polynesians. Trejaut et al. 2014 found O2a2b-P164(xO2a2b1-M134) in 26/146 = 17.8% of a pool of samples of Filipinos (4/8 = 50% Mindanao, 7/31 = 22.6% Visayas, 10/55 = 18.2% South Luzon, 1/6 = 17% North Luzon, 2/22 = 9.1% unknown Philippines, 2/24 = 8.3% Ivatan).
The distributions of other subclades of O2-M122 in the Philippines were sporadic, but it may be noted that O2a1b-JST002611 was observed in 6/24 = 25% of a sample of Ivatan and 1/31 = 3.2% of a sample from the Visayas, O2a2a1a2-M7 was observed in 1/6 = 17% of a sample from North Luzon, 1/55 = 1.8% of a sample from South Luzon, and 1/31 = 3.2% of a sample from the Visayas, and O2a2b1a1a-M133 was observed in 2/31 = 6.5% of a sample from the Visayas. A total of 45/146 = 30.8% of the sampled Filipinos were found to belong to Haplogroup O2-M122.
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. (Delfin et al. also observed O-M7 in 5/39 = 12.8% of a sample of Agta from Iriga in southeastern Luzon and 5/36 = 13.9% of a sample of Ati from Panay.)
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.
After the 16th century, the colonial period saw the influx of genetic influence from other populations. This is evidenced by the presence of a small percentage of the Y-DNA Haplogroup R1b (R-M343) present among the population of the Philippines. DNA studies vary as to how small these lineages are. A year 2001 study conducted by Stanford University Asia-Pacific Research Center stated that only 3.6% of the Philippine population had European Y-DNA. This however is contrasted by genetic studies done by Applied Biosystems and FamilyTreeDNA, wherein the R1b Y-DNA Haplotype common in Spain and Western Europe was also detected among 12-13% of the sample size of Filipinos, which had come to the area, via immigration from Spain and Latin America, as well as haplogroup I1 (I-M253) which came from Germanic Europeans and had spread to the Philippines mostly from Anglo-America (USA) and consisting to about 0.95% of the sample size. Also included is haplogroup H1a (H-L901), that came from South Asian sources.
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. Therefore implying that the mostly native majority population of the Philippines, still posses Spanish admixture in their genetics in minor percentages per person.
The analysis of the full autosomal genome of 1,082 individuals from the Philippines has shown that "in contrast to several other Spanish-colonized regions, Philippine demography appears to have remained largely unaffected by admixture with Europeans" (Larena et al. 2021). European admixture is found at a low level among individuals from lowland groups such as Ilocanos and Cebuanos, and reaches significant population-wide levels among urbanized lowlanders (who form half the population of the country), Bicolanos and Chavacano-speaking Mestizos.
One study found that the Y-DNA of 2 out of 64 sampled Filipino males belonged to Haplogroup Q-M242 (which has its highest frequency among Native Americans, Asian Siberians, and in Central Asians). Coincidentally, it is in a similar percentage to the previously mentioned National Geographic study, which stated that 2% of the population is Native American.
The Indian Mitochondrial DNA haplogroups, M52'58 and M52a are also present in the Philippines suggesting that there was Indian migration to the archipelago starting from the 5th Century AD.
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.
A recent genetic study found 10-20% of Cebuano ancestry is attributable to South Asian (Indian) descent, dated to a time when Precolonial Cebu practiced Hinduism.
Scientist, Matthew C. Go, in a Trihybrid Ancestry Variation Analysis approach to Admixture in Filipinos, published a study wherein it was discovered that upon exhuming the remains around the public cemetery of the "Manila North Cemetery" as well as other public cemeteries across the Philippines, and practicing forensic anthropology on them, Matthew C. Go estimated that 71% of the mean amount, among the samples exhumed, have attribution to Asian descent while 7% is attributable to European descent. Filipinos have significantly less Asian ancestry compared to other Asian nationalities like the Koreans who are 90% Asian, Japanese at 96%, Thai at 93%, and Vietnamese at 84%.
Nevertheless, a 2019 Anthropology Study by Beatrix Dudzik and also Matthew Go, while using skeletons collated by the University of the Philippines and sampled from all across the Philippines, thus published in the Journal of Human Biology, using physical anthropology, estimated that, 72.7% of Filipinos are Asian, 12.7% of Filipinos can be classified as Hispanic, 7.3% as Indigenous American, African at 4.5% and European at 2.7%. However, this is only according to an interpretation of the data wherein the reference groups, which were attributed to the Filipino samples; for the Hispanic category, were Mexican-Americans, and the reference groups for the European, African, and Indigenous American, categories, were: White Americans, Black Americans, and Native Americans from the USA, while the Asian reference groups were sourced from Chinese, Japanese, and Vietnamese origins.
In contrast, a different anthropology study using Morphoscopic ancestry estimates in Filipino crania using multivariate probit regression models by J. T. Hefner and also Matthew C. Go, published on year 2020, while analyzing Historic and Modern samples of skeletons in the Philippines, paint a different picture, in that, when the reference group for "Asian" was Thailand (Southeast Asians) rather than Chinese, Japanese, and Vietnamese; and the reference group for "Hispanic" were Colombians (South Americans) rather than Mexicans, the combined historical and modern sample results for Filipinos, yielded the following ratios: Asian at 48.6%, African at 32.9%, and only a small portion classifying as either European at 12.9%, and finally for Hispanic at 5.7%.
In 2017, a Japanese scientist, Nandar Yukyi, using a Multivariate Analysis of Craniometric Variation Of Modern Asian And Hispanic Individuals; as her graduate Thesis, found that Mexican and Filipino skeletal samples taken from prisons at Mexico and the Philippines, cluster together, when it comes to physical dimensions, in addition, samples from Guatemalans also misclassify as Filipino, and that there were several instances wherein Filipinos and Mexicans were misclassified into each other's racial categories, and the same happened to Ainu Japanese skeletal samples.
As for the general population of the Philippines, there are several data points elucidating that the Philippine population is racially diverse.
Of the Mexican ancestry in Filipinos, there are records to distill their general number, according to Stephanie Mawson in her M.Phil thesis entitled Between Loyalty and Disobedience: The Limits of Spanish Domination in the Seventeenth Century Pacific, in the 1600s there were thousands of Latin American settlers sent to the Philippines by the Spaniards per year and around that time frame the Spaniards had cumulatively sent 15,600 settlers from Peru and Mexico while there were only 600 Spaniards from Spain, that supplemented a Philippine population of only 667,612 people. Due to the initial low population count, people of Latin American and Hispanic descent quickly spread across the territory. Several hundred Tlaxcalan soldiers sailed to the islands in the 16th century, with some settling permanently and contributing numerous Nahuatl words to the Filipino languages. It was royal policy to use Peruvian and Mexican soldiers as colonists to the Philippines.
The book Intercolonial Intimacies Relinking Latin/o America to the Philippines, 1898–1964 by Paula C. Park cites "Forzados y reclutas: los criollos novohispanos en Asia (1756-1808)" gave a higher number of later Mexican soldier-immigrants to the Philippines, pegging the number at 35,000 immigrants in the 1700s, in a Philippine population which was only around 1.5 Million, thus forming 2.33% of the population.
In 1799, Friar Manuel Buzeta estimated the population of all the Philippine islands as 1,502,574. Despite the number of Mixed Spanish-Filipino descent being the lowest, they may be more common than expected as many Spaniards often had Filipino concubines and mistresses and they frequently produced children out of wedlock.
In the late 1700s to early 1800s, Joaquín Martínez de Zúñiga, an Agustinian Friar, in his Two Volume Book: "Estadismo de las islas Filipinas" compiled a census of the Spanish-Philippines based on the tribute counts (Which represented an average family of seven to ten children and two parents, per tribute) and came upon the following statistics:
The Spanish-Filipino population as a proportion of the provinces widely varied; with as high as 19% of the population of Tondo province (The most populous province and former name of Manila), to Pampanga 13.7%, Cavite at 13%, Laguna 2.28%, Batangas 3%, Bulacan 10.79%, Bataan 16.72%, Ilocos 1.38%, Pangasinan 3.49%, Albay 1.16%, Cebu 2.17%, Samar 3.27%, Iloilo 1%, Capiz 1%, Bicol 20%, and Zamboanga 40%. According to the data, in the Archdiocese of Manila which administers much of Luzon under it, about 10% of the population was Spanish-Filipino. Summing up all the provinces including those with no Spanish Filipinos, all in all, in the total population of the Philippines, mixed Spanish-Filipinos composed 5% of the population.
Meanwhile, government records show that 1.35 Million pure-bred Chinese live in the Philippines and 20% of the Philippines' total population were either half Chinese or mixed Chinese-Filipinos
In the 1860s to 1890s, in the urban areas of the Philippines, especially at Manila, according to burial statistics, as much as 3.3% of the population were pure European Spaniards and the pure Chinese were as high as 9.9%. The Spanish-Filipino and Chinese-Filipino mestizo populations may have fluctuated. Eventually, everybody belonging to these non-native categories diminished because they were assimilated into and chose to self-identify as pure Filipinos. Since during the Philippine Revolution, the term "Filipino" included anybody born in the Philippines coming from any race. That would explain the abrupt drop of otherwise high Chinese, Spanish and mestizo percentages across the country by the time of the first American census in 1903.