Genetic ancestry of Filipino people


Genetic ancestry of Filipino people are closest to the Ami tribe of Taiwan

Filipinos are often thought of as ethnically Austronesians (Malay, Indonesian, Pacific Islanders). However, recent gene tests indicate a stronger Chinese descent.

There are nine indigenous tribes of native Taiwan. The Saisiat, Atayal, Tsou, Amis, Bunun, Rukai, Puyuma, Paiwan, and Yami or Tao. The Filipino genes are closely related to the Ami tribe.

In short, Pinoys, particularly those from the northern parts, are more Chinese than their Malay or Indonesian counterparts in the South East.

The surprising discovery was again supported by a 2014 study published by Nature using whole genome sequencing (instead of only mtDNA). All ISEA (Island Southeast Asia) populations had genes originating from the aboriginal Taiwanese. 

Chinese origins of Filipino

It is estimated that 30–40% (although there are some estimates as high as 50%) of Filipinos have partial Han Chinese ancestry.

According to Jose Cruz, there are 16 diverse Taiwanese tribes and only four had contributed to the Austronesian diaspora outside the island. The ancestry of these tribes stems from the Han Chinese people.

A recent study published in 2020 at PNAS traced the origins of Guam’s first inhabitants to Taiwan and the Philippines (having Taiwanese ethnicity), based on DNA samples collected on the U.S. territory.

In other genetic tests, Eskimos and Navajos Indians of North America belonged to the same cluster of the Ami tribes. 

Shared language and culture of Chinese

The use of chopsticks is the easiest way to associate groups of people of Chinese ethnicity. Even though it is not native to Filipinos, we share about 2,000 or more Chinese words (Hokkien, which is widely spoken in Taiwan), as well as traditions and dishes.

Filipino terms of respect used by younger members of Filipino family members to address older siblings originated from the Chinese (Hokkien):

Hokkien (Fookien)Tagalog (Traditional)
A-Che or Ah-Chi (eldest sister)Ate
Ku-A or Ah-Hia (eldest brother)Kuya
Di-Chi (2nd older sister)Ditse
Di-Ku (2nd older brother)Diku
Sa-Chi (3rd older sister)Santse
Sa-ku 3rd (older brother)Sanku

Filipino Negritos: Pre-Austronesian from an African wave

Human presence in Southeast Asia dates back to at least 40,000 years ago. The Negritos in the Philippine Islands, Peninsular Malaysia, and the Andaman Islands are thought to represent the descendants of the pre-Austronesian out of Africa migration wave. [Nature

Austronesian influence on Filipinos

Austronesian peoples (Austronesian-speaking) include large groups of people from Taiwan (indigenous Chinese), Southeast Asia, Micronesia, coastal New Guinea, Polynesia, and Madagascar.

Smaller groups of people from Malaysia and Indonesia (Southeast Asia) relocated to the Philippines some 5,000-6,000 years ago although some Ami tribes (Taiwan) were earlier settlers some 8 to 10,000 years ago.

Austronesian ethnicity is evident in the similarity of some words and numerals. Here are examples:

Paiwan (Indigenous Taiwan, closest to the Philippines)Malagasy (Madagascar, farthest from the Philippines)CebuanoTagalog
The Filipino language was highly influenced by its Austronesian roots, but it is still distant compared to the original Austronesia language family that Indonesian, Malay, and Timor Islands use.

Filipino paternal lineage from Taiwan and China

The most frequently occurring Y-DNA haplogroups among modern Filipinos are haplogroup O1a-M119. It is found with maximal frequency among the indigenous peoples of Nias and Mentawi Islands (West coast of Sumatra), Northern Luzon (Especially Batanes), China, and Taiwan.

One logical reason is that the Han Chinese traders arrived in the Philippines via Fujian province almost 2000 years ago. This migration continued during Spanish colonization. Several of them settled and assimilated with the local Filipino-Spanish culture.

Eventually, a small Chinese community developed. Many became local artisans and wealthy Sangleys who even acquired the Don and Dona titles.

Han Chinese is assimilated into the much larger and dominant Austronesian population resulting in the average Filipino having about 25% Han Chinese genes and an estimated 30–40% of the Philippine population having partial Han Chinese ancestry (mainly from Fujian Province).

The connections between Filipinos and the Han Chinese run very deep, such that there are about 2000 or more Chinese words (Hokkien Dialect) in Filipino, and many cultural practices, beliefs and foods are shared.

Assimilation of the Chinese genes during the Spanish colonization

In 1798, almost 300 years after Spain colonized the country, the local Spanish government conducted a census. The result showed that 33% of the population in Luzon, the largest, were Mestizos of Spanish, Mexican, Latino, and Chinese (Sangleys) ancestry.

The comprehensive genetic map below shows that the average Filipino individual’s genome of the 2 largest ethnic groups of the Philippines(Tagalogs & Visayans) is made up of 21–23% Han Chinese genes, 2–3% European (mostly Spanish), and 1.5% Austroasiatic.

Filipinos of Spanish descent comprise only 2 to 3% of the average Filipino individual’s genes.

Filipinos of Spanish descent comprise only 2 to 3%.

Hispanized Chinese surnames

In 1787, Chinese mestizos were about 2,793 out of its local native population of 6,490. Intermarriage continued between Chinese and local natives which resulted in an increase of Chinese mestizos.

Interestingly, anyone born of a Chinese father with an Indio mother was classified as Chinese mestizo. A Chinese mestiza who married an Indio was listed, together with her children, as Indo.

Hence, some Spanish-sounding surnames, such as Cayetano, Villanueva, and Tomas among others, were listed as Chinese mestizos in an 1852 barangay record in Bacolod, according to author Antonio Tan.

The same was true in the Pampanga where hispanized names such as de Ocampo, Bassilo, Mesina, or de lost Reyes, among others, were classified as Chinese mestizo

Negros Iloilo had families such as Lacson, Jocson, and Yulo, among others like the Araneta, who were Chinese mestizo. In Cebu, we have the Velez, Osmena, and Climaco, among others, who are of Chinese descent.

In short, having a Spanish surname does not assume Castillian descent, but rather Chinese.

Some Chinese mestizo eventually dropped their romanized Chinese name to shorten it. For example, the descendant of Jose Castro Ongchengco just used Jose Castro. Mariano Velasco Chua Chengco, a wealthy merchant in the late 19th century, was popularly known as Mariano Velasco. [Tan, p145]

In the mid-19th century, there were 240,000 Chinese mestizos but only about 7,000 to 10,000 Spanish mestizos. [Archipel 32]

Standardizing the Filipino last name

In 1849, a Spanish edict (Catálogo Alfabético De Apellidos) standardized Filipinos who did not have surnames. A list was given for them to choose the surnames they prefer.

Those who already have their last name were able to keep it—provided they have been using it for the last four generations. In short, having a Spanish last name does not necessarily mean having Spanish blood.

Filipinos who have Spanish “religious last names” had to prove their Spanish ancestry. One example is the De la Resurreccion family. They reverted back apparently to their Chinese surname, Yan.

The Yan family was allegedly one of the earliest Chinese immigrants to Laguna, according to Roque Yan. The family has been using the Spanish surname for the last four generations.

The Yan principality first appeared during the interregnum between the Qin and Han period in China. The ethnic Han Chinese have been interacting with the indigenous people of the Philippine Islands since the 9th Century AD, engaging in trading and bartering.

The Yan family of Pagsanjan replaced their Spanish (religious sounding) surname De La Resurreccion in 1849. (PHOTO: Grandchildren of Manuel de la Resurecciόn (Born 1800) and Francisca Cosme (Born 1795) were the first to use the Yan surname, apparently reverting it back to their Chinese roots)

The distinction between Indonesian and Malay ethnicity

Genetic tests conducted by researchers around the world show Filipinos are ethnically and genetically distinct and separate from their Malaysian and Indonesian neighbors, despite having similar features and even dialects.

According to Cruz, there is actually no such thing as “The Malay Race” but only Malay ethnicity. These groups are found in the Malay Peninsula and Sumatra. About 2,465 km of water east of the Philippines.

The point is, that the Philippines is unique among its South East Asian neighbors. They are the only race that is considered direct descendants of people from Ancient East Asia via Taiwan. Thus share 75–100% of the genes of the Taiwanese Amis.

On the other hand, its neighbors Malaysia and Indonesia (Malay ethnicity) are primarily Austroasiatic (from mainland South East Asia) with significant Austronesian and Indian genetic admixture.

Filiipinos have a minuscule 1.5% Austroasiatic genes

Still, Filipinos have Malay influences such as words, dishes, and even facial features. After all, they are close neighbors.

Filipinos do not necessarily have Indonesian ethnicity

  • Filipinos do not cluster with Indonesians in genetic tests.
  • Indonesians are primarily Austroasiatic since they cluster with Austroasiatic.
  • The average Filipino’s genes only have a minuscule 1.5% Austroasiatic genes, which were also contributed by Vietnamese, Cambodians, and Malaysians who settled in the Philippines a few hundred years ago.

Malays and Indonesians are genetically Austroasiatics (Khmers, Vietnamese, etc.) who have undergone a language shift to Austronesian, and their Urheimat is in mainland South East Asia.

Therefore, the average Filipino genes consist of ancient East Ancient (north) and old East Asian (south), which were two genetically distinct peoples. (See Filipino ethnic origin from Southern China)

The charts below clearly show that Filipino genes cluster together with the Taiwanese and are distantly placed among Malays and Indonesians.


Polynesian and African roots of South East Asia

The Malagasy people of Madagascar, although now clustered with the Bantu Africans genetically, are genetically related to the people of South Borneo and more distantly to the Atayal tribe of Taiwan.

The Polynesians and Maoris are genetically linked to the Kankanaey tribe of northern Philippines and hence the Ami/Amis of Taiwan, just like the lowland and highland Filipinos.

It seems the westward journey of Austronesians to Indonesia, Malaysia, Sri Lanka, and Madagascar was dominated by the Atayal tribe while the eastward journey to New Zealand and Polynesia was dominated by the Amis tribe.

Cruz explained that some exceptions like the Mentawai, who live in isolation on an island off the west coast of Sumatra, exist.


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