The Supplament to the First Study in my original post also show some Indian and Hispanic (Spanish + Latin American) immigration to the Philippines too. But it's only minor compared to the 4 original waves: Negrito, Austroasiatic, Papuan and Austronesian.
https://www.pnas.org/content/pnas/suppl/2021/03/17/2026132118.DCSupplemental/pnas.2026132118.sapp.pdf
Here's the Indian segment...
(Page 28)
5.7 Detection of South Asian-genetic signal in Sama Dilaut
Various cultural communities of ISEA had long-distance historical trade with the Indian subcontinent via the Indian Ocean Trading Network since the 1st millennium BCE (80) until the commencement of colonial period. Along this period are various Hindu Buddhist Kingdoms or empires including, among others, Srivijaya (650-1377), Medang (732-1006), Kediri (1245-1221), Singhasari (1222-1292) and Majapahit (1293-1527). Both Srivijaya and Majapahit kingdoms had ruled over a wide geographical area covering coastal MSEA, western Indonesia, & Malaysia, and may have exerted
influences as far as Sulu archipelago of the Philippines. It is then not surprising to find South Asian genetic signal among lowlander Malays, Javanese, Balinese, Sumatran and Bajo populations of Indonesia, which provide evidence for the historical longdistance interactions between ISEA and the Indian subcontinent.
Admixture analysis of Phil_AsiaPacific_315K & Phil_HO_201K datasets in section (Figs. S2C,D) revealed a low amount of West Eurasian-like ancestry among Sama Dilaut ethnic groups, which can be attributed to gene flow from South Asian populations with high West Eurasian ancestry (5, 81-83). We then formally tested this by using the test D(Mbuti;X,AtaManobo,Sama), where we investigate whether any X South Asian or control population share more alleles with Sama-related ethnic groups relative to Ata Manobo (Table S6J). We find that Sama Dilaut sea nomads of Sulu archipelago and Sama coastal dwellers of Zamboanga peninsula exhibited evidence of gene flow from South Asians. The best surrogate for South Asian genetic signal are
populations with high West Eurasian ancestry or populations labelled as ‘Ancestral North Indian’ (9). The admixture date calculated via LD-based method, Malder, revealed a South Asian gene flow in Sama populations around 750 +/- 150 years ago,which is before the period of Spanish colonization, and well within the period whenISEA was involved in an active trading network with the Indian subcontinent (Table S6M)
SUMMARY: The Sama Bilaut and Badjao people of Southern Philippines have the most Indian descent.
And Spanish segment...
(Page 35)
The Philippines was a colony of Spain from 1565 until 1898, and subsequently under American rule from 1901 until 1946. In contrast to the Philippines, the genetic legacy of the Colonial Period in the Americas is readily apparent today through the detectable high West Eurasian ancestry among the majority of lowland and/or urbanized populations of Latin America (88, 89). In the Philippine context, however, admixture between Spanish and local indigenous populations is largely limited (Figs. S2B-D & Tables S2-4), and can only be detected at a population level, using the test D(Mbuti,CEU,Balangao,X), among Bicolano and Creole-speaking Chavacano ethnic groups (Table S7Y). The signal is likely driven by 4 out of 10 individuals tested among Chavacanos, and 1-2 individuals with high levels of West Eurasian ancestry out of 10 tested among Bicolanos. If the threshold of significance is set at Z > 3, the presence of West Eurasian ancestry was also detected in random individuals (n = 4) among Yogad, Ibaloi, Kapampangan, and Pangasinan populations. If the threshold of significance is stretched to Z > 2, the signal can also be detected in some indviduals from Bolinao, Cebuano, Ibaloi, Itabayaten, Ilocano, Ivatan, Kapampangan, Pangasinan, and Yogad populations. All of these aforementioned ethnic groups predominantly reside in lowland and/or urbanized areas (Table S7Y). No West Eurasian ancestry was detected among Negrito, Manobo, and almost all highland ethnic groups. The West Eurasian genetic signal detected among Sama-related ethnic groups can be attributed to South Asian (Ancestral North Indian with high West Eurasian ancestry) gene flow into these populations. Using Malder (Table S7Z), we were able to detect a single admixture event characterized as West Eurasian plus Cordilleran-related, 239 +/- 54 years BP in Bicolano, 156 +/- 36 years BP in Chavacano, 424 +/- 90 years BP in Cuyonon, 161 +/- 42 years BP in Itawis, 429 +/- 109 years BP in Tagalog, and 178 +/- 28 in Yogad, all of which fall within the period of Spanish Colonization (Table S7Z). The mean estimates for Kapampangan (548 +/- 153 years BP) and Hiligaynon (507 +/- 150 years BP) were older than the initial arrival of Spanish colonialists into the Philippines, but have wide confidence intervals where the lower limits still fall within the Spanish Colonial Period (392 and 357 years BP, respectively).
SUMMARY: The Chavacano and Bicolano people in Mid and East Philippines (The areas closest to Latin America) have the most Spanish ancestry with 4 out of 10 Chavacanos (Mostly Zamboangenos) having high amounts of Spanish descent and 2 out of 10 Bicolanos too. Lowland mainstream Filipinos also have it but not as much as the 20% and 40% of their populations as Bicolanos and Chavacanos have.
