The question involves whether or not Filipinos have some Negrito genes. The Negritos are the original Australoid peoples of the Philippines. The Filipinos are the modern, SE Asian Mongoloid types that we all familiar with.
SE Asian Australoids are people like Papuans, Melanesians and Negritos.
It is possible to be part this or that in your background, but it won’t show up in genes or in skulls. I think we are all aware that SE Asians in general are a mix of a Mongoloid type with more primitive Australoid types = Negrito or Melanesian types, that were already living there. But when we look at skulls, we see nothing. SE Asian skulls do not look Australoid, other than Negritos and the Senoi.
When we go looking for Australoid genes, we can’t seem to find much of those either. Just a few here and there along the coast of Vietnam, in Malaysia and in Indonesia. Though there are a lot more in Eastern Indonesia.
So, yeah, Filipinos may well be part Melanesian/Negrito going way back when (Heck, all SE Asians are) but there’s little to nothing obvious left of the Australoid presence, other than maybe some vague look in the faces won’t plot on a chart (Filipino skulls won’t plot with Australoid skulls on charts).
The analogy with Amerindians is a good one. Amerindians in the US have quite a bit of White genes. Most are only part Amerindian anymore. But Whites do not have a lot of Amerindian genes. Sure, we have some (I am 1/3000 Amerindian as I am related to Pocohontas), and perhaps a majority of Americans have Amerindian genes, but they only have small amounts of them.
Vast amounts of White genes went into the Amerindian population. Few Amerindian genes went into the White population. Both via genocide and genetic swamping effects.
A similar situation may have existed in the Philippines. Aeta genes now look Filipino, but Filipinos seem to have few Negrito genes that I am aware of.
The Negritos were simply genetically swamped out. Vast amounts of Filipino genes went into the Negritos, but few Negrito genes went into the Filipinos.
All of this is complicated by the fact that the original Austronesians may well have been Australoid types. At 5000 YBP, the Taiwanese aborigine Ami, the source of the Filipino population, are Australoid.
They transition to Mongoloid over the next 3000 years. Probably a similar transition occurred in the Philippines, as the Ami in the Philippines slowly turned into Mongoloids along with the rest of SE Asia.
It is true that there are Bornean genes from Borneo in the South of the Philippines, that is, the South Filipinos of Mindanao are part Bornean.
The proto-Daic genes from 15,000 YBP that make up 80% of the Indonesians were from an Australoid people. Proto-Daics (the ancestors of the present day Dai people of Yunnan in South China) 15,000 YBP were Australoids. I am not sure what they looked like. Maybe something like an Aborigine or a Melanesian. The Indonesians then transitioned to Mongoloid types over the next 13,000 years or so.
The Anuids or Ainu types probably passed through the Philippines two times.
The first time, going from Thailand as the Ainuid Jomonese to Japan on boats to form the Japanese Jomonese 16,000 YBP.
Possibly the same migration brought the Jomonese to Australia as the Ainuid Murrayans, a formative element in the Aborigines.