Panasian-Part III: Philippines

Third part of the Panasian run (excluding Yoruba, South Asians).
This post is about populations from the Philippine Archipelago:

About the populations:
Amis and Atayal are Taiwanese aborigines speaking Formosan Austronesian languages. It is generally believed the Austronesian language family derives from Taiwan, having spread into the Philippines, Indonesia and Polynesia as an agriculturally-driven expansion. Taiwanese "Aboriginals" are historically primitive farmers supplementing their diet with some hunting and fishing.
Until recently they were the main inhabitants of Taiwan, having been swamped by Fujianese Han groups only in the last few centuries (Minnan and Hakka). There is some evidence they shared the island with a minority of Taiwanese Negritos- possibly the true Paleolithic forager native inhabitants- who don't exist anymore as a distinct group today.

Filipino populations are farmers, speaking various Austronesian dialects. Tagalog is the dialect on which the National Language of the Philippines, "Filipino" is based. They live in Southern Luzon. Ilocano is spoken by related populations in more Northern regions of Luzon island. Visayan is a third Filipino group of dialects spoken in the Visayas (central group of Philippine islands) as well as in some parts of Mindanao. The sample represented here was from Visayan-speaking colonists from West Mindanao. These groups comprise the majority of the islands population, and are at the core of self-identification with the modern "Filipino" nationality.

Minanubu or Manobo; Iraya are incipient farmers using slash and burn methods in Mindanao and Mindoro respectively. They speak Austronesian languages. These peoples have been suffering pressure from neighbouring more agriculturally advanced and socially complex Filipino migrants (such as Visayans), and are being pushed out of the more fertile soil in their homelands.

Ayta, Agta, Ati and Mamanwa are Philippine Negritos, who are generally hunter-gatherers, at least until very recently. Ayta and Agta are from Luzon; Ati are from the Visayas; Mamanwa from Mindanao.

The diversity of populations in the Philippines seems to fit very well into the Neolithic expansion model I've been exploring. Three groups can be identified, with a degree of continuity between groups: advanced farmer "Filipinos"; slash-and-burn farmers such as Iraya and Minanubu; and forager Negritos.
1) Negritos probably represent the ancient (forager) population of the Philippines. They present varying hybridization with farmers (as seen in farmer-associated components).
The similar pattern of "forager-components" (Kensiu are SE Asian Negritos. Naasioi are Papuans) in Agta, Ati and Ayta may represent Philippine-Negrito unique genetic patterns that ADMIXTURE didn't pick out in this analysis (maybe due to a more inbred Mamanwa sample taking it's own component and non-represented variety in the other Negritos being allocated to related Naasioi and Kensiu-modal components- something similar often happens in Siberian peoples' ADMIXTURE runs).
2) The earliest "First Wave" farmer intrusion in the Philippines is probably associated with Austronesian languages. Taiwanese Aboriginal groups speak the most divergent and diverse Austronesian tongues, and they are modal for the darkgreen component found in much larger amounts in Philippine farmers than in foragers (Negritos). Iraya and Minanubu have large such components but mostly lack the red, blue and lightgreen ones - they may represent a "First Wave" stage of Austronesian Expansion proper.
3) Han Fujianese and Cantonese migration into the Philippines is historically documented even before the Spanish Conquest. A "Second Wave" process may be interpreted as being in full swing in the Philippines in recent centuries and up to today. Slash-and-burn agriculturalists such as Iraya and Minanubu seem to be in the process of assimilation or expulsion to more marginal lands. These more primitive agriculturalists also present larger forager-modal components than "Filipinos", though less than Negritos, just as expected.
4) "Filipino" populations of advanced agriculturalists have more significative red and lightgreen elements, in which I tend to see absorption of much Han admixture in the last few centuries. Interestingly, mestizos de Sangley have been historically prominent as advanced farmers and plantation owners. Filipino ethnogenesis may derive from admixture between ancient slash-and-burn agriculturalists and migrants from China. Some admixture with Europeans (Spaniards, Americans) may also have occurred, to a smaller degree than with the Han, but a much higher degree than in other regional populations.