Human Biology Filipino vs Indonesian DNA

@dyno

Southeast asians, in general, have a lot of genetic overlap but of course there would still be differences across populations.

Now it is true that Javanese are actually part austroasiatic like Thais and Viets compared to Filipinos that are mostly austronesians however based on studies, Javanese (or possibly Western Indonesians in general) are farther genetically from both Thais and Vietnamese. Interestingly, Filipinos are actually closer to Thais and Vietnamese than Indonesians are.

This is from a study on vietnamese genetic variation. Thais (TAI) and Viets (KHV) are closest genetically. Southern Chinese (CHS) are also closely related to Vietnamese people. Filipino (PI) on the other hand is also close to both Thais and Viets with a some of its sample close to southern chinese.

However, as you can see, both Malaysians (MY) and Javanese (ID-JV) form their own cluster and are quite far from either thais or viets. Some malaysians and javanese are quite close to Filipinos but these samples show no overlap between javanese and thais/viet. Filipinos samples are spread in between them.

There is however one austroasiatic population that is close to both Malaysians and Javanese, even closer than they are to Filipinos and that is the Cambodians.

Since this is an fst table, the closer you are to 0, the closer the populations are genetically. Indonesians are closest to cambodians, then filipinos then thais/viets. Filipinos on the other hand are closest to both Viets and Indonesians with almost the same fst value (just like the graph above).

The genetic overlap of Filipinos to both Indonesians and Viets who are quite far apart from each other might have something to do with where the Filipino sample was taken. Southern Filipinos particularly those that are geographically closer to Indonesia are more similar genetically (compared to Northern Filipinos.)

In summary, even though Javanese are part austroasiatic, they are still genetically far from either viets or thais. They are still closer to Austronesians. Filipinos are close genetically to both Thais/Viets and Indonesians. The austroasiatic population most closely related to Javanese are the Cambodians.

@dyno , the Southeast Asia & Oceania component is Australoid as in Negrito or Papuan related?  It says in the fine print that it's a component that arrived 40,000 years ago in Southeast Asia.  That sounds like the Australoid migration from Africa taking the southern route eastward (below the Himalayas through India) into Southeast Asia.  But don't other studies state that Filipinos, Malaysians, and Indonesians are predominantly Mongoloid, something in the range of 90-95% Mongoloid with only about 5-10% Other including Australoid?  I thought most of the Southeast Asian ancestry is derived from the group of Out-of-Africa migrants that took the northern route from Africa (i.e., above the Himalayas through Central Asia) into East Asia, and then migrating southward into Southeast Asia at a much later time. 

What also confuses me is how Southeast Asians despite their minimal Australoid ancestry cluster somewhat closely to Australoids as depicted in the linked plot below.  Moreover, the Australoids seem to be distant from South Asians.  I understand that South Asians are not pure Australoid as they have ANI (Ancient North Indian ancestry) and also East Eurasian ancestry.  Were the sampled Australoids heavily admixed with Southeast Asian or East Asian ancestry?  My guess is that the sampled Australoids are not heavily admixed and are very representative of a pure Australoid genetic component. But that would suggest that Southeast Asians have a large Australoid genetic component.  Are Southeast Asians therefore heavily admixed with Australoids?  Did our East Eurasian ancestors that arrived into East Asia via the northern route, interbreed heavily with Australoids as they migrated into Southeast Asia?  Is that the correct narrative?  If that's true, then why do many studies show only about 5-10% Other including Australoid?

https://images.app.goo.gl/KC2DbJECtdDLtP1D8

@zexsypmp23 Indonesians are unique indeed, Gene 2.0 isn't perfect but it's enough to give an idea.