Human Biology [Solved] Download Filipino genetic origins

very informative 

This is a great study.  I have to applaud everyone involved in it.  It really answers and clarifies a lot of our Filipino ancestry and history. 

Some of the biggest takeaways:

1)  There is actually a Manobo ancestry and migration separate from the Austronesian (Cordilleran), Negrito, and Austro-Asiatic (Sama) migrations.  Manobos have been this mysterious group of people largely living in Mindanao.  In the past I always thought of them as an early group of Filipinos that at least predated the arrival of the Visayans, but we now know that they actually even predate the arrival of the Austronesians (Cordillerans).  Some have even thought of them as being originally a Negrito group of people who heavily intermarried with the Austronesians (and although that's true also) but they were actually a Southern Mongoloid group whose origins originate from mainland Southeast Asia via Borneo probably.

2)  Some of the Cordillerans, in particular, the Central Cordillerans have not intermarried with anyone, and thus represent the least admixed descendants of Basal East Asians.

3)  Austro-Asiatic (Sama) ancestry is found on some Filipino groups in Southeastern Philippines.  We know now that the Austro-Asiatics did in fact reach the Philippines.  The Austro-Asiatics migrated from southern China to mainland Southeast Asia perhaps through the Mekong River, and onto the Sumatra and Java, and parts of eastern Borneo.  But we know now that they even went further. 

There are several more big and important takeaways such as Polynesians having Filipino ancestral links, Papuan-related ancestry in Southeastern Philippines, Indian ancenstry amont the Sama-related groups, and the largely cultural diffusion of Islam.  

Another important takeaway was the Spanish ancestral influence in the Philippines during the colonial period which on average was relatively small.

A few other takeaways that were not specifically elaborated in the body of the study are the following.  Also following are some questions of mine.  

1)  The Mangyans (Iraya, Hanunuo, Buhid, and Bangon) are mainly Cordilleran with a little bit of Negrito, and don't differ much from lowland Filipinos such as the Tagalogs.  I had always thought that the Mangyans were an early Southeast Asian Mongoloid group of people similar to the Manobos, but unlike the Manobos who have at least 3 ancestries, the Mangyans only have two ancestries, Cordilleran and Negrito.  So Mangyans (their Cordilleran ancestry at least) arrived the same time as other Austronesians.  Despite many of them living up in the interior hills of Mindoro today, the Mangyans should be viewed as a lowland Filipino group.

2)  The Tagalogs are virtually identical to Kapampangans according to Figure 5, but also to Figure 3 where the two groups are right next to each other.  Are the Tagalog samples used from the Metro Manila area only?  What about Tagalogs further south in Batangas, Quezon Province, and Marinduque, are they also closely matched with the Kapampangans?  The Tagalog language is part of the Central Philippine language subgroup which includes the Visayan languages, Bicolano languages, Mansakan languages, and Manide-Inagta languages, all of which hail in the southern half of the Philippines.  It's surprising that the Tagalogs (at least those in Batangas, Quezon, and Marinduque) would not show a significant enough genetic influence from their language kin in the south.  When we think of Kapampangans today, we think of the province of Pampanga, but in truth, the Kapampangan people were far more widespread in Southern Luzon in the pre-colonial past including Batangas, Quezon, and possibly Marinduque.  So it would not be too surprising if the Tagalogs there also showed a large Kapampangan ancenstral influence.  

3)  Chavacanos are next to the Tagalogs and Kapampangans in Figure 3.  Was there a large migration of Tagalogs or Kapampangans to Zamboanga?  

4)  Where do Manobos originate from prior to arriving in Mindanao?   They took the southern route according to the study, which likely means they went through Borneo or Sulawesi.  Is there Manobo ancestry in Borneo and Sulawesi today?

5)  The Visayans are thought to have originated in northern Borneo prior to their migration to the Philippines (in particular Central Philippines region).  Assuming the Manobos originate from Borneo (especially northern Borneo), why don't Visayans show any Manobo ancestry?  Austro-Asiatic (Sama) ancestry is also found in western Borneo and now in southwestern Philippines, why don't Visayans have any of this ancestry as well since Austro-Asiatic ancestry was nearby (or even possibly present) in northern Borneo?

Some other interesting revelations from Figure 3 in the study:

1)  It appears that Agutayans and Cuyonons are genetically closely related despite their languages belonging to two different subgroups of the Philippine languages.  The Agutayan language belongs to the Kalamian subgroup of the Philippine languages, and Cuyonon belongs to the Central Philippine subgroup (and more specifically to the Bisayan language subgroup, and even more specifically to the Western Bisayan language subgroup).  Moreover, Agutayans and Cuyonons are grouped together genetically with the Visayans in Figure 3 suggesting that the Agutayans have received a lot of Visayan admixture despite keeping their Kalamian language.  The Agutayan (Kalamian speaking) people and language arrived to Agutaya Island first an retained their language despite being genetically overrunned by Western Visayans.  

2)  The Cinamiguins who reside in Camiguin Island just north of Mindanao appear to be genetically closely related to Cebuanos and Warays (both can be referred to as Eastern Visayans).  The Cinamiguins speak the Kamigin (or Kinamigin) language which belongs to the Manobo subgroup of the Greater Philippine languages.  But Cebuanos and Warays speak languages that belongs to the Central Philippine subgroup (and more specifically the Bisayan subgroup) of the Greater Philippine languages.  The Manobo people and language likely arrived to Camiguin Island earlier (and likely much earlier) than the Eastern Visayan people, which  suggests that the Cinamiguins have acquired a lot of ancestry from the Cebuano and Waray like people but retained their Manobo language.

3)  Visayans and most Luzon groups (Tagalogs, Kapampangans, Pangasinans, Ilocanos, Bicolanos, Ivatans, and etc.) are more closely related to each other than any of them are to the Sama groups, Tausugs, Yakans, Subanen, Palawan groups, and Mangyans if I'm reading Figure 3 correctly.  Basically every group residing on the western portion of the Philippines and below Luzon is somehow less related to the rest of the Philippines.  How is that possible?  The Mangyans of Mindoro are the furthest from all Filipino groups (excluding Negritos).  But their admixture with Negritos are not that large.  Moreover, Mindoro Island is just south of Luzon.  How is this possible?    

4) Continued:  According to Figure 4 of the study, both Manobos and Sama (Austro-Asiatic groups) are theorized to have gone through northern Borneo before arriving to Mindanao.  So hopefully we can find genetic evidence to support this.  

Manobos are a mongoloid group that predate the arrival of the Austro-Asiatic speakers into Southeast Asia and the Philippines.  Doesn't anyone find this interesting?  It's earth shattering in my opinion.  Prior to this study, I had always thought that there were only two mongoloid groups that arrived into Southeast in prehistory, and they were the Austro-Asiatic speakers and then the Austronesians.  But now we have at least 3 groups with the Manobos.  Could there be more pre-historical mongoloid groups entering Southeast Asia other than Austro-Asiatic and Austronesian?   Have any others been identified.

Lastly, I find it interesting that the Manobos today have survived as an ethnic group albeit their original languages have disappeared.  Or have they?  Does anyone know of any non-Austronesian and non-Austro-Asiatic languages among the Manobos?  Or how about just some words in Manobo languages that are neither Austronesian or Austro-Asiatic in origin?  

Mindanao and perhaps the Philippines in general was a kind of refuge for many ethnic groups prior to the Austronesian expansion.  Prior to the Austronesian expansion, most mongoloid groups traveled via Mainland Southeast Asia to get to Island Southeast Asia.  The Manobos and perhaps other non-Austro-Asiatic groups found Mindanao and the Philippines as a kind of safe haven since it was far and hard to get to back then, and it required boating and sailing technology (either from Borneo to Mindanao, or from mainland China (to Taiwan and then) to Luzon).  Mindanao was already occupied by the Mamanwa (Southern Negritos) and also the Denisovans (although they may have already been absorbed into the Mamanwa people).  But the Manobos may have had the (economic and political) desire, the more advanced technology, and population numbers to allow them to settle into Mindanao, and the Manobos largely sat their in Mindanao comfortably along with the Mamanwas for several thousands of years.  The large Austro-Asiatic expansion which followed later did not enter into Mindanao much (restricted primarily in the Sulu Archipelago, southern tip of the Zamboanga peninsula. and southern tip of Palawan), and this may have had to do partly with the Manobos and Mamanwas.  Even the Papuan expansion into southeastern Philippines did not have a major effect, and again this is likely due to the presence of the Manobos and Mamanwas.  If we go back in time even further, the Mamanwas may have prevented the Northern Negritos from migrating south into Mindanao, and the Manobos may have had a contributing role in securing that when they later arrived.  Of course any migration or expansion has its inherent limits and preferences, so how far could have the Austro-Asiatic (Sama) people and Papuans have entered into Mindanao if it were completely empty of people in the first place?  I would argue that they would likely have settled more inland, and therefore the Manobos and Mamanwas did check their advance.  And this was good for the Manobos and Mamanwas, because it preserved them as a people, and this is proof that Mindanao (and the Philippines in general since the Northern Negritos have survived to this day since the Austronesian expansion came thousands of years later after their arrival, and the arrival of the Mamanwas and Manobos) was a type of refuge or sanctuary due to its geographical position.