1 Genetic origins of the Filipino People

12 Important Insights into the Genetic Origins and Diversity of the Filipino People

by Maximilian Larena, Carlo Ebeo, Adrian Albano, Edison Molanida, Trixie Cruz-Angeles, & Felipe Mendoza de Leon Jr. Who is a Filipino? How do we define ourselves as Filipinos? To address these questions, we took advantage of the state-of-the-art techniques in genomics and computational biology. Using these recent technological advances, we were able to unlock the story of our past that is encoded in our genetic heritage, our DNA. To do this, we scoured into the 2.3 million molecular DNA markers that were known to differ between populations. In addition, we applied a multi-disciplinary approach, and incorporated into the work the input of local indigenous historians and cultural workers as well as experts in various disciplines covering linguistics, anthropology, archeology, and geology. Our approach provided us the ability to engage in comprehensive and in-depth analyses, enabling us to shed light on the origins, genetic relatedness, and migration history of the Filipino people. Introduction How do we define a Filipino? One way to define ourselves as Filipinos is in terms of shared cultural characteristics. For instance, we love to connect with people, enjoy the company of our kapwa, and excel in activities that bring us together. This is reflected on our commitment and devotion to our families, where we regard families as our comfort zone and as our important source of happiness, given that connectedness to one another is strongest within families. Moreover, the desire to connect with others can also be linked to our sense of hospitality and our ease to provide a friendly welcoming smile to guests or strangers. The deep appreciation for social relationships can also be found in other Austronesian-speaking societies in the Asia-Pacific region. This is exemplified by the concept of pakikipagkapwa among Filipinos or inafa'maolek among the Chamorros of Guam. Both concepts value social cohesion and the sense of belonging, which in turn promote a shared identity in a group or in a community. Other shared social traits typical for Austronesian-speaking societies also include reverence for ancestors and respect for elders. Additionally, features of shared cultural heritage, especially in prehistoric times, are also observed. These include the practice of body art such as tattooing or dental modification, use of outrigger canoes for sailing, practice of jade carving, and application of shared patterns in artistic works. The latter may include various forms of artistic expressions such as pottery, rock art, or architecture. Despite these commonalities, we as Filipinos are also different in many ways. We speak more than 130 distinct languages, profess different faiths, and prepare unique regional cuisines. We also wear distinctive traditional dresses, weave distinct baskets and fabrics, or narrate timeless tales in various chants. These differences highlight our cultural diversity, which begs the following questions: How did this come out to be? Who is actually a Filipino? How different are we in terms of heritage? How related are we to each other? Do we share a common origin? To address these questions, we formed a multidisciplinary research team and took advantage of the latest advances in genomics and computational biology. We unlocked the story of our past that is encoded in our genetic heritage, our DNA. Additionally, we incorporated into the work the input of various partners including local indigenous historians and cultural workers as well as experts in various disciplines covering linguistics, anthropology, archeology, and geology.

This groundbreaking study was made possible through the partnership between Uppsala University of Sweden led by Prof. Mattias Jakobsson and Dr. Maximilian Larena and the National Commission for Culture and the Arts of the Philippines led by Prof. Felipe Mendoza de Leon. The valuable involvement of the NCCA is pursuant to its mandate to promote Filipino heritage, under the provisions of Philippine Republic Act 7356, or the Law Creating the NCCA. Aside from the extensive network of cultural workers provided by the NCCA, this scientific endeavor was also implemented in collaboration with indigenous cultural communities, local universities, local government units, non-governmental organizations, and/or regional offices of the National Commission for Indigenous Peoples. More importantly, this study is one of its kind in terms of the active involvement of the indigenous peoples, who are themselves co-authors of the research project, in recognition of their indigenous knowledge, shared responsibility, essential contribution, and ownership of the work. The report below serves as a companion report to the recently published scientific article entitled ‘Multiple migrations into the Philippines in the past 50,000 years’ in the journal Proceedings of the National Academy of the United States of America (PNAS). We present here the 12 most important insights on the genetic origins of the Filipino people. 1. The evolution of modern humans started in Africa. We are all rooted in Africa, the birthplace of modern human evolution. It is in Africa where we can find the oldest fossils of anatomically modern humans. It is also in Africa where we can find the present-day populations with the highest levels of genetic diversity. The oldest divergence in the modern human lineage happened in Africa around ~300 thousand years ago, between the ancestors of southern African Khoe-San ethnic groups and the common ancestor of the rest of sub-Saharan Africans (Figure 1a). After some time, around ~60 to 70 thousand years ago, a distinct subgroup split from East Africans. This subgroup spread out of Africa, and went on to wander into the far reaches of the planet, to become the Early Europeans, Ancestral North Eurasians, Basal East Asians, and Basal Australasians. An interesting aspect of the human family tree is the relationship between Africans and non-Africans: some Africans are more related to all of us Filipinos (or to any other East Asian, European, or any groups outside of Africa) than they are to other Africans (Figure 1b). This is due to the fact that the shared common

2 Genetic origins of the Filipino People

~200kyears

~70-80kyears

~50kyears

~8kyears

Southern African

Khoe-San

Central Africanforager

East African

European NortheastAsian

HanChinese

AmisTaiwan

Cordilleran Negrito Papuan

~200kyears

~300kyears

~70-80kyears

~50kyears

~8kyears

Southern African

Central African

East Africa

nEuropean

Papuan

CordilleranNegrito

Amis Taiwan

Han Chinese

Northeast Asia

Neandertal

Deni-sovan

Deepest split in modern humans

Out-of-Africaevent ~60-70k

~300kyears

East Africans are more related toEuropeans, Northeast Asians, EastAsians, and Australasians than theyare to South Africans. All non-Africansare a subset of East Africans.

Figure 1. Model of modern human expansion out-of-Africa starting ~60 to 70 thousand years ago, diverging into ancestral populations of European Hunter-Gatherers, North Eurasians, East Asians, and Australasians (a). Inferred topology of modern human populations, where all non-Africans form as a subset of East Africans (b). Philippine Negritos form a clade with Papuans, and received recent gene flow from non-Negritos represented by Philippine Cordillerans. Papuans diverged from Philippine Negritos ~40 to 50 thousand years ago, while Indigenous Taiwanese diverged from Cordillerans ~8 thousand years ago. ancestor of all populations outside of Africa is only an African subgroup who split from East Africans. This would mean, for example, that the Kenyan groups of East Africa are more genetically related to us or to any other East Asian or European population than they are to Khoe-San groups of southern Africa. After some time, the populations who migrated out of Africa differentially lost or retained certain versions of the gene responsible for specific physical or physiological traits. A classic example of this is the variation in skin pigmentation, which is reflected on the different shades of skin color found among modern human populations. Aside from skin color, other observable variations include, among others, having short or tall stature or having straight or curly hair. These variations may have been brought about by random chance or local adaptation. Given the long and complex migrational history of Filipinos as presented below, it is not surprising to find a gradient of diversity in physical traits among the more than a hundred Philippine ethnic groups. 2. All non-Africans, including all Filipinos, possess Neandertal ancestry. Following their exit out of Africa, the ancestors of modern humans encountered a distinct species of archaic humans known as the Neandertals. By that time, Neandertals already inhabited a wide geographic range in Eurasia, from western Europe to Southwest Asia and up to the Altai mountains of Siberia. They share some common features with modern humans, and are regarded as modern human’s evolutionary cousins. Although distinctively, in contrast to modern humans, Neandertals are characterized as having larger cranium, broader nose, more prominent brow ridge, and more robust physical built. Some of which are physical traits attributed to adaptation for the colder climate of their era. For reasons not entirely clear, Neandertals became extinct up until around ~30 to 40 thousand years ago, at the moment when modern humans just emerged into Eurasia a few millennia earlier. Various theories were put forward as the cause of their extinction: climate change, infectious disease, or being out-competed by the technology-advanced modern humans. However, other experts would contend that Neandertals did not in fact became fully extinct, but rather just became absorbed or assimilated into the larger population of modern humans through interbreeding. Such

model would dilute the levels of Neandertal ancestry, after generations of interbreeding. The assimilation theory has recently gained more traction, especially with the recent advances in ancient DNA technology. The genome of Neandertals were successfully sequenced, and was leveraged against the genomes of present-day populations. With strong evidence provided by Green et al., 2010 and others, it can be shown that all populations outside of Africa, including Filipinos, carry some levels of Neandertal ancestry . Using various computational approaches, the levels of detectable Neandertal ancestry among non-Africans can range between ~1–4%. As to when this interbreeding event likely happened has been a longstanding question of interest among experts. The uniform levels of Neandertal ancestry in non-Africans point to a very old interbreeding event into a common ancestor. Indeed, we already detect levels of Neandertal ancestry from ancient DNA extracted from 30 to 40 thousand year old East Asian and European individuals. This hard evidence sets the boundary for the Neandertals-modern human interbreeding event to be older than 40 thousand years ago. This is consistent with various findings based on computational modeling, which estimated the interbreeding event to happen around ~50 to 60 thousand years ago. This suggests that Neandertals interbred with modern humans likely in the Levant region of the Middle East, right after modern humans migrated out of Africa, and prior to the dispersal of modern humans into Europe and East Asia. 3) Negritos are the first modern human inhabitants of the Philippine Islands. Subsequent to interbreeding with Neandertals, the ancestral population of modern humans migrated into the far reaches of Eurasia. Some groups went westward into the European continent, in pulses and at different time points, contributing to the three ancestral components found in most Europeans today. Another group migrated eastward into Asia likely north of the Himalayas arch, who later diverged into the various subgroups of East Asians. Another major group also migrated eastward, however coursed through the southern sections of India likely via a coastal route. Based on the living

b a

3 Genetic origins of the Filipino People

Figure 2. Model for expansion of Australasian-related populations. A distinct clade in mainland Southeast Asia later became the present-day Malay Negritos and Andaman Island Negritos. Another clade gave rise to Basal Sunda group, who later diverged and entered the Philippines to become the present-day Northern and Southern Negritos, while another group migrated eastwards to become the present-day Papuans and Australian Aborigines. populations today, the latter are phenotypically characterized by their darker skin color, and are collectively referred to here as the Australasians. Some Australasians remained in southern India who later contributed to the ancestry of today’s Dravidian-speaking populations. Others migrated further eastwards and entered the Andaman Islands to become the Andaman Island Negritos, to Thailand to become the Maniq Negritos, and to peninsular Malaysia to become the Malay Negritos (Figure 2). A subgroup migrated further into the east and into Sundaland, a biogeographical region that was left unsubmerged during the Last Glacial Maximum (popularly known as Ice Age) when the sea levels were 60 to 120 meters below today’s levels. The extended shoreline kept the Sunda landmass to cover a vast area which interconnects the Malay peninsula to Borneo, Java, Sumatra, and all other small islands of western Island Southeast Asia. This facilitated a barrier-free pathway for migration of populations, may it be humans or animals, via the exposed land bridges. For instance, one subgroup migrated further into the eastern section of Sundaland (present-day Borneo). This subgroup, the Basal Sunda population, subsequently diverged. One group crossed multiple seas towards the eastern section of Island Southeast Asia, until they reached the Sahul continent to become the present-day Papuans and Australian Aborigines. The other group split from the ancestors of Papuans and Australian Aborigines around ~40 to 50 thousand years ago, and moved northward to enter the Philippines, to become the First Filipinos: the Philippine Negritos. Access to the Philippines by the ancestral Philippine Negrito population from Sundaland would only require minimal water crossings. Most of the Philippine Islands were interconnected to each other around the time of the last ice age. One possible pathway is via the northern route, crossing Palawan and Mindoro Islands to reach Luzon. The other tractable pathway is the southern route, crossing the Sibutu passage between Sabah and the Sulu archipelago land bridge to reach Zamboanga peninsula of Mindanao. This would suggest that, aside from the common ancestor of Papuans and Australian Aborigines, the ancestral population of Philippine Negritos were also likely one of the earliest modern human groups who engaged in sea navigation. The ancestral Negrito population who took the northern route is evident today as the Northern Negrito ancestry detected among the Batak of Palawan Island, Manygan Iraya of Mindoro Island, and Ayta, Agta, Atta, Alta, Arta, Manide, Dumagat and Remontado groups of Luzon Island. The other ancestral Negrito

population who took the southern route, the Southern Negritos, became the Mamanwa Negritos of Mindanao Island. Hence, the ancestral Northern Negritos and the ancestral Southern Negritos comprise the first two major waves of modern human migrations into the Philippines. Based on the genetic evidence presented above, it also needs to be emphasized that Philippine Negritos are more genetically related to East Asians than they are to Africans. For instance, the Ayta Negrito of Central Luzon are more genetically similar to Philippine Cordillerans, Han Chinese, or Kinh Vietnamese, than they are to any other African population. This would indicate that physical traits are not always a reliable indicator of genetic relatedness. The Philippine Negritos may share some physical features with Africans, such as darker skin color, but they are definitively more East Asian than African in their DNA. 4) Ancestors of Negritos interbred with another archaic human species: the Denisovans. The migration of Negrito groups into the Philippines did not happen inconsequentially. Along the way, they encountered another distinct species of archaic humans known as the Denisovans. This is evidenced by the discovery of ~2–4% Denisovan ancestry detected among Philippine Negritos, Australian Aborigines, Papuans, and non-Papuan Melanesians by Reich et al., (2011) and others. This indicates that the common ancestor of these Island Southeast Asian and Oceanian populations interbred with Denisovans sometime in the past. Recent findings also show that East Asians, Siberians, and Native Americans possess some Denisovan ancestry, albeit at very low levels of < 0.1%. The Denisovan group who interbred into these mainland Asian groups, referred to as Siberian Denisovans, are very different from the Denisovan group who interbred into the Island Southeast Asian and Oceanian groups, referred to as the Southern Denisovans. Hence, current evidence indicates that there are at least two distantly related Denisovans who interbred with modern humans. Despite these discoveries, our knowledge on Denisovans is still largely limited. Most of the information we have is coming from the available DNA evidence. These include the high-quality DNA recovered from a finger bone found in the Denisova Cave of Altai, Siberia (where the name ‘Denisovan’ came from), and more recently from some mitochondrial DNA recovered from a bone element and some sediments in the Baishiya Karst Cave of the Tibetan plateau. Until this time, due to the scarcity of fossil finds, we still do not have a comprehensive picture on how an actual Denisovan looks like. This may change in time given the pace of collaborative investigations currently underway. The revolutionary discoveries of Homo floresiensis and Homo luzonensis already gave indications that Island Southeast Asia is an important area for human evolution. Provided the Denisovan genetic signal detected in high amounts among ethnic groups of Island Southeast Asia, we are confident that it will only be a matter of time that a fossil of the so called Southern Denisovan will be discovered. 5) Postglacial migration of Manobo-related populations into southern Philippines. Basal East Asians who migrated north of the Himalayan arc after ~40 to 50 thousand years ago subsequently split into multiple groups. One went up north and interbred with Siberians / North Asians, and migrated into Beringia (the land bridge between Siberia and Alaska) around 25 thousand years ago, and contributed to the dual ancestral source of all Native Americans. Another group went eastward to later become the Tai-Kadai and Austronesian-speaking populations, and another went southeast via the Mekong river to later become the Austroasiatic-speaking populations.

4 Genetic origins of the Filipino People

PhCor Bontoc PhCor Kankanaey PhCor Balangao PhCor AyanganIfugao PhCor TuwaliIfugao PhCor Kalanguya PhCor Ibaloi PhCor Itneg PhCor Kalinga PhCor Apayao PhCag Gddang PhCag Malaweg PhCag Itawis PhCag Ibanag PhCag Yogad PhCag Gaddang PhIlo Ilocano PhBas Itbayaten PhBas Ibatan PhBas Ivatan PhCen Bolinao PhCor Pangasinan PhCor Bugkalot PhCen Sambal PhCen Kapampangan PhCen Tagalog PhCre Chavacano PhBik Bicolano PhNeg AgtaBulusan PhNeg AgtaMatnog PhVis Boholano PhVis Cebuano PhMbo Cinamiguin PhVis Waray PhBuk BinukidnonNegros PhKlm Agutaya PhVis Cuyonon PhMbo Kagayanen PhNeg AtiNegros PhNeg AtiPanay PhVis Hilgaynon PhVis Kinaray-a PhBuk Sulodnon PhSub Subanen PhSub Subanon PhDan Iranun PhDan Meranao PhDan Maguindanaon PhMbo ManoboDulangan PhMbo Lambanguian PhBil Teduray PhBil BlaanKoronadal PhBil Tboli PhBil Obo PhBil BlaanSarangani PhMbo ManoboSarangani PhMns Kalagan PhMns Tagakaolo PhBil BagoboKlata PhMbo ManoboTagabawa PhSan Sangil PhMbo Dibabaon PhMbo Manguangan PhMbo ManoboRK PhMns Mandaya PhMns Mansaka PhMns Kamayo PhVis Surigaonon PhMbo ManoboAgusan PhMbo BukidnonBinukid PhMbo BukidnonTalaandig PhMbo BukidnonHigaonon PhMbo BukidnonUmayamnon PhMbo BukidnonManobo PhMbo OvuManuvo PhMbo ManoboIlianen PhMbo BukidnonTigwahanon PhMbo BukdinonMatigsalug PhMbo AtaManobo PhMbo DavaoMatigsalug PhSam Yakan PhVis Tausug PhSam SamaBangingi PhSam SamaDeyaBonggao PhSam SamaKabingaan PhSam SamaDilautMampang PhSam SamaDilautBonggao PhSam SamaDilautTaluksangay PhPal Tagbanwa PhPal Molbog PhPal Palawano PhMyn MangyanIraya PhMyn MangyanHanunuo PhMyn MangyanBuhid PhMyn MangyanBangon PhNeg Mamanwa PhNeg Batak PhNeg AgtaManide PhNeg AgtaLopez PhNeg AgtaIriga PhNeg AgtaIraya PhNeg AgtaIsarog PhNeg AgtaDumagat PhNeg AgtaRemontado PhNeg AttaRizal PhNeg AgtaLabin PhNeg AgtaMaddela PhNeg Arta PhNeg AgtaCasiguran PhNeg AgtaDupaningan PhNeg AytaSambal PhNeg AytaMagbukon PhNeg AytaMag-antsi PhNeg AytaAmbala PhNeg AytaMag-indi

PhCor Bontoc PhCor Kankanaey PhCor Balangao PhCor AyanganIfugao PhCor TuwaliIfugao PhCor Kalanguya PhCor Ibaloi PhCor Itneg PhCor Kalinga PhCor Apayao PhCag Gddang PhCag Malaweg PhCag Itawis PhCag Ibanag PhCag Yogad PhCag Gaddang PhIlo Ilocano PhBas Itbayaten PhBas Ibatan PhBas Ivatan PhCen Bolinao PhCor Pangasinan PhCor Bugkalot PhCen Sambal PhCen Kapampangan PhCen Tagalog PhCre Chavacano PhBik Bicolano PhNeg AgtaBulusan PhNeg AgtaMatnog PhVis Boholano PhVis Cebuano PhMbo Cinamiguin PhVis Waray PhBuk BinukidnonNegros PhKlm Agutaya PhVis Cuyonon PhMbo Kagayanen PhNeg AtiNegros PhNeg AtiPanay PhVis Hilgaynon PhVis Kinaray-a PhBuk Sulodnon PhSub Subanen PhSub Subanon PhDan Iranun PhDan Meranao PhDan Maguindanaon PhMbo ManoboDulangan PhMbo Lambanguian PhBil Teduray PhBil BlaanKoronadal PhBil Tboli PhBil Obo PhBil BlaanSarangani PhMbo ManoboSarangani PhMns Kalagan PhMns Tagakaolo PhBil BagoboKlata PhMbo ManoboTagabawa PhSan Sangil PhMbo Dibabaon PhMbo Manguangan PhMbo ManoboRK PhMns Mandaya PhMns Mansaka PhMns Kamayo PhVis Surigaonon PhMbo ManoboAgusan PhMbo BukidnonBinukid PhMbo BukidnonTalaandig PhMbo BukidnonHigaonon PhMbo BukidnonUmayamnon PhMbo BukidnonManobo PhMbo OvuManuvo PhMbo ManoboIlianen PhMbo BukidnonTigwahanon PhMbo BukdinonMatigsalug PhMbo AtaManobo PhMbo DavaoMatigsalug PhSam Yakan PhVis Tausug PhSam SamaBangingi PhSam SamaDeyaBonggao PhSam SamaKabingaan PhSam SamaDilautMampang PhSam SamaDilautBonggao PhSam SamaDilautTaluksangay PhPal Tagbanwa PhPal Molbog PhPal Palawano PhMyn MangyanIraya PhMyn MangyanHanunuo PhMyn MangyanBuhid PhMyn MangyanBangon PhNeg Mamanwa PhNeg Batak PhNeg AgtaManide PhNeg AgtaLopez PhNeg AgtaIriga PhNeg AgtaIraya PhNeg AgtaIsarog PhNeg AgtaDumagat PhNeg AgtaRemontado PhNeg AttaRizal PhNeg AgtaLabin PhNeg AgtaMaddela PhNeg Arta PhNeg AgtaCasiguran PhNeg AgtaDupaningan PhNeg AytaSambal PhNeg AytaMagbukon PhNeg AytaMag-antsi PhNeg AytaAmbala PhNeg AytaMag-indi

BontocKankanaeyBalangaoAyangan IfugaoTuwali IfugaoKalanguyaIbaloiItnegKalingaApayaoGddangMalawegItawisIbanag

Ethnolinguistic group

YogadGaddangIlocanoItbayatenIbatanIvatanBolinaoPangasinanBugkalotSambalKapampanganTagalogChavacanoBicolanoAgta BulusanAgta MatnogBoholanoCebuanoCinamiguinWarayBukidnon NegrosAgutayaCuyononKagayanenAti NegrosAti PanayHiligaynonKinaray-aSulodnonSubanenSubanonIranunMeranaoMaguindanaonManobo DulanganLambaguianTedurayBlaan KoronadalTboliOboBlaan SaranganiManobo SaranganiKalaganTagakaoloBagobo KlataManobo TagabawaSangilDibabaonManguanganManobo Rajah KabungsuwanMandayaMansakaKamayoSurigaononManobo AgusanBukidnon BinukidBukidnon TalaandigBukidnon HigaononBukidnon UmayamnonBukidnon ManoboOvu ManuvoManobo IlianenBukidnon TigwahanonBukidnon MatigsaugAta ManoboDavao MatigsalugYakanTausugSama BangingiSama Deya BongaoSama KabingaanSama Dilaut MampangSama Dilaut BongaoSama Dilaut TaluksangayTagbanwaMolbogPalawanoMangyan IrayaMangyan HanunuoMangyan BuhidMangyan BangonMamanwaBatakManideAgta LopezAgta IrigaAgta IrayaAgta IsarogAgta DumagatAgta RemontadoAtta RizalAgta LabinAgta MaddelaArtaAgta CasiguranAgta DupaninganAyta Sambal

Ayta Ambala

Ayta MagbukonAyta Mag-antsi

Ayta Mag-indi

Genetic clusters

Geographic clusters

Negrito or non-Negritoclassification

Linguistic clusters

Cordilleran CentralCagayan ValleyIlocanoBashiicCentral LuzonChavacanoBikolanoVisayan EasternVisayan WesternSubanon / SubanenDanaoBilicSangilMansakanManoboSamaPalawanicMangyanSouthern NegritoBatak NegritoSoutheast Luzon NegritoSouthern Luzon Negrito Northeast Luzon Negrito 1Northeast Luzon Negrito 2Central Luzon Negrito

non-Negrito

Negrito

LuzonBatanes & BabuyanVisayasMindanaoSulu archipelagoPalawanMindoro

Northern Luzon - CordilleranNorthern Luzon - IlocanoNorthern Luzon - CagayanNorthern Luzon - ArtaBashiicChavacanoCentral LuzonTagalogUmiray DumagatBikolanoVisayan BinukidnonCalamianSubanonSamaMansakaDanaoSangilBilicManoboMamanwaManide

)))

A distinct group also split off 15 thousand years ago and migrated from mainland Southeast Asia into Sundaland likely via the extended coastline that was present during the last ice age. Low-lying sections of Sundaland started to become submerged from ~12 thousand years ago and stabilizing until ~8 thousand years ago, brought about by the rising sea levels of the Postglacial period. The dramatic change in climate likely played an important role in the movement, isolation and differentiation of various populations in the modifying landscape of Island Southeast Asia. One of such groups entered Mindanao Island, who later contributed to the Manobo-related (or Mindanao-related) ancestry detected in southern Philippines today. The ancestral Manobo population diverged and spread out into the various corners of Mindanao Island. They encountered and interbred with the resident Southern Negritos, which resulted in the detection of Negrito ancestry among all present-day Manobo ethnic groups. Some of them crossed the seas to reach Camiguin Island to become the Cinamiguin, and even as far as Cagayancillo (a remote island situated between Palawan and Negros Islands) to become the Kagayanen. Some millennia later, another major interbreeding event occurred, following the expansion of Cordilleran-related groups into Mindanao. The greatest impact of this migration is found among the coastal groups, where one can find a dilution of Manobo-related ancestry. Hence today, we can find the highest levels of Manobo-related ancestry among the inland ethnic groups of Mindanao, such as the Ata Manobo, Bukidnon Matigsalug, and Davao Matigsalug. All of these complex and differential admixture events between Manobo-related groups and Southern Negritos and Cordilleran-related populations (plus some Papuan-related gene flow into southeastern Mindanao presented in item 9 below) resulted in the formation of more than 20 culturally and linguistically diverse indigenous ethnic groups of Mindanao. 6) Entry of Sama-related populations into southwestern Philippines. Most Sama-related ethnic groups inhabit the islands and coastal areas of southwestern Philippines. They are at times named after their place of origin, for instance, Sama Davao, Sama Taluksangay, Sama Mampang, Sama Sulawesi, or Sama Mapun. Alternatively, Sama-related groups are also classified according to their place of settlement: i) Sama Deya or Inland Sama such as the urbanized Sama population of Bongao, Tawi-Tawi, ii) Sama Bihing or Shoreline Sama who live in stilt houses at coastal areas, and iii) Sama Dilaut or Sea Sama who traditionally live in intricately designed lepa boats. Sama Dilaut of Philippines are also known by their exonym ‘Bajao’ ‘Bajaw’ ‘Bajo’ or ‘Badjao’. It should be noted however that they preferred to be called as Sama Dilaut. Culturally, they are a distinct ethnic group, renowned for their navigation skills and ocean-based lifestyle. They are oftentimes referred to as the Philippine sea nomads. Moreover, Sama-Dilaut and other Sama-related ethnic groups speak a distinct language that is not classified under the Philippine languages, but instead is classified under the Barito languages (which include languages spoken by some indigenous groups in Borneo). The cultural and linguistic distinctiveness of Sama is also validated in their genetic ancestry. Our investigation revealed that Sama-related ethnic groups possess a unique genetic ancestry, heretofore referred to as the Sama-related ancestry. This ancestry is found in the highest amount or the least admixed form among the Sama Dilaut sea nomads of Sulu archipelago. As expected, Sama-related ancestry is also found among the inland Sama Deya of Bongao, Yakan of Basilan, and coastal Sama groups of Zamboanga (Sama Kabingaan and Sama Banguigi). In

Figure 3. Tree topology of 115 Philippine ethnic groups based on genetic relationships, without accounting for admixture between populations. An icon representing the genetic cluster is located at the left side of the name for each row of Filipino ethnic group, and icons representing Negrito or non-Negrito, geographic, or linguistic cluster groupings are located at the right. Figure adapted from Larena et al., (2021) PNAS with some modifications.

5 Genetic origins of the Filipino People

a b

c d

Philippine NEGRITOS as the First Migrants

after 50,000 years ago

BasalSunda

Basal East Asian

SouthernNegrito

NorthernNegrito

Entry of MANOBO-like groupsinto southern Philippines before 12,000 years ago

AncestralCordilleran

AncestralAustroasiatic

AncestralManobo

Basal EastAsian

Migration of Htin/Mlabri-relatedSAMA-like populations

~ 8,000 to 12,000 years ago

AncestralCordilleran

AncestralAustroasiatic

AncestralSama

Holocene expansion ofCORDILLERAN-related groups

before 7,000 years ago

AncestralCordilleran

addition, Sama-related ancestry is also detected among the Tausug of Sulu, Subanen/Subanon ethnic groups of Zamboanga Peninsula, Molbog, Palawano, and Tagbanwa ethnic groups of Palawan, and Bajo ethnic groups of Indonesia; indicating a complex history of inter-island exchanges between various ethnic groups of southwestern Philippines and Borneo. Sama Dilaut oral traditions point to peninsular Malaysia, specifically Johor, as their ancestral homeland. Interestingly, our analyses reveal a strong genetic affiliation of Sama Dilaut and Austroasiatic-speaking populations of mainland Southeast Asia (Htin and Mlabri populations), supporting the narrative of their oral traditions. The divergence time between Htin/Mlabri and Sama Dilaut ethnic groups was estimated to occur ~12 thousand years ago, which coincides with the climate-change driven modification of the landscape in Southeast Asia. The presence of Sama-related (or Austroasiatic-related) and Manobo-related (or Mindanao-related) ancestries in southern Philippines provides an incontrovertible evidence for a south-to-north migration of some ancient populations from mainland Southeast Asia into Indonesia and the Philippines. These findings are at odds with the exclusive Out-of-Taiwan view on the peopling of the Philippines, where it is claimed that all non-Negrito Filipinos originated from Taiwan. 7) Pulses of migration of Cordilleran-related groups from Taiwan-South China greater area into the Philippines. After the northward migrations of Northern Negrito, Southern Negrito, Manobo, and Sama-related groups, a southward migration of Cordilleran-related populations into the Philippines took place after 10 thousand years ago. This migration did not happen as one monolithic block, but instead likely occurred in pulses occurring between ~7 to 10 thousand years ago. In addition, these migrations originated from the Southern China-Taiwan greater area, coinciding with the geologic changes that took place at the time, when the land bridge between southern China and Taiwan gradually became submerged. This again is an example where climate change may have had a lasting impact on the mass dispersal of populations. It must be emphasized that the populations inhabiting Southern China ~4 to 5 thousand years ago (or earlier) are the ancestors of Cordilleran-related populations who likely speak a pre-Austronesian form of language. The Han Chinese, or what we refer to as the majority Chinese population, did not yet inhabit southern China during that time. In fact, based on ancient DNA evidence, the Fujian inhabitants of coastal southern China, dated to ~4 to 5 thousand years, are more genetically related to present-day indigenous Taiwanese and Cordillerans than they are to the Han Chinese. It was only after 2 thousand years ago when the Han Chinese started migrating southwards (originating from the Yellow river basin of northern China), and gradually inhabiting the geographic area of modern mainland China that we know of today. The arrival of Cordilleran-related (or Austronesian-related) groups resulted in interbreeding with resident groups who arrived earlier during the initial waves of migration. Remarkably, central Cordillerans (Kankanaey, Bontoc, Balangao, Tuwali, Ayangan, Kalanguya, and Ibaloi) remained as the only ethnic group within the Philippines, out of the 115 groups investigated, who did not display any sign of interbreeding with Negritos. This is unusual in human history, given the assumption that when two distinct populations meet, one way or the other, they will likely interbreed with each other at some point in time. As highlighted in this study, we find that this is not always the case. Our study places the central Cordillerans in a unique position in human evolutionary history, making them the least admixed (or “purest”) descendants of Basal East Asians.

One major impact of the migration of Cordilleran-related populations from South China-Taiwan area into the Philippines is the dominant influence on the linguistic landscape. All Philippine ethnic groups speak a language that is classified under the Malayo-Polynesian branch of the Austronesian language family. The arrival of Austronesian-speaking populations likely precipitated widespread linguistic replacement throughout the archipelago and beyond. This replaced the earlier non-Austronesian languages of the Negrito, Sama, and Manobo-related groups. However, it may not have been a complete replacement, as some items in the language may have been retained from the original non-Austronesian language. For instance, it was shown that some Negrito groups speak languages that potentially contain certain words that are not completely accounted for by any other Austronesian etymologies. This is also true with Land Dayak Austronesian-speakers of Borneo, where their languages contain certain words that are associated with Austroasiatic languages of mainland Southeast Asia. More comprehensive analysis still needs to be done to know if this is also true with Manobo and Sama-related populations, if there are non-Austronesian lexical elements in their languages. The migration of Cordilleran-related groups into the Philippines is likely not associated with farming expansion. This contradicts with the idea that people, language, and farming always go together in a single package, as argued by the proponents of the out-of-Taiwan hypothesis. The various Cordilleran-related groups already diverged from each other and from indigenous Taiwanese (~8 to 10 thousand years ago), earlier than the established archeological dates for the commencement of agriculture (~4.2 thousand years ago). Our findings are consistent with the recent

Figure 4. Migration history of the Philippine archipelago for the past 50,000 years adapted from Larena et al., (2021) PNAS, with some modifications. The suggested model depicts initial entry by Northern and Southern Negritos (a), followed by migration of Manobo-related groups (b), Sama-related groups (c), and culminating in expansion of Cordilleran-related groups (d).

6 Genetic origins of the Filipino People

archeological evidence, where it was shown that rice paddy field agriculture only appeared until recently (~2,500 years ago); and also with the phylogenetic evidence on rice, where it was shown that the divergence between various rice varieties within the Philippines only happened after ~2,500 years ago. 8) Polynesians and other Pacific Islanders are genetically linked to Filipinos. The Philippine Islands served as a crucial gateway for the spread of Austronesian-speaking populations into the rest of Southeast Asia and the remote islands of the Pacific. A series of ancient DNA studies since 2015 has provided a better picture on this important phase of Asia-Pacific prehistory. The first seminal study is the analyses on the oldest Lapita individuals of Vanuatu, dated ~3,000 years old, by Skoglund et al. (2015). The study revealed that the oldest Lapita individuals were most genetically linked to Filipinos. This is especially significant given that the Lapita culture is regarded as the predecessor of present-day Polynesian, some Micronesian, and some coastal Melanesian culture in the islands of the Pacific. Accordingly, the study portrays a lasting legacy of Filipinos into the genetic make-up of islander populations in the Pacific. Another study by Pugach et al., looked at the genetic profile of two ancient individuals from Guam, Mariana Islands in the western Pacific. The ancient individuals, dated ~2,200 years old, revealed to have a genetic ancestry that is linked to Filipino ethnic groups relative to all other worldwide set of populations. This suggests that the ancestor Chamorro people of Mariana Islands likely originated from a coastal population inhabiting the Philippines. Future work still needs to be done, including a comprehensive analysis on Philippine, Indonesian, and Taiwanese ancient populations. Such study with wide geographic coverage will aid us in pinpointing the specific coastal source population who migrated into the Marshall Islands and distantly into the coasts of Bismarck archipelago and Vanuatu Islands. 9) Gene flow of Papuan-related ancestry into southeastern Philippines. Papuans are the indigenous peoples of New Guinea, a large island southeast of Philippines which comprises the independent state of Papua New Guinea in the east and the West Papua province of Indonesia in the west. Papuans are one of the most ethnolinguistically diverse populations in the world, given the presence of at least 800 distinct languages. Genetically, Papuans share a common ancestry with Australian Aborigines, which diverged ~25 to 35 thousand years ago, prior to the climate change-driven separation of Sahul landmass into New Guinea and Australia. The Papuans were shown to have some evidence of sea voyaging skills as early as ~30,000 years ago, travelling between the mainland New Guinea and the nearby islands of the Bismarck archipelago. However, this is limited to short-distance travel where the islands were still visible from each other. It was not until after the arrival of Austronesian-related groups in the region ~3 to 3.5 thousand years ago, when the Papuan-related groups started to navigate into distant islands (which are not visible from the island of departure). It was argued that the Papuans may have acquired the long-distance navigation skills from the migratory Austronesian-speaking populations. Given this, Papuan-related ancestry started to appear in ancient individuals of Vanuatu Islands after 3,000 years ago, diluting the East Asian ancestry of the first Lapita people. Remarkably, aside from Papuan-related gene flow eastwards into the islands of Oceania, we also find a gradient of Papuan-related gene flow westward into Indonesia and southeastern Philippines. The Papuan-related signal is highest among the ethnic groups of eastern Indonesia covering Lesser Sunda Islands, North Maluku, Sulawesi, and East Kalimantan of Borneo. In the Philippines, this previously unappreciated Papuan-related ancestry is detected at

the highest levels among the Islamized Sangil ethnic group of Glan, Sarangani. Some Papuan-related signal is also detectable among Bilic-speaking groups (i.e. Blaan and Tboli), Manobo-related groups (i.e. Lambaguian and Manobo Sarangani), Mansakan-related groups (Kalagan and Tagakaolo), and Mamanwa. Our analyses indicate that the westward Papuan-related gene flow into southeastern Philippines must be older than two thousand years ago, which coincides with the eastward expansion of Papuan-related groups into Oceania. However, we cannot exclude whether this gene flow occurred way much older, or whether it happened prior to the arrival of Manobo-related groups. This model would require the interbreeding event to occur first between resident Southern Negritos and migrating Papuans, followed by an interbreeding event between the admixed Negrito-Papuan population and incoming Manobo-related groups. More analysis still needs to be done to refine the date of gene flow from Papuans into the ethnic groups of Indonesia and southeastern Philippines. 10) Cultural and genetic legacy of the Maritime Trading Network with India. Since the 1st millennium BCE, ethnic communities in India have established an extensive Ocean Trading network which lasted until the start of the colonial period. Part of this trading network extends to the island communities of Southeast Asia, where long-distance trade was made possible through the establishment of sea routes. Along this period is the founding of Hindu-Buddhist Kingdoms/empires in Southeast Asia. These include, among others, Srivijaya (650-1377 CE) and Majapahit (1293-1527 CE), which are kingdoms that ruled over a wide geographical area covering coastal mainland Southeast Asia, Malaysia, and western Indonesia, and may have exerted influences as far as Sulu archipelago of the Philippines. The genetic legacy of the Srivajaya and Majapahit empires can be observed in the detection of South Asian or Indian genetic signal in lowlander Malays, Javanese, Balinese, Sumatran and Bajo populations of Indonesia. Interestingly in our study, we also find the South Asian or Indian genetic signal among the Sama Dilaut sea nomads of Sulu archipelago and Sama coastal dwellers of Zamboanga peninsula, providing evidence for the historical long-distance interactions between the Indian subcontinent and Southeast Asia as far as the Philippines. Although we only find a significant population-level genetic signal of Indian ancestry in Sama-related groups, it will not be surprising to find this signal in random individuals among other lowlander or coastal populations. Our estimated date of gene flow from India into the Sama-related groups is between 500 to 1,000 years ago, which falls within the period of the Maritime Trading Network. Beyond the genetic legacy that was limited to the Sama-related groups, the cultural legacy of the Maritime Trading Network with India is recognizable all throughout the Philippine archipelago. This influence via cultural diffusion is patent in the incorporation of Sanskrit-based words in the Filipino language (e.g. Agham, Bansa, Bathala, Diwata, Guro, Katha, Mutya, etc.), use of Indian honorifics (e.g. Rajah, Maharlika, Datu, etc.), local adaptation of Indian folk literature (e.g. Meranao epic Maharadia Lawana), and use of Indic-based scripts. The Indic-based Suyat scripts of the Philippines (Basahan of Bicol, Baybayin of Tagalog, Badlit of Visayas, Kur-itan of Ilocos, Kulitan of Pampanga, Tagbanwa script, Buhid script, and Hanunuo script) are derived from the Kawi script of Java, which in turn was derived from the Pallava Brahmic script of India. The artifact Laguna copperplate inscription, which was declared as a National Cultural Treasure by the National Museum, is in fact an inscription based on Kawi script. Other artifacts or physical evidence of indirect Indian influences in the Philippines include the Garuda Gold Pendant of Tabon Cave and the 21-carat Golden Tara of Agusan.

7 Genetic origins of the Filipino People

Negrito-related orAustralasian-related ancestry

Cordilleran-related orAustronesian-related ancestry

Manobo-related orMindanao-related ancestry

Sama-related orAustroasiatic-related ancestry

Agta Dupaningan Atta Rizal Agta Labin Agta Casiguran Agta Maddela Arta Agta Dumagat Agta Remontado Agta Lopez Agta Manide Agta Iraya Agta Iriga a a a

Agta Isarog Agta Bulusan Agta Matnog Ayta Magbukon Ayta Ambala Ayta Mag-antsi Ayta Mag-indi Ayta Sambal Ati Panay Ati Negros Batak Mamanwa a a a

Ivatan Itbayaten Ibatan Ilocano Ibanag Itawis Malaweg Yogad Gaddang Gddang Apayao Kalinga Itneg Balangao Bontoc

Kankanaey Ayangan Ifugao Tuwali Ifugao Kalanguya Ibaloi Pangasinan Bugkalot Bolinao Sambal Kapampangan Tagalog Bicolano Mangyan Iraya Mangyan Hanunuo Mangyan Buhid

Mangyan Bangon Waray Boholano Cebuano Kinray-a Hiligaynon Sulodnon Bukidnon Negros Agutaya Cuyonon Molbog Tagbanwa Palawano Sama Deya Bonggao Sama Kabingaan

Sama Bangingi Yakan Sama Dilaut Bonggao Sama DilautTaluksangay

Sama DilautMampang

Tausug Subanon Subanen Surigaonon Chavacano Meranao Iranun Maguindanaon Mansaka Tagakaolo

Kalagan Mandaya Kamayo Kagayanen Cinamiguin Bukidnon Binukid Bukidnon Higaonon Bukidnon Talaandig Bukidnon Manobo BukidnonUmayamnon

BukidnonTigwahanon

Bukdinon Matigsalug Ata Manobo Davao Matigsalug Ovu Manuvo

Manobo Tagabawa Manobo Agusan Manguangan Dibabaon Manobo RajahKabungsuwan

Manobo Ilianen Manobo Dulangan Lambanguian A A A A A A A

Manobo Sarangani Blaan Sarangani Blaan Koronadal Tboli Obo Teduray Bagobo Klata Sangil A A A A A A A

Figure 5. Estimates of Negrito or Australasian-related, Cordilleran or Austronesian-related, Manobo or Mindanao-related, or Sama or Austroasiatic-related ancestries among Philippine ethnic groups. Archaic Neandertal and Denisovan as well minor European, South Asian, and Papuan-related ancestries are not taken into account in these estimates. The first two rows represent the self-identified Negrito ethnic groups arranged geographically from north to south of the Philippines. Rows three to nine represent non-Negrito ethnic groups arranged geographically from north to south: Batanic, Cagayan Valley, Cordilleran, Central Luzon, Bicol, Mindoro, Visayas, Palawan, Sulu archipelago, Western Mindanao, Northern Mindanao, Eastern Mindanao, Central Mindanao, and Southern Mindanao.

8 Genetic origins of the Filipino People

11) The spread of Islam is largely via cultural diffusion. Oral traditions point to the year 1380 CE as the earliest account of Islamization in southwestern Philippines. An Arab missionary and trader, Makhdum Karim, established a mosque in Simunul Island, Tawi-Tawi; now regarded as the oldest mosque in the Philippines. More than a century later, a Johore-native named Shariff Muhammed Kabungsuwan arrived in western Mindanao, and became the first sultan of Maguindanao in the early 15th century. Shariff is recognized as the person responsible for establishing Islam as the main religion the western Mindanao area. Unlike the South Asian gene flow detected among Sama sea nomads which is attributed to the spread of Hindu-Buddhist influences in southwestern Philippines, we do not find any genetic signal of Arabic / Middle Eastern genetic impact among the Islamized ethnic groups. This would imply that the spread of Islamic faith in the Philippines is largely due to cultural diffusion (i.e. an indigenous person converting to Islam), and not by mass movement of Muslims carrying Middle Eastern ancestry. This is also supported by the fact that the 9 Islamized ethnic groups analyzed in the study do not form a single genetic unit. For instance, the Islamized Molbog of Palawan are more related to the Palawano and Tagbanwa ethnic groups, than they are to other Islamized ethnic groups, such as the Tausug, Meranao, or Maguindanaoan. This implies that the Molbog did not descend from other Islamized groups, but rather descend from a common ancestor shared with the Palawano and Tagbanwa ethnic groups, and later converted to Islam. Our observations are consistent with the historical evidence of mainland Mindanao. The Iranun, Meranao, and the Maguindanaoan culture already exist even prior to the arrival of Islam. The vibrant pre-islamic Meranao culture, for instance, appears to be an amalgamation of various influences. Among others, the Meranao people speak a language that classified as Austronesian, design their furniture with intricate okir motifs that were likely influenced by the okil-okil decorative carvings of Sama, recite the Maharadia Lawana which is a locally adapted version of the Indian epic Ramayana, and chronicle their pre-Islamic customary beliefs and practices in Darangen (an epic poem declared as a National Cultural Treasure by the National Museum in 2002 and as a Masterpiece of the Oral and Intangible Heritage of Humanity by UNESCO in 2005). Likewise, the Yakan of Basilan, the Tausug of Sulu, and the Sama of Tawi-Tawi already reside in the islands of Sulu archipelago with their distinct cultures prior to the arrival of Islam. While they all group together in terms of genetic relatedness, the Tausug people interestingly speak a language that is different from the rest. The Yakan and the Sama-related groups speak a language that is more related to some Bornean languages (Barito languages), while the Tausug speak a language that is more related to the Butuanon and Surigaonon languages (South Visayan languages). Based on our analysis, we find the Tausug to have genetic affiliations with both Sama-related and Visayan-related groups, indicating a history of interbreeding prior the Islamization. 12) Limited genetic legacy of the Spanish Colonial Period. The Spanish colonization of the Americas has left a lasting genetic legacy among its populations. This is evident in the high levels of European ancestry detected among the majority lowland populations of Hispanic America. In contrast, the European genetic signal in the Philippines is only limited to ~1 percent of all individuals investigated, indicating that the majority of the Philippine ethnic groups did not have a history of interbreeding with Europeans. The only ethnic group where we can detect significant levels of European ancestry in our dataset at a population level are the Chavacanos. Moreover, we only detect European ancestry in few random individuals from other lowland or urbanized ethnic groups. We estimate the date of this

European admixture to happen around 150 – 450 years ago, which is well within the period of Spanish Colonial rule in the Philippines. The lasting influence of the Spanish Colonial Period in the Philippines from 1565-1898 is then only profoundly cultural. This is evident in the namesake of our country and as a people, in the Spanish surnames found among the majority of Filipinos, as well as the predominant practice of Catholic Christianity, which accounts for 81% of the population. Additional Spanish influences on Filipino culture include, among others, the cuisine (e.g. Afritada, Lechon, Leche Flan, Menudo, etc.), music (e.g. rondalla, harana, kundiman, etc), dance (e.g. Cariñosa), celebration of Christian festivities, and several Spanish loan words present in various indigenous Philippine languages. Future prospects As genomic data becomes more available in the future, the prehistory of the Philippines will likely become more refined. This is especially true provided the recent developments in ancient DNA techniques. The precise genetic relationships and the time of admixture between various ethnic groups of Taiwan, Island and Mainland Southeast Asia, Papua New Guinea, and the rest of the Pacific Islands remains to be known. It remains to be known in detail how Denisovans interacted with ancestral Filipino ethnic groups, where and when these interactions happened, and what magnitude it contributed to the genetic ancestry of present-day populations. It remains to be known whether these interactions resulted in adaptive introgression, where our ancestors were able to acquire genes from archaic humans to make them better adapt and survive in tropical island environments. It also remains to be known whether Homo floresiensis or the recently discovered Homo luzonensis are genetically related to Denisovans, or if they partially contributed to the genetic ancestry of the present-day ethnic groups of the Asia-Pacific region. The future availability of data from various time transects and from various geographic regions, may it be from archaic or modern human samples, will potentially provide us surprising findings and generate new insights on human origins and diversity. For this to happen, as we have experienced in this study, advancement of knowledge is made possible through mutual collaborations with various sectors as well as working closely in partnership with indigenous communities. Summary The complex demographic history of the Philippines presented here does not fit with the three-wave migration theory by Otley Beyer, nor does it fit with the models of either an exclusive out-of-Taiwan or out-of-Sundaland hypothesis (Figure 3 & 4). Instead, we find that the Philippines were populated by at least five major waves of migration, starting with the Northern and Southern Negritos, who entered the Philippines after ~40 to 50 thousand years ago to become the First Filipinos. Thereafter by the Manobo-related groups entering Mindanao after ~15 thousand years ago, and the Sama-related groups entering southwestern Philippines after ~12 thousand years ago, both of which occurring around the time when there were substantial changes in the landscape of Sundaland brought about by climate change. Cordilleran-related groups likely arrived in the Philippines ~7 to 10 thousand years ago following their split from Indigenous Taiwanese, around the time when there were climate change-induced geographical changes in the South China-Taiwan greater area. Remarkably, some Cordillerans remained to be the only ethnic group in the Philippines who did not show evidence of

9 Genetic origins of the Filipino People

historical interbreeding with Negritos, and consequently remained to be the only population in the world regarded as the unadmixed descendants of Basal East Asians We also find minor genetic signals of Papuan-related ancestry, Indian-related ancestry, and European ancestry in some ethnic groups. The Papuan-related ancestry, dated more than ~2,500 year ago, is found among the coastal ethnic groups of southeastern Philippines such as Sangil and Blaan. The Indian-related genetic signal, dated ~500 to 1000 years ago, is found among Sama Dilaut and other coastal Sama ethnic groups of southwestern Philippines, indicating some genetic impact of the historical Maritime Trading Network with India. Lastly, the European genetic signal, dated ~150 to 450 years ago, is found only ~1% of all individuals investigated, indicating a limited genetic legacy of the Spanish Colonial Period. In this work, we present an intricate prehistory of the Filipino people that is characterized by series of encounters between distinct populations across time. At times, these encounters resulted in interbreeding, contributing to the admixed genetic profile of present-day populations (Figure 5). At other times, these encounters only resulted in partial or exclusive transfer of culture and/or ideas, leaving a limited or undetectable trace of genetic ancestry. Both demographic and cultural processes altogether contribute to the diversity of the Philippine ethnic groups that we know of today.

All of these complexities in history have lasting implications on how we define ourselves as Filipinos. We may be inadvertently diverse, but we, in one way or the other, share a common thread in history. We as Filipinos may vary in creed, philosophy, language, style, culture and traditions, or in the color of our skin or of our politics, but one thing is for certain: we are all bound together by blood, sharing a tapestry of genetic heritage derived from a common ancestor in one historical moment of our convoluted past. Author information: Maximilian Larena is a population geneticist affiliated with the Human Evolution Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. Carlo Ebeo is the Vice Head of the NCCA National Committee on Cultural Education and Board of Trustee member of the National Museum of the Philippines. Adrian Albano is an anthropologist and a Kalanguya Cordilleran affiliated with the Ifugao State University. Trixie Cruz-Angeles graduated with a degree in Linguistics, a degree in Law and is working on her MA in Archaeology and a minor in International Relations. Edison Molanida is the Project Coordinator at the Office of the Executive Director of the NCCA. Felipe Mendoza de Leon Jr. is the former chairperson of the NCCA. To cite this work, please use the source material for this summary: Multiple migrations to the Philippines during the last 50,000 years published in PNAS. https://doi.org/10.1073/pnas.2026132118 See also the source material, both the main text and the supplementary material, for the complete list of acknowledgements and references.