Genetic study reveals some Aetas and Indians share ancient a...

Komodo Commander · 2022-01-19T01:49:49Z

According to Delfin, it is commonly accepted that the Asia-Pacific—including the Philippines—was peopled by human migration that passed through the coast of South Asia. But the mitochondrial DNA (mtDNA) Indian-Philippine genetic link that Delfin and his team found “can be a signal of shared ancestry that actually originated from India”. Two mtDNA sets, M52'58 and M52a, that both originate from Indian populations were found in the Aetas of Zambales and the Agtas of Iriga in the Philippines. These shared common haplogroups show a link between the populations of India and the Philippines that is about 5,000 to 20,000 years old. This suggests that these migratory groups from India arrived before the Austronesian people landed in Philippine shores and populated the prehistoric Philippine archipelago. Link found in female lineage Mitochondrial DNA or mtDNA are the parts of a person's genome passed on by mothers to their children; only women pass them from generation to generation. Common mtDNA haplogroups or specific lineages were found in some Philippine and Indian populations which suggest common origins between the two. Since mtDNA ancestry is matrilineal and not a combination of genetic material from both parents, tracing someone's lineage through the mtDNA is a somewhat straightforward process. Indian origins not found in other Southeast Asian groups This connection, science blogger Nathaniel Hermosa said, is noteworthy because it is unique to the Philippines. Established genetic studies showed that no such link has been found in other Southeast Asian groups. “We also studied about 1,700 other mtDNA genomes (samples or individuals) across the Asia-Pacific region and did not find these two haplogroups anywhere else,” Delfin said in an email interview with GMA News Online. Hermosa posed the question: “How did the people from South Asia travel to the Philippines without passing through the rest of Southeast Asia?” Other regions in Southeast Asia might have been undersampled in this study, he added. Delfin acknowledged this possibility, stating that, in reality, not all populations in the Asia-Pacific region have been studied. So other Southeast Asian haplogroups that could also share links to the Indian populations may not have been sampled yet. Another possibility, he says, is a phenomenon called “genetic drift” in which historical accidents—natural disasters, for example, like earthquakes or floods—wipeout entire populations, leaving lucky survivors. This means that the survivors pass on their genes largely as a result of chance rather than natural selection. Over time, the haplogroups that originated from India in other Asia-Pacific populations may have been eliminated, leaving only the ones observed between India and the Philippines. Arrival of migratory groups from India The same study also suggest “a genetic signal of a possible migration event that happened after the initial peopling of the Asia-Pacific region.” Somewhere between the initial peopling of Asia and Pacific regions and the Austronesian expansion, those migratory groups from India came to the Philippines. “This estimated age (5,000 to 20,000 years ago) is somewhat in between the estimated ages of the initial peopling of the Asia and Pacific regions (50,000 to 70,000 years ago) and the Austronesian expansion (5,000 to 7,000 years ago),” said Delfin. The latter are thought to be the two major peopling events of the Philippines. “Somehow after the ancestors of Asia-Pacific peoples first settled the region, there were subsequent population movements around the Asia-Pacific, that could have brought such Indian specific mtDNA haplogroups to the Philippines' prehistoric archipelago,” Delfin explained. Calls for further study Further investigation of this data will be done through an on-going project that focuses on different Negrito groups using autosomal single nucleotide polymorphism (aSNP) data, which unlike mtDNA data, is not limited to the female lineage and represents more the entirety of a person's genome. This project is funded by Department of Science and Technology, Philippine Council for Health Research and Development (DOST-PCHRD). The main proponent of this project is the Institute of Human Genetics, National Institutes of Health, UP Manila, (UP-NIH-IHG) headed by Dr. Eva Cutiongco-de la Paz, and is done in collaboration with the University of the Philippines Natural Sciences Research Institute DNA Analysis Laboratory (UP-NSRI-DAL) are collaborators in this project.— TJD, GMA News

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Ancient History, Filipino, genetics, India, Neolithic Philippines, ntDNA, Philippines

Three migrations were seen upon analysis of mtDNA genomes of 14 ethnolinguistic groups.

The plot thickens!

It still fascinates me how regions of the earth have been reached and populated by humans. Particularly, I am curious how humans ‘conquered’ the islands of the Philippines. Curious because it says where I, a Filipino, and the rest of Filipinos came from.

I’ve written two blog posts about this topic already (here and here). Let me first summarize what I think are notable points in these studies. The first post is about the diversity of mtDNA in the Philippines by K. A. Tabbada et al [1]. In that paper, they said that the Philippines was populated mostly via Austronesian expansion (~5 000 years ago) but they found out that there is also an ancient lineage that links the Filipinos to people in Near Oceania and Australia (whose founder age they estimate to be ~47 000 years ago). They point out that “there is evidence of substructuring within the lineages which means there is a pattern of long-term in situ evolution.”

The second post I wrote is about the human Y chromosome (NRY) diversity in the islands [2]. In that study, the authors obtained results similar to the mtDNA analysis such as the Austronesian expansion and a founder lineage. Moreover, they were able to connect different Filipino ethnolinguistic groups to different groups outside of the Philippines. Three things are clear in that study: 1) there is genetic diversity even within Philippine populations (even within negrito groups), 2) there is no simple distinction between negrito and non-negrito groups, and 3) there are recent and ancient connections to the people of neighboring countries including Near Oceania and Australia.

Now, a recent paper in the European Journal of Human Genetics studied complete mtDNA of 14 ethnolinguistic groups in the Philippines [3]. They have found out that different groups posses different genetic make-up and that these different genetic make up is caused by different waves of migration that are both recent and ancient and an in situ diversification. These conclusions are similar to the first two papers but what I find striking are the reporting of a direct Indian migration to the islands and the suggestion that every ethnolinguistic group has unique genetic history.

The Indian-Philippine link is noteworthy. The presence of these haplogroups that connect the Filipinos and Indians have NOT been observed in other Southeast Asian groups. AetaZ and Agta groups which posses these haplogroups, “seem to demonstrate a direct mtDNA link between India and the Philippines.” How did the people from South Asia travel to the Philippines without passing through the rest of Southeast Asia? Maybe other regions in Southeast Asia are undersampled?

Another reason why it is remarkable is that it says that the timing of this migration to the islands is in between the initial colonization and the Austronesian expansion. The timing of migration also coincides with a similar migration of South Asians to Australia [4].

There is more to look forward to. The authors said, “although the NRY and mtDNA landscapes of the Filipino population are now described, these genetic systems are just two loci and specifically reflect respectively, male and female genetic histories. A more comprehensive view of Filipino diversity and history can still be sought through genome-wide variation.”

I will be waiting for your results eagerly!

Reference:
[1] K. Tabbada, J. Trejaut, J. Loo, Y. Chen, M. Lin, M. Mirazon-Lahr, T. Kivisild, and M. C. De Ungria, Philippine Mitochondrial DNA Diversity: A Populated Viaduct between Taiwan and Indonesia? Mol. Biol. Evol. 27(1):21–31 (2010). DOI: 10.1093/molbev/msp215

[2] Delfin F, Salvador JM, Calacal GC, Perdigon HB, Tabbada KA, Villamor LP, Halos SC, Gunnarsdóttir E, Myles S, Hughes DA, Xu S, Jin L, Lao O, Kayser M, Hurles ME, Stoneking M, & De Ungria MC (2010). The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. European journal of human genetics : EJHG PMID: 20877414

[3] Delfin F, Min-Shan Ko A, Li M, Gunnarsdóttir ED, Tabbada KA, Salvador JM, Calacal GC, Sagum MS, Datar FA, Padilla SG, De Ungria MC, & Stoneking M (2013). Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region. European journal of

Abstract

Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent. The date of mixture is unknown but has implications for understanding Indian history. We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that India experienced a demographic transformation several thousand years ago, from a region in which major population mixture was common to one in which mixture even between closely related groups became rare because of a shift to endogamy.

Introduction

Genetic evidence indicates that most of the ethno-linguistic groups in India descend from a mixture of two divergent ancestral populations: Ancestral North Indians (ANI) related to West Eurasians (people of Central Asia, the Middle East, the Caucasus, and Europe) and Ancestral South Indians (ASI) related (distantly) to indigenous Andaman Islanders.¹ The evidence for mixture was initially documented based on analysis of Y chromosomes² and mitochondrial DNA^3–5 and then confirmed and extended through whole-genome studies.^6–8

Archaeological and linguistic studies provide support for the genetic findings of a mixture of at least two very distinct populations in the history of the Indian subcontinent. The earliest archaeological evidence for agriculture in the region dates to 8,000–9,000 years before present (BP) (Mehrgarh in present-day Pakistan) and involved wheat and barley derived from crops originally domesticated in West Asia.^9,10 The earliest evidence for agriculture in the south dates to much later, around 4,600 years BP, and has no clear affinities to West Eurasian agriculture (it was dominated by native pulses such as mungbean and horsegram, as well as indigenous millets¹¹). Linguistic analyses also support a history of contacts between divergent populations in India, including at least one with West Eurasian affinities. Indo-European languages including Sanskrit and Hindi (primarily spoken in northern India) are part of a larger language family that includes the great majority of European languages. In contrast, Dravidian languages including Tamil and Telugu (primarily spoken in southern India) are not closely related to languages outside of South Asia. Evidence for long-term contact between speakers of these two language groups in India is evident from the fact that there are Dravidian loan words (borrowed vocabulary) in the earliest Hindu text (the Rig Veda, written in archaic Sanskrit) that are not found in Indo-European languages outside the Indian subcontinent.^12,13

Although genetic studies and other lines of evidence are consistent in pointing to mixture of distinct groups in Indian history, the dates are unknown. Three different hypotheses (which are not mutually exclusive) seem most plausible for migrations that could have brought together people of ANI and ASI ancestry in India. The first hypothesis is that the current geographic distribution of people with West Eurasian genetic affinities is due to migrations that occurred prior to the development of agriculture. Evidence for this comes from mitochondrial DNA studies, which have shown that the mitochondrial haplogroups (hg U2, U7, and W) that are most closely shared between Indians and West Eurasians diverged about 30,000–40,000 years BP.^3,14 The second is that Western Asian peoples migrated to India along with the spread of agriculture; such mass movements are plausible because they are known to have occurred in Europe as has been directly documented by ancient DNA.^15,16 Any such agriculture-related migrations would probably have begun at least 8,000–9,000 years BP (based on the dates for Mehrgarh) and may have continued into the period of the Indus civilization that began around 4,600 years BP and depended upon West Asian crops.¹⁷ The third possibility is that West Eurasian genetic affinities in India owe their origins to migrations from Western or Central Asia from 3,000 to 4,000 years BP, a time during which it is likely that Indo-European languages began to be spoken in the subcontinent. A difficulty with this theory, however, is that by this time India was a densely populated region with widespread agriculture, so the number of migrants of West Eurasian ancestry must have been extraordinarily large to explain the fact that today about half the ancestry in India derives from the ANI.^18,19 It is also important to recognize that a date of mixture is very different from the date of a migration; in particular, mixture always postdates migration. Nevertheless, a genetic date for the mixture would place a minimum on the date of migration and identify periods of important demographic change in India.

Human Biology Genetic study reveals some Aetas and Indians share ancient ancestry

Complete mtDNA genomes of Filipinos reveal recent and ancient lineages

Genetic Evidence for Recent Population Mixture in India (nih.gov)

Abstract

Introduction