Ayta Negritos: Highest Levels of Denisovan DNA

Most historians point to the Bering Land Bridge Theory to explain the history of the Aetas. This theory suggests that the Aetas reached the Philippines because of the land bridges or narrow strait that connected all land masses in the world. According to this theory, hunters at the time crossed these land bridges but due to the movement of plates underneath the Earth’s surface, these migration paths eventually disappeared. Therefore, even those with no intent to colonize new lands, were unable to return to their original homes.





Their distinguishing characteristics and practices
Aetas are characterized by their skin color, height, and hair type. They mostly have dark to dark-brown skin, curly hair, and are usually below five-feet tall. Traditionally, Aetas are hunting and gathering indigenous people. They’re actually among the most skilled when it comes to jungle survival – they are even able to make use of plants as herbal medicine and possess tools and weapons. While they’re nomadic, they are able to build temporary houses made of sticks.

Most Aetas practice monotheism and are animists. They worship a Supreme Being and at the same time, also believe in environmental spirits. They believe that various places in our environment are being governed by both good and evil spirits.

As for their clothing, they wear plain and simple attire. Traditional Aetas, who are skilled in weaving and plating, wear wrap around skirts or bark cloth (for women) and loin cloths for men. They are also into music and the arts – making use of ornaments as accessories and have ensembles of instruments to create melodious rhythms.

Colonial resistance and unfortunate displacement
Because they are usually scattered in mountainous areas, the Spaniards had a hard time introducing Catholicism to their population. They mostly resisted to change, which made it difficult for the Spanish to colonize their areas. This is also one of the reasons why they were able to preserve their cultural traditions and beliefs through to today.



Most Aetas can be found in the northern part of Luzon. According to historical accounts, they have lived near Mount Pinatubo in Zambales for thousands of years. But, when Mount Pinatubo erupted in 1991, it devastated the Aeta population. The majority lost their homes while some re-settled in urban areas. This gave way to Aetas being modernly influenced by prevailing Filipino culture and practices. Some Aetas have already married Filipinos. Most Aetas also go to school nowadays.

Challenges today
In the Philippines, Aetas as well as other indigenous groups, belong to the marginalized sector of the country. They’re often displaced because their homelands have been destroyed due to illegal logging, mining, and slash-and-burn farming. Thus, these situations have forced them to relocate and leave their ancestral lands.



While the Philippine government has implemented mandates and acts such as the Indigenous Peoples’ Rights Act of 1997, it’s not enough to protect them and help them cope with matters such as access to jobs and livelihood support.

The main paternal haplogroup of the Negritos is K2b in the form of its rare primary clades K2b1* and P* (a.k.a. K2b2* or P-P295*). Most Aeta males (60%) carry K-P397 (K2b1), which is otherwise uncommon in the Philippines and is strongly associated with the indigenous peoples of Melanesia and Micronesia. Basal P* is rare outside the Aeta and some other groups within Maritime Southeast Asia. Some Negrito populations are Haplogroup D-M174*, a branch of D-M174 among Andaman Islanders, as well as Haplogroup O-P31 which is also common among the now Austroasiatic-speaking Negrito peoples, such as the Maniq and the Semang in Malaysia.

A 2017 study by Mondal et al. finds that the Riang people (a Tibeto-Burmese population) and the Andamanese share the same D clade (D1a3 also known as D2a2b), and have their closest lineages with other clades in East Asia. The Jarawa and Onge shared this D1a2b with each other within the last ~7000 years. The East Asian D1a2b had diverged from the Japanese D1a2a lineage ~53,000 years ago. The authors concluded that: ”This strongly suggests that haplogroup D does not indicate a separate ancestry for Andamanese populations. Rather, haplogroup D was part of the standing variation carried by the Eastern OOA expansion, and later lost from most of the populations except in Andaman and partially in Japan and Tibet”.

In contrast, the Riang (Tibeto-Burman-speaking) and Andamanese have their nearest neighbour lineages in East Asia. The Jarawa and Onge shared haplogroup D lineages with each other within the last ~7000 years, but had diverged from Japanese haplogroup D Y-chromosomes ~53000 years ago, most likely by a split from a shared ancestral population.

repositori.upf.edu/handle/10230/34399

Researchers have known from several lines of evidence that the ancient hominins known as the Denisovans interbred with modern humans in the distant past. Now researchers reporting in the journal Current Biology on August 12, 2021, have discovered that the Philippine Negrito ethnic group known as the Ayta Magbukon have the highest level of Denisovan ancestry in the world. In fact, they carry considerably more Denisovan DNA than the Papuan Highlanders, who were previously known as the present-day population with the highest level of Denisovan ancestry.

“We made this observation despite the fact that Philippine Negritos were recently admixed with East Asian-related groups—who carry little Denisovan ancestry, and which consequently diluted their levels of Denisovan ancestry,” said Maximilian Larena of Uppsala University. “If we account for and masked away the East Asian-related ancestry in Philippine Negritos, their Denisovan ancestry can be up to 46 percent greater than that of Australians and Papuans.”

In the new study, Larena and colleagues, including Mattias Jakobsson, aimed to establish the demographic history of the Philippines. Through a partnership between Uppsala University of Sweden and the National Commission for Culture and the Arts of the Philippines (NCCA), aided by collaboration with indigenous cultural communities, local universities, local government units, non-governmental organizations, and/or regional offices of the National Commission for Indigenous Peoples, they analyzed about 2.3 million genotypes from 118 ethnic groups of the Philippines including diverse self-identified Negrito populations. The sample also included high-coverage genomes of AustraloPapuans and Ayta Magbukon Negritos.

The study shows that Ayta Magbukon possess the highest level of Denisovan ancestry in the world, consistent with an independent admixture event into Negritos from Denisovans. Together with the recent discovery of a small-bodied hominin, called Homo luzonensis, the data suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans, and that these archaic groups may have been genetically related.

Altogether, the researchers say that the findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.

“This admixture led to variable levels of Denisovan ancestry in the genomes of Philippine Negritos and Papuans,” Jakobsson said. “In Island Southeast Asia, Philippine Negritos later admixed with East Asian migrants who possess little Denisovan ancestry, which subsequently diluted their archaic ancestry. Some groups, though, such as the Ayta Magbukon, minimally admixed with the more recent incoming migrants. For this reason, the Ayta Magbukon retained most of their inherited archaic tracts and were left with the highest level of Denisovan ancestry in the world.”

“By sequencing more genomes in the future, we will have better resolution in addressing multiple questions, including how the inherited archaic tracts influenced our biology and how it contributed to our adaptation as a species,” Larena said.

Introduction
Since their exit out of Africa, anatomically modern humans have overlapped and interbred with archaic hominins across time and space. Interactions with Neanderthals,1,2 Denisovans,3,4 and possibly other archaic hominins5,6 have left an indelible genetic trace in the genomes of present-day populations.7, 8, 9 All Eurasians possess uniform levels of Neanderthal ancestry, whereas Australasians uniquely have elevated levels of Denisovan ancestry relative to any other population. Denisovans were initially thought to have a simple shared demographic history with modern humans, through a single admixture event with the ancestor of Australasians (a collective term for the shared genetic ancestry between Philippine Negritos and Australopapuans).4,10,11

Later work suggested that Denisovans were likely deeply diverging structured populations who inhabited wide-ranging diverse environments, given that Denisovan ancestry can also be detected, albeit at lower levels, among East Asian, South Asian, Siberian, and Native American populations.7,12, 13, 14 Through analysis of recovered archaic tracts from population-level genomes, it was recently shown that modern humans admixed with Denisovans at least twice in the past, with Denisovan-like populations possessing varying degrees of genetic affiliation to the reference Altai Denisovan.15 Subsequent work revealed a third independent Denisovan introgression event that was exclusively found among Papuan-related populations, indicating an increasingly complex admixture history between Denisovans and Australasians.16

Although the intertwined demographic history between Denisovans and Australasians is being uncovered, our knowledge of their specific interactions in Island Southeast Asia (ISEA) remains limited. This is especially important given that some present-day populations of the Philippines, who self-identify as “Negritos” and who are genetically related to Australopapuans, display significant levels of Denisovan ancestry.4,17,18 To deepen our understanding of past Denisovan-Australasian interactions in the ISEA region, we comprehensively investigated the archaic ancestry of 1,107 individuals from 118 distinct ethnic groups of the Philippines, including 25 ethnolinguistically diverse Negrito populations (Figures 1A and S1; see STAR Methods).19



Figure 1
Indigenous Negrito ethnic groups of the Philippines

(A) Location of the 118 Philippine ethnic groups analyzed in this study. Negrito ethnic groups are labeled with red circular markers, whereas all other non-Negrito populations are labeled with yellow circular markers. Philippine Negritos are classified based on their genetic and/or geographical clusters: Northeast Luzon Negrito; Central Luzon Negrito; Southern Luzon Negrito; Southeast Luzon Negrito; and Southern Negrito.
(B) Principal-component analysis (PCA) of West Eurasians, Australasians, and East Asians. Philippine Negritos lie between the axis defined by East Asian and Australasian-related ancestries.
(C) Subset PCA showing the five distinct population clusters of Philippine Negritos.
(D) Proportion of Australasian-related versus East-Asian-related ancestries among Philippine Negritos estimated using qpAdm.
See also Figures S1 and S2.