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DNA of hunter-gatherer buried 7,000 years ago in Indonesia reveals story of Southeast Asian people

A team of archaeological geneticists has reconstructed the genome of a hunter-gatherer from the Indonesian archipelago, which sheds significant light on the history of the population of Southeast Asia.

This study reports the first known human genome of Leang Panninge to Wallacea, an oceanic island in the middle of the Sahul and Sunda continental shelves.

Although anatomically modern humans are believed to have crossed Australia from Asia 65,000 years ago, the earliest remains of Homo sapiens date back to only 13,000 years ago. One of the reasons is the tropical climate, which breaks down the natural tissues quite quickly and is therefore not very conducive to the conservation of remains. Previously, only two ancient human genomes, one from Laos and the other from Malaysia, had been sequenced in Southeast Asia.

Hunting and gathering is a way of life associated with the Paleolithic (3 million years ago to 10,000 years ago) in archaeological records. This way of life was largely replaced by the adoption of agriculture and the domestication of animals and plants, widely known as the Neolithic Revolution (10,000 to 8,000 years ago). However, some groups of hunter-gatherers have managed to survive to the present day and have been the subject of numerous anthropological investigations.

Reconstruction of genetic history

The present study used molecular markers with different modes of inheritance to examine the genetic history of Leang Panninge’s individual.

While nuclear DNA (nrDNA) is inherited in a biparental fashion, i.e. about half is from the mother and the other half from the father, mitochondrial DNA (mtDNA) shows uniparental inheritance. , that is, it is inherited exclusively from the mother. Studies targeting more molecular markers than a single one can better reconstruct the genetic history of a population.

DNA was sequenced from petrous bone, a small bone in the ear region of the skull. Petrous, in recent years, has been widely targeted for ancient DNA for its remarkable preservation of genetic material.

As there is a dearth of a large number of ancient individuals, any study of ancient DNA must be compared to the known genetic history of the current populations in the region, which in this case were Southeast Asia. East, Papua New Guinea, Australia and other Pacific Islands.

Who was his ancestor?

Genetic analyzes reveal that the individual shares significant genetic ancestry with current populations in Oceania – Australia, Papua New Guinea and other island groups.

Menu a, Sulawesi and Wallacea. The red rectangle indicates the region indicated in b. b, Leang Panninge. (Carlhoff, S., Duli, A., Nägele, K. et al. Nature)

Selina Carlhoff, lead author of the study, clarified in an email: “In direct comparisons, we show that these near Pacific Islander groups are more closely related to each other than to Leang Panninge… which would place Leang Panninge outside of this clade.

The populations of Oceania and Eurasia would have diverged 58,000 years ago, and the Papuan and Australian peoples around 37,000 years ago, also the date of the bifurcation of the individual Leang Panninge.

During this time, populations in these regions saw multiple introductions of genetic material from the Denisovans (the Denisovans are an extinct species of primitive hominids that extended across Asia in the Paleolithic).

Researchers have identified another ancestral genetic line in the individual’s old genome that appears to be more closely related to deep Asian lineages.

“Viewing the individual Leang Panninge as a mix between a lineage close to Oceania and a lineage related to deep East Asia may also explain the reduced amount of Denisovan-related ancestry compared to current Papuan groups.” , added Carlhoff.

Given the paucity of pre-Neolithic genomes in the region, it is difficult to underpin the exact source of the mixtures. It could be that this individual has ancestors of the first Homo sapiens inhabitants of Sulawesi around 50,000 years ago, or that a group from Southeast Asia related to the current Andamanese people brought genetic material.

The author is an independent science communicator. (mail[at]ritvikc[dot]with)

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