Southeast Asians Carry DNA of ‘Mysterious Southern Denisovans’

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two super-archaic species, Homo luzonensis and Homo floresiensis, were present around the time anatomically modern humans arrived in the region 50,000-60,000 years ago. In new research, an international team of scientists examined more than 400 modern human genomes to investigate ancient interbreeding events between super-archaic and modern human species. Their results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the fossil record.

A portrait of a juvenile female Denisovan based on a skeletal profile reconstructed from ancient DNA methylation maps. Image credit: Maayan Harel.

ISEA, also known as Maritime Southeast Asia, is a region that includes the countries of Brunei, Indonesia, Malaysia, the Philippines, Singapore, and East Timor.

It hosts a unique and diverse fossil record of hominin presence throughout the Pleistocene epoch.

The island of Java in modern Indonesia marks the southeastern extent of the range of Homo erectus, the first hominin species thought to have successfully dispersed outside Africa, where it maintained a presence from 1.49 million years ago until 117,000-108,000 years ago.

At least two additional endemic species lived in ISEA during the Pleistocene and are likely to have survived until the arrival of anatomically modern humans over 50,000 years ago: Homo floresiensis on Flores, in the Lesser Sunda Islands (also part of modern Indonesia), and Homo luzonensis on Luzon, in the northern Philippines.

Recent interpretations suggest that Homo floresiensis is either a close relative of Homo erectus, or alternatively represents an even more archaic species of Homo that independently reached ISEA in a separate dispersal event out Africa.

The current classification of Homo luzonensis is also uncertain; the available specimens share similarities with various hominin species including Australopithecus, Asian Homo erectus, Homo floresiensis and Homo sapiens.

This is an artist’s reconstruction of Homo erectus. Image credit: Yale University.

In the new study, University of Adelaide’s Dr. João Teixeira and colleagues examined the genomes of more than 400 modern humans, including over 200 from ISEA, to investigate the interbreeding events between the super-archaic species and modern human populations who arrived at ISEA 50,000-60,000 years ago.

In particular, they focused on detecting signatures that suggest interbreeding from deeply divergent species known from the fossil record of the area.

Their results showed no evidence of interbreeding; nevertheless, they were able to confirm previous results showing high levels of Denisovan ancestry in the region.

“While the known fossils of Homo erectus, Homo floresiensis and Homo luzonensis might seem to be in the right place and time to represent the mysterious southern Denisovans, their ancestors were likely to have been in Island Southeast Asia at least 700,000 years ago,” said Professor Chris Stringer, a researcher at the Natural History Museum, London.

“Meaning their lineages are too ancient to represent the Denisovans who, from their DNA, were more closely related to the Neanderthals and modern humans.”

Reconstruction of Homo floresiensis. Image credit: Elisabeth Daynes.

“These analyses provide an important window into human evolution in a fascinating region, and demonstrate the need for more archaeological research in the region between mainland Asia and Australia,” said Professor Kris Helgen, director of the Australian Museum Research Institute.

“We know from our own genetic records that the Denisovans mixed with modern humans who came out of Africa 50,000-60,000 years ago both in Asia, and as the modern humans moved through ISEA on their way to Australia,” Dr. Teixeira said.

“The levels of Denisovan DNA in contemporary populations indicate that significant interbreeding happened in ISEA.”

“The mystery then remains, why haven’t we found their fossils alongside the other ancient humans in the region? Do we need to re-examine the existing fossil record to consider other possibilities?”

The findings were published in the journal Nature Ecology and Evolution.


J.C. Teixeira et al. Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture. Nat Ecol Evol, published online March 22, 2021; doi: 10.1038/s41559-021-01408-0

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