Protein sequence analysis by SOKENDAI, University of Tokyo reveals Taiwan's oldest human fossil to be Denisovan

A research group led by Assistant Professor Takumi Tsutaya and Research Fellow Rikai Sawafuji (currently a Lecturer at Kyushu University) from the Graduate University for Advanced Studies (SOKENDAI), along with researchers from the University of Tokyo, the National Museum of Natural Science, Taiwan, and the University of Copenhagen (Denmark) and other collaborators, has announced that Taiwan's oldest human fossil originated from a male "Denisovan", an extinct archaic hominin group. This was determined by examining ancient protein sequences. The researchers also discovered morphological features of Denisovans that differ from other archaic hominins, including a thick, robust jaw and large molars. These findings contribute to the study of human evolution and were published in the April 11 issue of the international academic journal Science.

"Denisovan" is the provisional name of an archaic hominin group whose existence was demonstrated in 2010 through ancient genome analysis of fossils discovered in Denisova Cave in Siberia. They are thought to have diverged from Neanderthals more than 400,000 years ago. However, Denisovan fossils (dating from 195,000 to 48,000 years ago) have only been found, so far, in Siberia and Tibet. Moreover, most of these fossils were teeth and bone fragments, leaving their skeletal morphology unknown.

Research on modern human genomes suggests that Denisovans interbred with Homo sapiens (modern humans) in Southeast Asia and possibly Oceania tens of thousands of years ago. However, Denisovan fossils have only been discovered in northern Asia, with no molecular evidence showing their distribution extended to southern Asia.

Taiwan's oldest human fossil is a mandible reported by the research group in 2015 as "Penghu 1." It was retrieved by trawling nets from the sea bottom of Taiwan (Penghu Channel), which has been exposed as land for several periods over the past hundred thousand years. Its age is estimated at 190,000-100,000 years ago or 70,000-10,000 years ago. When it was discovered, it was considered to potentially be Asia's fourth archaic hominin due to its unique and partially archaic morphology. Extraction of ancient DNA was unsuccessful, leaving its phylogenetic position unclear.

In this study, the research group sampled a total of ∼25 milligrams of bone powder from the fossil and successfully extracted past, endogenous proteins (ancient proteins). They determined the sequences using mass spectrometry and obtained sequence information for 4,241 amino acid residues derived from 51 proteins. Among these, they discovered one "Denisovan"-specific variation and one semi-specific variation. Based on sequence phylogenetic analysis, they determined it belonged to the same lineage as a Denisovan from Siberia. Y-chromosome-specific proteins reflecting genetic sex were also detected in the dental enamel.

This provides fossil evidence that Denisovans were widely distributed across Asia, demonstrating their behavioral flexibility to adapt to diverse environments. By examining genetic information contained in proteins and DNA, there is potential for discovering additional "Denisovan" fossils among unclassified fossils found, especially in China and Asia.

Tsutaya commented: "I would like to continue developing analytical methods that can maximize the extraction of information such as ancient proteins from smaller samples with minimal destruction, in order to preserve valuable fossils as much as possible."

Journal Information
Publication: Science
Title: A male Denisovan mandible from Pleistocene Taiwan
DOI: 10.1126/science.ads3888