The Hominins We’ve Been Calling Denisovans Are More Diverse Than Previously Thought

Researchers have identified three distinct Denisovan lineages, including one that could constitute an entirely separate species

All of the Denisovan specimens found to date originated from a cave in Siberia Демин Алексей Барнаул via Wikimedia Commons under CC BY SA-4.0

A new DNA analysis of 161 modern human genomes spanning islands across Southeast Asia and New Guinea suggests the Denisovans, an elusive early hominin species identified in 2010, boasted a far more complex family tree than once believed. As a team of international researchers report in the journal Cell, the human cousins currently labeled as Denisovans comprised at least three diverse populations—including a lineage so distinct that it may even constitute an entirely separate species.

As Live Science’s Charles Q. Choi reports, scientists first realized the Denisovans had more than one lineage in 2018. This finding, also detailed in Cell, drew on modern DNA to reveal that the early hominins likely interbred with Homo sapiens in two waves, creating varied genetic legacies still seen in contemporary residents of Oceania and East Asia.

One of these lineages was closely related to the Denisovans whose fragmented bones were unearthed in Siberia’s Altai Mountain, or Denisova, cave in 2010, carrying DNA found in modern East Asians. The second lineage had more limited genetic ties with the Denisovan specimens known to science and carried DNA evident in Papua New Guineans and South Asians.

This latest study further diversifies the Denisovan lineage, revealing that the non-Altai group flourished alongside a population never previously identified. Dubbed D1 and D2, Dyani Lewis notes for Cosmos, these groups split off from the Altai Denisovans, or D0, some 283,000 years ago, and from each other around 363,000 years ago. As the researchers explain, the D1 population’s genetic legacy is largely restricted to Papuans, while D2’s has a “wider geographical distribution spanning much of Asia and Oceania.”

Crucially, senior author Murray Cox, a computational biologist at New Zealand’s Massey University, tells the Economist, the D2 group is “about as different from the individual found in the Denisova cave as it is from Neanderthals.”

“If we’re going to call Neanderthals and Denisovans by special names,” Cox continues, “this new group probably needs a new name, too.”

The researchers’ analysis points toward Denisovan and modern human interbreeding occurring as recently as 15,000 years ago. If supported, this would make the Denisovans, rather than the Neanderthals, the last hominin cousin to disappear from the planet.

Traces of Denisovan DNA found in contemporary humans have implications for health care in the tropical region of Southeast Asia. As Cox tells Live Science’s Choi, genetic variations passed down by early hominin interbreeding continue to influence the “health of people today, mostly positively, sometimes negatively.”

Moving forward, Cox says, the scientists hope to use their findings to improve health care for the millions of individuals who, thanks to the research bias toward those of European descent, have “essentially no” existing research foundation.

“What do these archaic variants do?” Cox asks. “Why do we still have them?”

The Denisovan team’s findings arrive close on the heels of another key addition to the increasingly complex timeline of human evolution. As a different team of scientists wrote in the journal Nature earlier this week, 13 bones and teeth found in a cave on the island of Luzon in the Philippines point toward the existence of a newly identified hominin species known as Homo luzonensis. Diminutive human ancestors who stood an estimated three to four feet tall, these individuals populated the Earth some 50,000 to 67,000 years ago.

Homo luzonensis, the newly discovered D2 lineage and Homo floresiensis—a hominin species discovered on the Indonesian island of Flores in 2003 and given the nickname "Hobbit" for its tiny size—testify to the significant, yet understudied role Southeast Asia played in the development of humanity.

“The genomes in [the Cell] paper … are the first genomes from Indonesia,” Cox explains to Discover magazine’s Nathaniel Scharping. “That’s pretty amazing because Indonesia is the world’s fourth largest country, it’s got 250 million people and it’s as big as continental Europe. It just shows that disparity between science that happens in the West versus science that happens in developing countries.”

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