DNA Analysis Reveals Ancient Humans Interbred with Denisovans Twice

Enter bachelor number two.

Whether we want to accept it or not, our fossil record shows that ancient humans regularly mated with Neanderthals. We now know that most non-Africans have at least a little bit of Neanderthal DNA, which is partially responsible for their unique habits and looks. On Thursday, however, scientists reported in Cell that our ancient history is even more scandalous than we thought. Neanderthals, it seems, weren’t the only other hominins that anatomically modern humans decided to screw.

Enter bachelor number two: the Denisovan.

The study shows that interbreeding with Denisovan hominins wasn’t an isolated affair, either. It was at least a two-wave event that happened in East Asia and Oceania. Before this study, scientists already knew that the genomes of Aboriginal people in Australia and Papua New Guinea contain fragments of Denisovan DNA. The new study shows there are uniquely different Denisovan genomes in the DNA of East Asian individuals, indicating that interbreeding with Homo sapiens happened in two independent episodes.

“In this work with East Asians, we find a second set of Denisovan ancestry that we do not find in the South Asians and Papuans,” senior author and University of Washington biostatistician Sharon Browning, Ph.D., explained in a statement released Thursday. “This Denisovan ancestry in East Asians seems to be something they acquired themselves.”

Artist rendering of ancient hominin breeding.

Browning et al.

Browning, along with a team of scientists from the University of Washington and Princeton University, came to this conclusion by comparing 5,600 whole genome sequences from people who live in Europe, Asia, Oceania, and the Americas to the Denisovan genome, pieced together from DNA extracted from the pinkie bone of a young Denisovan girl discovered in Siberia in 2008. In 2010, scientists who sequenced her genome declared she belonged to a group of archaic humans closely related to Neanderthals. Today, her genome is the reference point for all Denisovan ancestry.

In the current study, pieces of DNA from the Papuans matched with the Denisovan genome, but the DNA extracted from Han Chinese, Chinese Dai, and Japanese were a “much closer match.” This means that the Denisovan genome is more closely related to the modern East Asian population than to modern Papuans, although both do share Denisovan ancestry.

The Denisova cave, where the remains of the Denisovan girl was found.

Max Planck Institute

Browning concluded that two distinct Denisovan populations mated with humans. Both of these populations mated with the ancestors of East Asians, but one population mated with the ancestors of South Asians and Oceanians. The team assumes these hookups happened pretty soon after humans left Africa around 50,000 years ago, but they don’t know where it happened first. The fact that the Denisovan girl was found in Siberia but rare remnants of Denisovan DNA are found throughout Asia suggests the species ranged widely, but their population numbers were never very high.

Now, Browning and her team want to study more Asian populations, Africans, and Native Americans to seek out more Denisovan DNA.

“We want to look throughout the world to see if we can find evidence of interbreeding with other archaic humans,” says Browning. “There are signs that intermixing with archaic humans was happening in Africa, but given the warmer climate no one has yet found African archaic human fossils with sufficient DNA for sequencing.”

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