DNA Study Reveals We Have a Mystery Human Ancestor

A new method for analyzing modern and archaic human DNA has thrown up some fascinating results. It appears that modern humans ( Homo Sapiens ) mated earlier and more frequently with an archaic human ancestor, a species of extinct hominins. Moreover, they have found evidence the DNA of this mysterious archaic human ancestor is still part of our modern human genetic inheritance.

An American team of scientists, from leading American universities, embarked upon an ambitious plan to map the flow of genes between different species of hominids.  Gene flow is an indication of interbreeding between ancient human species. A new algorithm, known as ARGweaver-D, was developed by Melissa J. Hubisz to achieve the goals of the project. This algorithm allowed researchers to develop a model of the lineages of early humans. Adam Siepel, who took part in the study, stated that “We are trying to build a complete model for the evolutionary history of every segment of the genome, jointly across all of the analyzed individuals” according to Live Science .

Our Mysterious Archaic Human Ancestor and Extinct Humans

During the study, researchers compared the genomes of two Neanderthals, a Denisovan and two modern African individuals. The Neanderthals ( Homo neanderthalensis ) were an extinct species of humans that died out about 30000 years ago, and once inhabited vast areas of Eurasia. Denisovans are a mysterious species, only known through their DNA, who probably ranged across an area that covered Siberia and East Asia. The samples from modern Africans were selected because they are known not to have Neanderthal nor Denisovan genes.

The spread and evolution of Denisovans (John D. Croft / CC BY-SA 3.0)

The spread and evolution of Denisovans (John D. Croft / CC BY-SA 3.0 )

Based on the ground-breaking algorithm the researchers were able to develop an ancestral recombination graph, which “includes a tree that captures the relationships among all individuals at every position along the genome, and the recombination events that cause those trees to change from one position to the next,” Siepel told Live Science . The team were able to build up a picture of the extensive interbreeding between different species of hominids and gain insights even into their migration patterns.

DNA Reveals Our Mysterious Archaic Human Ancestor

The researchers wrote in PLOS Genetics that they ‘estimate that the gene flow occurred between 200-300 kya,’ which is 200,000 or 300,000 years ago. And research has already shown that modern humans, Denisovans, Neanderthals interbred in the ancient past. However, using the new algorithm, researchers were able to show that this interbreeding occurred much earlier than once believed. It seems likely that anatomically modern humans left Africa and migrated to Eurasia in an early wave and mated with Neanderthals, before they returned to Africa or died out.

The results from a sample of Denisovan DNA were remarkable. Inverse.com states that the ‘genome contained genetic material that came from an unexpected source – an archaic human ancestor that was neither human, nor Neanderthal, nor Denisovan.’ This was a mystery. Researchers have theorized that the genes may have come from Homo Erectus . An extinct hominin who emerged in Africa about two million years ago, Homo Erectus was the first archaic human to use fire and migrate out of Africa.

The Mystery of Homo Erectus

However, the “story” of Homo Erectus is unproven because we do not have any DNA from this long-extinct human species. Siepel told Live Science that “the genome of that extinct species of human has never been sequenced.” As a result, there is much we still don’t know about human evolution, including if H. Erectus (upright man) is our ancestor. It is also possible that the mysterious DNA found ‘nested’ in the genome sequences comes from a new and unknown archaic human ancestor species.

A reconstruction of Peking Man or Homo erectus pekinensis, a specimens of Homo erectus found in China dating from roughly 750,000 years ago. (Cicero Moraes / Public domain)

A reconstruction of Peking Man or Homo erectus pekinensis, a specimens of Homo erectus found in China dating from roughly 750,000 years ago. (Cicero Moraes / Public domain )

The new research indicates that the human tree is much more complex than first thought. Hundreds of thousands of years ago there were four species of humans and they interbred. It appears that the ranges of our archaic human ancestors overlapped and that because of their regular migrations they often mated with different human species. The study also shows the importance of migration in the evolution of both archaic and modern humans.

Modern Humans Are The Result of Multiple Hybrid Offspring

Siepel told Live Science that “A picture is emerging of a series of distinct but related populations moving around the globe and frequently interacting with one another, with occasional interbreeding events that produced hybrid offspring.” It is not known if these hybrids were fit enough to survive and have offspring. It seems likely that at least some survived and this accounts for the distinctive genetic inheritance of many groups. For example, Tibetans and Pacific Islanders show traces of Denisovan DNA.

These interbreeding events were very important in the evolution of modern humans.  Science Daily reports that “15% of these ‘super-archaic’ regions may have been passed down to modern humans.’’ This means that genes which flowed between different archaic human species are still part of modern people’s genetic make-up, including those from an unknown archaic human ancestor.

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Clearly, the newly developed algorithm can help researchers to delve deeper into the evolutionary history of archaic and modern humans. Siepel told Science Daily that “It seems to be especially powerful for detecting ancient introgression” or interbreeding between species. For example, the algorithm can be adapted to help experts to understand mating occurrences between prehistoric wolves and dogs. So far, this powerful algorithm has already shown the we modern humans likely have an archaic human ancestor who is still unknown and unnamed.

Top image: Male and female Neanderthals were one of our ancestors, but recent DNA research suggests we also have a mysterious archaic human ancestor.  Credit: Gorodenkoff / Adobe Stock

By Ed Whelan

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