AI Finds Traces of a Lost Species in Human DNA

Buried deep within the DNA of Asian individuals is a genetic clue pointing to the existence of an unknown human ancestor. Remarkably, it wasn’t a human who reached this startling conjecture, but rather an artificially intelligent algorithm. Welcome to archaeology in the 21st century.

New research published last week in Nature Communications suggests a yet-to-be discovered hominid interbred with modern humans tens of thousands of years ago. This mystery species eventually went extinct, but an AI developed by researchers from the Institute of Evolutionary Biology (IBE) and several other European institutions found traces of its existence in the DNA of present-day people with Asian ancestry. A press release issued by the Centre for Genomic Regulation said it’s the first time deep learning has been used to explain human history, “paving the way for this technology to be applied in other questions in biology, genomics and evolution.”

The mystery hominid is likely a hybrid species of Neanderthals and Denisovans, according to the new research. Neanderthals, who lived in Europe, and Denisovans, who spread to Siberia, southeast Asia, and Oceania, were a closely related group of early humans, diverging from a common ancestor around 744,000 years ago. When anatomically modern humans (Homo sapiens) spilled into Eurasia from Africa, they commingled and interbred with both Neanderthals and Denisovans, which we know through genetic research. In addition to the generous amount of DNA left behind by the Neanderthals, scientists have extracted Denisovan DNA from a well-preserved finger bone found in a Siberian cave. Today, we find traces of these extinct species in the DNA of non-African humans, though only Asians retain genetic remnants of the Denisovans.

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