Artificial Intelligence Finds Ancient ‘Ghosts’ in Modern DNA

Could deep learning help paleontologists and geneticists hunt for ghosts?

When modern humans first migrated out of Africa 70,000 years ago, at least two related species, now extinct, were already waiting for them on the Eurasian landmass. These were the Neanderthals and Denisovans, archaic humans who interbred with those early moderns, leaving bits of their DNA behind today in the genomes of people of non-African descent.

But there have been growing hints of an even more convoluted and colorful history: A team of researchers reported in Nature last summer, for instance, that a bone fragment found in a Siberian cave belonged to the daughter of a Neanderthal mother and a Denisovan father. The finding marked the first fossil evidence of a first-generation human hybrid.

Unfortunately, it’s very rare to find such fossils. (Our knowledge of Denisovans, for instance, is based on DNA extracted from a mere finger bone.) Many other ancestral pairings could easily have transpired, including ones that involved hybrid groups from earlier crosses — but they might be practically invisible when it comes to physical evidence. Clues to their occurrence may instead survive only in some people’s DNA, and even then, they may be subtler than the signs of Neanderthal and Denisovan genes there. Statistical models have helped scientists infer the existence of a couple of these populations without fossil data: ..Read More..

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