Footprint of new human ancestor detected by AI: All you need to know

A new AI-driven investigation into the genome of Asian populations has led to the discovery of what is believed to be a previously unknown human ancestor, which heightens the possibility that ancient species were interbreeding with modern humans millennia ago. The findings, in other words, show that humans had descendants with a species that is unknown to us.

Researchers have identified the footprint of a newly identified extinct hominid using a deep learning algorithm, which assisted in the understanding of its genetic structure.

According to the deep learning analysis of modern DNA material, it appears that two different species of human ancestor, the Neanderthal and Denisovan populations, had interbred to create this new hominid, which likely went on to breed with modern humans.

The team behind the study

Researchers used artificial intelligence and deep learning for the first time ever to account for human evolution, paving the way for the application of this technology in other questions in biology, genomics and evolution.

Conducted by the Institute of Evolutionary Biology (IBE), Centro Nacional de Análisis Genómico (CNAG-CRG) of the Centre for Genomic Regulation (CRG), and the Institute of Genomics at the University of Tartu, the latest discovery followed in the heels of a similar one concerning an offspring of a Neanderthal mother and Denisovan father. Both these populations are believed to have existed with modern humans 40,000 years ago in Eurasia.

Mayukh Mondal, an investigator from the University of Tartu, says, ‘Our theory coincides with the hybrid specimen discovered recently in Denisova,’ suggesting that such hominid hybrids may not have been all that uncommon after all. The latest research, published in Nature Communications, suggests that it wasn’t an isolated case but part of a more general introgression process.

AI and human evolution

The algorithm has helped pinpoint the transitions from DNA to the demographics of ancestral populations, which until recently, were difficult to explain. The origin of fragments within the human genome suggests the existence of a third ancestor, with the larger implication that intermingling took place tens of thousands of years ago.

The algorithm ‘imitates the way in which the nervous system of mammals works, with different artificial neurons that specialize and learn to detect, in data, patterns that are important for performing a given task,’ explains Òscar Lao, principal investigator at the CNAG-CRG.

‘Whenever we run a simulation we are travelling along a possible path in the history of humankind.

Implications on evolutionary theories

The ancient hominid has reportedly existed since ages, before breeding with modern humans arriving in Asia after the ‘Out of Africa’ migration about 80,000 years ago. This offered a watershed moment in the history of human population, causing half the world’s modern humans to abandon the African continent and migrate to other continents, giving rise to all the current populations, according to Jaume Bertranpetit, principal investigator at the IBE and head of Department at the UPF.

Although theories concerning cross-breeding with the Neanderthals (in all continents except Africa) and with the Denisovans (in Oceania and probably in South-East Asia) have existed for a while, the ‘evidence of cross-breeding with a third extinct species had not been confirmed with any certainty,’ he said. Further studies will prove if deep learning can make sense of the ancestral puzzle, which is currently a potpourri of unexplained theories and conjectures.

The most popular theory involves one which believes that the migration from Africa took place in a single wave, 60,000 years ago. This was presumably followed by a brief period of interbreeding with the Neanderthals, and came to explain why Europeans and Asians have ancient human DNA. But there is contention over what drove the Neanderthals to extinction, with theories ranging from tropical diseases carried by the African migrants, climate change, and competition over for survival.

Another school of thought believes that the migration occurred in several phases beginning 120,000 years ago. The recent discovery of a prehistoric ancestor we didn’t know about yet, may throw more weight behind this theory which proposes that different species developed into modern humans in several places at once.

Prarthana Mitra is a staff writer at Qrius

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