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In Human Genome, AI Discovered Unknown ‘Ghost’ Ancestor

Nobody knew who she was; all they knew was that she was unique. Scientists have never before encountered a teenage girl from more than 50,000 years ago who was so oddly distinctive that she seemed to be a hybrid ancestor to modern humans.

Only recently have scholars found proof that she wasn’t alone. In a 2019 study examining the complex prehistory of humanity, researchers used artificial intelligence (AI) to pinpoint an unidentified human ancestor species that modern humans may have encountered and interacted with during the protracted journey out of Africa thousands of years ago.

According to evolutionary biologist Jaume Bertranpetit of the Universitat Pompeu Fabra in Spain, the so-called Out of Africa event took place about 80,000 years ago when a portion of the human population, which already included modern humans, left the African continent and migrated to other continents, giving rise to all the current populations. Modern humans also fashioned other things by mating with ancient and extinct hominids from other species as they carved their way into the continent of Eurasia.Do humans have a 'ghost' ancestor? Artificial intelligence thinks so. - Genetic Literacy Project

Until recently, it was assumed that Neanderthals and Denisovans, the latter discovered in 2010, were these sporadic sexual partners. But in this study, deep learning algorithms combed through a complex mass of ancient and present human genetic code, isolating the third exon from a long time ago in Eurasian DNA.

The researchers discovered proof of what they term a “third introgression, a “ghost” archaic population that modern humans interbred with during the African exodus using the statistical method known as Bayesian inference. According to the researchers’ conclusions in their paper, This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage, suggesting that the third population in the sexual history of humanity may have been a hybrid of Neanderthals and Denisovans.

Although there is still work to be done and the study projects themselves aren’t directly related, it can be said that the teenage girl “hybrid fossil” discovered in 2018 is hypothetically supported in some ways by the deep learning approach. In a press release at the time of discovery, genomicist Mayukh Mondal from the University of Tartu in Estonia, one of the team members, said, “Our theory coincides with the hybrid specimen discovered recently in Denisova, although as yet we cannot rule out other possibilities.”

New scientific discoveries made at rapid rate

In addition to Denisovans and Neanderthals, a third group of researchers found evidence of what they called a “definite third interbreeding event” in 2018. A pair of papers released in early 2019 traced the timeline of how those extinct species intersected and interbred with more clarity than ever before.

There is still a ton of study to be done in this area. In the study of human lineage, using this kind of AI analysis is a distinctly novel technique, and the known fossil material we’re dealing with is remarkably scarce.
According to the study, however, what the team has discovered explains more than just a long-forgotten introgression process; it’s a dalliance that, in its own unique way, contributes to who we are now.

In the genome, Bertranpetit and his team thought we’d try to find these places of high divergence, see which are Neanderthal and which are Denisovan, and then see whether these explain the whole picture. In fact, even after removing the Neanderthal and Denisovan components, the genome still contains some highly divergent regions.


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