The role of artificial intelligence in identifying the footprint of an extinct human species

In his 2005 New York Times Bestseller Sapiens, Yuval Noah Harari posited that, no one "... knows how many lost relatives of ours are waiting to be discovered ..." And recent scientific findings are showing his prescience.

Homo sapiens was known to have encountered Homo neanderthalis on their Out-of-Africa journey (which commenced approximately 80,000 years ago) because a number of non-Africa-resident human populations have 2% (on average) Neanderthal DNA in their genomes. According to a Max Planck Institute for Evolutionary Anthropology study, DNA from Neanderthals may be influencing skin tone, ease of tanning, hair color, and sleeping patterns of present-day Europeans. Current-day Africans have very little Neanderthal DNA in their genes as they did not make the trek through Eurasia.

In 2010 a previously unknown human species was discovered as a result of DNA analysis on a  fossilized finger fragment found in the Denisova Cave in Siberia. The cave is known to have been occupied by Neanderthals but the analysis showed the fragment belonging to a hitherto unknown species, a species that was eventually named Homo denisova. Comparison of the Denisova reference data to human population genomes shows Denisovan DNA resident in some current Asian human populations.

John D. Croft at English Wikipedia [CC BY-SA 3.0
(https://creativecommons.org/licenses/by-sa/3.0)]

A more recent study compared 5,500 genomes of modern humans living in Europe, Asia, and Oceania looking for the presence of archaic DNA. The findings were as follows (Browning, et al.):

• All groups had clusters of Neanderthal DNA that matched Altai Neanderthal DNA
• Some populations had DNA clusters that matched the Altai Denisovan DNA
• There was a third DNA cluster that was unlike the Neanderthal DNA and only partially resembled the Denisovan DNA.

The authors concluded, based on the foregoing, that ancestral humans encountered, and mated with, two separate groups of Denisovans, providing two infusions of Denisovan DNA into the human genome. The hypothesis is that the first infusion occurred in present-day China, Japan, and Vietnam while the second infusion was taken on by the humans who continued into Southeast Asia. The impact of Denisovan DNA in modern-day humans is realized in the immune system and fat and blood sugar levels.

Analysis of a recent skeletal fragment from a 13-year-old girl who died 50,000 years ago showed that she had a Neanderthal mother and a Denisovan father, proof that these two species had interbred (Scientists surmise that Denisovans and Neanderthals diverged 390,000 years ago into distinct but closely related populations.).

She was not alone. A recent artificial-intelligence-driven study has identified the DNA footprint of an extinct hominid who interbred with ancestors of current-day Asiatics. The AI analysis posits that this extinct species is a Neanderthal-Denisovan hybrid; in other words a species with a DNA profile similar to that of the 13-year-old girl mentioned in the preceding paragraph.

The techniques used to ferret out the above information is called Deep Learning. According to the Center for Genomic Regulation:

Deep Learning is an algorithm that imitates the way in which the nervous system of mammals work, with different artificial neurons that specialise and learn to detect, in data, patterns that are important for performing a certain task. ... "We have used this property to get the algorithm to learn to predict human demographics using genomes obtained through hundreds of thousands of simulations. Whenever we run a simulation, we are traveling along a possible path in the history of humankind."

If the foregoing findings are borne out, a previously unknown, extinct human species will have been surfaced, much as Sapiens predicted.

Bibliography
Sharon Browning, et al., Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture, Cell, March 15, 2018.
Center for Genomic Regulation, Artificial Intelligence applied to the genome identifies an unknown human ancestor, Press Release.
Peter Doehill, Artificial Intelligence has found an Unknown Ghost Ancestor in the Human Genome, Science Alert.
Ben Guarino, Ancient Humans had sex with more than just Neanderthals, Scientists find, Washington Post, 11/11/19.
Yuval Noah Harari, Sapiens: A Brief History of Humankind, Harper Collins, 2015.
Greta Jochem, Neanderthal Genes Help Shape How Many Modern Humans Look, NPR, 10/5/2017.
Michelle Starr, This Ancient Teenager had Parents from Two Different Species, ScienceAlert, 8/22/18.


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