As is well known, our ancestors once mixed with their archaic relatives. This is now also becoming apparent in the gorillas, researchers report: the genome of the eastern lowland gorillas and mountain gorillas bears traces of hybridization with a lineage of these great apes that is now extinct. Genetic evidence also suggests that certain hereditary traits of these "ghost ancestors" gave the gorillas survival advantages after introgression, the scientists say.
In a way, they live on in us: Studies in recent years have shown that when Homo sapiens met his cousins who still existed at the same time, there was interbreeding. Clear traces of the genome of Neanderthals or Denisovans in the genome of some of today's human groups bear witness to this. It is also becoming apparent that the former crossings could have had a positive effect on the genetic profile of the people. Could something similar happen to our closest relatives in the animal kingdom? In the case of the pygmy chimpanzee - the bonobo - scientists have already discovered evidence of a genetic influence of an extinct lineage in the genome. An international team of researchers is now demonstrating this in gorillas as well.
Trace genes of a "ghost population"
This group of great apes is made up of two species - the western and eastern gorillas. Both also have subspecies: Western gorillas include western lowland gorillas and Cross River gorillas. The second species includes the eastern lowland gorillas and the closely related mountain gorillas. For the study, the researchers have now subjected the genome of all four subspecies to a special analysis technique. Among them were newly sequenced mountain gorilla genomes from Bwindi National Park in Uganda. Innovative statistical methods and artificial intelligence were used to uncover peculiarities in the genome sequences. Based on certain characteristics, it is also possible to draw conclusions as to when certain genetic changes occurred.
As the researchers report, they actually found traces of “archaic” elements in the genomes of the eastern lowland gorillas and the mountain gorillas. According to the genetic evidence, they entered the genome of the common ancestor of both subspecies about 40,000 years ago. The studies showed that this gene flow apparently did not exist in the ancestors of the western gorillas.
However, it remains unclear which extinct gorilla representative the contribution came from. In contrast to their human cousins - the Neanderthals and Denisovans - there is no ancient DNA from extinct relatives for comparison purposes in the great apes due to a lack of corresponding fossil records. As the team reports, however, the genetic characteristics at least allow conclusions to be drawn as to how old the "ghost lineage" was: it had separated from the common ancestors of all modern-day gorillas more than three million years ago. Sometime later, the ancestors of the eastern gorillas encountered these archaic relatives and mated with them - similar to the case of humans and Neanderthals. "As a result, up to three percent of the genomes of today's two eastern gorilla groups now carry remnants of genes from this "ghost population," says senior author Martin Kuhlwilm from the University of Vienna.
Gene flow with an enriching effect?
As the scientists continue to report, they have also found indications that the former crossbreeding could have done the eastern gorillas genetically good. They say this is exemplified by a gene introduced by the ghost population that encodes a specific bitter taste receptor. This hereditary disposition also shows signs of positive selection after transmission. As the researchers explain, this gene could have helped the two eastern gorilla subspecies avoid certain bitter-tasting poisonous plants in their habitat. "Eastern gorillas typically feed more on plants than westerns, on the other hand more on fruits, so taste receptors in eastern gorillas are plausible targets of adaptive introgression," the scientists write.
On the other hand, it also seems possible that certain hereditary traits of the ghost population were superfluous or even had an unfavorable effect on the crossbreed offspring. As the team reports, it is becoming apparent that the corresponding genetic material has been eliminated from the X chromosome over time: The analysis data shows that this genetic material carrier in the eastern gorillas has very little DNA from the ghost population. Thus, the X chromosome in particular appears to have been subject to negative selection. Interestingly, this has also become apparent in humans and other species. A possible reason for this is that this genetic material carrier is only present in male individuals in contrast to the others in one copy. Therefore, unfavorable gene variants can have a stronger effect, the researchers explain.
Finally, the scientists once again emphasize the importance of the study: "The history of interbreeding with groups that are now extinct in various species such as humans, bonobos and now also gorillas is an important aspect of evolution, about which we have now gained new knowledge". First author Harvinder Pawar from the Institute for Evolutionary Biology in Barcelona adds: "Evolutionary genetics is important so that we can learn more about what differentiates us humans from other great apes," says the scientist.
Source: University of Vienna, specialist article: Nature Ecology and Evolution, doi: 10.1038/s41559-023-02145-2