We used to think that the evolutionary history of hominids is linear with different species coming and going until the modern man emerged. Of course, the more we discover about our ancestors, the clearer it becomes that mankind's evolutionary history is anything but linear. In recent studies, scientists (by sequencing genomes in 2010 and 2014) were able to discover clues of swapped segments of DNA that we shared with ancient species of humans through mating. This discovery opened a lot of opportunities for further studies especially in finding out how much of our hominid relatives remain in each of us today or if the presence of ancient hominid DNA gave any advantages or disadvantages in adaptation.
In recent studies, it was proven that ancient hominid genes can give adaptation advantages such is the case of high-altitude adaptation of people from Tibet which they inherited directly from the ancient Denisovans. This is a classic case of a DNA swapping or genomic introgression.
READ: From Lucy to Lola: Human Evolution Has Gone A Long Way and So Is Our Understanding of Our Origins
However, in cases of dealing with diseases, unpacking the contributions of ancient hominid DNA is quite a difficult task for scientists. In a new study published in Molecular Biology and Evolution, Alexandre Gouy and Laurent Excoffier developed new computational tools for analyzing human genome datasets. Through these new computational tools, scientists were able to find more evidence of adaptation genomes received from our hominid ancestors particularly to fight infectious diseases like malaria. The authors explained that their findings confirm that the archaic genome introgression is widespread in immunity-related genes and that the pathogens represent a strong selective pressure which can be one of the major reasons for adaptive evolution in humans. The archaic introgression, according to scientists behind this study, also affected human metabolism and the ability to respond to different types of pathogens may it be bacteria, viruses, or protists.
Gouy and Excoffier analyzed the latest archaic introgression maps that are recently made available based on samples from the 1000 Genomes project and 35 Melanesian individuals. According to Gouy, the results of the analysis not only showed that introgression is found in genes with the same functions but also showed that some of these introgressions are co-selected.
Instead of analyzing these genes individually, the duo focused on developing methods that will detect patterns of introgression that are based on biological pathway analysis and data sets of connected genes and subnetworks. Using the methods enabled the duo to identify highly introgressed subnetworks among three primary biological pathway databases: KEGG, NCI, and Reactome. They also identified highly introgressed networks among East Asians, Europeans, and Papua New Guineans. Excoffier explained that one of the most striking evidence of adaptive introgression is the high possibility of malaria resistance among Papua New Guineans.
Aside from resistance to infectious diseases, Gouy and Excoffier were able to find evidence of introgression in genes that are related to porphyrins involved in the respiratory chain and the binding of iron and oxygen in red blood cells and muscles. Neanderthal introgression among European populations is found in the olfactory receptors as well. The authors also tackled the controversial topic of modern human behavior and cognition, albeit with caution, and explained that although their study is still preliminary, there is evidence of introgression among gene networks that are involved in behavior and cognition.
The results of their study are based on earlier studies that are able to identify Neanderthal variants present at two SLC loci. These variants are previously associated with behavioral traits such as depression, mood disorders, and smoking. Gouy narrates that they have found genes showing an excess of introgression that are associated with susceptibility to autism and attention-deficit/hyperactivity disorder or ADHD. However, findings in this area are still incomplete and further explorations will be needed to identify their contributions to human health and disease.
Although these introgressions with Neanderthal and Denisovan genome are low in modern humans, their presence continues to build the case that the ancient hominid DNA that remains in the system of modern humans has helped them in adapting to their environment.
