Scientific discoveries are always an exciting accomplishment. Recently, Nature Ecology & Evolution published a landmark study on resurrecting the alternative splicing landscape of archaic hominins using machine learning. This study used SpliceAI, a computer-based system to analyse high-coverage genomes from three Neanderthals and a Denisovan in order to detect putative archaic splice-altering variants (SAVs). The researchers identified 5,950 SAVs, of which 2,186 were those specific to the archaic hominins and 3,607 were shared with modern humans through introgression and shared ancestry.
The investigators observed that the archaic-specific SAVs were enriched in genes that were associated with adaptations such as the epidermis, respiration and spinal rigidity. Contrary to that, the shared SAVs occurred in sites under greater negative selection. Furthermore, the authors noticed that SAVs were more common in Neanderthal populations with lower effective population sizes in comparison to Denisovan and shared SAVs. All of this evidence point to the fact that splicing plays a major role in the phenotypic differences between the ancient and modern hominin species.
In addition to the details of the study, one of the authors, Dr. David Reich, is a professor at Harvard Medical School, a Howard Hughes Medical Institute Investigator, and a member of the US National Academy of Sciences. Dr. Reich is an expert in human population genetics, archaeogenetics, and climate change. He has pioneered numerous advancements in the field of human evolution, including the discovery of Neanderthal gene flow into modern Europeans.
The scientists hope that their findings will help to elucidate further the evolutionary process that hominins underwent in order to adapt and survive in their respective environments. This research is particularly important due its implications in the study of diverse medical conditions. The findings of this research open up the potential to assess how the process of splicing contributes to genetic differences between hominins and potentially leads to the better understanding of certain diseases.
