Impact of Archaic Introgression in the X Chromosome in Southeast Asian and Near Oceanian Populations

Denisovans and Neanderthals are our most closely related species, with evidence we interbred with them now being widely supported by genetic studies. However, little focus has been placed on Southeast Asian and Near Oceanian populations, despite evidence suggesting these populations have the highest level of Denisovan admixture. In this study we aim to advance our understanding of archaic admixture with Denisovans and Neanderthals in the X chromosomes of Southeast Asian and Oceanian populations. We observe variable levels of admixture in X chromosome data from Papuan, Filipino, Thai and Taiwanese individuals, from undetectable signal to approximately 2% Denisovan and 2,5% Neanderthal ancestry as identified by SPrime. These segments are predominantly located in the intergenic and intronic regions according to ANNOVAR, although low levels of archaic admixture can also be identified in protein-coding regions. Notably, these regions were identified by KEGG as being primarily associated with pathways involved in cancer, infection and immunity, suggesting that admixture events may have played a role in the diversification of the immune system of modern humans. We propose future studies to determine whether selection or genetic drift is responsible for the retention of these regions in present-day populations. Additionally, we recommend a more detailed investigation of how the methodological approaches for detecting archaic segments may impact the results in these types of studies.