Impact of mitochondrial epistatic interactions on evolution of different human subpopulations

Studies of human mitochondrial (mt) genome variation may be undertaken to investigate the human history and natural selection. By analyzing nucleotide co-occurrence over the entire human mt-genome, we have developed a network model to describe human evolutionary patterns. Using 7,424 unique polymorphic sites, we found evidence that mutation biases at second codon position and RNA genes were critical to producing continental-level heterogeneity among human subpopulations. Further, the analysis highlighted richer co-mutation regions of the mt-genome and thus provided evidence of epistasis. Specifically, a large portion of COX genes co-mutate in Asian and American populations whereas, in African, European and Oceanic populations, there was greater epistasis in hypervariable regions. Very interestingly, this study demonstrated hierarchical modularity as a crucial agent for a nucleotide co-occurrence network make-up. More profoundly, our ancestry-based nucleotide module analyses showed that nucleotide co-changes cluster preferentially in known mitochondrial haplogroups. It was also conceived that contemporary human mt-genome nucleotides most closely resembled the ancestral state and very few of them were ancestral-variants. Overall, these results demonstrated that subpopulation based factors such as intra-species evolution do exert selection on mitochondrial genes by favoring specific epistatic genetic variants.