We have analyzed the sequence divergence amongst the three species that is, gorilla, chimpanzee and human varying from Hominidae and Pongidae. Apart from the genomic phylogeny, we compared the protein and rRNA phylogenies to increase the importance of phylogenetic analysis. The proteins selected are from the mitochondrial origin as mtDNA which codes for mitochondrial proteins, mutate at a higher rate compared to nuclear DNA, so as to give a more useful, magnified view of the diversity present in a population, and its history. The phylogenetic analysis of the mitochondrial genome, rRNA and proteins are done using parsimony, BIONJ and PHYML methods which $resulted into variable results. The proteins that were able to infer the already stated phylogeny between these members were ATP synthase subunit 6 and 8, cytochrome b, cytochrome oxidase subunit 1 and 3 and NADH dehydrogenase subunit 2, 3 and 5. Although BIONJ and PHYML methods predicted similar results most often parsimony was found to be predicting contradictory phylogeny with respect to above two methods. To verify the results as obtained from various methods and to further analyze the evolutionary relationship between these members, we applied the method of calculating sequence divergence using bioinformatics tools. Taking into account that local point mutations generate a considerable genetic variation and this variation being very high in mitochondrial DNA, we analyzed the sequence divergence between these three species using 0, ±1 and ±2 error in identical cut sites by different restriction enzymes. No identical site between chimpanzee-human clade at different errors indicated gorilla to be common ancestor of these two members. At ±2 error, an identical sequence divergence was obtained between the chimpanzee-gorilla and human-gorilla clades but overall results suggest chimpanzee to be a closer relative of gorilla than human.
Key words: Sequence divergence, In silico restriction digestion, phylogeny.
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