| Estimating nonsynonymous (Ka) and synonymous (Ks) substitution rates is of great significance in reconstructing phylogeny and understanding evolutionary dynamics of protein-coding sequences across closely related and yet divergent species. Since Ka and Ks represent the numbers of substitutions per nonsynonymous and synonymous site, respectively, the Ka/Ks ratio (denoted as ω) is widely used to detect selective pressure acting on protein-coding sequences. Because of the long time spent in accumulating nucleotide variants, those variants could not be observed easily in a short period. Early studies using this criterion took the approach of pairwise sequence comparison, averaging dS and dN over all codons in the gene sequence and over the whole Neutral and adaptive protein evolution time period separating the two sequences. However, one may expect most sites in a functional protein to be constrained during most of the evolutionary time. Positive selection, if it occurs, should affect only a few sites and occur in an episodic fashion. Thus the pairwise averaging approach rarely detects positive selection.Ka/Ks ratio of the orthologs between human, chimpanzee, and mouse was calculated, which was regarded as a criterion to filter out exons that may be under positive selective pressure. Furthermore, protein functional domain prediction was constructed to determine whether every individual exon encode domain or not. Therefore, we got a exon list in which were exons under positive selection and encoding functional domain. LY96 was selected for in-depth analysis, we compared coding sequences from 13 vertebrates and evaluated the molecular evolution of LY96 gene in these species and concluded that natural selection at exon4 has indeed played a role in shaping the function of LY96 in the course of evolution. Two branch nodes with Ka/Ks ratios greater than 1 were observed:the one leading to cow and pig, and the other to rabbit and the primates. |
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