Additional file 8.

Supplementary figure S5. Comparisons of the evolutionary distances by two methods. Number of non-synonymous substitutions per non-per synonymous site (dS). Panel A: Distance method modified Nei-Gojorbori(JC) k = 2.5; panel B: ML method the codon model (pairwise). The estimated synonymous substitution reached plateau from the analysis by Nei Gojobori method. However there was no such tendency from the analysis by the maximum likelihood method. It means that although there were many multiple substitutions at the synonymmous sites, the maximum likelihood effectively correct the numbers of the multiple substitutions.

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Watanabe et al. BMC Evolutionary Biology 2011 11:322   doi:10.1186/1471-2148-11-322