Phylogenetic relationship among the section Stenophora in the genus Dioscorea based on the analysis of nucleotide sequence variation in the phosphoglucose isomerase(Pgi)locus

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To determine the phylogenetic relationship of six species (Dioscorea gracillima, D. nipponica, D. quinqueloba, D. septemloba, D. tenuipes, and D. tokoro) in the section of Stenophora in the genus of Dioscorea, nucleotide sequence variation in 1073 bp of coding region of the phosphoglucose isomerase (Pgi) locus was analyzed. Estimates of nucleotide diversity (π) for D. gracillima, D. quinqueloba, D. tenuipes, and D. tokoro were 0.0020, 0.0005, 0.0025, and 0.0013, respectively. Deviation from neutrality in the pattern of polymorphism in these four species was not detected by the Tajimas test. The difference in the pattern of amino acid substitutions between divergence and polymorphism was not observed by McDonald and Kreitman test. The obtained phylogenetic trees indicated that D. tokoro and D. tenuipes belonged to a monophyletic clade, while the other four species formed a separate monophyletic group. The branch lengths of phylogenetic tree varied among species. D. nipponica had a significantly faster substitution rate compared to D. gracillima, D. quinqueloba, and D. septemloba.
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