Sequence Divergence in the MtDNA Control Region of Amphidromous and Landlocked Forms of Ayu

Abstract

We investigated mitochondrial DNA divergence for amphidromous and landlocked forms of ayu Plecoglossus altivelis to describe their genetic status and search for genetic markers discriminating the two forms. The first half of the control region was sequenced for 60 fish, 15 individuals from each of 2 amphidromous and 2 landlocked populations. These sequences were found to be highly variable, suggesting their utility for the analysis of intra-specific divergence. The landlocked form was genetically more homogeneous than the amphidromous form in terms of the number of polymorphic sites and the magnitude of nucleotide diversity. Intra-form net nucleotide substitutions were 0.024% in the landlocked and -0.062% in the amphidromous, showing that intra-form genetic differentiations were small. In contrast, inter-form net nucleotide substitutions were considerably higher, 0.241-0.527%, indicating some genetic heterogeneity in the mitochondrial genome between the two forms. Nearly 80% of fish were distinguishable as amphidromous or landlocked by the nucleotide substitutions at hyper-variable sites.