Abstract
Landlocked ayu stocks in the Biwa Lake system were investigated using a mitochondrial DNA marker to evaluate their genetic structure. Samples examined consisted of spring migrants (o-ayu), fall migrants (ko-ayu), and juvenile residents in the lake at a predifferentiated stage. Compared to amphidromous fish, the landlocked fish, overall, were characterized by a lower genetic diversity that has resulted from lower haplotype diversity and a higher similarity in nucleotide sequences between haplotypes. Some nucleotide diversities that were unique to the samples showed that the landlocked ayu are not genetically homogeneous, suggesting the occurrence of a single metapopulation throughout the Biwa Lake system. The pairwise fixation index inferred different respective local populations for the o-ayu and ko-ayu ascending the same stream in the same year class, as well as the isolation by distance among local populations of ko-ayu. For conservation practices during transplantation with fish from non-native stocks, it should be taken into account that the Biwa Lake stocks have a high probability of not being genetically uniform.
