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Sequence analyses of the non-coding, control region (CR) and coding region of the ND4-tRNA(Ser) genes in the mitochondrial DNA (mtDNA) were conducted for populations of the ayu Plecoglossus altivelis altivelis and the Ryukyu-ayu P. a. ryukyuensis. The level of genetic differentiation between the two subspecies evaluated from the CR data was substantially low, when comparing with that estimated from ND4-tRNA(Ser) gene region data, as well as those from nuclear genome data sets. By contrast, the differentiation between subspecies in the ND4-tRNA(Ser) gene region was substantial, being consistent with the results from the previous nuclear genome analyses. Results of UPGMA and minimum spanning network analyses also implied the unexpected ceiling of genetic differentiation in the CR. These results suggest that the CR does not reflect accurately the level of overall genetic differentiation between the populations of the ayu, but other coding regions of the mtDNA do reflect it so that the mtDNA on the whole may function as a rich source of useful markers for genetic assessment of populations of this species.

The migratory fish ayu, Plecoglossus altivelis, has two forms: an amphidromous form found throughout the Japanese islands and a landlocked form found in Lake Biwa. Because Lake Biwa is one of the sources of the Yodo River, which flows into Osaka Bay, it is likely that there has been contact between the two forms within the Yodo River system. To examine the effects of such contact, 573 ayu were collected from the Yodo River system and several other rivers and compared through an extensive investigation of microsatellite genotyping. Multivariate and individual admixture analyses of microsatellite data showed that samples of upstream migrants collected from the Yodo River in May 2003 included many individuals assigned to the amphidromous form, although fish collections in June and July 2003 were primarily composed of individuals of the landlocked form. Samples of drifting larvae, which we considered to be derived from eggs spawned in the Yodo River system, were mostly assigned to the amphidromous form. These results imply that an indigenous population of the amphidromous form exists and reproduces in the Yodo River system. It is likely that upstream migrants of the landlocked Lake Biwa form are supplied annually as well-developed larvae drifting out from Lake Biwa, but contribute very little to the next generation.

The population genetic structure of a reef-dwelling aeolid nudibranch, Pteraeolidia ianthina ( Angas, 1864 ) (Gastropoda, Mollusca), was investigated by analyzing the nuclear ribosomal RNA gene region, including 18S and 5.8S rRNA genes and the ITS1 region (545 bp). Among 235 individuals from 10 localities in the northwestern Pacific, two genetically distinct groups were detected: Groups A and B, which are separated by a minimum sequence difference of 5.3% (p-distance). The marked genetic differentiation of these two groups, even in localities where both co-occur, suggests that they are distinct species, although intergroup hybrids were observed in very low frequency. Within-population genetic variability was low in Group A, but high in Group B. Geographic analysis of between-population genetic distance and "allele" sharing data indicated three subgroups within Group A (temperate Japan, Ryukyus + Philippines, and Guam), whose distribution ranges appear to have some relationship to climate zones (temperate and subtropics + tropics) and ocean currents (Kuroshio and North Equatorial Currents). Within Group B detected only from three subtropic and tropic localities, however, genetic distances between populations were much smaller than those in Group A, and thus no significant geographic pattern was found. These differences in genetic variability and population structure between Groups A and B may reflect differences in biological features between them, such as the duration of the pelagic larval stage. Furthermore, some morphological differences were observed between Groups A and B. These observations provide further support for the suggestion that the two groups are separate species.