Genetic diversity and population structure of Japanese populations of the oval squid, Sepioteuthis cf. lessoniana, were compared with populations from Taiwan and Vietnam using nucleotide sequences of the mitochondrial DNA non-coding region 2. In total, 402 nucleotide sequences representing 242 individuals from Japanese waters (Ishikawa, Japan Sea coast of Honshu; Tokushima, eastern Shikoku; Nagasaki, western Kyushu; and Okinawajima and Ishigakijima Island, in the Ryukyu Archipelago) and the East and South China Seas (Keelung, northern Taiwan; Vietnam, Gulf of Tonkin) were examined. Among the 29 haplotypes recognized, haplotype no. 1 was shared by more than 75% of individuals from Japanese localities, whereas it was found in less than 13% of specimens from the East and South China Seas populations. Conversely, the East and South China Seas populations included more than 30% individuals with haplotype no. 2, whereas less than 10% of haplotype no. 2 individuals were from Japanese localities. The differences of haplotype and nucleotide diversities between pooled Japanese populations (0.2639, 0.23%) and the East and South China Seas populations (0.7900, 1.01%) indicate that S. cf. lessoniana from Japanese waters exhibits lower genetic diversity. An analysis of molecular variance between the Japanese populations and the East and South China Seas populations was highly significant. A minimum spanning tree of 29 haplotypes and an Unweighted Pair Group Method with Arithmetic mean (UPGMA) tree based on pairwise F ST comparisons also supported the separation between Japanese and the East and South China Seas populations. We suggest that the Kuroshio Current physically limits gene flow and has thus caused the differences in genetic diversity among the populations examined.

SUMMARY “Monitoring Sites 1000” – Japan's long‐term monitoring survey was established in 2003, based on the Japanese Government policy for the conservation of biodiversity. Ecological surveys have been conducted on various types of ecosystems at approximately 1000 sites in Japan for 15 years now and are planned to be carried out for 100 years. Since 2008, seaweed communities had been monitored at six sites, featuring the kelp (e.g. Saccharina and Ecklonia; Laminariales) and Sargassum (Fucales) communities in the subarctic and temperate regions of Japan. Annual surveys were carried out during the season when these canopy‐forming seaweeds are most abundant. A non‐destructive quadrat sampling method, with permanent quadrats placed along transects perpendicular to the shoreline, was used to determine species composition, coverage, and vertical distribution of seaweeds at these sites; while destructive sampling was done every 5 years to determine biomass. The occurrence of canopy‐forming species Saccharina japonica (var. japonica) and Ecklonia cava have appeared to be stable at the Muroran (southwestern part of Hokkaido Island) and Shimoda (Pacific coast of middle Honshu Island) sites, respectively; whereas the coverage of Ecklonia radicosa (= Eckloniopsis radicosa) at the Satsuma‐Nagashima site in southern part of Kyushu Island was highly variable until its sudden disappearance from the habitat in 2016. Thalli of E. radicosa lost most of their blades through browsing by herbivorous fish, and thus, this may be one of the causes of the decline. A shift in the community structure related to environmental changes had also been observed at some other sites. Pre‐ and post‐disaster data revealed the impact of the 2011 earthquake and tsunami disasters, including a shift in the vertical distribution of Ecklonia bicyclis (= Eisenia bicyclis) to shallower depths at the Shizugawa site in the Pacific coast of northern Honshu Island, due to seafloor subsidence.

Restriction fragment length polymorphism analysis was performed on polymerase chain reaction-amplified DNA fragments containing the D-loop, ND2, and CO I genes of fiddler crab Uca arcuata mitochondrial DNA. In total, 316 individuals from six populations in Japan and two populations in Taiwan were analyzed using five restriction endonucleases (AfaI, BcnI, Cfr13I, HaeIII and HinfI), yielding 85 haplotypes. Samples were taken from Nakagusuku Bay, Okinawajima Island, which is the only known distribution of U. arcuata in the Ryukyu Archipelago. The Okinawajima Island population is isolated geographically from others and showed a marked low genetic variability (h = 0.2539, p = 0.0005) and significant differentiation from other population samples in haplotype composition. We suggest that a substantial decrease in the genetic variability of the Okinawajima Island population was caused by genetic drift under the conditions of small population size and low gene flow from other populations. It is important to conserve the intertidal zone in Nakagusuku Bay for the maintenance of this endangered population.

We compared the breeding season and genetic population structure of six sentinel crab (Macrophthalmus banzai) populations in southwestern Japan. Ovigerous females from Northern group populations (Wakayama, Kochi, and Tanega-shima) were observed from March to September, whereas ovigerous females from Southern group populations (Amami-oshima, Okinawa-jima, and Iriomote-jima) were observed from October to May. Genetic analysis using two markers corresponding to mitochondrial DNA encoding cytochrome oxidase subunit I (COI) and the large subunit of ribosomal RNA (16Sr-RNA) revealed a marked genetic difference between the Northern and Southern groups. A genetic boundary exists between the Tanega-shima and Amami-oshima populations, which is consistent with the interpopulation difference in the breeding season.

Broad scale studies in seagrass benthic macrofauna are important for future regional marine conservation. We examined spatial variation in the community structure of seagrass‐associated benthic macroinvertebrates collected by sediment coring in 2010 at six seagrass sites of Japan covering the latitudinal range of 24°–43°N. Total species richness and ES(50) at site level did not show clear site variations and relationship with latitude. At core level, site variations of mean species richness, ES(50), Simpson diversity and abundance showed inconsistent pattern, but with more cases of statistically significant association with latitude. Variations were generally influenced by the seagrass species, often among subtropical species, among temperate Zostera species, and between Zostera and subtropical species. Finally, the community composition differed significantly across all sites and community similarity decreased rapidly with geographic distance, with only 5% similarity retained at the distance of 400 km. The dissimilarity among sites was higher with the similar distance compared to other types of coastal communities such as rocky intertidal assemblages, which is associated with minor occurrence of species with broad distributional range.