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On 11 March 2011, a catastrophic earthquake and subsequent tsunami hit the Pacific coast of northern Japan, devastating many of the towns, villages and coastal ecosystems located along the shoreline. To assess the impacts of the disaster, we investigated temporal dynamics of fish and epibenthic megafaunal community structure in relation to changes in a range of physical, biological and anthropogenic variables between 2007 and 2018 in Onagawa Bay. Commercially important fish such as greenlings, Japanese anchovy, flatfishes, rockfishes were consistently abundant in both larval and adult fish assemblages. While abundance, species richness, and Shannon index H' for adult fish and epibenthic megafaunal assemblages increased significantly soon after the disaster to peak values towards the end of the study period, the same metrics did not change accordingly for larval fish assemblages. Temporal dynamics of larval fish community clearly demonstrated significant seasonal variation along with changes in large-scale environmental conditions such as temperature and nutrients. However, anthropogenic components such as decline in human population, reduction in fishing pressure and the recovery of aquaculture operations significantly explained the observed post-disaster change in adult fish and epibenthic megafaunal communities. The pelagic and benthic components of Onagawa Bay appeared to have responded to the 2011 disaster very differently, and this study suggests the post-disaster recovery and dynamics of the coastal ecosystems may be regulated by how human societies respond to the impacts of a tsunami catastrophe through their influences on benthic habitat of ecosystems.

Massive tsunami disturbances have potentially detrimental effects on genetic diversity and effective population size of coastal marine species, and evaluating these effects can be useful for devising conservation strategies for coastal marine environments. Local populations of the intertidal goby Chaenogobius annularis, which are distributed on scattered rocky beaches of the Japanese Archipelago, show demographic independence without overlapping generations, making this an ideal species with which to study the effects of tsunami disturbance on genetic diversity. Some of these populations were affected by the tsunami of the 2011 off the Pacific coast of Tohoku Earthquake. Here, we investigated the change in genetic diversity of a local population of this species, which was located close to the epicenter of the earthquake, across the cohorts before and after the tsunami and evaluated the impact of the tsunami disturbance. Genetic diversity was maintained after the tsunami, and no change in the effective population size was observed. Our results suggest that the tsunami disturbance has had no marked impact on the genetic diversity of C. annularis.

Marine organisms with a planktonic larval stage can passively disperse long distance and are thus expected to have a wider distribution range and lower geographic variation. However, recent molecular phylogenetic studies have revealed that they often display a clear geographic genetic structure or even form a geographically fragmented species complex. These genetic divergences can be facilitated by the presence of dispersal barriers such as oceanic currents and/or by the limitation of suitable habitats. Using comprehensive phylogenetic analyses, we evaluate how such dispersal barriers shape genetic divergence and speciation in the intertidal snail genus Monodonta. Our phylogenetic analysis revealed various patterns of cladogenesis in Monodonta in East Asia. Genetic segregation between the Japanese and Ryukyu Archipelagos are detected in M. labio and M. perplexa perplexa. However, the relationship of geographical border and lineages does not correspond to those two because they show different habitat preference. M. labio distributed in the Japanese mainland is separated by the boundary corresponding to the point from which oceanic currents split into different directions. In contrast, species inhabiting various environments such as M. confusa are not genetically separated in Japan. In the peripheral oceanic Ogasawara Islands, two Monodonta species form each endemic lineage, although these two underwent different colonization processes to the islands. These findings suggest that the genus Monodonta has been genetically diversified around Japan, probably due to its correlations with dispersal ability, oceanic current, and habitat preferences. These factors may be effective causes for diversification of marine gastropods with a planktonic stage.

Chlamys farreri , which is naturally distributed along the coasts of East Asia, is a commercially important mollusk in China, and its mariculture has been prevalent since the 1970s with the decrease of natural resources in the 1960s. To conserve its genetic resources and avoid genetic disturbance, the population structure of the natural population in Japan and genetic condition of the stock population in China were investigated using morphological, microsatellite, and mtDNA markers. Analysis of morphological variance in C . farreri revealed no distinct difference between the presumed 2 subspecies ( C . farreri akazara and C . farreri nipponensis ) or between the natural and cultured scallops. Population genetic analysis using 2 DNA markers showed that wild scallops in Japan could be divided into a northern group and a southern group with 2 subgroups. The magnitude of genetic divergence between these groups was below the subspecies level, suggesting that C . farreri comprises 1 species with geographic subpopulations. Analysis of the mtDNA markers indicated the genetic divergence between populations of Japan and China, while that of the microsatellite markers showed that 3 Chinese populations (Qingdao, Weihai, and Yantai) were genetically similar to the northern Japanese group, suggesting the possibility of introduction of foreign genomes from the Tohoku area. On the basis of the present results, the northern and southern groups in Japan and Dalian population in China should ideally be regarded as separate units for management and conserved as the source populations for breeding programs. In addition, the genetic relationship among natural and cultured populations in China and natural populations in Japan should be further investigated for a better genetic management of this species.

The Japanese sea cucumber Apostichopus japonicus has a pelagic-lecithotrophic larva. Here, we clarify larval dispersal among Japanese sea cucumber populations by describing the levels of distinctiveness and gene flow among red and green variant populations of A. japonicus across Toyama Bay using 11 polymorphic microsatellite markers. Samples of Japanese sea cucumber populations were collected from three localities (Noto, Shinminato, and Uozu) around Toyama Bay. Geographically separated populations of red and green variants were determined to be genetically distinct, supported by phylogenetic analysis and the distinctiveness range values of pairwise multilocus estimates of F ST. Contemporary migration analyses indicated that the majority of estimated migration events occurred within A. japonicus populations comprised of only either red or green variants. In a historical gene flow analysis, two best-fit models (n-island and stepping stone models) showed circulation for the gene migration in Toyama Bay among red variant populations. Our results provide useful information on the genetic structure of Japanese sea cucumber populations and will be helpful for genetic conservation and fisheries management of sea cucumber populations in Toyama Bay.

Elucidating the scale of gene flow among populations is an important challenge for understanding the ecological dynamics and local adaptation of marine organisms. We assessed whether gene flow is restricted even at a small spatial scale in the Japanese common intertidal goby Chaenogobius annularis, using highly polymorphic DNA markers, involving the mitochondrial DNA (mtDNA) control region and 15 microsatellite DNA (msDNA), because past ecological studies have suggested low dispersal ability for rocky intertidal fishes. We found significant heterogeneities between four neighboring local populations by both mtDNA and msDNA analyses. In addition, no genetic heterogeneity was detected by either method across generations within a population; it was considered that such genetic differentiation is retained across generations and that the gene flow of this species is restricted to within a radius of a few kilometers. This is the first report showing a clear genetic subdivision in rocky intertidal fish.

Genetic differentiation in the intertidal goby Chaenogobius annularis was studied using allozyme markers. Samples were collected from six localities along the coasts of Japanese islands and the Korean Peninsula. Six out of 13 loci showed allelic variation in at least one population. Although the predominant alleles of 12 loci were the same among all populations, Mdh-1 showed clear differences among the populations located along the coasts of the Pacific Ocean and the Sea of Japan. These two possible geographic groups, the Pacific Ocean and the Sea of Japan groups, were characterized by diagnostic alleles of Mdh-1, namely Mdh-1 100 and Mdh-1 70.

To demonstrate inbreeding depression in various traits of Pacific abalone Haliotis discus hannai, 12 inbreeding full-sib families (brother-sister mating) and 13 outbreeding full-sib families were produced by factorial mating using the parents from two full-sib families. All 25 full-sib families were reared for 158 days after settlement, and 8 of the inbred and outbred full-sib families were reared until 3 y 4 mo of age. Inbreeding depression traits between inbred and outbred crosses were compared. No significant differences in fertilization rate, hatchability, and veliger survival rate were observed between the inbreeding and outbreeding crosses. Deformity rate in veliger larvae from the inbred crosses was significantly higher than that among the outbred crosses (t-test, P < 0.01). Significantly lower survival rates were observed in the inbreeding crosses at 109 days after settlement (t-test, P < 0.01) and between 1 y 4 mo-old and 3 y 4 mo-old crosses (t-test, P < 0.05). Mean increases in shell l...

‘Inbreeding depression’ may be an avoidable phenomenon for abalone culture. However, only a few studies have been carried out on inbreeding depression. In the present study, using six families produced in 1994, a factorial mating system including inbreeding and outbreeding was constructed in order to demonstrate inbreeding depression traits of the Pacific abalone. In total, 24 inbreeding and 21 outbreeding crosses were produced during three years (1999–2001) and these off-spring were reared for approximately one year. Significant differences in fertilization rate and growth were not observed between inbreeding and outbreeding corsses. However, the deformity rate of veliger larvae was always higher in inbreeding crosses than that of outbreeding crosses in all experiments. Moreover, a significantly high deformity rate was observed in some full-sib families of inbreeding. Alternatively, the survival rates of inbreeding crosses were much lower than for outbreeding crosses after about 4 months and one year in two rearing localities. These results indicate that inbreeding depression is observed in the traits of deformity rate and survival, but not in fertilization rate nor growth in the first generation of a full-sib family of the Pacific abalone.

Correspondance: Molecular Ecology Resources Primer Development Consortium, E-mail: editorial.office@molecol.com; International audience; This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

Nei's (1972) genetic distance were estimated among 21 populations of the common freshwater shrimp Paratya compressa improvisa, living in the northern part of Japan. The estimates were based on examination of 18 enzyme loci by starch-gel electrophoresis. These shrimp populations were genetically classified into three geographic groups on the basis of predominating alleles typical for two loci Fdp-1 and Fdp-2. The "Kanto group" consisted of individuals having Fdp-1a and Fdp-2c, the "Japan Sea group" having Fdp-1b and Fdp-2a, and the "Pacific Ocean group" having Fdp-1b and Fdp-2c. Nei's genetic distance among the three different geographic groups, varied from 0.0572 to 0.2136. Average genetic distances were 0.1001 between Pacific Ocean and Japan Sea groups, 0.0851 between Pacific Ocean and Kanto groups, and 0.1990 between Japan Sea and Kanto groups. These values of genetic distance among the three groups are comparable with those among different subspecies.

The gene consitution of an individual river population of the chum salmon was compared with that of other river populations by geneitc distance calculated from the allelic frequencies at six isozymic loci, Idh-A2, Idh-B2, Ldh-A1, Mdh-B1, Pgm-B2 and Aat-A1, which are surveyed by starch gel electrophoresis. A matrix of genetic distances among river populations indicated that an indivdual river population could not be regarded as a completely genetic isolated population because of exchange of individuals with neighbouring river populations. Analysis of a correlation between geographic and genetic distance among river populations revealed three routes of homing migration for spawning. The correlation also revealed that gene constiutions of two river populations separated by more that about 600km along the homing migration routes could be regarded as practically independent of each other.

Genetic variability in native and sown populations, including 10 collections, of the Japanese scallop Patinopecten yessoensis on the Okhotsk Sea coast of Hokkaido in Japan was surveyed by starch gel electrophoresis for 19 genetic loci. As a whole, the proportion of polymorphicloci averaged 0.405±0.008 and the average heterozygosity 0.158±0.002, and these values were remarkably higher than those estimated for fish. Any two of the 10 collections showed clear differences in gene frequencies at more than one locus except for a few combinations, indicating that they have a breeding structure independent of each other. The mean genetic distance was larger among native populations than among sown populations. The genetic distance was 0.0035±0.0003 on the average for all populations, the value being smaller than 0.01 that is considered as the level of local race. However, the mean genetic distance between native Notoro Lake population and the other native populations was 0.0077±0.0008, the value being the largest. These results suggest that the scallop population has a structure capable of being split into a number of local subpopulations.