Contrasting population genetic structure of three semi-terrestrial brachyuran crabs on the coast of the Japanese archipelago.

Anthropogenic activities have reduced ecotones between the ocean and land, which is likely to threaten the population of brackish-water brachyuran crabs. To assess the current status of these crabs, we examine the population genetic structures of three semi-terrestrial brachyuran crabs widely distributed along the coast of the Japan and to clarify factors determining their genetic structures. We collected 184 Orisarma dehaani, 252 Chiromantes haematocheir, and 151 Helice tridens crabs from 36 localities of the Japanese archipelago. Genome-wide SNP data from these crabs were analyzed using MIG-seq. Bayesian clustering of STRUCTURE and DAPC analysis were used to identify genetically disturbed populations and to visualize genetic differentiation between local populations. Genetic population structure showed clear differentiation between populations on the Pacific coast of the Tohoku region and on other Japanese coasts in O. dehaani, but not in C. haematocheir or H. tridens. The inbreeding coefficient of O. dehaani was significantly higher on the Pacific coast of the Tohoku region compared to other Japanese coasts. C. haematocheir and H. tridens had homogeneous genetic structures along the Japanese coast, but showed genetic differentiation of a local population at their range limits. Thus, O. dehaani showed little gene flow and clear genetic differentiation between populations in the Tohoku Pacific region and those on other Japanese coasts due to ocean currents. Although such a regional differentiation was not found in C. haematocheir and H. tridens, one population of C. haematocheir was genetically isolated at the edge of its distribution range and likely vulnerable to environmental changes.

Invasions of an obligate asexual daphnid species support the nearly neutral theory.

To verify the "nearly neutral theory (NNT)," the ratio of nonsynonymous to synonymous substitutions (dN/dS) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual Daphnia pulex invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed the whole-genome sequences of 18 genotypes, including those of the two independently invaded D. pulex lineages (JPN1 and JPN2) and compared the dN/dS ratio between the lineages. The base substitution rate of each genotype demonstrated that the JPN1 lineage having a larger distribution range diverged earlier and thus was older than the JPN2 lineage. Comparisons of the genotypes within lineages revealed that changes in dN/dS occurred after the divergence and were larger in the younger lineage, JPN2. These results imply that the JPN1 lineage has been more effectively subjected to purification selections, while slightly deteriorating mutations are less purged in JPN2 with smaller population size. Altogether, the lineage-specific difference in the dN/dS ratio for the obligate asexual D. pulex was well explained by the NNT.

Long-term dynamics of a cladoceran community from an early stage of lake formation in Lake Fukami-ike, Japan.

An increase in nutrient levels due to eutrophication has considerable effects on lake ecosystems. Cladocerans are intermediate consumers in lake ecosystems; thus, they are influenced by both the bottom-up and top-down effects that occur as eutrophication progresses. The long-term community succession of cladocerans and the effects cladocerans experience through the various eutrophication stages have rarely been investigated from the perspective of the early-stage cladoceran community assemblage during lake formation. In our research, long-term cladoceran community succession was examined via paleolimnological analysis in the currently eutrophic Lake Fukami-ike, Japan. We measured the concentration of total phosphorus and phytoplankton pigments and counted cladoceran and other invertebrate subfossils in all layers of collected sediment cores, and then assessed changes in the factors controlling the cladoceran community over a 354-year period from lake formation to the present. The cladoceran community consisted only of benthic taxa at the time of lake formation. When rapid eutrophication occurred and phytoplankton increased, the benthic community was replaced by a pelagic community. After further eutrophication, large Daphnia and high-order consumers became established. The statistical analysis suggested that bottom-up effects mainly controlled the cladoceran community in the lake's early stages, and the importance of top-down effects increased after eutrophication occurred. Total phosphorus and phytoplankton pigments had positive effects on pelagic Bosmina, leading to the replacement of the benthic cladoceran community by the pelagic one. In contrast, the taxa established posteutrophication were affected more by predators than by nutrient levels. A decrease in planktivorous fish possibly allowed large Daphnia to establish, and the subsequent increase in planktivorous fish reduced the body size of the cladoceran community.

Evolution of asexual Daphnia pulex in Japan: variations and covariations of the digestive, morphological and life history traits.

BACKGROUND: Several genetic lineages of obligate parthenogenetic Daphnia pulex, a common zooplankton species, have invaded Japan from North America. Among these, a lineage named JPN1 is thought to have started colonization as a single genotype several hundred to thousand years ago and subsequently produced many genotypes in Japan. To examine the phenotypic variations due to ecological drivers diverging the genotypes in new habitats, we measured heritability and variation in 17 traits, including life history, morphology and digestive traits, and the genetic distance among the D. pulex JPN1 genotypes in Japan. RESULTS: We found that most of the traits measured varied significantly among the genotypes and that heritability was highest in the morphological traits, followed by the digestive and life history traits. In addition, 93% of the variation in these traits was explained by the first three components in the principal component analysis, implying that variation of these heritable traits is not random but rather converged into a few directions. These relations among traits revealed the potential importance of predation pressures and food conditions as factors for diverging and selecting different genotypes. However, the magnitude of the difference in any single trait group did not correlate with the genetic distance. CONCLUSIONS: Our findings show that the divergent traits evolved within D. pulex JPN1 lineage without genetic recombination, since their ancestral clone invaded Japan. Large variations and covariations of the phenotypic traits, irrespective of the genetic distance among the genotypes, support the view that the invasive success of D. pulex JPN1 was promoted by a genetic architecture that allowed for large phenotypic variations with a limited number of functionally important mutations without recombination.

Rediscovery after Almost 120 Years: Morphological and Genetic Evidence Supporting the Validity of Daphnia mitsukuri (Crustacea: Cladocera).

We examined the morphology of Daphnia individuals maintained in our laboratory for several years, originally collected in Lake Inbanuma, Chiba, Japan. We determined partial sequences of the mitochondrial cytochrome c oxidase subunit I and 12S rRNA genes from specimens in the cultured material. These animals are morphologically similar to D. obtusa Kurz, 1874 , but genetically distinct from this species. Our detailed observation shows that the morphological characteristics in the female and male individuals of our material are highly congruent with those of D. mitsukuri Ishikawa, 1896 , which has not been identified positively for more than 120 years since its original description, with its taxonomic identity having been questioned for almost 90 years. Based on our morphological and genetic data, we conclude that D. mitsukuri should be regarded as a taxonomically valid species. A search among public DNA sequence databases suggests D. mitsukuri is also distributed in China, although these Chinese sequences have been labeled as 'Daphnia pulex', representing misidentification.

Effects of light environment during growth on the expression of cone opsin genes and behavioral spectral sensitivities in guppies (Poecilia reticulata).

BACKGROUND: The visual system is important for animals for mate choice, food acquisition, and predator avoidance. Animals possessing a visual system can sense particular wavelengths of light emanating from objects and their surroundings and perceive their environments by processing information contained in these visual perceptions of light. Visual perception in individuals varies with the absorption spectra of visual pigments and the expression levels of opsin genes, which may be altered according to the light environments. However, which light environments and the mechanism by which they change opsin expression profiles and whether these changes in opsin gene expression can affect light sensitivities are largely unknown. This study determined whether the light environment during growth induced plastic changes in opsin gene expression and behavioral sensitivity to particular wavelengths of light in guppies (Poecilia reticulata). RESULTS: Individuals grown under orange light exhibited a higher expression of long wavelength-sensitive (LWS) opsin genes and a higher sensitivity to 600-nm light than those grown under green light. In addition, we confirmed that variations in the expression levels of LWS opsin genes were related to the behavioral sensitivities to long wavelengths of light. CONCLUSIONS: The light environment during the growth stage alters the expression levels of LWS opsin genes and behavioral sensitivities to long wavelengths of light in guppies. The plastically enhanced sensitivity to background light due to changes in opsin gene expression can enhance the detection and visibility of predators and foods, thereby affecting survival. Moreover, changes in sensitivities to orange light may lead to changes in the discrimination of orange/red colors of male guppies and might alter female preferences for male color patterns.

Historical changes in the ecosystem condition of a small mountain lake over the past 60 years as revealed by plankton remains and Daphnia ephippial carapaces stored in lake sediments.

To examine if changes in species composition of a plankton community in the past due to anthropogenic activities can be clarified in lakes without any monitoring data, we analyzed genetically ephippial carapaces of Daphnia with plankton remains stored in the bottom sediments of Lake Hataya Ohunma in Japan. In the lake, abundance of most plankton remains in the sediments was limited and TP flux was at low levels (2-4 mg/m2/y) before 1970. However TP flux increased two-fold during the period from 1980s to 1990 s. In parallel with this increase, abundance of most plankton remains increased although abundance of benthic testate amoebae's remains decreased, indicating that the lake trophic condition had changed from oligo- to mesotrophic for the past 60 years. According to cluster analysis, the stratigraphic sediments were divided into two periods with different features of the phytoplankton composition. Chronological comparison with events in the watershed suggested that eutrophication occurred because of an increase in visitors to the watershed and deposition of atmospheric dust. In this lake more than 50% of resting eggs produced by Daphnia over the past 60 years hatched. However, genetic analysis of the ephippial carapaces (remains) showed that the Daphnia population was originally composed of D. dentifera but that D. galeata, or its hybrid with D. dentifera, invaded and increased the population density when the lake was eutrophied. Subsequently, large D. pulex established populations in the 1980s when largemouth bass were anonymously introduced. These results indicated that the Lake Hataya Ohunma plankton community underwent significant changes despite the fact that there were no notable changes in land cover or land use in the watershed. Since increases in atmospheric deposition and release of fish have occurred in many Japanese lakes, the changes in the plankton community described here may be widespread in these lakes.

Expression of the nos gene and firefly flashing: a test of the nitric-oxide-mediated flash control model.

Fireflies (Coleoptera: Lampyridae) emit various types of light that differ among species and populations of the same species. Their lights are assumed to be biological properties that play important ecological and evolutionary roles. Some species in the Lampyridae emit periodic luminescence, the patterns of which are characterized by species-specific intervals. In previous work, it was predicted that the nitric oxide (NO) regulates the oxygen supply required for the bioluminescence reaction of fireflies. Here, the expression of the NO synthase (NOS) mRNA in some fireflies was examined to verify the predictive model of nitric-oxide-mediated flash control in these insects. The expression of the nos gene in the lantern organ was observed not only in nocturnal flashing species but also in diurnal non-flashing species. It was shown that the expression levels of nos were higher in the lantern of Luciola cruciata (Motschulsky) larvae, which that emits continuous light, than in other body parts, although expression in the lantern of the adults, who flash periodically, was not high. Furthermore, there was no significant difference in expression levels among adults of Luciola cruciata characterized by different flashing intervals. The data do not support the model of an NO-mediated flash control mechanism, during which oxygen becomes available for the luciferin-luciferase reaction through NO-mediated inhibition of mitochondrial respiration. It is also indicated that flash patterns do not co-vary with NOS production. However, high nos expression in the larval lantern suggests that NO may play a role in producing continuous light by functioning as a neurotransmitter signal for bioluminescence.

Size-dependent foraging gene expression and behavioral caste differentiation in Bombus ignitus.

BACKGROUND: In eusocial hymenopteran insects, foraging genes, members of the cGMP-dependent protein kinase family, are considered to contribute to division of labor through behavioral caste differentiation. However, the relationship between foraging gene expression and behavioral caste in honeybees is opposite to that observed in ants and wasps. In the previously examined eusocial Hymenoptera, workers behave as foragers or nurses depending on age. We reasoned that examination of a different system of behavioral caste determination might provide new insights into the relationship between foraging genes and division of labor, and accordingly focused on bumblebees, which exhibit size-dependent behavioral caste differentiation. We characterized a foraging gene (Bifor) in bumblebees (Bombus ignitus) and examined the relationship between Bifor expression and size-dependent behavioral caste differentiation. FINDINGS: A putative open reading frame of the Bifor gene was 2004 bp in length. It encoded 668 aa residues and showed high identity to orthologous genes in other hymenopterans (85.3-99.0%). As in ants and wasps, Bifor expression levels were higher in nurses than in foragers. Bifor expression was negatively correlated with individual body size even within the same behavioral castes (regression coefficient = -0.376, P < 0.001, all individuals; -0.379, P = 0.018, within foragers). CONCLUSION: These findings indicate that Bifor expression is size dependent and support the idea that Bifor expression levels are related to behavioral caste differentiation in B. ignitus. Thus, the relationship between foraging gene expression and behavioral caste differentiation found in ants and wasps was identified in a different system of labor determination.

Nitric oxide synthase (NOS) in the Japanese fireflies Luciola lateralis and Luciola cruciata.

Species-specific flash patterns in firefly species are important for the investigation of the evolution of Lampyridae. Since nitric oxide synthase (NOS) is one of the key enzymes controlling flash patterns, we determined the cDNA sequences of NOS in the Japanese fireflies Luciola lateralis and L. cruciata. The identity of the NOS sequences was very high between these 2 species. Firefly NOS also exhibited a high identity with those of other insect species, and the cofactor-binding domains were particularly well conserved. Many negatively selected sites were detected throughout the NOS sequences; however, no positive selection was detected. The phylogenetic relationship of insect NOS was different from that of the general classification system, although the lineages corresponded to the major recognized taxonomic groups.