Methyl farnesoate regulatory mechanisms underlying photoperiod-dependent sex determination in the freshwater crustacean Daphnia magna.

Freshwater zooplankton Daphnia magna has been widely used in ecotoxicology studies. During the last 20 years, it has been demonstrated that the topical application of juvenile hormone (JH) or JH analogs to mother daphnids induce male offspring production. Based on this finding, an in vivo screening validation method for chemicals with JH agonistic effect has developed. Although this screening system successfully identified a number of JH-like chemicals, molecular mechanisms underlying the male sex-determining process remain largely unknown. To address this issue, we established a reliable male- or female-producing system using Daphnia pulex WTN6 strain by changing the rearing photoperiod. Taking advantage of this rearing system, we successfully found several factors involving male sex determination such as ionotropic glutamate receptors, protein kinase C and pantothenate. Here, we used two D. magna strains that can also control the production of female or male offspring by photoperiod differences as model species for ecotoxicology studies. We demonstrated that either treatment of antagonist of ionotropic glutamate receptors or inhibitor of protein kinase C strongly suppressed male offspring production even under male-producing conditions. Moreover, we revealed that male sex-determining processes are likely diverged between D. magna and D. pulex based on the current experiment. This study provides a fine experimental method for in vivo screening not only JH agonists but also JH antagonists. Moreover, using daphnids with photoperiod-dependent sex determination manner will hugely contribute to understanding the mode-of-action of JH in daphnids.

Isolation and characterization of 13 microsatellite loci for the Neotropical otter, Lontra longicaudis, by next generation sequencing.

The Neotropical otter, Lontra longicaudis, is an ecologically important species for freshwater ecosystems that is threatened due to habitat destruction and hunting. However, there is limited information regarding the population sizes, genetic diversity, genetic structure and gene flow of the species, which is crucial for the elaboration of conservation plans. The aim of this study was to isolate and characterize microsatellites for L. longicaudis, using Illumina paired-end-sequencing. Initial amplification tests were performed in 48 loci, out of which, 13 yielded high-quality PCR products and thus were further evaluated. Genetic diversity and discrimination power of the 13 microsatellite loci was assessed using 19 non-invasive samples collected in the Jamapa basin in Veracruz, Mexico and blood samples from six captive individuals. All loci were polymorphic, the number of alleles per locus ranged from 4 to 10, the observed heterozygosity from 0.21 to 0.69, and the expected heterozygosity from 0.55 to 0.82. The combined set of 13 microsatellites showed a high power for discriminating among individuals (probability of identity PID = 1.551 × 10-16) and among siblings (probability of identity of siblings PIDSIB = 3.349 × 10-06). A combination of nine loci are sufficient to discriminate among siblings with high confidence (PIDSIB < 0.0001). The new set of microsatellites for the Neotropical otter reported here will provide a useful genetic tool to assess population genetic patterns and ecological parameters of the species.

Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data.

BACKGROUND: A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-absence data, we evaluate species co-occurrences that help elucidate relationships among organisms and environments. To summarize similarity between occurrences of species, we routinely use the Jaccard/Tanimoto coefficient, which is the ratio of their intersection to their union. It is natural, then, to identify statistically significant Jaccard/Tanimoto coefficients, which suggest non-random co-occurrences of species. However, statistical hypothesis testing using this similarity coefficient has been seldom used or studied. RESULTS: We introduce a hypothesis test for similarity for biological presence-absence data, using the Jaccard/Tanimoto coefficient. Several key improvements are presented including unbiased estimation of expectation and centered Jaccard/Tanimoto coefficients, that account for occurrence probabilities. The exact and asymptotic solutions are derived. To overcome a computational burden due to high-dimensionality, we propose the bootstrap and measurement concentration algorithms to efficiently estimate statistical significance of binary similarity. Comprehensive simulation studies demonstrate that our proposed methods produce accurate p-values and false discovery rates. The proposed estimation methods are orders of magnitude faster than the exact solution, particularly with an increasing dimensionality. We showcase their applications in evaluating co-occurrences of bird species in 28 islands of Vanuatu and fish species in 3347 freshwater habitats in France. The proposed methods are implemented in an open source R package called jaccard (https://cran.r-project.org/package=jaccard). CONCLUSION: We introduce a suite of statistical methods for the Jaccard/Tanimoto similarity coefficient for binary data, that enable straightforward incorporation of probabilistic measures in analysis for species co-occurrences. Due to their generality, the proposed methods and implementations are applicable to a wide range of binary data arising from genomics, biochemistry, and other areas of science.

Amphibious flies and paedomorphism in the Jurassic period.

The species of the Strashilidae (strashilids) have been the most perplexing of fossil insects from the Jurassic period of Russia and China. They have been widely considered to be ectoparasites of pterosaurs or feathered dinosaurs, based on the putative presence of piercing and sucking mouthparts and hind tibio-basitarsal pincers purportedly used to fix onto the host's hairs or feathers. Both the supposed host and parasite occur in the Daohugou beds from the Middle Jurassic epoch of China (approximately 165 million years ago). Here we analyse the morphology of strashilids from the Daohugou beds, and reach markedly different conclusions; namely that strashilids are highly specialized flies (Diptera) bearing large membranous wings, with substantial sexual dimorphism of the hind legs and abdominal extensions. The idea that they belong to an extinct order is unsupported, and the lineage can be placed within the true flies. In terms of major morphological and inferred behavioural features, strashilids resemble the recent (extant) and relict members of the aquatic fly family Nymphomyiidae. Their ontogeny are distinguished by the persistence in adult males of larval abdominal respiratory gills, representing a unique case of paedomorphism among endopterygote insects. Adult strashilids were probably aquatic or amphibious, shedding their wings after emergence and mating in the water.

COE loss-of-function analysis reveals a genetic program underlying maintenance and regeneration of the nervous system in planarians.

Members of the COE family of transcription factors are required for central nervous system (CNS) development. However, the function of COE in the post-embryonic CNS remains largely unknown. An excellent model for investigating gene function in the adult CNS is the freshwater planarian. This animal is capable of regenerating neurons from an adult pluripotent stem cell population and regaining normal function. We previously showed that planarian coe is expressed in differentiating and mature neurons and that its function is required for proper CNS regeneration. Here, we show that coe is essential to maintain nervous system architecture and patterning in intact (uninjured) planarians. We took advantage of the robust phenotype in intact animals to investigate the genetic programs coe regulates in the CNS. We compared the transcriptional profiles of control and coe RNAi planarians using RNA sequencing and identified approximately 900 differentially expressed genes in coe knockdown animals, including 397 downregulated genes that were enriched for nervous system functional annotations. Next, we validated a subset of the downregulated transcripts by analyzing their expression in coe-deficient planarians and testing if the mRNAs could be detected in coe+ cells. These experiments revealed novel candidate targets of coe in the CNS such as ion channel, neuropeptide, and neurotransmitter genes. Finally, to determine if loss of any of the validated transcripts underscores the coe knockdown phenotype, we knocked down their expression by RNAi and uncovered a set of coe-regulated genes implicated in CNS regeneration and patterning, including orthologs of sodium channel alpha-subunit and pou4. Our study broadens the knowledge of gene expression programs regulated by COE that are required for maintenance of neural subtypes and nervous system architecture in adult animals.

Effects of differential habitat warming on complex communities.

Food webs unfold across a mosaic of micro and macro habitats, with each habitat coupled by mobile consumers that behave in response to local environmental conditions. Despite this fundamental characteristic of nature, research on how climate change will affect whole ecosystems has overlooked (i) that climate warming will generally affect habitats differently and (ii) that mobile consumers may respond to this differential change in a manner that may fundamentally alter the energy pathways that sustain ecosystems. This reasoning suggests a powerful, but largely unexplored, avenue for studying the impacts of climate change on ecosystem functioning. Here, we use lake ecosystems to show that predictable behavioral adjustments to local temperature differentials govern a fundamental structural shift across 54 food webs. Data show that the trophic pathways from basal resources to a cold-adapted predator shift toward greater reliance on a cold-water refuge habitat, and food chain length increases, as air temperatures rise. Notably, cold-adapted predator behavior may substantially drive this decoupling effect across the climatic range in our study independent of warmer-adapted species responses (for example, changes in near-shore species abundance and predator absence). Such modifications reflect a flexible food web architecture that requires more attention from climate change research. The trophic pathway restructuring documented here is expected to alter biomass accumulation, through the regulation of energy fluxes to predators, and thus potentially threatens ecosystem sustainability in times of rapid environmental change.

Stoichiometric control of organic carbon-nitrate relationships from soils to the sea.

The production of artificial fertilizers, fossil fuel use and leguminous agriculture worldwide has increased the amount of reactive nitrogen in the natural environment by an order of magnitude since the Industrial Revolution. This reorganization of the nitrogen cycle has led to an increase in food production, but increasingly causes a number of environmental problems. One such problem is the accumulation of nitrate in both freshwater and coastal marine ecosystems. Here we establish that ecosystem nitrate accrual exhibits consistent and negative nonlinear correlations with organic carbon availability along a hydrologic continuum from soils, through freshwater systems and coastal margins, to the open ocean. The trend also prevails in ecosystems subject to substantial human alteration. Across this diversity of environments, we find evidence that resource stoichiometry (organic carbon:nitrate) strongly influences nitrate accumulation by regulating a suite of microbial processes that couple dissolved organic carbon and nitrate cycling. With the help of a meta-analysis we show that heterotrophic microbes maintain low nitrate concentrations when organic carbon:nitrate ratios match the stoichiometric demands of microbial anabolism. When resource ratios drop below the minimum carbon:nitrogen ratio of microbial biomass, however, the onset of carbon limitation appears to drive rapid nitrate accrual, which may then be further enhanced by nitrification. At low organic carbon:nitrate ratios, denitrification appears to constrain the extent of nitrate accretion, once organic carbon and nitrate availability approach the 1:1 stoichiometry of this catabolic process. Collectively, these microbial processes express themselves on local to global scales by restricting the threshold ratios underlying nitrate accrual to a constrained stoichiometric window. Our findings indicate that ecological stoichiometry can help explain the fate of nitrate across disparate environments and in the face of human disturbance.

Integrative taxonomy detects cryptic and overlooked fish species in a neotropical river basin.

The great freshwater fish diversity found in the neotropical region makes management and conservation actions challenging. Due to shortage of taxonomists and insufficient infrastructure to deal with such great biodiversity (i.e. taxonomic impediment), proposed remedies to accelerate species identification and descriptions include techniques that combine DNA-based identification and concise morphological description. The building of a DNA barcode reference database correlating meristic and genetic data was developed for 75 % of the Mucuri River basin's freshwater fish. We obtained a total of 141 DNA barcode sequences from 37 species belonging to 30 genera, 19 families, and 5 orders. Genetic distances within species, genera, and families were 0.74, 9.5, and 18.86 %, respectively. All species could be clearly identified by the DNA barcodes. Divergences between meristic morphological characteristics and DNA barcodes revealed two cryptic species among the Cyphocharax gilbert and Astyanax gr. bimaculatus specimens, and helped to identify two overlooked species within the Gymnotus and Astyanax taxa. Therefore, using a simplified model of neotropical biodiversity, we tested the efficiency of an integrative taxonomy approach for species discovery, identification of cryptic diversity, and accelerating biodiversity descriptions.

The Influence of the Disturbed Continuity of the River and the Invasive Species--Potamopyrgus antipodarum (Gray, 1843), Gammarus tigrinus (Sexton, 1939) on Benthos Fauna: A Case Study on Urban Area in the River Ruda (Poland).

The progressive degradation of aquatic ecosystems and ecohydrological role of rivers is one of the most important global environmental issues. The loss of the ability of rivers to self-purify waters due to the disturbances of river continuity cause a lack of biological life in parts of rivers or even in an entire river. The appearance of alien species in degraded aquatic environments is an increasingly common phenomenon and constitutes one of the threats to biodiversity. The aim of the study was to evaluate the possible impact of alien species Potamopyrgus antipodarum (Gray, 1843) and Gammarus tigrinus (Sexton, 1939) on native invertebrates as well as the influence of environmental factors on the occurrence benthos fauna including also alien species. The study conducted in industrial area, in the River Ruda (Poland), showed that at the sites at which the occurrence of the two alien species was observed, the density of native benthos and diversity decreased significantly. CCA analysis showed that non-native species occurred in fast water velocity and that their presence was associated with high values of conductivity, hardness, and a high chloride content. The arrival of new species from other geographical areas is one of the factors that influences the species balance in native aquatic fauna. The number of alien species in freshwater ecosystems probably will increase in the future as new aliens are moved outside of their native ranges.

Effect of Dactylogyrus catlaius (Jain 1961) infection in Labeo rohita (Hamilton 1822): innate immune responses and expression profile of some immune related genes.

The monogenean ectoparasite, Dactylogyrus sp. is a major pathogen in freshwater aquaculture. The immune responses in parasitized fish were analyzed by quantitation of innate immune factors (natural agglutinin level, haemolysin titre, antiprotease, lysozyme and myeloperoxidase activities) in serum and immune-relevant gene expression in gill and anterior kidney. The antiprotease activity and natural agglutinin level were found to be significantly higher and lysozyme activity was significantly lower in parasitized fish. Most of the genes viz., beta2-microglobulin (beta2M), major histocompatibility complex I (MHCI), MHCII, tumor necrosis factor alpha (TNFalpha) and toll-like receptor 22 (TLR22) in gill samples were significantly down-regulated in the experimental group. In the anterior kidney, the expression of superoxide dismutase and interleukin 1beta (IL1beta) were significantly up-regulated whereas a significant down regulation of MHCII and TNFalpha was also observed. The down-regulation of most of the genes viz, MHCI, beta2M, MHCII, TLR22 and TNFalpha in infected gills indicated a well evolved mechanism in this parasite to escape the host immune response. The modulation of innate and adaptive immunity by this parasite can be further explored to understand host susceptibility.

The identity of the Sarawak freshwater crab Parathelphusa oxygona Nobili, 1901, with description of a new species, Parathelphusa nobilii, from Western Kalimantan, Indonesia, Borneo (Crustacea: Brachyura: Gecarcinucidae).

The identity of the common lowland freshwater crab in western Sarawak, Borneo, East Malaysia, Parathelphusa oxygona Nobili, 1901 (family Gecarcinucidae), is clarified. The species is redescribed and figured, and its taxonomy discussed. Specimens from western Kalimantan, Borneo, Indonesia, which have been referred to P. oxygona are here referred to a new species, Parathelphusa nobilii. The new species can be differentiated from congeners by its relatively more swollen branchial regions of the carapace, wider and lower external orbital tooth, relatively more slender male abdomen and a straight male first gonopod. 

Migration confers survival benefits against avian predators for partially migratory freshwater fish.

The importance of predation risk in shaping patterns of animal migration is not well studied, mostly owing to difficulties in accurately quantifying predation risk for migratory versus resident individuals. Here, we present data from an extensive field study, which shows that migration in a freshwater fish (roach, Rutilus rutilus) that commonly migrates from lakes to streams during winter confers a significant survival benefit with respect to bird (cormorant, Phalacrocorax carbo spp.) predation. We tagged over 2000 individual fish in two Scandinavian lakes over 4 years and monitored migratory behaviour using passive telemetry. Next, we calculated the predation vulnerability of fish with differing migration strategies, by recovering data from passive integrated transponder tags of fish eaten by cormorants at communal roosts close to the lakes. We show that fish can reduce their predation risk from cormorants by migrating into streams, and that probability of being preyed upon by cormorants is positively related to the time individuals spend in the lake during winter. Our data add to the growing body of evidence that highlights the importance of predation for migratory dynamics, and, to our knowledge, is one of the first studies to directly quantify a predator avoidance benefit to migrants in the field.

Fish fins as non-lethal surrogates for muscle tissues in freshwater food web studies using stable isotopes.

RATIONALE: Dorsal white muscle is the standard tissue analysed in fish trophic studies using stable isotope analyses. However, sampling white muscle often implies the sacrifice of fish. Thus, we examined whether the non-lethal sampling of fin tissue can substitute muscle sampling in food web studies. METHODS: Analysing muscle and fin δ(15)N and δ(13)C values of 466 European freshwater fish (14 species) with an elemental analyser coupled with an isotope ratio mass spectrometer, we compared the isotope values of the two tissues. Correlations between fin and muscle isotope ratios were examined for all fish together and specifically for 12 species. We further proposed four methods of assessing muscle from fin isotope ratios and estimated the errors made using these muscle surrogates. RESULTS: Despite significant differences between isotope values of the two tissues, fin and muscle isotopic signals are strongly correlated. Muscle values, estimated with raw fin isotope ratios (1st method), induce an error of ca. 1‰ for both isotopes. In comparison, specific (2nd method) or general (3rd method) correlations provide meaningful corrections of fin isotope ratios (errors <0.6‰). On the other hand, relationships, established for Australian tropical fish, only give poor muscle estimates (errors >0.8‰). CONCLUSIONS: There is little chance that a global model can be created. However, the 2nd and 3rd methods of estimating muscle values from fin isotope ratios should provide an acceptable level of error for the studies of European freshwater food web. We thus recommend that future studies use fin tissue as a non-lethal surrogate for muscle.

Recent changes in a remote Arctic lake are unique within the past 200,000 years.

The Arctic is currently undergoing dramatic environmental transformations, but it remains largely unknown how these changes compare with long-term natural variability. Here we present a lake sediment sequence from the Canadian Arctic that records warm periods of the past 200,000 years, including the 20th century. This record provides a perspective on recent changes in the Arctic and predates by approximately 80,000 years the oldest stratigraphically intact ice core recovered from the Greenland Ice Sheet. The early Holocene and the warmest part of the Last Interglacial (Marine Isotope Stage or MIS 5e) were the only periods of the past 200,000 years with summer temperatures comparable to or exceeding today's at this site. Paleoecological and geochemical data indicate that the past three interglacial periods were characterized by similar trajectories in temperature, lake biology, and lakewater pH, all of which tracked orbitally-driven solar insolation. In recent decades, however, the study site has deviated from this recurring natural pattern and has entered an environmental regime that is unique within the past 200 millennia.

Bacterial diversity on different surfaces in urban freshwater.

Microbial loads in freshwater systems have important implications in biogeochemical cycling in urban environments. Immersed surfaces in freshwaters provide surfaces for bacterial attachment and growth. Microorganisms that adhere initially to these surfaces play a critical role in biofilm formation and sustenance. Currently, there is little understanding on the type of organisms that initially adhere to different surfaces in urban canals. In this study, water from an urban stormwater canal was employed to allow bacteria to attach to different surfaces in a flowcell apparatus and understand the differences and changes in bacterial community structure. Bacterial communities were highly diverse on different surfaces as indicated by Jaccard's indices of 0.14-0.56. Bacteria on aluminium were the most diverse and on Plexiglas the least. Bacterial communities were highly dynamic in the early attachment phase and it changed by 59% between 3 and 6 h on aluminium. Specificity of attachment to surfaces was observed for some bacteria. Judicious use of materials in urban aquatic environment would help mitigate microbial load in urban waters.

Genetic and morphological variation of three freshwater lake populations of Coilia ectenes (Engraulidae).

Population structure of the important commercial fish, Coilia ectenes, was investigated in samples from three freshwater lakes in the Eastern China using a multivariate approach of morphometrics and mitochondrial DNA control region sequencing. A total of eighteen morphological distances of truss method and eight morphometric variables were taken from each fish. Multivariate analyses of the morphometric data revealed significant morphological differences among the three lake populations, especially for those samples from Taihu Lake. Discriminant functions were used to compare sites, and these permitted an 83% success rate in distinguishing fish from the three sites. However, no obviously geographical differentiation was found among those populations of C. ectenes based on the genetic data. In the AMOVA analysis, only 2.2% genetic variability came from different populations, and most of them were present within the sub-populations. Experience a recent population expansion and some movement of fish among those areas, quite possibly enough to bring about relative genetic homogeneity, but there is insufficient to prevent the three populations from differing phenotypically. The diversified environmental factors may be playing an important role in shaping morphological variations among those populations.

Memory and obesity affect the population dynamics of asexual freshwater planarians.

Asexual reproduction in multicellular organisms is a complex biophysical process that is not yet well understood quantitatively. Here, we report a detailed population study for the asexual freshwater planarian Schmidtea mediterranea, which can reproduce via transverse fission due to a large stem cell contingent. Our long-term observations of isolated non-interacting planarian populations reveal that the characteristic fission waiting time distributions for head and tail fragments differ significantly from each other. The stochastic fission dynamics of tail fragments exhibits non-negligible memory effects, implying that an accurate mathematical description of future data should be based on non-Markovian tree models. By comparing the effective growth of non-interacting planarian populations with those of self-interacting populations, we are able to quantify the influence of interactions between flatworms and physical conditions on the population growth. A surprising result is the non-monotonic relationship between effective population growth rate and nutrient supply: planarians exhibit a tendency to become 'obese' if the feeding frequency exceeds a critical level, resulting in a decreased reproduction activity. This suggests that these flatworms, which possess many genes homologous to those of humans, could become a new model system for studying dietary effects on reproduction and regeneration in multicellular organisms.

Quantity and quality: unifying food web and ecosystem perspectives on the role of resource subsidies in freshwaters.

Although the study of resource subsidies has emerged as a key topic in both ecosystem and food web ecology, the dialogue over their role has been limited by separate approaches that emphasize either subsidy quantity or quality. Considering quantity and quality together may provide a simple, but previously unexplored, framework for identifying the mechanisms that govern the importance of subsidies for recipient food webs and ecosystems. Using a literature review of > 90 studies of open-water metabolism in lakes and streams, we show that high-flux, low-quality subsidies can drive freshwater ecosystem dynamics. Because most of these ecosystems are net heterotrophic, allochthonous inputs must subsidize respiration. Second, using a literature review of subsidy quality and use, we demonstrate that animals select for high-quality food resources in proportions greater than would be predicted based on food quantity, and regardless of allochthonous or autochthonous origin. This finding suggests that low-flux, high-quality subsidies may be selected for by animals, and in turn may disproportionately affect food web and ecosystem processes (e.g., animal production, trophic energy or organic matter flow, trophic cascades). We then synthesize and review approaches that evaluate the role of subsidies and explicitly merge ecosystem and food web perspectives by placing food web measurements in the context of ecosystem budgets, by comparing trophic and ecosystem production and fluxes, and by constructing flow food webs. These tools can and should be used to address future questions about subsidies, such as the relative importance of subsidies to different trophic levels and how subsidies may maintain or disrupt ecosystem stability and food web interactions.