Hidden biodiversity in Neotropical streams: DNA barcoding uncovers high endemicity of freshwater macroinvertebrates at small spatial scales.

Aquatic macroinvertebrates play a crucial role in freshwater ecosystems, but their diversity remains poorly known, particularly in the tropics. This "taxonomic void" limits our understanding of biodiversity patterns and processes in freshwater ecosystems, and the scale at which they operate. We used DNA barcoding to estimate lineage diversity (and the diversity of unique haplotypes) in 224 specimens of freshwater macroinvertebrates at a small spatial scale within the Panama Canal Watershed (PCW). In addition, we compiled available barcoding data to assess macroinvertebrate diversity at a broader spatial scale spanning the Isthmus of Panama. Consistently across two species delimitation algorithms (i.e., ABGD and GMYC), we found high lineage diversity within the PCW, with ~ 100-106 molecular operational taxonomic units (MOTUs) across 168 unique haplotypes. We also found a high lineage diversity along the Isthmus of Panama, but this diversity peaked within the PCW. However, our rarefaction/extrapolation approach showed that this diversity remains under-sampled. As expected, these results indicate that the diversity of Neotropical freshwater macroinvertebrates is higher than previously thought, with the possibility of high endemicity even at narrow spatial scales. Consistent with previous work on aquatic insects and other freshwater taxa in this region, geographic isolation is likely a main factor shaping these patterns of diversity. However, other factors such as habitat variability and perhaps local adaptation might be reshaping these patterns of diversity at a local scale. Although further research is needed to better understand the processes driving diversification in freshwater macroinvertebrates, we suggest that Neotropical streams hold a high proportion of hidden biodiversity. Understanding this diversity is crucial in the face of increasing human disturbance.

Evidence of an ancient connectivity and biogeodispersal of a bitterling species, Rhodeus notatus, across the Korean Peninsula.

The modern-day distribution of freshwater fishes throughout multiple rivers is likely the result of past migration during times when currently separate drainages were once connected. Here, we used mitochondrial and microsatellite analyses for 248 individuals of Rhodeus notatus collected from seven different rivers to obtain better understand historical gene flow of freshwater fish on the Korean Peninsula. Based on our phylogenetic analyses, this Korean species originated through the paleo-Yellow River from China and first colonized near the west coast. These genetic data also provided evidence of estuary coalescences among the rivers flowing to the west and southwest coast on well-developed continental shelf. In addition, the pattern of population structure revealed the biogeodispersal route from the west coast to the south coast. It could be inferred that massive migration was not involved in the formation of southern populations, since the signature of historical genetic drift was clearly observed. Our study is the first genetic attempt to confirm hypotheses describing the migration of freshwater species towards the end of East Asia, which have previously been developed using only geological reasoning.

Biologia Futura: integrating freshwater ecosystem health in water resources management.

Sustainable water use implies the simultaneous protection of water quality and quantity. Beyond their function to support human needs such as drinking water provision, transportation and recreation freshwater bodies are also habitats. Conceiving them as water users on their own with respective biological, physico-chemical and morphological requirements could help maintaining their healthy state. Healthy freshwater ecosystems are also attractive for high-value human uses. Dwindling per capita availability of water, increasing demands, human well-being and climate change lead to competition for, and pressures on freshwater ecosystems. This has been conceptualized through the modification of the drivers-pressures-state-impacts-responses framework. This distinguishes between pressures, associated with the achievement of human well-being, and stressors, which are defined as the negative effect of excessive pressures or combination thereof on aquatic ecosystems. Guidelines usually specify threshold values to classify water bodies as appropriate for certain utilitarian uses. However, only few guidelines focus on freshwater ecosystem health. Eight guidelines for monitoring of freshwater ecosystem health were analysed in the UNEP-funded project "International Water Quality Guidelines for Ecosystems". Based on this review, general benchmark values are proposed for key physico-chemical indicators. Furthermore, adaptive pathways towards improved monitoring and protection of the health of freshwater ecosystems are recommended. In this paper, we review the main findings of the report and also review its recent uptake. Water quality guidelines for freshwater ecosystems cannot be conceived without societal consensus and vision. Different climatic, geographical and socioeconomic contexts are to be considered too. Their development is embedded in an adaptive cycle. Its multiple phases and steps indicate a long-term approach including reassessment and potential revisions.

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.

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.

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.

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.

Hot spring siliceous stromatolites from Yellowstone National Park: assessing growth rate and laminae formation.

Stromatolites are commonly interpreted as evidence of ancient microbial life, yet stromatolite morphogenesis is poorly understood. We apply radiometric tracer and dating techniques, molecular analyses and growth experiments to investigate siliceous stromatolite morphogenesis in Obsidian Pool Prime (OPP), a hot spring in Yellowstone National Park. We examine rates of stromatolite growth and the environmental and/or biologic conditions that affect lamination formation and preservation, both difficult features to constrain in ancient examples. The "main body" of the stromatolite is composed of finely laminated, porous, light-dark couplets of erect (surface normal) and reclining (surface parallel) silicified filamentous bacteria, interrupted by a less-distinct, well-cemented "drape" lamination. Results from dating studies indicate a growth rate of 1-5 cm year(-1) ; however, growth is punctuated. (14)C as a tracer demonstrates that stromatolite cyanobacterial communities fix CO(2) derived from two sources, vent water (radiocarbon dead) and the atmosphere (modern (14)C). The drape facies contained a greater proportion of atmospheric CO(2) and more robust silica cementation (vs. the main body facies), which we interpret as formation when spring level was lower. Systematic changes in lamination style are likely related to environmental forcing and larger scale features (tectonic, climatic). Although the OPP stromatolites are composed of silica and most ancient forms are carbonate, their fine lamination texture requires early lithification. Without early lithification, whether silica or carbonate, it is unlikely that a finely laminated structure representing an ancient microbial mat would be preserved. In OPP, lithification on the nearly diurnal time scale is likely related to temperature control on silica solubility.

[Nonparametric methods for comparative assessment of species diversity as applied to riverine macrozoobenthic communities].

Models for relationship between sampling effort and estimates of species number and other characteristics of species diversity are considered and evaluated. In the analysis, different randomization algorithms and other statistical methods of monitoring data processing are used including jackknife and bootstrap procedures, algorithms ICE and Chao2, Colwell-Mao interpolation model, Mikhaelis-Menten curves, and others. A comparative analysis of overall species richness in macrozoobenthic communities using streams of the Lower Volga basin as a case study is performed with the aid of different extrapolation models, and the resulting estimates are discussed. The relationships are analyzed between sampling effort (number of hydrobiological samples) and cumulative estimates of species richness and basic indices of species diversity. The means towards improvement of conclusions substantiation when ranking riverine communities by species diversity are considered.

Understanding behavioral responses of fish to pheromones in natural freshwater environments.

There is an abundance of experimental studies and reviews that describe odorant-mediated behaviors of fish in laboratory microcosms, but research in natural field conditions has received considerably less attention. Fish pheromone studies in laboratory settings can be highly productive and allow for controlled experimental designs; however, laboratory tanks and flumes often cannot replicate all the physical, physiological and social contexts associated with natural environments. Field experiments can be a critical step in affirming and enhancing understanding of laboratory discoveries and often implicate the ecological significance of pheromones employed by fishes. When findings from laboratory experiments have been further tested in field environments, often different and sometimes contradictory conclusions are found. Examples include studies of sea lamprey (Petromyzon marinus) mating pheromones and fish alarm substances. Here, we review field research conducted on fish pheromones and alarm substances, highlighting the following topics: (1) contradictory results obtained in laboratory and field experiments, (2) how environmental context and physiological status influences behavior, (3) challenges and constraints of aquatic field research and (4) innovative techniques and experimental designs that advance understanding of fish chemical ecology through field research.

[The model of development of science by the example of limnology].

Limnology--the science about lakes is the young and relatively closed area of studies; its existence is owing to several hundreds of scientists. The International Society of Limnologists holds its meetings since 1922. We used materials of these meetings to find out the main stages of development of this science; among these stages there were both fast and relatively calm periods. Based on analysis of these data, we constructed a model of development of the science, the same data being used for tuning and verification of the model. We have suggested that the main regularities and of development of limnology can be extrapolated to other sciences. The main "acting person" in the model is population of scientists. Each scientist, with some probability, can propose new ideas as well as use in his elaborations some particular complex of the already accumulated knowledge and ideas. The model also takes into consideration how the scientific information is spreading, specifically some individual peculiarities of model scientists, such as age, experience, communicability. After the model parameters had been chosen in such a way that is described adequately the development of limnology, we performed a series of experiments by changing some of the characteristics and obtained rather unexpected results published preliminary in the short work (Levchenko V. F and Menshutkin V. V. Int. J. Comp. Anticip. Syst., 2008, vol. 22, p. 63-75) and discussed here in the greater detail. It is revealed, that the development of science is passing irregularly and sharply decelerated at low level of scientists communication and absence of scientific schools, and that the age of "scientific youth" of scientist begins usually only after 40 years.

Bioactive phenols in algae: the application of pressurized-liquid and solid-phase extraction techniques.

A new extraction technique based on the off-line combination of pressurized-liquid with solid-phase extraction (PLE-SPE) is described. The method was used for the extraction of bioactive phenolic acids (protocatechuic, p-hydroxybenzoic, 2,3-dihydroxybenzoic, chlorogenic, vanillic, caffeic, p-coumaric, salicylic acid), cinnamic acid and hydroxybenzaldehydes (p-hydroxybenzaldehyde, 3,4-dihydroxybenzaldehyde, vanillin) from in vitro culture of two freshwater algae (Anabaena doliolum and Spongiochloris spongiosa) and from food products of marine macroalgae Porphyra tenera (nori) and Undaria pinnatifida (wakame). For the identification and quantification of the compounds the molecular ions [M-H](-) and specific fragments were analyzed by quadrupole mass spectrometry analyzer connected on-line with a reversed-phase HPLC system. Our analysis showed that the freshwater algae and marine algal products contained submicrogram or microgram level of above-mentioned phenols per gram of lyophilized sample. In addition, the total phenol content (Folin-Ciocalteu assay) and antioxidant activity (TEAC assay, Trolox equivalent antioxidant capacity assay) of the PLE-SPE extracts were determined and discussed.