Interfibrillar stiffening of echinoderm mutable collagenous tissue demonstrated at the nanoscale

The mutable collagenous tissue (MCT) of echinoderms (e.g., sea cucumbers and starfish) is a remarkable example of a biological material that has the unique attribute, among collagenous tissues, of being able to rapidly change its stiffness and extensibility under neural control. However, the mechanisms of MCT have not been characterized at the nanoscale. Using synchrotron small-angle X-ray diffraction to probe time-dependent changes in fibrillar structure during in situ tensile testing of sea cucumber dermis, we investigate the ultrastructural mechanics of MCT by measuring fibril strain at different chemically induced mechanical states. By measuring a variable interfibrillar stiffness (E(IF)), the mechanism of mutability at the nanoscale can be demonstrated directly. A model of stiffness modulation via enhanced fibrillar recruitment is developed to explain the biophysical mechanisms of MCT. Understanding the mechanisms of MCT quantitatively may have applications in development of new types of mechanically tunable biomaterials

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL

Hybrid off-river augmentation system as an alternative raw water resource: the hydrogeochemistry of abandoned mining ponds

The use of water from abandoned mining ponds under a hybrid off-river augmentation system (HORAS) has been initiated as an alternative water resource for raw water. However, it raises the questions over the safety of the use of such waters. In this study, the hydrogeochemical analysis of the waters is presented to assess the degree to which the water has been contaminated. Comparisons were made between sampling sites, i.e. abandoned mining ponds, active sand mining ponds and the receiving streams within Bestari Jaya, Selangor River basin. The aqueous geochemistry analysis showed different hydrochemical signatures of major elements between sites, indicating different sources of minerals in the water. Discharges from the sand mining ponds were found to contain elevated availability of dissolved concentrations of iron, manganese, lead, copper and zinc, among others. However, the quality of the water (from the main river) that is supplied for potable water consumption is at a satisfactory level despite being partly sourced from the abandoned mining ponds. In fact, all the metal concentrations detected were well below the Malaysia Ministry of Health guideline limits for untreated raw water. In addition, the results of the geochemical index analysis (i.e. geoaccumulation index, enrichment factor and modified contamination factor) showed that the rivers and abandoned mining ponds were generally unpolluted with respect to the metals found in sediments

Larval survivorship and settlement of crown-of-thorns starfish (Acanthaster cf. solaris) at varying algal cell densities

The dispersal potential of crown-of-thorns starfish (CoTS) larvae is important in understanding both the initiation and spread of population outbreaks, and is fundamentally dependent upon how long larvae can persist while still retaining the capacity to settle. This study quantified variation in larval survivorship and settlement rates for CoTS maintained at three different densities of a single-celled flagellate phytoplankton, Proteomonas sulcata (1 x 10^3, 1 x 10^4, and 1 x 10^5 cells/mL). Based on the larval starvation hypothesis, we expected that low to moderate levels of phytoplankton prey would significantly constrain both survival and settlement. CoTS larvae were successfully maintained for up to 50 days post-fertilization, but larval survival differed significantly between treatments. Survival was greatest at intermediate food levels (1 x 10^4 cells/mL), and lowest at high (1 x 10^5 cells/mL) food levels. Rates of settlement were also highest at intermediate food levels and peaked at 22 days post-fertilization. Peak settlement was delayed at low food levels, probably reflective of delayed development, but there was no evidence of accelerated development at high chlorophyll concentrations. CoTS larvae were recorded to settle 17–43 days post-fertilization, but under optimum conditions with intermediate algal cell densities, peak settlement occurred at 22 days post-fertilization. Natural fluctuations in nutrient concentrations and food availability may affect the number of CoTS that effectively settle, but seem unlikely to influence dispersal dynamics

Understanding ‘it depends’ in ecology: A guide to hypothesising, visualising and interpreting statistical interactions

Ecologists routinely use statistical models to detect and explain interactions among ecological drivers, with a goal to evaluate whether an effect of interest changes in sign or magnitude in different contexts. Two fundamental properties of interactions are often overlooked during the process of hypothesising, visualising and interpreting interactions between drivers: the measurement scale – whether a response is analysed on an additive or multiplicative scale, such as a ratio or logarithmic scale; and the symmetry – whether dependencies are considered in both directions. Overlooking these properties can lead to one or more of three inferential errors: misinterpretation of (i) the detection and magnitude (Type-D error), and (ii) the sign of effect modification (Type-S error); and (iii) misidentification of the underlying processes (Type-A error). We illustrate each of these errors with a broad range of ecological questions applied to empirical and simulated data sets. We demonstrate how meta-analysis, a widely used approach that seeks explicitly to characterise context dependence, is especially prone to all three errors. Based on these insights, we propose guidelines to improve hypothesis generation, testing, visualisation and interpretation of interactions in ecology

Disentangling nonrandom structure from random placement when estimating β-diversity through space or time

There is considerable interest in understanding patterns of β-diversity that measure the amount of change in species composition through space or time. Most hypotheses for β-diversity evoke nonrandom processes that generate spatial and temporal within-species aggregation; however, β-diversity can also be driven by random sampling processes. Here, we describe a framework based on rarefaction curves that quantifies the nonrandom contribution of species compositional differences across samples to β-diversity. We isolate the effect of within-species spatial or temporal aggregation on beta-diversity using a coverage standardized metric of β-diversity (βC). We demonstrate the utility of our framework using simulations and an empirical case study examining variation in avian species composition through space and time in engineered versus natural riparian areas. The primary strengths of our approach are that it provides an intuitive visual null model for expected patterns of biodiversity under random sampling that allows integrating analyses across α-, γ-, and β-scales. Importantly, the method can accommodate comparisons between communities with different species pool sizes, and it can be used to examine species turnover both within and between meta-communities

Synthesis reveals approximately balanced biotic differentiation and homogenization

This work was supported by the German Research Foundation (FZT 118, to S.A.B., T.E., A.S., R.v.K., W.-B.X., and J.M.C.) and ERC GA 101044975 and the Leverhulme Centre for Anthropocene Biodiversity (to M.D.). This work was also supported by the German Research Foundation (DFG) project “Establishment of the National Research Data Infrastructure (NFDI)” in the consortium NFDI4Biodiversity (project number 442032008) (to T.E.), European Union Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 894644 (to I.S.M.), USDA Hatch grant MAFES #1011538 and NSF EPSCOR Track II grant #2019470 (to B.M.), and NSF Track II grant #2019470 (to N.J.G.).It is commonly thought that the biodiversity crisis includes widespread declines in the spatial variation of species composition, called biotic homogenization. Using a typology relating homogenization and differentiation to local and regional diversity changes, we synthesize patterns across 461 metacommunities surveyed for 10 to 91 years, and 64 species checklists (13 to 500+ years). Across all datasets, we found that no change was the most common outcome, but with many instances of homogenization and differentiation. A weak homogenizing trend of a 0.3% increase in species shared among communities/year on average was driven by increased numbers of widespread (high occupancy) species and strongly associated with checklist data that have longer durations and large spatial scales. At smaller spatial and temporal scales, we show that homogenization and differentiation can be driven by changes in the number and spatial distributions of both rare and common species. The multiscale perspective introduced here can help identify scale-dependent drivers underpinning biotic differentiation and homogenization.Peer reviewe

Supplementary information files for Regional occupancy increases for widespread species but decreases for narrowly distributed species in metacommunity time series

Supplementary files for article Regional occupancy increases for widespread species but decreases for narrowly distributed species in metacommunity time series   While human activities are known to elicit rapid turnover in species composition through time, the properties of the species that increase or decrease their spatial occupancy underlying this turnover are less clear. Here, we used an extensive dataset of 238 metacommunity time series of multiple taxa spread across the globe to evaluate whether species that are more widespread (large-ranged species) differed in how they changed their site occupancy over the10-90 years the metacommunities were monitored relative to species that are more narrowly distributed (small-ranged species). We found that on average, large-ranged species tended to increase in occupancy through time, whereas small-ranged species tended to decrease. These relationships were stronger in marine than in terrestrial and freshwater realms. However, in terrestrial regions, the directional changes in occupancy were less extreme in protected areas. Our findings provide evidence for systematic decreases in occupancy of small-ranged species, and that habitat protection could mitigate these losses in the face of environmental change.</p

Six years of demography data for 11 reef coral species

Scleractinian corals are colonial animals with a range of life history strategies, making up diverse species assemblages that define coral reefs. We tagged and tracked approximately 30 colonies from each of 11 species during seven trips spanning six years (2009-2015) in order to measure their vital rates and competitive interactions on the reef crest at Trimodal Reef, Lizard Island, Australia. Pairs of species were chosen from five growth forms where one species of the pair was locally rare (R) and the other common (C). The sampled growth forms were massive [Goniastrea pectinata (R) and G. retiformis (C)], digitate [Acropora humilis (R) and A. cf. digitifera (C)], corymbose [A. millepora (R) and A. nasuta (C)], tabular [A. cytherea (R) and A. hyacinthus (C)] and arborescent [A. robusta (R) and A. intermedia (C)]. An extra corymbose species with intermediate abundance, A. spathulata was included when it became apparent that A. millepora was too rare on the reef crest, making the 11 species in total. The tagged colonies were visited each year in the weeks prior to spawning. During visits, two or more observers each took 2-3 photographs of each tagged colony from directly above and on the horizontal plane with a scale plate to track planar area. Dead or missing colonies were recorded and new colonies tagged in order to maintain approximately 30 colonies per species throughout the six years of the study. In addition to tracking tagged corals, 30 fragments were collected from neighboring untagged colonies of each species for counting numbers of eggs per polyp (fecundity); and fragments of untagged colonies were brought into the laboratory where spawned eggs were collected for biomass and energy measurements. We also conducted surveys at the study site to generate size structure data for each species in several of the years. Each tagged colony photograph was digitized by at least two people. Therefore, we could examine sources of error in planar area for both photographers and outliners. Competitive interactions were recorded for a subset of species by measuring the margins of tagged colony outlines interacting with neighboring corals. The study was abruptly ended by Tropical Cyclone Nathan (Category 4) that killed all but nine of the over 300 tagged colonies in early 2015. Nonetheless, these data will be of use to other researchers interested in coral demography and coexistence, functional ecology, and parametrizing population, community and ecosystem models. The data set is not copyright restricted, and users should cite this paper when using the data.Publisher PDFPeer reviewe

Disentangling nonrandom structure from random placement when estimating β-diversity through space or time

There is considerable interest in understanding patterns of β-diversity that measure the amount of change in species composition through space or time. Most hypotheses for β-diversity evoke nonrandom processes that generate spatial and temporal within-species aggregation; however, β-diversity can also be driven by random sampling processes. Here, we describe a framework based on rarefaction curves that quantifies the nonrandom contribution of species compositional differences across samples to β-diversity. We isolate the effect of within-species spatial or temporal aggregation on beta-diversity using a coverage standardized metric of β-diversity (βC). We demonstrate the utility of our framework using simulations and an empirical case study examining variation in avian species composition through space and time in engineered versus natural riparian areas. The primary strengths of our approach are that it provides an intuitive visual null model for expected patterns of biodiversity under random sampling that allows integrating analyses across α-, γ-, and β-scales. Importantly, the method can accommodate comparisons between communities with different species pool sizes, and it can be used to examine species turnover both within and between meta-communities