Annotation of Tribolium nuclear receptors reveals an evolutionary overacceleration of a network controlling the ecdysone cascade

The Tribolium genome contains 21 nuclear receptors, representing all of the six known subfamilies. When compared to other species, this first complete set for a Coleoptera reveals a strong conservation of the number and identity of nuclear receptors in holometabolous insects. Two novelties are observed: the atypical NR0 gene knirps is present only in brachyceran flies, while the NR2E6 gene is found only in Tribolium and in Apis. Using a quantitative analysis of the evolutionary rate, we discovered that nuclear receptors could be divided into two groups. In one group of 13 proteins, the rates follow the trend of the Mecopterida genome-wide acceleration. In a second group of five nuclear receptors, all acting together at the top of the ecdysone cascade, we observed an overacceleration of the evolutionary rate during the early divergence of Mecopterida. We thus extended our analysis to the twelve classic ecdysone transcriptional regulators and found that six of them (ECR, USP, HR3, E75, HR4 and Kr-h1) underwent an overacceleration at the base of the Mecopterida lineage. By contrast, E74, E93, BR, HR39, FTZ-F1 and E78 do not show this divergence. We suggest that coevolution occurred within a network of regulators that control the ecdysone cascade. The advent of Tribolium as a powerful model should allow a better understanding of this evolution

Annotation of Tribolium nuclear receptors reveals an increase in evolutionary rate of a network controlling the ecdysone cascade

Special Issue on the Tribolium GenomeThe Tribolium genome contains 21 nuclear receptors, representing all of the six known subfamilies. This first complete set for a coleopteran species reveals a strong conservation of the number and identity of nuclear receptors in holometabolous insects. Two novelties are observed: the atypical NR0 gene knirps is present only in brachyceran flies, while the NR2E6 gene is found only in Tribolium and in Apis. Using a quantitative analysis of the evolutionary rate, we discovered that nuclear receptors could be divided into two groups. In one group of 13 proteins, the rates follow the trend of the Mecopterida genome-wide acceleration. In a second group of five nuclear receptors, all acting early during the ecdysone cascade, we observed an even higher increase of the evolutionary rate during the early divergence of Mecopterida. We thus extended our analysis to the twelve classic ecdysone transcriptional regulators and found that six of them (ECR, USP, HR3, E75, HR4 and Kr-h1) underwent an increase in evolutionary rate at the base of the Mecopterida lineage. By contrast, E74, E93, BR, HR39, FTZ-F1 and E78 do not show this divergence. We suggest that coevolution occurred within a network of regulators that control the ecdysone cascade. The advent of Tribolium as a powerful model should allow a better understanding of this evolutionary event

Caged Gammarus fossarum (crustacea) as a robust tool for the characterization of bioavailable contamination levels in continental waters. Toward the determination of threshold values

We investigated the suitability of an active biomonitoring approach, using the ecologically relevant species Gammarus fossarum, to assess trends of bioavailable contamination in continental waters. Gammarids were translocated into cages at 27 sites, in the Rhône-Alpes region (France) during early autumn 2009. Study sites were chosen to represent different physico-chemical characteristics and various anthropic pressures. Biotic factors such as sex, weight and food availability were controlled in order to provide robust and comparable results. After one week of exposure, concentrations of 11 metals/metalloids (Cd, Pb, Hg, Ni, Zn, Cr, Co, Cu, As, Se and Ag) and 38 hydrophobic organic substances including polycyclic aromatic hydrocarbons (PAHs), polychlorobiphenyles (PCBs), pentabromodiphenylethers (PBDEs) and organochlorine pesticides, were measured in gammarids. All metals except Ag, and 33 organic substances among 38 were quantified in G. fossarum, showing that this species is relevant for chemical biomonitoring. The control of biotic factors allowed a robust and direct inter-site comparison of the bioavailable contamination levels. Overall, our results show the interest and robustness of the proposed methodological approach for assessing trends of bioavailable contamination, notably for metals and hydrophobic organic contaminants, in continental waters. Furthermore, we built threshold values of bioavailable contamination in gammarids, above which measured concentrations are expected to reveal a bioavailable contamination at the sampling site. Two ways to define such values were investigated, a statistical approach and a model fit. Threshold values were determined for almost all the substances investigated in this study and similar values were generally derived from the two approaches. Then, levels of contaminants measured in G. fossarum at the 27 study were compared to the threshold values obtained using the model fit. These threshold values could serve as a basis for further implementation of quality grids to rank sites according to the extent of the bioavailable contamination, with regard to the applied methodology

Life-history phenology strongly influences population vulnerability to toxicants: a case study with the mudsnail Potamopyrgus antipodarum.

International audienceOne of the main objectives of ecological risk assessment is to evaluate the effects of toxicants on ecologically relevant biological systems such as populations or communities. However, the effects of toxicants are commonly measured on selected subindividual or individual endpoints due to their specificity against chemical stressors. Introducing these effects into population models is a promising way to predict impacts on populations. The models currently employed are very simplistic, and their environmental relevance needs to be improved to establish the ecological relevance of hazard assessment. The present study with the gastropod Potamopyrgus antipodarum combines a field experimental approach with a modeling framework. It clarifies the role played by seasonal variability of life-history traits in the population's vulnerability to the alteration of individual performance, potentially due to toxic stress. The present study comprised 3 steps: 1) characterization of the seasonal variability in life-history traits of a local population over 1 yr by using in situ experiments on caged snails, coupled with a demographic follow-up; 2) development of a periodic matrix population model that visualizes the monthly variability of population dynamics; and 3) simulation of the demographic consequences of an alteration in life-history traits (i.e., fertility, juvenile, and adult survival). The results revealed that demographic impacts strongly depend on the season when alterations of individual performance occur. Model analysis showed that this seasonal variability in population vulnerability is strongly related to the phenology of the population. The authors emphasize that improving the realism of population models is a major objective for ecological risk assessment, and that taking into account species phenology in modeling approaches should be a priority

Dynamic Habitat Disturbance and Ecological Resilience (DyHDER): Modeling Population Responses to Habitat Condition

Understanding how populations respond to spatially heterogeneous habitat disturbance is as critical to conservation as it is challenging. Here, we present a new, free, and open‐source metapopulation model: Dynamic Habitat Disturbance and Ecological Resilience (DyHDER), which incorporates subpopulation habitat condition and connectivity into a population viability analysis framework. Modeling temporally dynamic and spatially explicit habitat disturbance of varying magnitude and duration is accomplished through the use of habitat time‐series data and a mechanistic approach to adjusting subpopulation vital rates. Additionally, DyHDER uses a probabilistic dispersal model driven by site‐specific habitat suitability, density dependence, and directionally dependent connectivity. In the first application of DyHDER, we explore how fragmentation and projected climate change are predicted to impact a well‐studied Bonneville cutthroat trout metapopulation in the Logan River (Utah, USA). The DyHDER model predicts which subpopulations are most susceptible to disturbance, as well as the potential interactions between stressors. Further, the model predicts how populations may be expected to redistribute following disturbance. This information is valuable to conservationists and managers faced with protecting populations of conservation concern across landscapes undergoing changing disturbance regimes. The DyHDER model provides a valuable and generalizable new tool to explore metapopulation resilience to spatially and temporally dynamic stressors for a diverse range of taxa and ecosystems

Aggregation methods in dynamical systems and applications in population and community dynamics

Approximate aggregation techniques allow one to transform a complex system involving many coupled variables into a simpler reduced model with a lesser number of global variables in such a way that the dynamics of the former can be approximated by that of the latter. In ecology, as a paradigmatic example, we are faced with modelling complex systems involving many variables corresponding to various interacting organization levels. This review is devoted to approximate aggregation methods that are based on the existence of different time scales, which is the case in many real systems as ecological ones where the different organization levels (individual, population, community and ecosystem) possess a different characteristic time scale. Two main goals of variables aggregation are dealt with in this work. The first one is to reduce the dimension of the mathematical model to be handled analytically and the second one is to understand how different organization levels interact and which properties of a given level emerge at other levels. The review is organized in three sections devoted to aggregation methods associated to different mathematical formalisms: ordinary differential equations, infinite-dimensional evolution equations and difference equations

Interactive Effects of Pesticides and Nutrients on Microbial Communities Responsible of Litter Decomposition in Streams

Global contamination of streams by a large variety of compounds, such as nutrients and pesticides, may exert a high pressure on aquatic organisms, including microbial communities and their activity of organic matter decomposition. In this study, we assessed the potential interaction between nutrients and a fungicide and herbicide [tebuconazole (TBZ) and S-metolachlor (S-Met), respectively] at realistic environmental concentrations on the structure (biomass, diversity) and decomposition activity of fungal and bacterial communities (leaf decay rates, extracellular enzymatic activities) associated with Alnus glutinosa (Alnus) leaves. A 40-day microcosm experiment was used to combine two nutrient conditions (mesotrophic and eutrophic) with four pesticide treatments at a nominal concentrations of 15 μg L-1 (control, TBZ and S-Met, alone or mixed) following a 2 × 4 full factorial design. We also investigated resulting indirect effects on Gammarus fossarum feeding rates using leaves previously exposed to each of the treatments described above. Results showed interactive effects between nutrients and pesticides, only when nutrient (i.e., nitrogen and phosphorus) concentrations were the highest (eutrophic condition). Specifically, slight decreases in Alnus leaf decomposition rates were observed in channels exposed to TBZ (0.01119 days-1) and S-Met (0.01139 days-1) than in control ones (0.01334 days-1) that can partially be explained by changes in the structure of leaf-associated microbial communities. However, exposition to both TBZ and S-Met in mixture (MIX) led to comparable decay rates to those exposed to the pesticides alone (0.01048 days-1), suggesting no interaction between these two compounds on microbial decomposition. Moreover, stimulation in ligninolytic activities (laccase and phenol oxidase) was observed in presence of the fungicide, possibly highlighting detoxification mechanisms employed by microbes. Such stimulation was not observed for laccase activity exposed to the MIX, suggesting antagonistic interaction of these two compounds on the ability of microbial communities to cope with stress by xenobiotics. Besides, no effects of the treatments were observed on leaf palatability for macroinvertebrates. Overall, the present study highlights that complex interactions between nutrients and xenobiotics in streams and resulting from global change can negatively affect microbial communities associated with leaf litter, although effects on higher trophic-level organisms remains unclear

Unexpected Novel Relational Links Uncovered by Extensive Developmental Profiling of Nuclear Receptor Expression

Nuclear receptors (NRs) are transcription factors that are implicated in several biological processes such as embryonic development, homeostasis, and metabolic diseases. To study the role of NRs in development, it is critically important to know when and where individual genes are expressed. Although systematic expression studies using reverse transcriptase PCR and/or DNA microarrays have been performed in classical model systems such as Drosophila and mouse, no systematic atlas describing NR involvement during embryonic development on a global scale has been assembled. Adopting a systems biology approach, we conducted a systematic analysis of the dynamic spatiotemporal expression of all NR genes as well as their main transcriptional coregulators during zebrafish development (101 genes) using whole-mount in situ hybridization. This extensive dataset establishes overlapping expression patterns among NRs and coregulators, indicating hierarchical transcriptional networks. This complete developmental profiling provides an unprecedented examination of expression of NRs during embryogenesis, uncovering their potential function during central nervous system and retina formation. Moreover, our study reveals that tissue specificity of hormone action is conferred more by the receptors than by their coregulators. Finally, further evolutionary analyses of this global resource led us to propose that neofunctionalization of duplicated genes occurs at the levels of both protein sequence and RNA expression patterns. Altogether, this expression database of NRs provides novel routes for leading investigation into the biological function of each individual NR as well as for the study of their combinatorial regulatory circuitry within the superfamily

De <i>novo </i>transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups

Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species