Exposure, but not timing of exposure, to a sulfonylurea herbicide alters larval development and behaviour in an amphibian species.

Environmental contamination is one of the major causes of biodiversity loss. Wetlands are particularly susceptible to contamination and species inhabiting these habitats are subjected to pollutants during sensitive phases of their development. In this study, tadpoles of a widespread amphibian, the spined toad (Bufo spinosus), were exposed to environmental concentrations of nicosulfuron (0 µg/L; 0.15 ± 0.05 µg/L and 0.83 ± 0.04 µg/L), a sulfonylurea herbicide, during different phases of development. Tadpoles were exposed during embryonic (12.98 ± 0.90 days) or larval development (93.74± 0.85 days), or throughout both phases, and we quantified development duration, morphological traits and behavioural features as responses to exposure. Developing tadpoles exposed to nicosulfuron were larger, but with smaller body, and had shorter but wider tail muscles. They were also more active and swam faster than control tadpoles and showed diverging patterns of behavioural complexity. We showed that higher concentrations had greater effects on individuals than lower concentrations, but the timing of nicosulfuron exposure did not influence the metrics studied: Exposure to nicosulfuron triggered similar effects irrespective of the developmental stages at which exposure occurred. These results further indicate that transient exposure (e.g., during embryonic development) can induce long-lasting effects throughout larval development to metamorphosis. Our study confirms that contaminants at environmental concentrations can have strong consequences on non-target organisms. Our results emphasize the need for regulation agencies and policy makers to consider sublethal concentrations of sulfonulyrea herbicides, such as nicosulfuron, as a minimum threshold in their recommendations.

Selective extinction against redundant species buffers functional diversity.

The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional redundancy. However, current knowledge is based on short timescales and an understanding of how functional diversity responds to long-term biodiversity dynamics has been limited by the availability of deep-time, trait-based data. Here, we compile an exceptional trait dataset of fossil molluscs from a 23-million-year interval in the Caribbean Sea (34 011 records, 4422 species) and develop a novel Bayesian model of multi-trait-dependent diversification to reconstruct mollusc (i) diversity dynamics, (ii) changes in functional diversity, and (iii) extinction selectivity over the last 23 Myr. Our results identify high diversification between 23-5 Mya, leading to increases in both functional richness and redundancy. Conversely, over the last three million years, a period of high extinction rates resulted in the loss of 49% of species but only 3% of functional richness. Extinction rates were significantly higher in small, functionally redundant species suggesting that competition mediated the response of species to environmental change. Taken together, our results identify long-term diversification and selective extinction against redundant species that allowed functional diversity to grow over time, ultimately buffering the ecological functions of biological communities against extinction.

Oceanic thermal structure mediates dive sequences in a foraging seabird.

Changes in marine ecosystems are easier to detect in upper-level predators, like seabirds, which integrate trophic interactions throughout the food web.Here, we examined whether diving parameters and complexity in the temporal organization of diving behavior of little penguins (Eudyptula minor) are influenced by sea surface temperature (SST), water stratification, and wind speed-three oceanographic features influencing prey abundance and distribution in the water column.Using fractal time series analysis, we found that foraging complexity, expressed as the degree of long-range correlations or memory in the dive series, was associated with SST and water stratification throughout the breeding season, but not with wind speed. Little penguins foraging in warmer/more-stratified waters exhibited greater determinism (memory) in foraging sequences, likely as a response to prey aggregations near the thermocline. They also showed higher foraging efficiency, performed more dives and dove to shallower depths than those foraging in colder/less-stratified waters.Reductions in the long-term memory of dive sequences, or in other words increases in behavioral stochasticity, may suggest different strategies concerning the exploration-exploitation trade-off under contrasting environmental conditions.

Simultaneous Bayesian inference of phylogeny and molecular coevolution.

Patterns of molecular coevolution can reveal structural and functional constraints within or among organic molecules. These patterns are better understood when considering the underlying evolutionary process, which enables us to disentangle the signal of the dependent evolution of sites (coevolution) from the effects of shared ancestry of genes. Conversely, disregarding the dependent evolution of sites when studying the history of genes negatively impacts the accuracy of the inferred phylogenetic trees. Although molecular coevolution and phylogenetic history are interdependent, analyses of the two processes are conducted separately, a choice dictated by computational convenience, but at the expense of accuracy. We present a Bayesian method and associated software to infer how many and which sites of an alignment evolve according to an independent or a pairwise dependent evolutionary process, and to simultaneously estimate the phylogenetic relationships among sequences. We validate our method on synthetic datasets and challenge our predictions of coevolution on the 16S rRNA molecule by comparing them with its known molecular structure. Finally, we assess the accuracy of phylogenetic trees inferred under the assumption of independence among sites using synthetic datasets, the 16S rRNA molecule and 10 additional alignments of protein-coding genes of eukaryotes. Our results demonstrate that inferring phylogenetic trees while accounting for dependent site evolution significantly impacts the estimates of the phylogeny and the evolutionary process.

CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates.

The study of molecular coevolution, due to its potential to identify gene regions under functional or structural constraints, has recently been subject to numerous scientific inquiries. Particular efforts have been conducted to develop methods predicting the presence of coevolution in molecular sequences. Among these methods, a few aim to model the underlying evolutionary process of coevolution, which enable to differentiate the shared history of genes to coevolution and thus improve their accuracy. However, the usage of such methods remains sparse due to their expensive computational cost and the lack of resources alleviating this issue. Here we present CoevDB (http://phylodb.unil.ch/CoevDB), a database containing the result of a large-scale analysis of intramolecular coevolution of 8201 protein-coding genes of bony vertebrates. The web interface of CoevDB gives access to the results to 800 millions of statistical tests corresponding to all the pairs of sites analyzed. Several type of queries enable users to explore the database by either targeting specific genes or by discovering genes having promising estimations of coevolution.

Reproductive performance and diving behaviour share a common sea-ice concentration optimum in Adélie penguins (Pygoscelis adeliae).

The Southern Ocean is currently experiencing major environmental changes, including in sea-ice cover. Such changes strongly influence ecosystem structure and functioning and affect the survival and reproduction of predators such as seabirds. These effects are likely mediated by reduced availability of food resources. As such, seabirds are reliable eco-indicators of environmental conditions in the Antarctic region. Here, based on 9 years of sea-ice data, we found that the breeding success of Adélie penguins (Pygoscelis adeliae) reaches a peak at intermediate sea-ice cover (ca. 20%). We further examined the effects of sea-ice conditions on the foraging activity of penguins, measured at multiple scales from individual dives to foraging trips. Analysis of temporal organisation of dives, including fractal and bout analyses, revealed an increasingly consistent behaviour during years with extensive sea-ice cover. The relationship between several dive parameters and sea-ice cover in the foraging area appears to be quadratic. In years of low and high sea-ice cover, individuals adjusted their diving effort by generally diving deeper, more frequently and by resting at the surface between dives for shorter periods of time than in years with intermediate sea-ice cover. Our study therefore suggests that sea-ice cover is likely to affect the reproductive performance of Adélie penguins through its effects on foraging behaviour, as breeding success and most diving parameters share a common optimum. Some years, however, deviated from this general trend, suggesting that other factors (e.g. precipitation during the breeding season) might sometimes become preponderant over the sea-ice effects on breeding and foraging performance. Our study highlights the value of monitoring fitness parameters and individual behaviour concomitantly over the long-term to better characterize optimal environmental conditions and potential resilience of wildlife. Such an approach is crucial if we want to anticipate the effects of environmental change on Antarctic penguin populations.

Accelerating Bayesian inference for evolutionary biology models.

Motivation: Bayesian inference is widely used nowadays and relies largely on Markov chain Monte Carlo (MCMC) methods. Evolutionary biology has greatly benefited from the developments of MCMC methods, but the design of more complex and realistic models and the ever growing availability of novel data is pushing the limits of the current use of these methods. Results: We present a parallel Metropolis-Hastings (M-H) framework built with a novel combination of enhancements aimed towards parameter-rich and complex models. We show on a parameter-rich macroevolutionary model increases of the sampling speed up to 35 times with 32 processors when compared to a sequential M-H process. More importantly, our framework achieves up to a twentyfold faster convergence to estimate the posterior probability of phylogenetic trees using 32 processors when compared to the well-known software MrBayes for Bayesian inference of phylogenetic trees. Availability and Implementation: https://bitbucket.org/XavMeyer/hogan. Contact: nicolas.salamin@unil.ch. Supplementary information: Supplementary data are available at Bioinformatics online.

Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.

BACKGROUND: Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial and probabilistic methods that look for coevolving positions in nucleotide or amino acid sequences. RESULTS: We have developed a web-based platform that gives a user-friendly access to two phylogenetic-based methods implementing the Coev model: the evaluation of coevolving scores and the simulation of coevolving positions. We have also extended the capabilities of the Coev model to allow for the generalization of the alphabet used in the Markov model, which can now analyse both nucleotide and amino acid data sets. The simulation of coevolving positions is novel and builds upon the developments of the Coev model. It allows user to simulate pairs of dependent nucleotide or amino acid positions. CONCLUSIONS: The main focus of our paper is the new simulation method we present for coevolving positions. The implementation of this method is embedded within the web platform Coev-web that is freely accessible at http://coev.vital-it.ch/, and was tested in most modern web browsers.

Different risk thresholds in pedestrian road crossing behaviour: a comparison of French and Japanese approaches.

When crossing the road, pedestrians have to make a trade-off between saving time and avoiding any risk of injuries. Here, we studied how culture influences an individual's perception of risks when crossing a street, using survival analysis. This study is the first to use this analysis to assess cognitive mechanisms and optimality of decisions underlying road crossing behaviour. We observed pedestrian behaviour in two city centres: Inuyama (Japan) and Strasbourg (France). In each city, observations were made at a safe site consisting of a crosswalk and a street light and at an unsafe site (i.e. no crosswalk or street light). At the unsafe site, we measured the time needed by a pedestrian to take a decision (Tdec). During Tdec, a pedestrian estimates whether he can (Tsafe) or cannot (Trisk) cross the road. Using survival analysis, we studied the distributions of these three time variables and showed that French pedestrians took more risks than Japanese pedestrians, and that males took more risks than females, but only in Japan. More studies would considerably broaden our understanding on how culture may affect decision-making processes under risky circumstances.