Signs of stabilisation and stable coexistence

Many empirical studies motivated by an interest in stable coexistence have quantified negative density dependence, negative frequency dependence, or negative plant–soil feedback, but the links between these empirical results and ecological theory are not straightforward. Here, we relate these analyses to theoretical conditions for stabilisation and stable coexistence in classical competition models. By stabilisation, we mean an excess of intraspecific competition relative to interspecific competition that inherently slows or even prevents competitive exclusion. We show that most, though not all, tests demonstrating negative density dependence, negative frequency dependence, and negative plant–soil feedback constitute sufficient conditions for stabilisation of two‐species interactions if applied to data for per capita population growth rates of pairs of species, but none are necessary or sufficient conditions for stable coexistence of two species. Potential inferences are even more limited when communities involve more than two species, and when performance is measured at a single life stage or vital rate. We then discuss two approaches that enable stronger tests for stable coexistence‐invasibility experiments and model parameterisation. The model parameterisation approach can be applied to typical density‐dependence, frequency‐dependence, and plant–soil feedback data sets, and generally enables better links with mechanisms and greater insights, as demonstrated by recent studies.     

Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors

Acute myeloid leukemia (AML) is characterized by fast progression and low survival rates, in which Fms-like tyrosine kinase 3 (FLT3) receptor mutations have been identified as a driver mutation in cancer progression in a subgroup of AML patients. Clinical trials have shown emergence of drug resistant mutants, emphasizing the ongoing need for new chemical matter to enable the treatment of this disease. Here, we present the discovery and topological structure-activity relationship (SAR) study of analogs of isoquinolinesulfonamide H-89, a well-known PKA inhibitor, as FLT3 inhibitors. Surprisingly, we found that the SAR was not consistent with the observed binding mode of H-89 in PKA. Matched molecular pair analysis resulted in the identification of highly active sub-nanomolar azaindoles as novel FLT3-inhibitors. Structure based modelling using the FLT3 crystal structure suggested an alternative, flipped binding orientation of the new inhibitors.     

Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists

Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1–S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research.

This is part of the PLOS Computational Biology Education collection.

     

The intertidal mudflats of Barr Al Hikman,Sultanate of Oman,as feeding,reproduction and nursery grounds for brachyuran crabs

Brachyuran crabs are an important ecological and economical, yet often unstudied aspect of intertidal mudflats of the Arabian Peninsula. Here we provide baseline density estimates of crabs at the relatively pristine intertidal mudflats of Barr Al Hikman (Sultanate of Oman) and provide information on their life cycle and habitat preference. Across the winters of 2012–2015 crabs were sampled on a grid covering the entire intertidal depth gradient. 29 species were found and average densities varied between 12 and 54 crabs/m². Deposit-feeding and herbivorous crabs were the most abundant species across all winters. Size frequency data and the presence of ovigerous females show that most crabs species reproduce in the intertidal area. P. segnis, the most important crab for local fisheries, was found to use the intertidal area as a nursery ground. We analysed the relationships between the two most abundant crab species, Macrophthalmus sulcatus and Thalamita poissonii and the environmental variables: seagrass density, tidal elevation, median grain size and sediment depth using Random Forest models. The predictive capacity of the models and the relative importance of the environmental predictors varied between years, but crab densities in general were positively associated with seagrass density, presumably because seagrass offers feeding habitat.

     

Sod cutting and soil biota effects on seedling performance

Sod cutting (i.e. top soil removal) is a restoration management option for enhancing seedling establishment and for lowering the nutrient concentration in eutrophicated soils of nutrient-poor species-rich grasslands. Removal of the upper soil changes not only abiotic soil properties but may also affect the resident soil community. We investigated the effects of sod cutting on the establishment and performance of two endangered plant species (Cirsium dissectum and Succisa pratensis) while simultaneously manipulating the interaction between seedlings and soil biota. In intact grassland and sod-cut areas at two localities, seedlings were grown in plastic tubes. Half of the tubes had a filter that excluded roots but allowed entry of fungal hyphae and soil microorganisms. The other tubes were closed (i.e. no contact with the surrounding soil). In a greenhouse experiment we studied the effect of soil solutions (with or without fungal tissue) from three grasslands and three sod-cut areas on seedling growth. Sod cutting had a positive net effect on seedling growth for S. pratensis. Access to (mycorrhizal) fungi and other soil biota resulted in a negative impact on seedling growth of both plant species, both in grassland and sod-cut areas. The greenhouse experiment confirmed that the soil biota in these meadows reduced seedling growth. Although sod cutting did not mitigate negative plant-soil feedback, it enhanced seedling growth, presumably by decreasing competition for light. Sod cutting is therefore very useful when seedling establishment needs to be stimulated.     

The Community Structure of the European Network of Interlocking Directorates 2005–2010

The boards of directors at large European companies overlap with each other to a sizable extent both within and across national borders. This could have important economic, political and management consequences. In this work we study in detail the topological structure of the networks that arise from this phenomenon. Using a comprehensive information database, we reconstruct the implicit networks of shared directorates among the top 300 European firms in 2005 and 2010, and suggest a number of novel ways to explore the trans-nationality of such business elite networks. Powerful community detection heuristics indicate that geography still plays an important role: there exist clear communities and they have a distinct national character. Nonetheless, from 2005 to 2010 we observe a densification of the boards interlocks network and a larger transnational orientation in its communities. Together with central actors and assortativity analyses, we provide statistical evidence that, at the level of corporate governance, Europe is getting closer.     

Investigating Incipient Speciation in Arabidopsis lyrata from Patterns of Transmission Ratio Distortion

Our understanding of the development of intrinsic reproductive isolation is still largely based on theoretical models and thorough empirical studies on a small number of species. Theory suggests that reproductive isolation develops through accumulation of epistatic genic incompatibilities, also known as Bateson–Dobzhansky–Muller (BDM) incompatibilities. We can detect these from marker transmission ratio distortion (TRD) in hybrid progenies of crosses between species or populations, where TRD is expected to result from selection against heterospecific allele combinations in hybrids. TRD may also manifest itself because of intragenomic conflicts or competition between gametes or zygotes. We studied early stage speciation in Arabidopsis lyrata by investigating patterns of TRD across the genome in F₂ progenies of three reciprocal crosses between four natural populations. We found that the degree of TRD increases with genetic distance between crossed populations, but also that reciprocal progenies may differ substantially in their degree of TRD. Chromosomes AL6 and especially AL1 appear to be involved in many single- and two-locus distortions, but the location and source of TRD vary between crosses and between reciprocal progenies. We also found that the majority of single- and two-locus TRD appears to have a gametic, as opposed to zygotic, origin. Thus, while theory on BDM incompatibilities is typically illustrated with derived nuclear alleles proving incompatible in hybrid zygotes, our results suggest a prominent role for distortions emerging before zygote formation.     

Field experiments on seed dispersal by wind in ten umbelliferous species (Apiaceae)

This report presents data from experiments on seed dispersal by wind for ten species of the family Apiaceae. Seed shadows were obtained in the field under natural conditions, using wind speeds between four and ten m/s. The flight of individual seeds was followed by eye, and seed shadows were acquired, with median distances varying from 0.7 to 3.1 m between species. Multiple regression models of wind speed and seed weight on dispersal distance were significant for six out of ten species; wind speed had significant effects in seven cases, but seed weight only once. A good correlation between mean terminal falling velocity of the seeds of a species and median dispersal distance, indicates the promising explanatory power that individual terminal velocity data might have on dispersal distance, together with wind speed and turbulence. The theory that seeds that seem to be adapted to wind dispersal travel much longer distances than seeds that have no adaptation was tested. Flattened and winged seeds were indeed found to be transported further by wind, but not much further. Moreover, the species with wind-adapted seeds were also taller, being an alternative explanation since their seeds experienced higher wind speeds at these greater heights. Furthermore, flattened and winged seeds were disseminated from ripe umbels at lower wind speeds in the laboratory. This means that the observed difference in dispersal distance would have been smaller when species specific thresholds for wind speed were incorporated in the field experiments. We argue therefore, that seed morphology is not always the best predictor in classifying species in groups with distinctly different dispersal ability.     

Random processes and geographic species richness patterns: why so few species in the north?

In response to the suggestion that the latitudinal gradient in species richness is the result of stochastic processes of species distributions, we created a computer simulation program that enabled us to study random species distributions over irregularly shaped areas. Our model could not explain latitudinal variation in species richness of New World mammals and created species richness patterns that differed dramatically from previous stochastic models. The interplay of speciation and species migration in our simulation generated the highest species richness in the middle of a landmass, not in the middle of its latitudinal stretch as was found in previous one-dimensional models. The discrepancy between the results of this study and previous empirical studies suggests that the effect of randomness in species-richness distribution is on a continental scale restricted by other, dominant determinants that limit the effect of chance.     

The temperature‐size rule in Daphnia magna across different genetic lines and ontogenetic stages: Multiple patterns and mechanisms

Ectotherms tend to grow faster, but reach a smaller size when reared under warmer conditions. This temperature‐size rule (TSR) is a widespread phenomenon. Despite the generality of this pattern, no general explanation has been found. We therefore tested the relative importance of two proposed mechanisms for the TSR: (1) a stronger increase in development rate relative to growth rate at higher temperatures, which would cause a smaller size at maturity, and (2) resource limitation placing stronger constraints on growth in large individuals at higher temperatures, which would cause problems with attaining a large size in warm conditions. We raised Daphnia magna at eight temperatures to assess their size at maturity, asymptotic size, and size of their offspring. We used three clonal lines that differed in asymptotic size and growth rate. A resource allocation model was developed and fitted to our empirical data to explore the effect of both mechanisms for the TSR. The genetic lines of D. magna showed different temperature dependence of growth and development rates resulting in different responses for size at maturity. Also, at warm temperatures, growth was constrained in large, but not in small individuals. The resource allocation model could fit these empirical data well. Based on our empirical results and model explorations, the TSR of D. magna at maturity is best explained by a stronger increase in development rate relative to growth rate at high temperature, and the TSR at asymptotic size is best explained by a size‐dependent and temperature‐dependent constraint on growth, although resource limitation could also affect size at maturity. In conclusion, the TSR can take different forms for offspring size, size at maturity, and asymptotic size and each form can arise from its own mechanism, which could be an essential step toward finding a solution to this century‐old puzzle.