Nutrient management and structural shifts in fish assemblages: Lessons learned from an Area of Concern in Lake Ontario

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Landmarking and strong Allee thresholds

Mate-finding difficulties in small populations are often postulated to create strong demographic Allee effects that increase the probability of extinction of native species or, similarly, decrease the probability that non-native species will successfully invade. Many species make use of a restricted number of mating locations, detectable from long-distance, that are not selected for habitat reasons (e.g., hilltopping in butterflies). This ‘landmarking’ strategy may specifically address the problem of overcoming mate-finding difficulties. Using a variant of the birthday problem, we demonstrate that populations which locate a restricted number of mate-finding sites using landmark features may have high probability of successful mating even at very low population densities. Therefore, a strong Allee threshold, if it exists, may be very small, and non-native species that make use of this strategy may have a very good chance of population establishment at low density.     

Drivers of future alien species impacts: An expert‐based assessment

Understanding the likely future impacts of biological invasions is crucial yet highly challenging given the multiple relevant environmental, socio‐economic and societal contexts and drivers. In the absence of quantitative models, methods based on expert knowledge are the best option for assessing future invasion trajectories. Here, we present an expert assessment of the drivers of potential alien species impacts under contrasting scenarios and socioecological contexts through the mid‐21st century. Based on responses from 36 experts in biological invasions, moderate (20%–30%) increases in invasions, compared to the current conditions, are expected to cause major impacts on biodiversity in most socioecological contexts. Three main drivers of biological invasions—transport, climate change and socio‐economic change—were predicted to significantly affect future impacts of alien species on biodiversity even under a best‐case scenario. Other drivers (e.g. human demography and migration in tropical and subtropical regions) were also of high importance in specific global contexts (e.g. for individual taxonomic groups or biomes). We show that some best‐case scenarios can substantially reduce potential future impacts of biological invasions. However, rapid and comprehensive actions are necessary to use this potential and achieve the goals of the Post‐2020 Framework of the Convention on Biological Diversity.     

Hysteresis in an experimental phytoplankton population

The road to recovery of a deteriorated system is often different, and fraught with more barriers, than the path to the system's deterioration. This phenomenon is called hysteresis, and is inherent to systems presenting alternative stable states. In such systems, the stability of a given state is the product of positive feedback loops. A broad range of natural systems have been predicted to show hysteretic behaviour, but hysteresis has so far only been unambiguously demonstrated at cellular or metabolic levels, not yet at the population or ecosystem level. To extend our understanding of hysteresis at the population level, we performed an experiment on light‐stressed cyanobacteria and found hysteresis between alternative stable states. Furthermore, during the experiment, the cyanobacteria adapted physiologically to high light levels, and deviated from their theoretically predicted pathway of hysteresis, therewith also avoiding extinction. Our experiment confirmed that a population that loses resilience due to deteriorating external conditions can show a delayed – hysteretic – recovery‐response when conditions are improved. This population‐level study also indicates that the slowness of these systems may obscure the true state they are in, which is important to factor into ecosystem monitoring. Additionally, we show that adaptation can drastically alter the systems’ predicted behaviour to ecosystem management. Flexibility of species and slowness should, therefore, be included in the monitoring and prediction of ecosystem responses to environmental changes.     

Scaffolding pre-assembled contigs using SSPACE

SUMMARY: De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield a number of contigs. Using paired-read sequencing data it is possible to assess the order, distance and orientation of contigs and combine them into so-called scaffolds. Although the latter process is a crucial step in finishing genomes, scaffolding algorithms are often built-in functions in de novo assembly tools and cannot be independently controlled. We here present a new tool, called SSPACE, which is a stand-alone scaffolder of pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. SSPACE shows promising results on both prokaryote and eukaryote genomic testsets where the amount of initial contigs was reduced by at least 75%.     

Cell type-specific regulation of ion channels within the maize stomatal complex

The stomatal complex of Zea mays is composed of two pore-forming guard cells and two adjacent subsidiary cells. For stomatal movement, potassium ions and anions are thought to shuttle between these two cell types. As potential cation transport pathways, K(+)-selective channels have already been identified and characterized in subsidiary cells and guard cells. However, so far the nature and regulation of anion channels in these cell types have remained unclear. In order to bridge this gap, we performed patch-clamp experiments with subsidiary cell and guard cell protoplasts. Voltage-independent anion channels were identified in both cell types which, surprisingly, exhibited different, cell-type specific dependencies on cytosolic Ca(2+) and pH. After impaling subsidiary cells of intact maize plants with microelectrodes and loading with BCECF [(2',7'-bis-(2-carboxyethyl)-5(and6)carboxyflurescein] as a fluorescent pH indicator, the regulation of ion channels by the cytosolic pH and the membrane voltage was further examined. Stomatal closure was found to be accompanied by an initial hyperpolarization and cytosolic acidification of subsidiary cells, while opposite responses were observed during stomatal opening. Our findings suggest that specific changes in membrane potential and cytosolic pH are likely to play a role in determining the direction and capacity of ion transport in subsidiary cells.     

Evaluating experimental bias and completeness in comparative phosphoproteomics analysis

Unraveling the functional dynamics of phosphorylation networks is a crucial step in understanding the way in which biological networks form a living cell. Recently there has been an enormous increase in the number of measured phosphorylation events. Nevertheless, comparative and integrative analysis of phosphoproteomes is confounded by incomplete coverage and biases introduced by different experimental workflows. As a result, we cannot differentiate whether phosphosites indentified in only one or two samples are the result of condition or species specific phosphorylation, or reflect missing data. Here, we evaluate the impact of incomplete phosphoproteomics datasets on comparative analysis, and we present bioinformatics strategies to quantify the impact of different experimental workflows on measured phosphoproteomes. We show that plotting the saturation in observed phosphosites in replicates provides a reproducible picture of the extent of a particular phosphoproteome. Still, we are still far away from a complete picture of the total human phosphoproteome. The impact of different experimental techniques on the similarity between phosphoproteomes can be estimated by comparing datasets from different experimental pipelines to a common reference. Our results show that comparative analysis is most powerful when datasets have been generated using the same experimental workflow. We show this experimentally by measuring the tyrosine phosphoproteome from Caenorhabditis elegans and comparing it to the tyrosine phosphoproteome of HeLa cells, resulting in an overlap of about 4%. This overlap between very different organisms represents a three-fold increase when compared to dataset of older studies, wherein different workflows were used. The strategies we suggest enable an estimation of the impact of differences in experimental workflows on the overlap between datasets. This will allow us to perform comparative analyses not only on datasets specifically generated for this purpose, but also to extract insights through comparative analysis of the ever-increasing wealth of publically available phosphorylation data.