Additional file 2 of Parameter inference for stochastic single-cell dynamics from lineage tree data

A ZIP file containing the raw datasets obtained from the MCMC runs presented. (ZIP 449 kb

Data from: Prudent behavior rather than chemical deception enables a parasite to exploit its ant host

Many parasites display complex strategies to evade host detection. The principal view is that parasites of social insects deceive their host by means of advanced chemical adaptations such as mimicking the cuticular host recognition cues, being chemically odorless, or emitting manipulative volatiles. Apart from these chemical adaptations, parasites of social insects may also use simpler behavioral strategies to evade host detection. As yet, such behavior has rarely been studied. Here we tested which chemical and behavioral strategies the unspecialized parasitic rove beetle Thiasophila angulata uses to avoid detection by its aggressive Formica rufa red wood ant host. Chemical comparisons of the beetle’s and the host ants’ cuticular hydrocarbons showed that the beetle carried an idiosyncratic cuticular profile that was clearly different from that of its host. Beetles that were isolated from their host or were placed in the nests of another Formica species perfectly retained their original cuticular profiles and provoked equal levels of aggression. These results suggest that the beetles do not avoid host detection through chemical deception. In contrast, the beetle adapted its behavior to avoid aggression by the ants. In the presence of ants, the beetle behaved much more prudently by hiding more frequently and engaging in less risky runs. Overall, these results highlight that for relatively unspecialized parasites, general strategies such as prudent behavior can be equally effective as more specialized deception strategies to evade host detection.,Effect of beetle isolation or transplantation on F. rufa aggressionEffect of the host on the beetle’s chemical profileBeetle behavior in absence vs presence of F. rufa

Data from: Stressor fluxes alter the relationship between beta-diversity and regional productivity

Dispersal of organisms can influence the relationship between beta-diversity and regional productivity in heterogeneous environments. However, many ecosystems are also linked by fluxes of stressors, with an unknown influence on this relationship. In this study, we assess the relationship between beta-diversity (measured as Bray-Curtis dissimilarity) and regional productivity (measured as biovolume) under various levels of a stressor flux in meta-ecosystems that were composed of two marine micro-algae communities. We created heterogeneity by exposing one of the two communities to a herbicide and manipulated regional diversity by applying a dispersal gradient, which decreased beta-diversity. We applied four stressor flux levels, which homogenized the herbicide concentration between the communities over time. The stressor flux changed the relationship between beta-diversity and regional productivity by changing the effect of dispersal on regional productivity. In absence of the stressor flux, the relationship between beta-diversity and regional productivity was mostly not significant, but positive at the end of the experiment. This positive relationship was generated by a negative effect of dispersal on regional productivity, probably because dispersal disrupted local dynamics by removing organisms from the most-productive unstressed community. In presence of the stressor flux, the relationship between beta-diversity and regional productivity was often negative as dispersal now increased regional productivity. Dispersal increased regional productivity by increasing the productivity of the stressed community. This positive effect was stronger in the presence than in the absence of the stressor flux because the stressor flux reduced the concentration of the herbicide in the stressed community, where it facilitated recovery. Our study shows that stressor fluxes can strongly interact with the effects of dispersal on productivity and thus influence diversity-productivity relationships.,main experiment algae countsIn this experiment, we aim to evaluate the effect of a stressor flux and dispersal on the relationship between beta-diversity and regiuonal productivity. To do so, communities with marine diatoms were used, of which 1 community contained the chemical stressor atrazine. We applied 5 levels of dispersal and 4 levels of the stress flux in a full-factorial design. Each treatment was replicated 3 times.main_experiment_algae_counts.txtdata_monoculturesGrowth (biovolume/ml) of 6 algae strains at different atrazine concentrations at different times.

Supplementary material from "Elevated compositional change in plant assemblages linked to invasion"

Alien species are widely linked to biodiversity change, but the extent to which they are associated with the reshaping of ecological communities is not well understood. One possible mechanism is that assemblages where alien species are found exhibit elevated temporal turnover. To test this, we identified assemblages of vascular plants in the BioTIME database for those assemblages in which alien species are either present or absent and used the Jaccard measure to compute compositional dissimilarity between consecutive censuses. We found that, although alien species are typically rare in invaded assemblages, their presence is associated with an increase in the average rate of compositional change. These differences in compositional change between invaded and uninvaded assemblages are not linked to differences in species richness but rather to species replacement (turnover). Rapid compositional restructuring of assemblages is a major contributor to biodiversity change, and as such, our results suggest a role for alien species in bringing this about

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis. Availability: The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench.© The Author(s) 201

Genomic Correlates of Relationship QTL Involved in Fore- versus Hind Limb Divergence in Mice

Divergence of serially homologous elements of organisms is a common evolutionary pattern contributing to increased phenotypic complexity. Here, we study the genomic intervals affecting the variational independence of fore- and hind limb traits within an experimental mouse population. We use an advanced intercross of inbred mouse strains to map the loci associated with the degree of autonomy between fore- and hind limb long bone lengths (loci affecting the relationship between traits, relationship quantitative trait loci [rQTL]). These loci have been proposed to interact locally with the products of pleiotropic genes, thereby freeing the local trait from the variational constraint due to pleiotropic mutations. Using the known polymorphisms (single nucleotide polymorphisms [SNPs]) between the parental strains, we characterized and compared the genomic regions in which the rQTL, as well as their interaction partners (intQTL), reside. We find that these two classes of QTL intervals harbor different kinds of molecular variation. SNPs in rQTL intervals more frequently reside in limb-specific cis-regulatory regions than SNPs in intQTL intervals. The intQTL loci modified by the rQTL, in contrast, show the signature of protein-coding variation. This result is consistent with the widely accepted view that protein-coding mutations have broader pleiotropic effects than cis-regulatory polymorphisms. For both types of QTL intervals, the underlying candidate genes are enriched for genes involved in protein binding. This finding suggests that rQTL effects are caused by local interactions among the products of the causal genes harbored in rQTL and intQTL intervals. This is the first study to systematically document the population-level molecular variation underlying the evolution of character individuation

Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations

The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress.© The Author(s) 201

Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris

A parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agriculture globally. Nevertheless, no genome sequence of a parasitic plant has been reported to date. Here we describe the genome sequence of the parasitic field dodder, Cuscuta campestris. The genome contains signatures of a fairly recent whole-genome duplication and lacks genes for pathways superfluous to a parasitic lifestyle. Specifically, genes needed for high photosynthetic activity are lost, explaining the low photosynthesis rates displayed by the parasite. Moreover, several genes involved in nutrient uptake processes from the soil are lost. On the other hand, evidence for horizontal gene transfer by way of genomic DNA integration from the parasite’s hosts is found. We conclude that the parasitic lifestyle has left characteristic footprints in the C. campestris genome.© The Author(s) 201

Dataset Figure_5: Whi5-GFP intensity versus size and time in a synchronous G1 population

Whi5-GFP intensity as a function of time for the different FOV of elutriated cells. This dataset contains: 1. Raw TIF_images_NADH – These are autofluorescence images taken at each time point for the purposes of calculating cell size. Time points were every 10 minutes except at 30 minutes which had to be discarded due to poor focus. 2. Raw TIF_images_WHI5 – These raw image files correspond to images of Whi5-GFP excited at 1000 nm fpr all 11 time points of different FOV obtained at 3 different z positions (1-3) (0, -0.5 um, + 0.5 um). Whi5-GFP intensity values for each nucleus were taken for the z-position that gave the highest intensity for each nucleus. 3. NADHDATA_with_time plot.xlsx is the analysis of the raw images of auto-fluorescence exciting at 750 nm. The only relevant information for the Figure is in Colume C sheet 1. It is the cell area in total pixels. 4. Whi5Data_BestFocusPlanes_All_FOV.xlsx is the analysis of the Whi5-GFP images for Whi5-GFP intensity vs time and size for each time point (which corresponds to a different FOV)