Find research datasets worth reusing

opencc-zeroFeb 2024View details →

Genetically identical mice express alternative reproductive tactics depending on social conditions in the field

In many species, establishing and maintaining a territory is critical to survival and reproduction, and an animal's ability to do so is strongly influenced by the presence and density of competitors. Here we manipulate social conditions to study the alternative reproductive tactics displayed by genetically identical, age-matched laboratory mice competing for territories under ecologically realistic social environmental conditions. We introduced adult males and females of the laboratory mouse strain (C57BL/6J) into a large, outdoor field enclosure containing defendable resource zones under one of two social conditions. We first created a low-density social environment, such that the number of available territories exceeded the number of males. After males established stable territories, we introduced a pulse of intruder males and observed the resulting defensive and invasive tactics employed. In response to this change in social environment, males with large territories invested more in patrolling but were less effective at excluding intruder males as compared to males with small territories. Intruding males failed to establish territories and displayed an alternative tactic featuring greater exploration as compared to genetically identical territorial males. Alternative tactics did not lead to equal reproductive success—males that acquired territories experienced greater survival and had greater access to females.

opencc-by-4.0Oct 2019View details →

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network

In this repository we provide raw and processed datasets for the article: “Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network” by Arantxa Urchueguía, Luca Galbusera, Dany Chauvin, Gwendoline Bellement, Thomas Julou  and Erik van Nimwegen. A preprint is available under the following DOI: <a href="https://doi.org/10.1101/795369">https://doi.org/10.1101/795369</a>.  The repository consists of the following datasets:  1. preprocessed_datasets.zip(~22GB) <ul> <li>This dataset contains raw data from the flow cytometry experiments (FACS Canto II, BD Bioscience) in all measured conditions in RData format. Raw fcs files were processed with the tools described in the publication ''Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria" published here: <a href="https://doi.org/10.1371/journal.pone.0240233">https://doi.org/10.1371/journal.pone.0240233</a>. The tools themselves are available here: <a href="https://github.com/vanNimwegenLab/E-Flow">https://github.com/vanNimwegenLab/E-Flow</a>.  Included in the files are the outputs of these processing tools together with all raw values that came directly from the flow cytometer. The file directory_structure_in_preprocessed contains information about how the files are organized.</li> </ul> 2. info_files: This is a set of csv files containing detailed information about the experiments done to acquire the preprocessed_datasets as well as annotation files that we used to retrieve promoter information.  3. processed_datasets: These files correspond to the processed datasets from the raw Rdata files under 1 above.  The processed data provide mean and variance estimates in fluorescence of E.coli promoters across the different growth conditions. Note that we discarded  flow cytometry measurements from promoter/growth-condition combinations that  contained abnormal fluorescence distributions (due to contamination) as well as measurements from reporters with annotation mismatches. The folder contains the following clean dataset files that were used in the paper: <ul> <li>FULL_dataset_mean_var_wreplicates: In this dataset we include the processed means and variances (in both logarithmic and linear scale) of all  promoters in each condition. Included as well are replicate measurements for some conditions.. We also include the name and Blattner number of the gene immediately downstream of each promoter, the DNA sequence of each promoter, and regulatory information (number of unique inputs for transcription factors sites and their names) which we obtained from RegulonDB v 10.5 (<a href="https://doi.org/10.1093/nar/gky1077">https://doi.org/10.1093/nar/gky1077</a>). </li> <li>dataset_with_noise_estimates: In this dataset we provide noise estimates for all promoters expressed above an expression threshold (mean GFP fluorescence at least as large as autofluorescence). Note that the noise estimate correspond to the difference between the promoter’s variance in log-expression and the minimal variance as a function of its mean expression (i.e. the so called noise floor was subtracted). Apart from the mean, variance, noise and promoter features (sequence, name of gene downstream, number of unique regulatory inputs and name of the TFs binding), we also include the parameters used for fitting the minimal noise, i.e. noise floor,  in each of the conditions. </li> <li>time_course_data_SI: This dataset contains mean and variance measurements of one of the plates of the library measured at different time points during growth in Minimal media 0.4M NaCl: 0h (just after dilution), 1h, 2h, 3h, 5h, 6.5h, 8.5h, 10h and 11h. </li> <li>growth_curves_SI: Growth data (OD600 as a function of time) for a subset of the promoters from the library across different growth conditions.</li> <li>singlecell_areas_SI: Single-cell areas estimated using agar patches of cells growing in each condition. Each row of the table contains data for a single-cell. </li> <li>synthetic_promoters_dataset: This dataset contains mean, variance and noise measurements of a set of constitutive promoters from  <a href="https://doi.org/10.7554/eLife.05856.001">https://doi.org/10.7554/eLife.05856.001</a> across different conditions.</li> <li>MARA_results:  All transcription factor activities results explaining measured noise levels in each condition. This data has been obtained after performing Motif Activity Response Analysis on the noise levels of all measured promoters in each condition.</li> </ul>

opencc-zeroApr 2022View details →

Effects of genetic vs. environmental quality on condition-dependent morphological and life history traits in a neriid fly

Condition is assumed to reflect both genes and environment, enabling condition-dependent signals to reveal genetic quality. However, because the phenotypic effects of variation in genetic quality could be masked by environmental heterogeneity, the contribution of genetic quality to phenotypic variation in fitness-related traits and condition-dependent signals remains unclear. We compared effects of ecologically relevant manipulations of environmental quality (nutrient dilution in the larval diet) and genetic quality (one generation of inbreeding) on male and female morphology, life history and reproductive performance in the neriid fly Telostylinus angusticollis. We found that larval diet quality had strong, positive effects on male and female body size, male secondary sexual traits, and aspects of male and female reproductive performance. By contrast, inbreeding had weak effects on most traits, and no trait showed clear and consistent effects of both environmental and genetic quality. Indeed, inbreeding effects on body size and male competitive performance were of opposite sign in rich vs. poor larval diet treatment groups. Our results suggest that environmental quality strongly affects condition, but the effects of genetic quality are subtle and environment-dependent in this species. These findings raise questions about the genetic architecture of condition and the potential for condition-dependent traits to function as signals of genetic quality.

opencc-zeroMay 2022View details →

Personality, sperm traits and a test for their combined dependence on male condition in guppies

There is evidence that animal personality traits can have spill-over effects for sexual selection, with studies reporting that male behavioural types are associated with success during pre- and post-copulatory sexual selection. Given these links between personality and sexual traits, and the evidence that their expression can depend on an individual's nutritional status (i.e. condition), a novel prediction is that changes in a male's diet should alter both the average expression of personality and sexual traits, and their covariance. We tested these predictions using the guppy Poecilia reticulata, a species previously shown to exhibit strong condition dependence in ejaculate traits and a positive correlation between sperm production and individual variation in boldness. Contrary to expectation, we found that dietary restriction – when administered in mature adult males – did not affect the expression of either behavioural (boldness and activity) or ejaculate traits, although we did find that males subjected to dietary stress exhibited a positive association between sperm velocity and boldness that was not apparent in the unrestricted diet group. This latter finding points to possible context-dependent patterns of covariance between sexually selected and personality traits, which may have implications for patterns of selection and evolutionary processes under fluctuating environmental conditions.

opencc-by-4.0Feb 2021View details →

Рис. 11. Зависимость чисΛенности Heterodera glycines от засоренности поΛей Fig. 11. Dependence of the number of Heterodera glycines on the field weediness in Reproductive potential of Soybean Cyst Nematode Heterodera glycines - quarantine pest of soybean - in Primorsky Region conditions

Рис. 11. Зависимость чисΛенности Heterodera glycines от засоренности поΛей Fig. 11. Dependence of the number of Heterodera glycines on the field weediness

opencc-zeroAug 2021View details →

Condition-dependent sexual reproduction is driven by benefits, not costs of sex

Facultative sexual organisms must allocate resources to both asexual and sexual reproduction. Optimal patterns of investment in sex depend on the relative costs and benefits of each reproductive mode, and may consequently be context- and condition-dependent. Two proposed explanations for the observed variation in investment in sex among facultative sexual lineages invoke alternative condition-dependent scenarios. Under the 'fitness-associated sex' hypothesis, sex is predicted when individuals are in poor condition or experience stressful environments. Under the 'resource-demanding sex' hypothesis, sex is only affordable to individuals in good condition experiencing favourable environments. Direct tests of these contrasting hypotheses are rare; moreover, investment in different components of sexual reproduction responds differently to cues promoting sex, and may be subject to different energetic constraints. Using genotypes of facultative sexual Daphnia carinata that differ in their level of investment in sex, we manipulated resource availability while accounting for day length (a seasonal cue for sex) to evaluate these hypotheses. The sexual response to day length depended on resource availability: increased day lengths and reduced food availability increased the production of sexual eggs, and relative investment in males, in a manner consistent with the fitness-associated sex hypothesis. The pattern of condition-dependence was specific to each component of reproductive investment – while male production covaried with asexual fecundity across genotypes, increased sexual egg production was associated with reduced asexual reproduction. Our results suggest that investment in sex is determined largely by its context-dependent advantages, and that this investment is not moderated by immediate costs to asexual reproduction.

Fig. 5 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil

Fig. 5. Relationships between total (black symbols) and gutted weight (g) (grey symbols) for male (above) and females (below) of Rioraja agassizi.

Fig. 2 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil

Fig. 2. Maps of Southeast Brazil, showing the fishing hauls by month, conducted by a total of eight fishing vessels. Symbols represent the fishing hauls from where samples of Rioraja agassizi were collected (dotted circles), or when this information was not available, the total hauls recorded by the skippers (crosses).

Fig. 6 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil

Fig. 6. Median condition factor by month (from March, 2005 to March, 2006) considering total (black line) and gutted weight (g) (grey line) for males (above) and females (below) of Rioraja agassizi. Vertical bars represent the data interval.

Fig. 4 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil

Fig. 4. Relationship of disc width (cm) as a dependent variable of total length (cm) for males (black symbols) and females (grey symbols) of Rioraja agassizi.

Fig. 1 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil

Fig. 1. Map of the study area, southeast Brazil, south-western Atlantic Ocean. Symbols represent all the fishing hauls from where samples of Rioraja agassizi were collected.

opencc-zeroMay 2023View details →

The trait-mediated trade-off between growth and survival depends on tree sizes and environmental conditions

Interspecific relationships between growth and survival are critical determinants of tree species diversity maintenance in forests. The trade-offs between growth and survival in co-occurring tree species are believed to arise along a continuum of life-history strategies. For example, co-occurring species range from those that grow slowly and survive well in resource-poor environments to those that grow quickly but have low survival rates in resource-rich environments. However, uncertainties remain regarding how growth-survival trade-offs are related to species traits, tree sizes, or environmental conditions. We examined how the relationships between species traits and growth–survival relationships shift in response to changes in stem sizes and across census periods with different climate conditions (frequency of strong winds, drought intensity) across 45 co-occurring tree species based on 23 years of growth and survival records in a warm temperate rain forest on Yakushima Island, Japan. We developed hierarchical Bayesian models of relative growth and survival rates, including leaf traits, wood density, and 95-percentile maximum stem diameter as explanatory variables. We tested the relationships between estimated trait-mediated growth–survival relationships and the intensities of climate events during five census periods. Each trait's effects on growth–survival relationships differed across the five census periods in response to climate conditions. Interspecific growth–survival relationships affected by a single trait axis for leaves or wood tended to be negative. In contrast, those affected by the maximum stem diameter tended to be positive. Such trends increased with more frequent strong winds or more intense droughts. The single-trait effects on growth–survival relationships were stronger for smaller sizes than for larger sizes. For all traits combined, we found a significant growth–survival trade-off only for small-sized stems in three of five census periods. Synthesis: Our results indicate that the effect of species traits on the growth–survival relationships depended on tree sizes, the census periods, or both in response to the frequency or intensity of climate events. We argue the importance of incorporating spatial and temporal variations in environmental conditions into long-term data from tree census to predict forest dynamics.