Find research datasets worth reusing

opencc-by-4.0Sep 2021View details →

Constrained Fitness Landscape Analysis of Vehicle Routing Problems

The repository is a set of Jupyter notebooks and datasets used in the article titled: “Constrained Fitness Landscape Analysis for Capacitated Vehicle routing problems.” The main objective is to give the tools for reproducing the results shown in the paper.

Making sense of virus size and the tradeoffs shaping viral fitness

Viruses span an impressive size range, with genome length varying a thousandfold and virion volume nearly a millionfold. For cellular organisms the scaling of traits with size is a pervasive influence on ecological processes, but whether size plays a central role in viral ecology is unknown. Here we focus on viruses of aquatic unicellular organisms, which exhibit the greatest known range of virus size. We outline hypotheses within a quantitative framework, and analyze data where available, to consider how size affects the primary components of viral fitness. We argue that larger viruses have fewer offspring per infection and slower contact rates with host cells, but a larger genome tends to increase infection efficiency, broaden host range, and potentially increase attachment success and decrease decay rate. These countervailing selective pressures may explain why a breadth of sizes exist and even coexist when infecting the same host populations. Oligotrophic ecosystems may be enriched in "giant" viruses, because environments with resource-limited phagotrophs at low concentrations may select for broader host range, better control of host metabolism, lower decay rate, and a physical size that mimics bacterial prey. Finally, we describe where further research is needed to understand the ecology and evolution of viral size diversity.

Data from: Predator performance and fitness Is dictated by herbivore prey type plus indirect effects of their host plant

Animals, including herbivores and predators, use diet-mixing to balance their macro- and micronutrient intake. Recent work demonstrated that lady beetles fed only pea aphids from fava beans had reduced fitness caused by a deficiency of dietary sterols. However, beetles redressed this deficit by eating fava bean leaves. In the current study we used Coccinella septempunctata as a model to test the hypotheses that pea aphids are a poor sterol resource independent of their host plant, and that fava beans produce low quality prey regardless of aphid species. Additionally, we tested the reproductive rescue capacity of alfalfa and barley foliage compared to fava, and profiled the sterols of phloem exudates, foliage, and aphids reared on these different hosts. Beetle fecundity and egg viability was significantly better when provided pea aphids reared on alfalfa (compared to fava beans) and green peach aphids reared on fava plants. Alfalfa and barley leaves were not consumed by beetles and did not support beetle reproduction. The sterol profile of aphids largely reflected their host plant phloem. However, green peach aphids from fava acquired 125-times more sterol than pea aphids from fava. Our findings show how the sterol content of different host-plants can affect the third trophic level. Our results suggest that 1) prey quality varies depending on prey species, even when they occur on the same plant, 2) plant species can mediate prey quality, 3) host plant-mediated effects on prey quality partially drive omnivory, and 4) diet-mixing benefits growth and reproduction by redressing micronutrient deficits.

Photosynthesis from stolen chloroplasts can support sea slug reproductive fitness

Some sea slugs are able to steal functional chloroplasts (kleptoplasts) from their algal food sources, but the role and relevance of photosynthesis to the animal host remain controversial. While some researchers claim that kleptoplasts are slowly digestible 'snacks', others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis show light-dependent incorporation of 13C and 15N in the albumen gland and gonadal follicles of the sea slug Elysia timida, representing translocation of photosynthates to kleptoplast-free reproductive organs. Long-chain polyunsaturated fatty acids with reported roles in reproduction were produced in the sea slug cells using labelled precursors translocated from the kleptoplasts. Finally, we report reduced fecundity of E. timida by limiting kleptoplast photosynthesis. The present study indicates that photosynthesis enhances the reproductive fitness of kleptoplast-bearing sea slugs, confirming the biological relevance of this remarkable association between a metazoan and an algal-derived organelle.

Environmental effects on the genetic architecture of fitness components in a simultaneous hermaphrodite

Understanding how environmental change affects genetic variances and covariances of reproductive traits is key to formulate firm predictions on evolutionary responses. This is particularly true for sex-specific variance in reproductive success, which has been argued to affect how populations can adapt to environmental change. Our current knowledge on the impact of environmental stress on sex-specific genetic architecture of fitness components is still limited and restricted to separate-sexed organisms. However, hermaphroditism is widespread across animals and may entail interesting peculiarities with respect to genetic constraints imposed on the evolution of male and female reproduction. We explored how food restriction affects the genetic variance-covariance (G) matrix of body size and reproductive success of the simultaneously hermaphroditic freshwater snail Physa acuta. Our results provide strong evidence that the imposed environmental stress elevated the opportunity for selection in both sex functions. However, the G matrix remained largely stable across the tested food treatments. Importantly, our results provide no support for cross-sex genetic correlations suggesting no strong evolutionary coupling of male and female reproductive traits. We discuss potential implications for the adaptation to changing environments and highlight the need for more quantitative genetic studies on male and female fitness components in simultaneous hermaphrodites.

opencc-zeroOct 2022View details →

Parasitism shapes selection by drastically reducing host fitness and increasing host fitness variation

Determining the effects of parasites on host reproduction is key to understanding how parasites affect the underpinnings of selection on hosts. Although infection is expected to be costly, reducing mean fitness, infection could also increase variation in fitness costs among hosts, both of which determine the potential for selection on hosts. To test these ideas, we used a phylogenetically informed meta-analysis of 118 studies to examine how changes in the mean and variance in the outcome of reproduction differed between parasitized and non-parasitized hosts. We found that parasites had severe negative effects on mean fitness, with parasitized hosts suffering reductions in fecundity, viability, and mating success. Parasite infection also increased variance in reproduction, particularly fecundity and offspring viability. Surprisingly, parasites had similar effects on viability when either the male or female was parasitized. These results not only provide the first synthetic, comparative, and quantitative summary of the strong deleterious effects of parasites on host reproductive fitness, but also reveal a consistent role for parasites in shaping the opportunity for selection.

Data for: Testing for fitness epistasis in a transplant experiment identifies a candidate adaptive locus in Timema stick insects

Identifying the genetic basis of adaptation is a central goal of evolutionary biology. However, identifying genes and mutations affecting fitness remains challenging because a large number of traits and variants can influence fitness. Selected phenotypes can also be difficult to know a priori, complicating top-down genetic approaches for trait mapping that involve crosses or genome-wide association studies. In such cases, experimental genetic approaches, where one maps fitness directly and attempts to infer the traits involved afterward, can be valuable. Here, we re-analyse data from a transplant experiment involving Timema stick insects, where five physically clustered SNPs associated with cryptic body colouration were shown to interact to affect survival. Our analysis covers a larger genomic region than past work and revealed a locus previously not identified as associated with survival. This locus resides near a gene, Punch (Pu), involved in pteridine pigments production, implying that it could be associated with an unmeasured colouration trait. However, by combining previous and newly obtained phenotypic data, we show that this trait is not eye or body colouration. We discuss the implications of our results for the discovery of traits, genes, and mutations associated with fitness in other systems, as well as for supergene evolution.

Fitness landscapes reveal context-dependent benefits of oviposition behaviour

Resource choice behaviour has enormous fitness consequences and can drive niche expansion. However, individual behavioural choices are often mediated by context, determined by past experience. Do such context-dependent behaviours reflect maladaptive variation, or are they locally adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition behaviour reflects distinct, context-specific local fitness peaks. We measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviours (i.e., combinations of fecundity and resource preference) in a habitat containing optimal and suboptimal resource patches. We did this by experimentally manipulating female egg allocation across patches, which allowed us to assess behaviours not typically observed in the laboratory. We found that females from different age and competition contexts exhibit distinct behaviours which optimize different fitness components, linked in a tradeoff. With prior exposure to strong competition and increasing age, females produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young naïve females produce significantly more (but slower-developing) offspring, which is beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioural optimality and offers predictive power in novel contexts.

opencc-by-4.0Nov 2022View details →

No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host - Phenotype dataset

The present dataset contains all the phenotype data (.csv files) and R scripts used for data analysis, and to generated the figures (Figures 2 to 5) present in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host". The uploaded archive (.zip) contains 4 folders corresponding to the 4 Figures present in the manuscript (Figure 2, Figure 3, Figure 4 and Figure 5). Each folder contains the phenotype data tables (.csv files), a R script used to analyze the data and to generate the Figures and a readme file, explaining how the phenotype data tables are organized.

Recovery from heat-induced infertility: A study of reproductive tissue responses and fitness consequences in male Drosophila melanogaster

The predicted temperature increase caused by climate change is a threat to biodiversity. Across animal taxa, male reproduction is often sensitive to elevated temperatures leading to fertility loss and in more adverse scenarios, this can result in sterility when males reach their upper thermal fertility limit. Here we investigate temperature-induced changes in reproductive tissues, fertility reduction, sterility, and the associated fitness loss during the subsequent recovery phase in male Drosophila melanogaster. We heat-stressed males during development and either allowed them to recover or not in early adulthood, while measuring several determinants of male reproductive success. We found significant differences in recovery rate, organ sizes, sperm production, and other key reproductive traits among males from our different temperature treatments. Sperm maturation was impaired before reaching the upper thermal sterility threshold. While some effects were reversible, this did not compensate for the fitness loss due to damage imposed during development. Surprisingly, developmental heat stress was damaging to accessory gland growth, and female post-mating responses mediated by seminal fluid proteins were impaired regardless of the possibility of recovery. We suggest that sub-lethal thermal sterility and the subsequent fertility reduction is caused by a combination of inefficient functionality of both the accessory gland and testes.

Estimating total species richness: fitting rarefaction by asymptotic approximation

Estimating the number of species in a community is important for assessments of biodiversity. Previous species richness estimators are mainly based on non-parametric approaches. Although parametric asymptotic models have been applied, they received limited attention due to specific limitations. Here, we introduce parametric models fitting the probability-based rarefied species richness curve that allow us to estimate the 'Total Expected Species' (TES) in a community based on species' abundance data. We develop two approaches to calculate TES (termed 'TESa' and 'TESb'), based on two slightly different mathematical assumptions regarding Expected Species (ES) models. We provide R functions to calculate both these estimation approaches and their standard deviation. The function also enables users to visualize the estimation. We test the performance of TESa, TESb and their average (TESab) across simulated and empirical data, and compare their bias, precision and accuracy with other, commonly used, non-parametric species richness estimators; the bias-corrected (bc-)Chao1 and the Abundance-based Coverage Estimator (ACE). Simulation reveals that in small samples, TESa shows a tendency to over-estimate and TESb to under-estimate overall species richness. TESab performs well in bias, precision and accuracy when compared to (bc-)Chao1 and ACE estimators. Results from empirical data shows that the variance generated from TES estimates is comparable to that for (bc-)Chao1 and ACE. Our study demonstrates that rarefaction theory in combination with parametric approximation models provides a valuable new approach to estimate the species richness of incompletely sampled communities. <a name="_Hlk114347649"></a>Robust estimates are likely to be obtained where the observed number of species is greater than half of the TES estimation. When the ratio of TESa to the observed richness is >> 2, we suggest the use of TESb or TESab. Although more comprehensive comparisons with other estimators are suggested, we encourage researchers to consider the TES approach in their biodiversity studies as a complement to current existing estimators.

Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution

Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity towards other antibiotics, offers novel treatment opportunities to constrain or reverse the evolution of antibiotic resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here we address this issue in the Gram-positive pathogen Streptococcus pneumoniae by measuring collateral and fitness effects of clinically relevant gyrA and parC alleles, and their combinations, that confer resistance to fluoroquinolones. We integrated these results in a mathematical model which allowed us to evaluate how different in silico combination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of different gyrA and parC alleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic-specific pharmacodynamics, revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects of different antibiotics and suggest that these need to be considered in models examining CS-based therapies.

opencc-zeroDec 2022View details →

Data for: Fitness costs of female competition linked to resource defence and relatedness of competitors

Female reproductive success is often limited by access to resources and this can lead to social competition both within and between kin groups. Theory predicts that both resource availability and relatedness should influence the fitness consequences of social competition. However, testing key predictions requires differentiating the effects of these two factors. Here we achieve this experimentally by manipulating the social environment of house mice, a facultative communal breeding species with known kin discrimination ability. Our results support the hypothesis that resource defence can be costly for females, potentially trading off against maternal investment. When competition for nest sites was more intense, subjects: 1) were more active during resting phases, 2) responded more strongly to simulated territory intrusions via competitive signalling, and 3) produced smaller weaned offspring. However, we found no evidence that the propensity for kin to cooperate was influenced by relatedness of rivals. Communal breeding between sisters occurred independently of the relatedness of competitors, and costs of competition with non-kin were not mitigated by greater inclusive fitness benefits. Rather, communally breeding sisters weaned fewer offspring when competing with unrelated females, indicating that competition with non-kin is more costly overall. Our findings thus demonstrate that social competition has fitness costs and that associating with kin is beneficial to avoid negative fitness consequences of competing with non-kin, in addition to more widely recognised kin-selected benefits.

opencc-zeroDec 2022View details →

Different proxies, different stories? Imperfect correlations and different determinants of fitness in bighorn sheep

Measuring individual fitness empirically is required to assess selective pressures and predict evolutionary changes in nature. There is, however, little consensus on how fitness should be empirically estimated. As fitness proxies vary in their underlying assumptions, their relative sensitivity to individual, environmental, and demographic factors may also vary. Here, using a long-term study, we aimed at identifying the determinants of individual fitness in bighorn sheep (Ovis canadensis) using seven fitness proxies. Specifically, we compared four-lifetime fitness proxies: lifetime breeding success, lifetime reproductive success, individual growth rate, and individual contribution to population growth, and three multi-generational proxies: number of granddaughters, individual descendance in the next generation, and relative genetic contribution to the next generation. We found that all proxies were positively correlated, but the magnitude of the correlations varied substantially. Longevity was the main determinant of most fitness proxies. Individual fitness calculated over more than one generation was also affected by population density and growth rate. Because they are affected by contrasting factors, our study suggests that different fitness proxies should not be used interchangeably as they may convey different information about selective pressures and lead to divergent evolutionary predictions. Uncovering the mechanisms underlying variation in individual fitness and improving our ability to predict evolutionary change might require the use of several, rather than one, proxy of individual fitness.

opencc-zeroFeb 2023View details →

The impact of dietary breadth on bumblebee colony fitness

The current decline of pollinators may disrupt ecosystems and ecosystem services with potentially harmful effects on nature and human society. While the importance of habitat loss and fragmentation, pollution and increased disease risk in driving pollinator decline has been clearly demonstrated, the impact of resource diversity is less well understood. In this study, we investigated the effect of pollen diversity and composition on reproductive success and fitness of Bombus terrestris colonies. We asked the question whether a higher plant diversity results in a more diverse diet, lower pathogen incidence and a higher colony fitness. To answer these questions, colonies of lab-reared bumblebees were placed in species-poor heathland and species-rich semi-natural grasslands that strongly differed in plant community composition and diversity. We examined pollen loads on the bodies of foragers and identified the plant taxa present in the realized diet via DNA metabarcoding of the ITS2 marker. Liquid chromatography-mass spectrometry (LC-MS) was used to compare peptide composition of pollen samples from both habitats. Colony fitness was assessed by counting the number of sexuals produced by the colony at the end of its cycle. At the same time, colonies were examined for parasite incidence. Pollen composition and diversity on pollinators' bodies differed significantly between bees foraging in grasslands and heathlands. Concomitantly, peptide composition differed significantly between pollen samples from grasslands and heathlands. Colonies developed significantly better in heathland sites than in grasslands. In addition, colony fitness was only weakly related to pollen diversity and effects in some cases depended on the habitat where the bees were foraging. Pathogen incidence was very low and not affected by habitat. Overall, our results indicate that plant diversity is not necessarily a good predictor of colony fitness, and that vegetation composition and associated differences in both the quantity and quality of pollen are more important than pollen diversity per se.

opencc-by-4.0Jun 2022View details →

Supplementary Data: Global fits of vector-mediated s-channel simplified models for scalar and fermionic dark matter with GAMBIT

This record contains the YAML files, data files, and some of the plotting scripts for: "Global fits of vector-mediated s-channel simplified models for scalar and fermionic dark matter with GAMBIT". The paper can be found at https://arxiv.org/abs/2209.13266. Samples have been created using GAMBIT and figures can be reproduced with pippi.

opencc-zeroMar 2023View details →

Data for: Phenotypic plasticity increases exposure to extreme climatic events that reduce individual fitness

Climate models, and empirical observations, suggest that anthropogenic climate change is leading to changes in the occurrence and severity of extreme climatic events (ECEs). Effects of changes in mean climate on phenology, movement, and demography in animal and plant populations are well documented. In contrast, work exploring the impacts of ECEs on natural populations is less common, at least partially due to the challenges of obtaining sufficient data to study such rare events. Here, we assess the effect of changes in ECE patterns in a long-term study of great tits, near Oxford, over a 56-year period between 1965 and 2020. We document marked changes in the frequency of temperature ECEs, with cold ECEs being twice as frequent in the 1960s than at present, and hot ECEs being ~three times more frequent between 2010 and 2020 than in the 1960s. While the effect of single ECEs was generally quite small, we show that increased exposure to ECEs often reduces reproductive output, and that in some cases, the effect of different types of ECE is synergistic. We further show that long-term temporal changes in phenology, resulting from phenotypic plasticity, lead to an elevated risk of exposure to low-temperature ECEs early in reproduction, and hence suggest that changes in ECE exposure may act as a cost of plasticity. Overall, our analyses reveal a complex set of risks of exposure and effects as ECE patterns change and highlight the importance of considering responses to changes in both mean climate and extreme events. Patterns in exposure and effects of ECEs on natural populations remain underexplored and continued work will be vital to establish the impacts of ECEs on populations in a changing climate.

opencc-by-4.0Mar 2023View details →

Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"

The tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making. All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow. The source code is publicly available on GitHub: <a href="https://github.com/radical-collaboration/MDFF-EnTK">https://github.com/radical-collaboration/MDFF-EnTK </a> The preprint of this research is submitted on bioRxiv, doi: <a href="https://doi.org/10.1101/2021.12.07.471672">https://doi.org/10.1101/2021.12.07.471672 </a> To obtain maximum compression of the data, the tar command used to generate this tarball was: <pre><code class="language-bash">GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/</code></pre>

opencc-by-4.0Mar 2023View details →

Fits Data of "Multiple Rings and Asymmetric Structures in the Disk of SR 21"

This is the fits data of the paper "Multiple Rings and Asymmetric Structures in the Disk of SR 21".