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GB GMOS gri-band coadded and fully calibrated FITS images
<p>These are the Gemini/GMOS-N and GMOS-S coadded FITS images, taken in gri filters, of the 17 Green bean galaxies published in Schirmer+ 2016.</p>
Fitness of mCherry Reporter Tick-Borne Encephalitis Virus in Tick Experimental Models
<p>Figures and open datasets from the publication about the reporter TBEV in tick experimental models by Kevély et al., 2022 (<a href="https://doi.org/10.3390/v14122673">https://doi.org/10.3390/v14122673</a>)</p>
Data for: Simulating animal space use from fitted integrated Step-Selection Functions (iSSF)
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Fits and plot data for the paper: "Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants"
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Supplemental material for the paper, "Entropy, Search Trajectories, and Explainability for Frequency Fitness Assignment"
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THE IMPACT OF PHYSICAL FITNESS ON THE PSYCHOLOGICAL HEALTH OF CADETS IN HIGHER EDUCATION INSTITUTIONS
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Evolutionary mechanisms underpinning fitness response to multiple stressors in Daphnia
<p>Multiple stressors linked to anthropogenic activities can influence how organisms adapt and evolve. So far, a consensus on how multiple stressors drive adaptive trajectories in natural populations has not been reached. Some meta-analysis reports show predominance of additive effects of stressors on ecological endpoints (e.g. fecundity, mortality), whereas others show synergistic effects more frequently. Moreover, it is unclear what mechanisms of adaptation underpin responses to complex environments.</p> <p>Here, we use populations of the crustacean <i>Daphnia magna</i> resurrected from different times in the past to investigate mechanisms of adaptation to multiple stressors, and to understand how historical exposure to environmental stress shapes adaptive responses of modern populations. Using common garden experiments on resurrected modern and historical populations, we investigate: i) whether exposure to one stress results in higher tolerance to a second stressor; ii) the mechanisms of adaptation underpinning long-term evolution to multistress (genetic evolution, plasticity, evolution of plasticity); and iii) the interaction effects of multiple stressors on fitness (synergism, antagonism, additivity). We measure the combined impact of different levels of resource availability (algae) and biocides on fitness-linked life history traits and interpret these results in light of historical environmental exposures. We show that exposure to one stressor can alter tolerance to a second stressors and that the interaction effect depends on the severity of either stressor. We also show that mechanisms of adaptation underpinning phenotypic evolution significantly differ in single stress and multistress scenarios. These adaptive responses are driven largely by synergistic effects on fecundity and size at maturity, and additive effects on age at maturity. Exposure to multiple stressors shifts the trade-offs among fitness-linked life history traits, with a stronger effect on <i>Daphnia </i>populations when low resource availability and high biocide levels are experienced. Our study indicates that mitigation interventions based on single stress analysis may not capture realistic threats.</p>
Mosquito-bacteria interactions during larval development trigger metabolic changes with carry-over effects on adult fitness
<p>In animals with distinct life stages such as holometabolous insects, adult phenotypic variation is often shaped by the environment of immature stages, including their interactions with microbes colonizing larval habitats. Such carry-over effects were previously observed for several adult traits of the mosquito <i>Aedes aegypti</i> after larval exposure to different bacteria, but the mechanistic underpinnings are unknown. Here, we investigated the molecular changes triggered by gnotobiotic larval exposure to different bacteria in <i>Ae. aegypti</i>. We initially screened a panel of 16 bacterial isolates from natural mosquito breeding sites to determine their ability to influence adult life-history traits. We subsequently focused on four bacterial isolates (belonging to <i>Flavobacterium</i>, <i>Lysobacter</i>, <i>Paenibacillus</i>, and <i>Enterobacteriaceae</i>) with significant carry-over effects on adult survival and found that they were associated with distinct transcriptomic profiles throughout mosquito development. Moreover, we detected carry-over effects at the level of gene expression for the <i>Flavobacterium</i> and <i>Paenibacillus</i> isolates. The most prominent transcriptomic changes in gnotobiotic larvae reflected a profound remodeling of lipid metabolism, which translated into phenotypic differences in lipid storage and starvation resistance at the adult stage. Together, our findings indicate that larval exposure to environmental bacteria trigger substantial physiological changes that impact adult fitness, uncovering a possible mechanism underlying carry-over effects of mosquito-bacteria interactions during larval development.</p>
Dataset of the bacterial fitness estimation values and mutation identifications from: Rapid decline of adaptation of Pseudomonas fluorescens to soil biotic environment
<p>Interactions between microbes can both constrain and enhance adaptation, but to date, most studies employ simplified communities and environments. We measured fitness of populations of the soil bacterium Pseudomonas fluorescens that have been evolved in both the presence and absence of a natural potting soil microbial community. Populations from both environments showed similar fitness increases with respect to the ancestor in the absence of the community, suggesting no significant cost of evolving with the community. By contrast, fitness in the presence of the community increased for community-evolved populations, but decreased considerably below the ancestral state for populations evolved in the absence of the community. This suggests some abiotic beneficial mutations are costly in the presence of the community, while others are not, with the former only selected against in the presence of the community. Most mutations underpinning fitness changes were clone specific, supporting the view that there are multiple genetic pathways to adaptation in this complex environment. Such extreme mutational effects have not been observed in comparable in vitro studies that employ much simpler abiotic and biotic environments, and suggest that a caution is need when extrapolating results from simplified in vitro systems to real-world contexts.</p>
Fitness benefit plays a vital role in the retention of the Pi-ta susceptible alleles
<p>In plants, large numbers of <i>R</i> genes, which segregate as loci with alternative alleles conferring different resistance to pathogens, have been maintained over a long evolutionary time. In theory, there seem to be no reason for hosts to harbor susceptible alleles in view of their null contribution to resistance. As such, why should populations support disease-susceptible individuals along with disease-resistant individuals? In rice, a single copy gene <i>Pi-at</i> segregates for two expressed clades of alleles, one resistant and the other susceptible. We simulated loss-of-function of the <i>Pi-ta</i> susceptible allele using the CRISPR/Cas9 system to detect subsequent fitness changes and obtained insights into fitness effects on retention of the <i>Pi-ta</i> susceptible allele. Our creation of artificial knockout of the <i>Pi-ta</i> susceptible allele suffered a fitness decline of up to 49% in term of filled grains yield upon the loss of <i>Pi-ta</i>'s function. The <i>Pi-ta</i> susceptible alleles might serve as an off-switch to the downstream immune signaling, thus contributing to fine-tuning of plant defense response. These findings highlight the interplay between genetic architecture and fitness effects of segregating <i>R</i> gene alleles and also provide a plausible explanation how host genomes can tolerate the possible genetic load associated with a vast repertoire of <i>R</i> genes. This attempt to evaluate the fitness effect of the <i>R</i> gene in crop will bring some clues to researchers and breeders that not all disease resistant genes will bring fitness cost as universally acknowledged.</p>
Fitness data for control autotomized and regenerated crabs Hemigrapsus nudus
<p>The capacity of certain animals to regrow a lost appendage has been exploited as a powerful tool to study development. As a result, we now understand many of the proximate details of the regeneration process. Ironically, despite being one of the oldest studied developmental phenomena, regeneration is not often considered in the context of natural selection and evolution. Why do select species retain the capacity to shed and regrow body parts, whereas more derived lineages do not? We conducted a comprehensive study on the costs and benefits of autotomy and regeneration on <i>Hemigrapsus nudus</i>, the purple shore crab. In the realms of feeding and locomotion, regeneration restored fitness to what it otherwise would have been; autotomized animals showed decreases in feeding and locomotion, but regenerated animals performed no differently than intact crabs. However, for fecundity and male-male competition, regenerated animals had the lowest fitness compared to control and autotomized crabs. Our results raise the intriguing possibility that tradeoffs associated with reproduction may have led to the loss of regenerative abilities in derived lineages such as mammals and birds. Future work on the hundreds of species that regenerate lost body parts will reveal if and how this hypothesis can address the pervasive speculation plaguing the ultimate causes of regenerative losses.</p>
Effects of primary seed dormancy on life-time fitness of Arabidopsis thaliana in the field
<p class="MsoNoSpacing"><strong>Background and Aims</strong><em> </em>Seed dormancy determines the environmental niche of plants in seasonal environments, and has consequences for plant performance that potentially go far beyond the seed and seedling stages. In this study, we examined the cascading effects of seed dormancy on the expression of subsequent life-history traits and fitness in the annual herb <em>Arabidopsis thaliana</em>.<em> </em></p> <p class="MsoNoSpacing"><strong>Methods </strong>We planted seeds of >200 recombinant inbred lines (RIL) derived from a cross between two locally adapted populations (Italy and Sweden), and both parental genotypes at the native site of the Swedish population in three consecutive years. We quantified the relationship between primary seed dormancy and the expression of subsequent life-history traits and fitness in the RIL population with path analysis. To examine effects of differences in dormancy on relative fitness of the two parental genotypes, we planted dormant seeds during the seed dispersal period and non-dormant seeds during the germination period of the local population.</p> <p class="MsoNoSpacing"><strong>Key Results </strong>In the RIL population,<strong> </strong>strong primary dormancy was associated with high seedling survival, but with low adult survival and fecundity, and the path analysis indicated that this could be explained by effects on germination timing, rosette size, and flowering start. The relationship between primary seed dormancy and germination proportion varied among years, and this was associated with differences in seasonal changes in soil moisture. The planting of dormant and nondormant seeds indicated that the lower primary dormancy of the local Swedish genotype contributed to its higher germination proportion in two years, and to its higher fecundity in one year. </p> <p class="MsoNoSpacing"><strong>Conclusions </strong>Our results show that seed dormancy affects trait expression and fitness components across the life cycle, and suggest that among-year variation in the incidence of drought during the germination period should be considered when predicting the consequences of climatic change for population growth and evolution.</p>
What is the best fitness measure in wild populations? A case study on the power of short-term fitness proxies to predict reproductive value
<p>Fitness is at the core of evolutionary theory, but it is difficult to measure accurately. One way to measure long-term fitness is by calculating the individual's reproductive value, which represents the expected number of allele copies an individual passes on to distant future generations. However, this metric of fitness is scarcely used because the estimation of individual's reproductive value requires long-term pedigree data, which is rarely available in wild populations where following individuals from birth to death is often impossible. Wild study systems therefore use short-term fitness metrics as proxies, such as the number of offspring produced. This study obtained three frequently used short-term proxies for fitness obtained at different offspring life stages (eggs, hatchlings, fledglings and recruits), and compared their ability to predict reproductive values derived from the genetic pedigree of a wild passerine bird population. We used twenty years of precise field observations and a near-complete genetic pedigree to calculate reproductive success, individual growth rate and de-lifed fitness as lifetime fitness measures, and as annual de-lifed fitness. We compared the power of these metrics to predict reproductive values and lineage survival to the end of the study period. The three short-term fitness proxies predict the reproductive values and lineage survival only when measured at the recruit stage. There were no significant differences between the different fitness proxies at the same offspring stages in predicting the reproductive values and lineage survival. Annual fitness at one year old predicted reproductive values equally well as lifetime de-lifed fitness. However, none of the short-term fitness proxies was strongly associated with the reproductive values. In summary, the commonly short-term fitness proxies capture long-term fitness with intermediate accuracy at best, if measured at recruitment stage. As lifetime fitness measured at recruit stage and annual fitness in the first year of life were the best proxies of long-term fitness, we encourage their future use.</p>
Culling data fit
<p>Supplementary file (Workspace, culling data application)</p>
Data from: The distribution of fitness effects in an uncertain world
The distribution of fitness effects (DFE) among new mutations plays a critical role in adaptive evolution and the maintenance of genetic variation. While fitness landscape models predict several key features of the DFE, most theory to date focuses on predictable environmental conditions, while ignoring stochastic environmental fluctuations that feature prominently in the ecology of many organisms. Here, we derive an extension of Fisher's geometric model that incorporates two common effects of environmental variation: (1) non-adaptive genotype-by-environment interactions (GxE), in which the phenotype of a given genotype varies across environmental contexts; and (2) random fluctuation of the fitness optimum, which generates fluctuating selection. We show that both factors cause a mismatch between the DFE within single generations and the distribution of geometric mean fitness effects (averaged over multiple generations) that governs long-term evolutionary change. Such mismatches permit strong evolutionary constraints – despite an abundance of beneficial fitness variation within single environmental contexts – and to conflicting DFE estimates from direct versus indirect inference methods. Finally, our results suggest an intriguing parallel between the genetics and ecology of evolutionary constraints, with environmental fluctuations and pleiotropy placing qualitatively similar limits on the availability of adaptive genetic variation.
Figure 5 in Fitness Effects of Founder Female Number of Trichogramma papilionis Reared on Ephestia kuehniella
Figure 5. Mean (± SEM) number of Ephestia eggs parasitized per Trichogramma papilionis female for the three founder treatments (1, 2 and 10 founder females). No significant difference (P> 0.050).
Figure 3 in Fitness Effects of Founder Female Number of Trichogramma papilionis Reared on Ephestia kuehniella
Figure 3. Trichogramma papilionis sex ratios of progeny from three founder female treatments (1, 2, and 10 founder females). Values are estimated mean (± SEM). Bars not connected by the same letter are significantly different.
Fig. 1. Mean longevity when female Anagyrus pseudococci were provided with 1 in The effect of buckwheat flowers and cahaba vetch extrafloral nectaries on fitness of the vine mealybug parasitoid Anagyrus pseudococci (Hymenotpera: Encyrtidae)
Fig. 1. Mean longevity when female Anagyrus pseudococci were provided with 1 potted vetch (Vicia sativa) plant, 1 potted buckwheat (Fagopyrum esculentum) plant, or only water in the laboratory. Different letters indicate significant differences (Tukey's studentized range test: P <0.05) between treatment foods (ANOVA: F = 5.56, df = 2, P <0.001).
Fig. 2. Total offspring produced when female Anagyrus pseudococci were provided with 1 in The effect of buckwheat flowers and cahaba vetch extrafloral nectaries on fitness of the vine mealybug parasitoid Anagyrus pseudococci (Hymenotpera: Encyrtidae)
Fig. 2. Total offspring produced when female Anagyrus pseudococci were provided with 1 potted vetch (Vicia sativa) plant, 1 potted buckwheat (Fagopyrum esculentum) plant, or only water in the laboratory. Different letters indicate significant differences (Tukey's studentized range test: P <0.05) between treatment foods (ANOVA: F = 14.93, df = 2, P <0.0001).
Fig. 7 in Female remating inhibition and fitness of Bactrocera dorsalis (Diptera: Tephritidae) associated with male accessory glands
Fig. 7. Lifetime mean numbers (± S.E.) of offspring produced by Bactrocera dorsalis females of various mating statuses. G2, females mated once (n = 18); G3, females mated twice with different virgin males (n = 20); G4, females mated with non-virgin males (n = 18); G5, females housed with males with a sex ratio of 1: 1 (n = 18); G6, females housed with males with a sex ratio of 1♀: 23 (n = 19). Data for the unfertilized eggs laid by virgin females in group G1 and for females that produced fewer than 30 eggs and/or five offspring in total were not analyzed. Different letters indicate significant differences.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.