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53 results for “fitness measures”
Code from: Fitness as the organismal performance measure guiding adaptive evolution
<p>A long-standing problem in evolutionary theory is to clarify in what sense (if any) natural selection cumulatively improves the design of organisms. Various concepts, such as fitness and inclusive fitness, have been proposed to resolve this problem. In addition, there have been attempts to replace the original problem with more tractable questions such as whether a given gene or trait is favoured by selection. Here we ask what theoretical properties the concept of fitness should possess to encapsulate the improvement criterion required to talk meaningfully about adaptive evolution. We argue that natural selection tends to shape phenotypes based on the causal properties of individuals and that this tendency is, therefore, best captured by a fitness concept that focuses on these properties. We highlight a fitness concept that meets this role under broad conditions but requires adjustments in our conceptual understanding of adaptive evolution. These adjustments combine elements of Dawkinsian gene selectionism and Egbert Leigh's "Parliament of Genes".</p>
Data and fitting script for "Direct measurement of a sin(2φ) current phase relation in a graphene superconducting quantum interference device"
<p>This repository contains data and Python analysis scripts used for the publication "Direct measurement of a sin(2\phi) current phase relation in a graphene superconducting quantum interference device (https://doi.org/10.48550/arXiv.2405.13642).</p> <p>The repository is organized as follows: the raw data are encapsulated in a QCoDes database (https://microsoft.github.io/Qcodes/) named 'D-SQUID-06.db'. Post-treated critical current data are included as .csv files and are indexed by measurement ids.</p> <p>The principal analysis is realized in the Jupyter notebook 'Fits_and_Figures.ipynb', which includes all article figures as well as fit functions for fitting both critical currents Ic- and Ic+ simulatenously, first using analytical expression from equation 3 then using numerical expression from equation 5. All fits mentionned in the article are performed there. The repository includes a generic notebook "Extract_Critical_Current.ipynb" used to explore the raw data in the Qcodes database and features an enhanced peak detection script that we used to automatically extract critical current data despite having some artifacts on raw differential conductance versus bias current and magnetic field.</p> <p>We acknowledge the contribution of R. Kerjouan for developing the Python fitting script.</p>
Different measures of niche and fitness differences tell different tales
<p>In Modern Coexistence Theory, species coexistence can either arise via strong niche differences or weak fitness differences. Having a common currency for interpreting these mechanisms is essential for synthesizing knowledge across different studies and systems. However, several methods for quantifying niche and fitness differences exist, with little guidance on how and why these methods differ. Here, we first organize the available methods into three groups and review their differences from a conceptual point of view.Next, we apply four methods to quantify niche and fitness differences to one simulated and one empirical data set. We show that these methods do not only differ quantitatively, but affect how we interpret coexistence. Specifically, the different methods disagree on how resource supply rates (simulated data) or plant traits (empirical data) affect niche and fitness differences. We argue for a better theoretical understanding of what connects and sets apart different methods and more precise empirical measurements to foster appropriate method selection in coexistence theory.</p>
Code from: Fitness as the organismal performance measure guiding adaptive evolution
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Different measures of niche and fitness differences tell different tales
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Data for: Constitutive expression of the Type VI secretion system carries no measurable fitness cost in Vibrio cholerae
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Growth and fitness measures of cytoplasmic male sterility (CMS) of Physa acuta
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Best fit parameters describing net CO2 flux light response curves measured during the ITEX CO2 flux survey 2003-2009.
Ecosystem CO2 flux light response curves were measured on 1m x 1m plots ( some 0.3m x 0.3m plots in 2006 and some 0.7m x0.7m plots in 2009) across the arctic. This file contains the best fit parameters that describe these light response curves, together with corresponding NDVI data for each curve. Survey plots were located in the Toolik Lake LTER fertilization experiment in Alaska; at Imnavait Creek, Alaska; at Paddus, Latnjajaure and the Stepps site near Abisko in northern Sweden; at various sites in Adventdalen, Svalbard; in the Zackenberg valley, Northeast Greenland; at BEO near Barrow, Alaska and at the Anaktuvuk River Burn in Alaska. Measurements were made during the growing seasons 2003 to 2009.
Fitness measures of maternal transplants (seed fitness) and of the F1 generation (rosette diameter) of three translocated populations of Arnica montana in southern Belgium
<p>Fitness data measured in the framework of a genetic monitoring of translocated populations of the critically endangered Arnica montana. See Van Rossum et al. (2020) in Molecular Ecology for more details.</p>
Data S1. Laboratory behavioral data from: Measuring the fitness advantage conferred by autotomy in the wild
<p>Data S1. Laboratory behavioral data. The composition is summarized in figure S1.</p> <p>Autotomy, the self-amputation of body parts, serves as an anti-predator defense in many taxonomic groups of animals. However, its adaptive value has seldom been quantified. Here, we propose a novel modeling approach for measuring the fitness advantage conferred by the capability for autotomy in the wild. Using a predator-prey system where a land snail autotomizes and regenerates its foot specifically in response to snake bites, we conducted a laboratory behavioral experiment and a 3-year multi-event capture–mark–recapture (CMR) study. Combining these empirical data, we developed a hierarchical model and estimated the basic life history parameters of the snail. Using samples from the posterior distribution, we constructed the snail's life table as well as that of a snail variant incapable of foot autotomy. As a result of our analyses, we estimated the monthly encounter rate with snake predators at 3.3% (95% CI: 1.6–4.9%), the contribution of snake predation to total mortality until maturity at 43.3% (15.0–95.3%), and the fitness advantage conferred by foot autotomy at 6.5% (2.7–11.5%). This study demonstrated the utility of the multi-method hierarchical modeling approach for the quantitative understanding of the ecological and evolutionary processes of anti-predator defenses in the wild.</p>
Data S2. CMR data from: Measuring the fitness advantage conferred by autotomy in the wild
<p>Data S2. CMR data. The composition is summarized in tables S2, S3, and S10.</p> <p>Autotomy, the self-amputation of body parts, serves as an anti-predator defense in many taxonomic groups of animals. However, its adaptive value has seldom been quantified. Here, we propose a novel modeling approach for measuring the fitness advantage conferred by the capability for autotomy in the wild. Using a predator-prey system where a land snail autotomizes and regenerates its foot specifically in response to snake bites, we conducted a laboratory behavioral experiment and a 3-year multi-event capture–mark–recapture (CMR) study. Combining these empirical data, we developed a hierarchical model and estimated the basic life history parameters of the snail. Using samples from the posterior distribution, we constructed the snail's life table as well as that of a snail variant incapable of foot autotomy. As a result of our analyses, we estimated the monthly encounter rate with snake predators at 3.3% (95% CI: 1.6–4.9%), the contribution of snake predation to total mortality until maturity at 43.3% (15.0–95.3%), and the fitness advantage conferred by foot autotomy at 6.5% (2.7–11.5%). This study demonstrated the utility of the multi-method hierarchical modeling approach for the quantitative understanding of the ecological and evolutionary processes of anti-predator defenses in the wild.</p>
A Test of the Repeatability of Measurements of Relative Fitness in the Long-Term Evolution Experiment with Escherichia coli
<p>Experimental studies of evolution using microbes have a long tradition, and these studies have increased greatly in number and scope in recent decades. Most such experiments have been short in duration, typically running for weeks or months. A venerable exception, the long-term evolution experiment (LTEE) with <i>Escherichia coli</i> has continued for 30 years and 70,000 bacterial generations. The LTEE has become one of the cornerstones of the field of experimental evolution, in general, and the BEACON Center for the Study of Evolution in Action, in particular. Science laboratories and experiments usually have finite lifespans, but we hope that the LTEE can continue far into the future. There are practical issues associated with maintaining such a long-term experiment. One issue, which we address here, is whether key measurements made at one time and place are reproducible, within reasonable limits, at other times and places. This issue comes to the forefront when one considers moving an experiment like the LTEE from one lab to another. To that end, the Barrick lab at the University of Texas at Austin, measured the fitness values of samples from the 12 LTEE populations at 2,000, 10,000, and 50,000 generations and compared the new data to data previously obtained at Michigan State University. On balance, the datasets agree very well. More generally, this finding shows the value of simplicity in experimental design, such as using a chemically defined growth medium and appropriately storing samples from microbiological experiments. Even so, one must be vigilant in checking assumptions and procedures given the potential for uncontrolled factors (e.g., water quality) to affect outcomes. This vigilance is perhaps especially important for a trait like fitness, which integrates all aspects of organismal performance and may therefore be sensitive to any number of subtle environmental influences.</p>
Genetic and fitness measurements of Brighamia accessions for APPS
<p><span><span><strong>Premise of the study:</strong><i> </i>Living collections maintained for generations are at risk of diversity loss, inbreeding, and adaptation to cultivation. To address these concerns the zoo community uses pedigrees to track individuals and implement crosses that maximize founder contributions and minimize inbreeding. Using a pedigree management approach in an exceptional plant, we demonstrate how conducting such strategic crosses can minimize genetic issues that have arisen under current practices. </span></span></p> <p><span><span><strong>Methods:</strong> We performed crosses between these collections and compared the fitness of progeny, including plant performance and reproductive health. We genotyped the progeny and paternal accessions to measure changes in diversity and relatedness within and between accessions. </span></span></p> <p><span><span><strong>Results:</strong><i> </i>The mean relatedness among individuals of an accession, suggests they are full siblings. As a result there was high inbreeding and low diversity within an accession, although less so among accessions. Progeny from the wider crosses had increased genetic diversity, while selfed accessions were smaller and less fertile. </span></span></p> <p><span><span><strong>Discussion:</strong> Institutions which hold exceptional species should consider how diversity is maintained within their collections. Implementing a pedigree-based approach to managing reproduction of ex situ plants will slow the inevitable loss of genetic diversity and in turn, result in healthier collections. </span></span></p>
Fitness measures of seed progeny from seven natural populations of Campanula glomerata.
<p>Fitness (rosette diameter in cm) and HL for seed progeny of seven wild populations of <em>Campanula glomerata </em>from southern Belgium and north-eastern France. For details see Van Rossum et al. (2022) in Frontiers in Conservation Science.</p>
[Dataset] Difference spectrum fitting of the ion-neutral collision frequency from dual-frequency EISCAT measurements
<p>Dataset used for "Difference spectrum fitting of the ion-neutral collision frequency from dual-frequency EISCAT measurements"</p>
Data S1. Laboratory behavioral data from: Measuring the fitness advantage conferred by autotomy in the wild
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A Test of the Repeatability of Measurements of Relative Fitness in the Long-Term Evolution Experiment with Escherichia coli
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Genetic and fitness measurements of Brighamia accessions for APPS
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Data S2. CMR data from: Measuring the fitness advantage conferred by autotomy in the wild
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Data from: Measuring the effect of environmental stress on inbreeding depression alone obscures the relative importance of inbreeding-stress interactions on overall fitness in Callosobruchus maculatus
<p>Environmental stress can have a profound effect on inbreeding depression. Quantifying this effect is of particular importance in threatened populations, which are often simultaneously subject to both inbreeding and environmental stress. But while the prevalence of inbreeding-stress interactions is well known, the importance and broader applicability of such interactions in conservation are not clearly understood. We used seed beetles, Callosobruchus maculatus, as a model system to quantify how environmental stressors (here host quality and temperature stress) interact with inbreeding as measured by changes in the magnitude of8inbreeding depression, δ, as well as the relative importance of inbreeding-stress interactions to overall fitness. We found that while both environmental stressors caused substantial inbreeding-stress interactions as measured by change in δ, the relative importance of these interactions to overall survival was modest. This suggests that assessing inbreeding-stress interactions within the framework of δ alone may give an inaccurate representation of the relevance of interactions to population persistence. Furthermore, we found that the effect of environmental stress on fitness, but not inbreeding depression, varied strongly among populations. These results suggest that the outcomes of inbreeding-stress interactions are not easily generalized, an important consideration in conservation settings.</p>
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Allen Brain Atlas
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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.