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7 results for “selection coefficient”
Supplementary Table S1. Combined analysis of variance containing the degrees of freedom (DF), mean squares (MS), P value (P val.), mean, coefficient of experimental variation (CEV%) and selective accuracy (SA) for the traits of luminosity (L*), chromaticity a* (a*), chromaticity b* (b*), grain length (length, mm), grain width (width, mm), grain thickness (thickness, mm), mass of 100 grains (Mass, g), normal grains (Ng, %), water absorption (absorption, %), cooking time (Ct, min:s), and concentrations of potassium (K, g kg-1 dry matter - DM), phosphorus (P, g kg-1 DM), calcium (Ca, g kg-1 DM), magnesium (Mg, g kg-1 DM), iron (Fe, mg kg-1 DM), zinc (Zn, mg kg-1 DM), and copper (Cu, mg kg-1 DM) obtained in 25 common bean cultivars evaluated in four experiments carried out from 2019 to 2021
<p><strong><span>Table S1.</span></strong><span> Combined analysis of variance.</span></p> <p><strong><span>Indirect selection for multiple technological and nutritional traits in common bean cultivars under different degrees of multicollinearity</span></strong></p> <p><strong><span>Bragantia, 2024.</span></strong></p>
Data from: The relationship between dN/dS and scaled selection coefficients
Numerous computational methods exist to assess the mode and strength of natural selection in protein-coding sequences, yet how distinct methods relate to one another remains largely unknown. Here, we elucidate the relationship between two widely-used phylogenetic modeling frameworks: dN/dS models and mutation-selection (MutSel) models. We derive a mathematical relationship between dN/dS and scaled selection coefficients, the focal parameters of MutSel models, and use this relationship to gain deeper insight into the behaviors, limitations, and applicabilities of these two modeling frameworks. We prove that, if all synonymous changes are neutral, standard MutSel models correspond to dN/dS < 1. However, if synonymous codons differ in fitness, dN/dS can take on arbitrarily high values even if all selection is purifying. Thus, the MutSel modeling framework cannot necessarily accommodate positive, diversifying selection, while dN/dS cannot distinguish between purifying selection on synonymous codons and positive selection on amino acids. We further propose a new benchmarking strategy of dN/dS inferences against MutSel simulations and demonstrate that the widely-used Goldman-Yang-style dN/dS models yield substantially biased dN/dS estimates on realistic sequence data. By contrast, the less frequently used Muse-Gaut-style models display much less bias. Strikingly, the least-biased and most-precise dN/dS estimates are never found in the models with the best fit to the data, measured through both AIC and BIC scores. Thus, selecting models based on goodness-of-fit criteria can yield poor parameter estimates if the models considered do not precisely correspond to the underlying mechanism that generated the data. In conclusion, establishing mathematical links among modeling frameworks represents a novel, powerful strategy to pinpoint previously unrecognized model limitations and strengths.
Data for: Assessment of estimating selection coefficients in non-Wright-Fisher populations
<p>Selection coefficients are a useful parameter in evolutionary studies. Given that most tools to estimate selection coefficients assume population dynamics of a Wright-Fisher model, but most real-world populations violate Wright-Fisher model assumptions, the accuracy of these tools under more realistic scenarios of evolution is debatable. In this study, we test a common tool (WFABC) to assess estimates of selection coefficients in simulated populations which do and do not adhere to typical Wright-Fisher assumptions. Specifically, we look at simulated non-Wright-Fisher populations which experience evolutionary rescue. We see that fluctuating demography plays an important role in our ability to infer natural selection. Increased rates of sweeps due to bottlenecks increase error in estimates of selection by up to 5.45 times relative to typical WF-adhering populations. In a moderately polygenic model of adaptation, more severe bottlenecks produce harder sweeps such that selected sites interact with surrounding sites, including other selected sites, to increase error in estimates. This may lead to an erroneous excess of the estimated number of sites under selection within a population experiencing evolutionary rescue. Our results place an emphasis on thoughtful analyses of estimates of selection obtained from real-world populations which don't adhere to typical model assumptions.</p>
Data from: The relationship between dN/dS and scaled selection coefficients
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Data for: Assessment of estimating selection coefficients in non-Wright-Fisher populations
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Data from: Do males pay for sex? Sex-specific selection coefficients suggest not
Selection acting on males can reduce mutation load of sexual relative to asexual populations, thus mitigating the two-fold cost of sex, provided that it seeks and destroys the same mutations as selection acting on females, but with higher efficiency. This could happen due to sexual selection – a potent evolutionary force that in most systems predominantly affects males. We used replicate populations of red flour beetles (Tribolium castaneum) to study sex-specific selection against deleterious mutations introduced with ionizing radiation. We found no evidence for selection being stronger in males than in females; in fact, we observed a non-significant trend in the opposite direction. This suggests that selection on males does not reduce mutation load below the level expected under the (hypothetical) scenario of asexual reproduction. Additionally, we employed a novel approach, based on a simple model, to quantify the relative contributions of sexual and offspring viability selection to the overall selection observed in males. We found them to be similar in magnitude; however, only the offspring viability component was statistically significant. In summary, we found no support for the hypothesis that selection on males in general, and sexual selection in particular, contributes to the evolutionary maintenance of sex.
Data from: Do males pay for sex? Sex-specific selection coefficients suggest not
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