Selection history is relative.
Ontology highlight
ABSTRACT:
SUBMITTER: Liao MR
PROVIDER: S-EPMC7484361 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Plants must precisely time flowering to capitalize on favorable conditions. Although we know a great deal about the genetic basis of flowering phenology in model species under controlled conditions, the genetic architecture of this ecologically important trait is poorly understood in nonmodel organisms. Here, we evaluated the transition from vegetative growth to flowering in Boechera stricta, a perennial relative of Arabidopsis thaliana. We examined flowering time QTLs using 7920 recombinant inbred individuals, across seven laboratory and field environments differing in vernalization, temperature, and photoperiod. Genetic and environmental factors strongly influenced the transition to reproduction. We found directional selection for earlier flowering in the field. In the growth chamber experiment, longer winters accelerated flowering, whereas elevated ambient temperatures delayed flowering. Our analyses identified one large effect QTL (nFT), which influenced flowering time in the laboratory and the probability of flowering in the field. In Montana, homozygotes for the native allele at nFT showed a selective advantage of 6.6%. Nevertheless, we found relatively low correlations between flowering times in the field and the growth chambers. Additionally, we detected flowering-related QTLs in the field that were absent across the full range of laboratory conditions, thus emphasizing the need to conduct experiments in natural environments.
| S-EPMC3155413 | biostudies-literature
Project description:Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self-sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery-farmed) or naturalized/wild oysters to move onto a farm (naturalized-farmed). It is therefore important to understand genetic variation among populations and farm types. Here, we genotype naturalized/wild populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double-digest RAD-sequencing in 182 naturalized, 112 hatchery-farmed, and 72 naturalized-farmed oysters (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean F ST = 0.0019) and low differentiation between countries in the Japan-Canada-France historical translocation lineage (France-Canada F ST = 0.0024; Japan-Canada F ST = 0.0060). Chinese populations were more differentiated (China-Japan F ST = 0.0241). Hatchery-propagated populations had higher interindividual relatedness suggesting family structure. Within-population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate were lower in one farm population. Moving oysters from nature onto farms did not result in strong within-generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting nonlocal origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. Top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery-farmed oysters depend on whether naturalized populations are valued as a locally adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question.
| S-EPMC7359842 | biostudies-literature
Project description:Habitat-selection analysis lacks an appropriate measure of the ecological significance of the statistical estimates-a practical interpretation of the magnitude of the selection coefficients. There is a need for a standard approach that allows relating the strength of selection to a change in habitat conditions across space, a quantification of the estimated effect size that can be compared both within and across studies. We offer a solution, based on the epidemiological risk ratio, which we term the relative selection strength (RSS). For a "used-available" design with an exponential selection function, the RSS provides an appropriate interpretation of the magnitude of the estimated selection coefficients, conditional on all other covariates being fixed. This is similar to the interpretation of the regression coefficients in any multivariable regression analysis. Although technically correct, the conditional interpretation may be inappropriate when attempting to predict habitat use across a given landscape. Hence, we also provide a simple graphical tool that communicates both the conditional and average effect of the change in one covariate. The average-effect plot answers the question: What is the average change in the space use probability as we change the covariate of interest, while averaging over possible values of other covariates? We illustrate an application of the average-effect plot for the average effect of distance to road on space use for elk (Cervus elaphus) during the hunting season. We provide a list of potentially useful RSS expressions and discuss the utility of the RSS in the context of common ecological applications.
| S-EPMC5528224 | biostudies-other
Project description:Recent studies have shown that past selection history affects the allocation of attention on target selection. However, it is unclear whether context-driven selection history can modulate the efficacy of attention allocation on working memory (WM) representations. This study tests the influences of selection history on WM capacity. A display of one item (low load) or three/four items (high load) was shown for the participants to hold in WM in a delayed response task. Participants then judged whether a probe item was in the memory display or not. Selection history was defined as the number of items attended across trials in the task context within a block, manipulated by the stimulus set-size in the contexts with fewer possible stimuli (4-item or 5-item context) or more possible stimuli (8-item or 9-item context) from which the memorized content was selected. The capacity measure (i.e., the K measure) was estimated to reflect the number of items that can be held in WM. Across four behavioral experiments, the results revealed that the capacity was significantly reduced in the context with more possible stimuli relative to the context with fewer possible stimuli. Moreover, the reduction in capacity was significant for high WM load and not observed when the focus was on only a single item. Together, these findings indicate that context-driven selection history and focused attention influence WM capacity.
| S-EPMC5053993 | biostudies-literature
Project description:The purpose of this study was to thoroughly examine the performance of three information-based fit indices-Akaike's Information Criterion (AIC), Bayesian Information Criterion (BIC), and sample-size-adjusted BIC (SABIC)-using the log-linear cognitive diagnosis model and a set of well-known item response theory (IRT) models. Two simulation studies were conducted to examine the extent to which relative fit indices can identify the generating model under a variety of data conditions and model misspecifications. Generally, indices performed better when item quality was stronger. When the IRT was the generating model, all three indices correctly selected the IRT model for all replications. When the true model was a diagnostic classification model, for all three fit indices, the multidimensional IRT model was incorrectly selected as frequently as 70% of the replications. The results of this study identify situations for researchers where commonly used-and typically well-performing-fit indices may not be appropriate to compare models for selection.
| S-EPMC5978522 | biostudies-literature
Project description:Selection, recombination, and the demographic history of a species can all have profound effects on genomewide patterns of variability. To assess the impact of these forces in the genome of Drosophila miranda, we examine polymorphism and divergence patterns at 62 loci scattered across the genome. In accordance with recent findings in D. melanogaster, we find that noncoding DNA generally evolves more slowly than synonymous sites, that the distribution of polymorphism frequencies in noncoding DNA is significantly skewed toward rare variants relative to synonymous sites, and that long introns evolve significantly slower than short introns or synonymous sites. These observations suggest that most noncoding DNA is functionally constrained and evolving under purifying selection. However, in contrast to findings in the D. melanogaster species group, we find little evidence of adaptive evolution acting on either coding or noncoding sequences in D. miranda. Levels of linkage disequilibrium (LD) in D. miranda are comparable to those observed in D. melanogaster, but vary considerably among chromosomes. These patterns suggest a significantly lower rate of recombination on autosomes, possibly due to the presence of polymorphic autosomal inversions and/or differences in chromosome sizes. All chromosomes show significant departures from the standard neutral model, including too much heterogeneity in synonymous site polymorphism relative to divergence among loci and a general excess of rare synonymous polymorphisms. These departures from neutral equilibrium expectations are discussed in the context of nonequilibrium models of demography and selection.
| S-EPMC1698658 | biostudies-literature
Project description:Male genitalia often show remarkable differences among related species in size, shape and complexity. Across poeciliid fishes, the elongated fin (gonopodium) that males use to inseminate females ranges from 18 to 53% of body length. Relative genital size therefore varies greatly among species. In contrast, there is often tight within-species allometric scaling, which suggests strong selection against genital-body size combinations that deviate from a species' natural line of allometry. We tested this constraint by artificially selecting on the allometric intercept, creating lines of males with relatively longer or shorter gonopodia than occur naturally for a given body size in mosquitofish, Gambusia holbrooki. We show that relative genital length is heritable and diverged 7.6-8.9% between our up-selected and down-selected lines, with correlated changes in body shape. However, deviation from the natural line of allometry does not affect male success in assays of attractiveness, swimming performance and, crucially, reproductive success (paternity).
| S-EPMC4873965 | biostudies-literature
Project description:Object perception is inherently multidimensional: information about color, material, texture and shape all guide how we interact with objects. We developed a paradigm that quantifies how two object properties (color and material) combine in object selection. On each experimental trial, observers viewed three blob-shaped objects-the target and two tests-and selected the test that was more similar to the target. Across trials, the target object was fixed, while the tests varied in color (across 7 levels) and material (also 7 levels, yielding 49 possible stimuli). We used an adaptive trial selection procedure (Quest+) to present, on each trial, the stimulus test pair that is most informative of underlying processes that drive selection. We present a novel computational model that allows us to describe observers' selection data in terms of (1) the underlying perceptual stimulus representation and (2) a color-material weight, which quantifies the relative importance of color vs. material in selection. We document large individual differences in the color-material weight across the 12 observers we tested. Furthermore, our analyses reveal limits on how precisely selection data simultaneously constrain perceptual representations and the color-material weight. These limits should guide future efforts towards understanding the multidimensional nature of object perception.
| S-EPMC6490924 | biostudies-literature
Project description:Making decisions based on choice-outcome history is a crucial, adaptive ability in life. However, the neural circuit mechanisms underlying history-dependent decision-making are poorly understood. In particular, history-related signals have been found in many brain areas during various decision-making tasks, but the causal involvement of these signals in guiding behavior is unclear. Here we addressed this issue utilizing behavioral modeling, two-photon calcium imaging, and optogenetic inactivation in mice. We report that a subset of neurons in the posterior parietal cortex (PPC) closely reflect the choice-outcome history and history-dependent decision biases, and PPC inactivation diminishes the history dependency of choice. Specifically, many PPC neurons show history- and bias-tuning during the inter-trial intervals (ITI), and history dependency of choice is affected by PPC inactivation during ITI and not during trial. These results indicate that PPC is a critical region mediating the subjective use of history in biasing action selection.
| S-EPMC5663966 | biostudies-literature
Project description:Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant. This method focuses selection on the haplotype and optimizes the breeding program toward its end goal of generating an elite fixed line. We rigorously tested OHV selection breeding programs, using computer simulation, and show that it results in up to 0.6 standard deviations more genetic gain than genomic selection. At the same time, OHV selection preserved a substantially greater amount of genetic diversity in the population than genomic selection, which is important to achieve long-term genetic gain in breeding populations.
| S-EPMC4574260 | biostudies-literature