Testing the low-density hypothesis for reversed sex change in polygynous fish: experiments in Labroides dimidiatus.
Ontology highlight
ABSTRACT:
SUBMITTER: Kuwamura T
PROVIDER: S-EPMC3952142 | biostudies-other | 2014
REPOSITORIES: biostudies-other
Similar Datasets
Project description:The measurement of individual change has been an important topic in both education and psychology. For instance, teachers are interested in whether students have significantly improved (e.g., learned) from instruction, and counselors are interested in whether particular behaviors have been significantly changed after certain interventions. Although classical test methods have been unable to adequately resolve the problems in measuring change, recent approaches for measuring change have begun to use item response theory (IRT). However, all prior methods mainly focus on testing whether growth is significant at the group level. The present research targets a key research question: Is the "change" in latent trait estimates for each individual significant across occasions? Many researchers have addressed this research question assuming that the latent trait is unidimensional. This research generalizes their earlier work and proposes four hypothesis testing methods to evaluate individual change on multiple latent traits: a multivariate Z-test, a multivariate likelihood ratio test, a multivariate score test, and a Kullback-Leibler test. Simulation results show that these tests hold promise of detecting individual change with low Type I error and high power. A real-data example from an educational assessment illustrates the application of the proposed methods.
| S-EPMC5985704 | biostudies-literature
Project description:Recent developments in high throughput genomic assays have opened up the possibility of testing hundreds and thousands of genes simultaneously. However, adhering to the regular statistical assumptions regarding the null distributions of test statistics in such large-scale multiple testing frameworks has the potential of leading to incorrect significance testing results and biased inference. This problem gets worse when one combines results from different independent genomic experiments with a possibility of ending up with gross false discoveries of significant genes. In this article, we develop a meta-analysis method of combining p-values from different independent experiments involving large-scale multiple testing frameworks, through empirical adjustments of the individual test statistics and p-values. Even though, it is based on various existing ideas, this specific combination is novel and potentially useful. Through simulation studies and real genomic datasets we show that our method outperforms the standard meta-analysis approach of significance testing in terms of accurately identifying the truly significant set of genes.
| S-EPMC5663489 | biostudies-literature
Project description:Human pharmaceuticals present in the environment have the potential to cause adverse effects on non-target organisms. The "read-across hypothesis" stipulates that pharmaceuticals will exhibit similar biological effects across species (e.g. human and fish) if the molecular target has been conserved and the effective drug concentrations are reached (Cmax). We tested this hypothesis by evaluating if ibuprofen, a non-selective inhibitor of prostaglandins and the cyclooxygenase (COX) enzyme, can mimic its primary effect in humans, on fish, at comparable plasma concentrations. The endpoints, prostaglandin E metabolite (PGEM) levels and the mRNA expression of COX (ptgs) gene, were measured in the gills of control and exposed fathead minnows (Pimephales promelas), using enzyme-immunoassay and quantitative real-time PCR (qPCR). Fish were exposed, for 24-72 h, to measured water concentrations of 9 (n = 12), 370 (n = 40) and 470 ?g ibuprofen/L (n = 12). Water and blood plasma concentrations were determined using LC-MS/MS. Results showed that PGEM levels in fish exposed to 370 and 470 ?g ibuprofen/L were significantly decreased compared to control fish, when mean plasma ibuprofen concentrations were 1.8-5.6-fold below the Cmax. The plasma ibuprofen concentrations and PGEM levels varied greatly between individuals. In fish exposed to 9 ?g ibuprofen/L, when the mean plasma ibuprofen concentration was 224-fold below Cmax, no change in PGEM levels was observed. These data provide evidence for the read-across hypothesis, but suggest establishing a direct dose-response between internal plasma and PGEM is difficult, and would require significantly larger numbers of fish to overcome the inter-individual variation.
| S-EPMC5034852 | biostudies-other
Project description:Sequentially hermaphroditic fish change sex from male to female (protandry) or vice versa (protogyny), increasing their fitness by becoming highly fecund females or large dominant males, respectively. These life-history strategies present different social organizations and reproductive modes, from near-random mating in protandry, to aggregate- and harem-spawning in protogyny. Using a combination of theoretical and molecular approaches, we compared variance in reproductive success (V k*) and effective population sizes (N e) in several species of sex-changing fish. We observed that, regardless of the direction of sex change, individuals conform to the same overall strategy, producing more offspring and exhibiting greater V k* in the second sex. However, protogynous species show greater V k*, especially pronounced in haremic species, resulting in an overall reduction of N e compared to protandrous species. Collectively and independently, our results demonstrate that the direction of sex change is a pivotal variable in predicting demographic changes and resilience in sex-changing fish, many of which sustain highly valued and vulnerable fisheries worldwide.
| S-EPMC5567342 | biostudies-literature
Project description:BackgroundSustained research on the problem of determining which genes are differentially expressed on the basis of microarray data has yielded a plethora of statistical algorithms, each justified by theory, simulation, or ad hoc validation and yet differing in practical results from equally justified algorithms. Recently, a concordance method that measures agreement among gene lists have been introduced to assess various aspects of differential gene expression detection. This method has the advantage of basing its assessment solely on the results of real data analyses, but as it requires examining gene lists of given sizes, it may be unstable.ResultsTwo methodologies for assessing predictive error are described: a cross-validation method and a posterior predictive method. As a nonparametric method of estimating prediction error from observed expression levels, cross validation provides an empirical approach to assessing algorithms for detecting differential gene expression that is fully justified for large numbers of biological replicates. Because it leverages the knowledge that only a small portion of genes are differentially expressed, the posterior predictive method is expected to provide more reliable estimates of algorithm performance, allaying concerns about limited biological replication. In practice, the posterior predictive method can assess when its approximations are valid and when they are inaccurate. Under conditions in which its approximations are valid, it corroborates the results of cross validation. Both comparison methodologies are applicable to both single-channel and dual-channel microarrays. For the data sets considered, estimating prediction error by cross validation demonstrates that empirical Bayes methods based on hierarchical models tend to outperform algorithms based on selecting genes by their fold changes or by non-hierarchical model-selection criteria. (The latter two approaches have comparable performance.) The posterior predictive assessment corroborates these findings.ConclusionsAlgorithms for detecting differential gene expression may be compared by estimating each algorithm's error in predicting expression ratios, whether such ratios are defined across microarray channels or between two independent groups.According to two distinct estimators of prediction error, algorithms using hierarchical models outperform the other algorithms of the study. The fact that fold-change shrinkage performed as well as conventional model selection criteria calls for investigating algorithms that combine the strengths of significance testing and fold-change estimation.
| S-EPMC3224549 | biostudies-literature
Project description:For many dose-response studies, large samples are not available. Particularly, when the outcome of interest is binary rather than continuous, a large sample size is required to provide evidence for hormesis at low doses. In a small or moderate sample, we can gain statistical power by the use of a parametric model. It is an efficient approach when it is correctly specified, but it can be misleading otherwise. This research is motivated by the fact that data points at high experimental doses have too much contribution in the hypothesis testing when a parametric model is misspecified. In dose-response analyses, to account for model uncertainty and to reduce the impact of model misspecification, averaging multiple models have been widely discussed in the literature. In this article, we propose to average semiparametric models when we test for hormesis at low doses. We show the different characteristics of averaging parametric models and averaging semiparametric models by simulation. We apply the proposed method to real data, and we show that P values from averaged semiparametric models are more credible than P values from averaged parametric methods. When the true dose-response relationship does not follow a parametric assumption, the proposed method can be an alternative robust approach.
| S-EPMC5495511 | biostudies-other
Project description:Fish are the most species-rich vertebrate group, displaying vast ecological, anatomical and behavioural diversity, and therefore are of major interest for the study of behaviour and its evolution. However, with respect to other vertebrates, fish are relatively underrepresented in psychological and cognitive research. A greater availability of easily accessible, flexible, open-source experimental platforms that facilitate the automation of task control and data acquisition may help to reduce this bias and improve the scalability and refinement of behavioural experiments in a range of different fish species. Here we present GoFish, a fully automated platform for behavioural experiments in aquatic species. GoFish includes real-time video tracking of subjects, presentation of stimuli in a computer screen, an automatic feeder device, and closed-loop control of task contingencies and data acquisition. The design and software components of the platform are freely available, while the hardware is open-source and relatively inexpensive. The control software, Bonsai, is designed to facilitate rapid development of task workflows and is supported by a growing community of users. As an illustration and test of its use, we present the results of two experiments on discrimination learning, reversal, and choice in goldfish (Carassius auratus). GoFish facilitates the automation of high-throughput protocols and the acquisition of rich behavioural data. Our platform has the potential to become a widely used tool that facilitates complex behavioural experiments in aquatic species.
| S-EPMC10794453 | biostudies-literature
Project description:Pain perception in non-mammalian vertebrates such as fish is a controversial issue. We demonstrate that, in the fish Leporinus macrocephalus, an imposed restraint can modulate the behavioral response to a noxious stimulus, specifically the subcutaneous injection of 3% formaldehyde. In the first experiment, formaldehyde was applied immediately after 3 or 5 min of the restraint. Inhibition of the increase in locomotor activity in response to formaldehyde was observed, which suggests a possible restraint-induced antinociception. In the second experiment, the noxious stimulus was applied 0, 5, 10 and 15 min after the restraint, and both 3 and 5 min of restraint promoted short-term antinociception of approximately 5 min. In experiments 3 and 4, an intraperitoneal injection of naloxone (30 mg.kg(-1)) was administered 30 min prior to the restraint. The 3- minute restraint-induced antinociception was blocked by pretreatment with naloxone, but the corresponding 5-minute response was not. One possible explanation for this result is that an opioid and a non-preferential ?-opioid and/or non-opioid mechanism participate in this response modulation. Furthermore, we observed that both the 3- and 5- minutes restraint were severely stressful events for the organism, promoting marked increases in serum cortisol levels. These data indicate that the response to a noxious stimulus can be modulated by an environmental stressor in fish, as is the case in mammals. To our knowledge, this study is the first evidence for the existence of an endogenous antinociceptive system that is activated by an acute standardized stress in fish. Additionally, it characterizes the antinociceptive response induced by stress in terms of its time course and the opioid mediation, providing information for understanding the evolution of nociception modulation.
| S-EPMC3728202 | biostudies-literature
Project description:Climate change is increasing global temperatures and intensifying the frequency and severity of extreme heat waves. How organisms will cope with these changes depends on their inherent thermal tolerance, acclimation capacity, and ability for evolutionary adaptation. Yet, the potential for adaptation of upper thermal tolerance in vertebrates is largely unknown. We artificially selected offspring from wild-caught zebrafish (Danio rerio) to increase (Up-selected) or decrease (Down-selected) upper thermal tolerance over six generations. Selection to increase upper thermal tolerance was also performed on warm-acclimated fish to test whether plasticity in the form of inducible warm tolerance also evolved. Upper thermal tolerance responded to selection in the predicted directions. However, compared to the control lines, the response was stronger in the Down-selected than in the Up-selected lines in which evolution toward higher upper thermal tolerance was slow (0.04 ± 0.008 °C per generation). Furthermore, the scope for plasticity resulting from warm acclimation decreased in the Up-selected lines. These results suggest the existence of a hard limit in upper thermal tolerance. Considering the rate at which global temperatures are increasing, the observed rates of adaptation and the possible hard limit in upper thermal tolerance suggest a low potential for evolutionary rescue in tropical fish living at the edge of their thermal limits.
| S-EPMC7776906 | biostudies-literature
Project description:Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected from two ecologically similar species living along the eastern coast of South Africa: one gonochoristic, the 'santer' sea bream Cheimerius nufar, and one protogynous (female-first) sex changer, the 'slinger' sea bream Chrysoblephus puniceus. For both species, no evidence of genetic structuring, nor significant variation in genetic diversity, was found in the study area. Estimates of contemporary Ne were significantly lower in the protogynous species, but the same pattern was not apparent over historical timescales. Overall, our results show that sequential hermaphroditism may affect Ne differently over varying time frames, and that demographic signatures inferred from genetic markers with different inheritance modes also need to be interpreted cautiously, in relation to sex-changing life histories.
| S-EPMC5026757 | biostudies-literature