Foraging behavior in stochastic environments

How do temporally stochastic environments affect risk sensitivity in foraging behavior? We build a simple model of foraging under predation risks in stochastic environments, where the environments change over generations. We analyze the effects of stochastic environments on risk sensitivity of foraging animals by means of the difference between the geometric mean fitness and the arithmetic mean fitness. We assume that foraging is associated with predation risks whereas resting in the nest is safe because it is free of predators. In each generation, two different environments with given food amounts and predation risks occur with a certain probability. The geometric mean optimum is independent of food amounts. In most cases of stochastic environments, risk-averse tendency is increased, but in some limited conditions, more risk-prone behavior is favored. Specifically, risk-prone tendency is increased when the variation in food amount increases. Our results imply that the optimal behavior depends on the probability distribution of environmental effects under all selection regimes.     

Genetic architecture of plastic methyl jasmonate responses in Arabidopsis thaliana

The ability of a single genotype to generate different phenotypes in disparate environments is termed phenotypic plasticity, which reflects the interaction of genotype and environment on developmental processes. However, there is controversy over the definition of plasticity genes. The gene regulation model states that plasticity loci influence trait changes between environments without altering the means within a given environment. Alternatively, the allelic sensitivity model argues that plasticity evolves due to selection of phenotypic values expressed within particular environments; hence plasticity must be controlled by loci expressed within these environments. To identify genetic loci controlling phenotypic plasticity and address this controversy, we analyzed the plasticity of glucosinolate accumulation under methyl jasmonate (MeJa) treatment in Arabidopsis thaliana. We found genetic variation influencing multiple MeJa signal transduction pathways. Analysis of MeJa responses in the Landsberg erecta x Columbia recombinant inbred lines identified a number of quantitative trait loci (QTL) that regulate plastic MeJa responses. All significant plasticity QTL also impacted the mean trait value in at least one of the two "control" or "MeJa" environments, supporting the allelic sensitivity model. Additionally, we present an analysis of MeJa and salicylic acid cross-talk in glucosinolate regulation and describe the implications for glucosinolate physiology and functional understanding of Arabidopsis MeJa signal transduction.     

The fitness effect of mutations across environments: a survey in light of fitness landscape models

The fitness effects of mutations on a given genotype are rarely constant across environments to which this genotype is more or less adapted, that is, between more or less stressful conditions. This can have important implications, especially on the evolution of ecological specialization. Stress is thought to increase the variance of mutations' fitness effects, their average, or the number of expressed mutations. Although empirical evidence is available for these three mechanisms, their relative magnitude is poorly understood. In this paper, we propose a simple approach to discriminate between these mechanisms, using a survey of empirical measures of mutation effects in contrasted environments. This survey, across various species and environments, shows that stress mainly increases the variance of mutations' effects on fitness, with a much more limited impact on their average effect or on the number of expressed mutations. This pattern is consistent with a simple model in which fitness is a Gaussian function of phenotypes around an environmentally determined optimum. These results suggest that a simple, mathematically tractable landscape model may not be quantitatively as unrealistic as previously suggested. They also suggest that mutation parameter estimates may be strongly biased when measured in stressful environments.     

The fitness effect of mutations across environments: Fisher's geometrical model with multiple optima

When are mutations beneficial in one environment and deleterious in another? More generally, what is the relationship between mutation effects across environments? These questions are crucial to predict adaptation in heterogeneous conditions in a broad sense. Empirical evidence documents various patterns of fitness effects across environments but we still lack a framework to analyze these multivariate data. In this article, we extend Fisher's geometrical model to multiple environments determining distinct peaks. We derive the fitness distribution, in one environment, among mutants with a given fitness in another and the bivariate distribution of random mutants’ fitnesses across two or more environments. The geometry of the phenotype‐fitness landscape is naturally interpreted in terms of fitness trade‐offs between environments. These results may be used to fit/predict empirical distributions or to predict the pattern of adaptation across heterogeneous conditions. As an example, we derive the genomic rate of substitution and of adaptation in a metapopulation divided into two distinct habitats in a high migration regime and show that they depend critically on the geometry of the phenotype‐fitness landscape.     

Statistical Analysis of Factorial Diallel Design over Environments

Starting from the experimental situation that in each of a environments all mp combinations between m maternal and p paternal genotypes are raised in b replications (blocks), a linear model is formulated for a quantitative character. On the basis of this model formulae for the analysis of variance are given. The expectations of mean squares as well as the estimations of effects (general and specific combining ability and their interaction terms with environments) and their variances are given for different combinations of fixed and random factors.     

Maternal investment in egg size: environment- and population-specific effects on offspring performance

Geographic variation in maternal investment in offspring size can be adaptive if differences in investment translate into improved offspring performance in the given environments. We compared two moor frog, Rana arvalis, populations in the laboratory to test the hypothesis that investment in large eggs in populations originating from stressful (acid) environments improves offspring performance when reared in stressful (acid) conditions. We found that large initial size (hatchling mass) had moderate to strong, environment-dependent positive effects on larval and metamorphic traits in the acidic origin population, but only weak effects in the neutral origin population. Our results suggest that interactions between environmental conditions and initial size can be important determinants of individual performance, and that investment in large eggs is adaptive in acid environments. These findings emphasize the role of maternal effects as adaptations to environmental stress.     

Lipid modulation of nicotinic acetylcholine receptor function: the role of neutral and negatively charged lipids.

The effects of negatively charged and neutral lipids on the function of the reconstituted nicotinic acetylcholine receptor from Torpedo californica were determined with two assays using acetylcholine receptor-containing vesicles: the ion flux response and the affinity-state transition. The receptor was reconstituted into three different lipid environments, with and without neutral lipids: (1) phosphatidylcholine/phosphatidylserine; (2) phosphatidylcholine/phosphatidic acid; and (3) phosphatidylcholine/cardiolipin. Analysis of the ion flux responses showed that: (1) all three negatively charged lipid environments gave fully functional acetylcholine receptor ion channels, provided neutral lipids were added; (2) in each lipid environment, the neutral lipids tested were functionally equivalent to cholesterol; and (3) the rate of receptor desensitization depends upon the type of neutral lipid and negatively charged phospholipid reconstituted with the receptor. The functional effects of neutral and negatively charged lipids on the acetylcholine receptor are discussed in terms of protein-lipid interactions and stabilization of protein structure by lipids.     

Influence of day-length and isolates of Phytophthora infestans on field resistance to late blight of potato

Main and interaction effects of day-length and pathogen isolate on the reaction and expression of field resistance to Phytophthora infestans were analyzed in a sample of standard clones for partial resistance to potato late blight, and in the BCT mapping population derived from a backcross of Solanum berthaultii to Solanum tuberosum. Detached leaves from plants grown in field plots exposed to short- and long day-length conditions were independently inoculated with two P. infestans isolates and incubated in chambers under short- and long photoperiods, respectively. Lesion growth rate (LGR) was used for resistance assessment. Analysis of variance revealed a significant contribution of genotype × isolate × day-length interaction to variation in LGR indicating that field resistance of genotypes to foliar late blight under a given day-length depended on the infecting isolate. An allele segregating from S. berthaultii with opposite effects on foliar resistance to late blight under long- and short day-lengths, respectively, was identified at a quantitative trait locus (QTL) that mapped on chromosome 1. This allele was associated with positive (decreased resistance) and negative (increased resistance) additive effects on LGR, under short- and long day-length conditions, respectively. Disease progress on whole plants inoculated with the same isolate under field conditions validated the direction of its effect in short day-length regimes. The present study suggests the occurrence of an isolate-specific QTL that displays interaction with isolate behavior under contrasting environments, such as those with different day-lengths. This study highlights the importance of exposing genotypes to a highly variable population of the pathogen under contrasting environments when stability to late blight resistance is to be assessed or marker-assisted selection is attempted for the manipulation of quantitative resistance to late blight.     

Viability in a pink environment: why "white noise" models can be dangerous

Analysis of long time series suggests that environmental fluctuations may be accurately represented by 1/ f   noise (pink noise), where temporal correlation is found at several scales, and the range of fluctuations increases over time. Previous studies on the effects of coloured noise on population dynamics used first or second order autoregressive noise. I examined the importance of coloured noise for extinction risk using true 1/ f   noise. I also considered the problem of estimating extinction risk with a limited sample of environmental variation. Pink noise environments increased extinction risk in random walk models where environmental variation affected the growth rate. However, pink noise environments decreased extinction risk in the Ricker model where environmental variation modified the carrying capacity. Underestimation of environmental variance almost always yielded underestimation of extinction risk. For either population viability analysis or management, we should carefully consider the long-term behaviour of the environment as well as how we include environmental noise in population models.     

Sex- and trait-specific silver-spoon effects of developmental environments,on ageing

Evolutionary Ecology - The environment organisms experience during development can have effects which carry over into their adult lives. These environments not only affect adult traits at a given...     

Nonparametric Comparison of Longitudinal Response Patterns from Paired Samples Using Configural Frequency Analysis

Nonparametric methods of Configural Frequency Analysis (CFA) for comparing longitudinal response patterns are discussed. Characteristics of diagonally symmetric frequency distributions are mapped with hypotheses on the locus of treatment effects. Test statistics for the analysis of local dependencies are discussed. In particular, applications to paired samples are considered. A biomedical example is given from research on the effects of spasmolytic drugs. Local CFA-testing is compared with global testing. Alternative strategies of testing and the respective underlying assumptions are discussed.     

Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure

A key issue in evolutionary biology is an improved understanding of the genetic mechanisms by which species adapt to various environments. Using DNA sequence data, it is possible to quantify the number of adaptive and deleterious mutations, and the distribution of fitness effects of new mutations (its mean and variance) by simultaneously taking into account the demography of a given species. We investigated how selection functions at eight housekeeping genes of four closely related, outcrossing species of wild tomatoes that are native to diverse environments in western South America (Solanum arcanum, S. chilense, S. habrochaites and S. peruvianum). We found little evidence for adaptive mutations but pervasive evidence for strong purifying selection in coding regions of the four species. In contrast, the strength of purifying selection seems to vary among the four species in non-coding (NC) regions (introns). Using F(ST)-based measures of fixation in subdivided populations, we suggest that weak purifying selection has affected the NC regions of S. habrochaites, S. chilense and S. peruvianum. In contrast, NC regions in S. arcanum show a distribution of fitness effects with mutations being either nearly neutral or very strongly deleterious. These results suggest that closely related species with similar genetic backgrounds but experiencing contrasting environments differ in the variance of deleterious fitness effects.     

Gene action of canopy temperature in bread wheat under diverse environments

While canopy temperature (CT) shows a strong and reliable association with yield under drought and heat stress and is used in wheat breeding to select for yield, little is known of its genetic control. The objective of this study was to determine the gene action controlling CT in five wheat populations grown in diverse environments (heat, drought, and well-irrigated conditions). CT showed negative phenotypic correlations with grain yield under drought and well-irrigated environments. Additive × additive effects were most prevalent and significant for all crosses and environments. Dominance and dominance × dominance gene actions were also found, though the significance and direction was specific for each environment and genotypic cross. The use of CT as a selection criterion to improve tolerance to drought was supported by its significant association with grain yield and the genotype differences observed between cultivars. Our results indicated that genetic gains for CT in wheat could be achieved through conventional breeding. However, given some dominance and epistatic effects, it would be necessary to delay the selection process until the frequency of heterozygous loci within families is reduced.     

A MARKER-BASED METHOD FOR INFERENCES ABOUT QUANTITATIVE INHERITANCE IN NATURAL POPULATIONS

A marker-based method for studying quantitative genetic characters in natural populations is presented and evaluated. The method involves regressing quantitative trait similarity on marker-estimated relatedness between individuals. A procedure is first given for estimating the narrow sense heritability and additive genetic correlations among traits, incorporating shared environments. Estimation of the actual variance of relatedness is required for heritability, but not for genetic correlations. The approach is then extended to include isolation by distance of environments, dominance, and shared levels of inbreeding. Investigations of statistical properties show that good estimates do not require great marker polymorphism, but rather require significant variation of actual relatedness; optimal allocation generally favors sampling many individuals at the expense of assaying fewer marker loci; when relatedness declines with physical distance, it is optimal to restrict comparisons to within a certain distance; the power to estimate shared environments and inbreeding effects is reasonable, but estimates of dominance variance may be difficult under certain patterns of relationship; and any linkage of markers to quantitative trait loci does not cause significant problems. This marker-based method makes possible studies with long-lived organisms or with organisms difficult to culture, and opens the possibility that quantitative trait expression in natural environments can be analyzed in an unmanipulative way.     

Social effects for locomotion vary between environments in Drosophila melanogaster females

Despite strong purifying or directional selection, variation is ubiquitous in populations. One mechanism for the maintenance of variation is indirect genetic effects (IGEs), as the fitness of a given genotype will depend somewhat on the genes of its social partners. IGEs describe the effect of genes in social partners on the expression of the phenotype of a focal individual. Here, we ask what effect IGEs, and variation in IGEs between abiotic environments, has on locomotion in Drosophila. This trait is known to be subject to intralocus sexually antagonistic selection. We estimate the coefficient of interaction, Ψ, using six inbred lines of Drosophila. We found that Ψ varied between abiotic environments, and that it may vary across among male genotypes in an abiotic environment specific manner. We also found evidence that social effects of males alter the value of a sexually dimorphic trait in females, highlighting an interesting avenue for future research into sexual antagonism. We conclude that IGEs are an important component of social and sexual interactions and that they vary between individuals and abiotic environments in complex ways, with the potential to promote the maintenance of phenotypic variation.     

Fitness, genetic load and purging in experimental populations of the housefly

The relative effects of purging of the genetic load versus thefixation of deleterious alleles, under inbreeding, will influencea population's probability of extinction. The relative contributionof these two phenomena is expected to depend upon the rate ofinbreeding. A further complication is due to the fact that a purgingof the genetic load in one environment does not necessarily implya purging of the genetic load in other environments. To addressthese two issues, we compare fitness and genetic load in populationsexperiencing similar levels of inbreeding, but occurring as either ashort-term bottleneck or as a consequence of long-term reducedpopulation size, over a range of environments. Inbred populationshave consistently lower fitness than outbred populations acrossall environments tested. However, the bottlenecked populationssuffer less inbreeding depression for a given level of inbreeding,whether or not challenged by novel environments, than populationskept at a constant small size. The results of this study demonstratethat populations initiated from a small number of founders are ableto recover fitness and survive novel environmental challenges,provided that habitat is available for rapid population growth.     

POPULATION AND GENOTYPE NICHE WIDTH IN CLONAL PHLOX PANICULATA

We use a model population comprised of five genotypes of Phlox paniculata L. to investigate the contribution of individuals to the response breadth (niche) of the population on a light gradient and a moisture gradient. Analysis of within- and between-genotype components of population response width showed up to 20% of the response is due to between-genotype effects, depending upon the character considered. Since the only way a sedentary organism can deal with a variable environment is through plasticity of response, differences in levels of phenotypic plasticity between genotypes on the two resource gradients were also investigated. There was no correlation between level of phenotypic plasticity and success over a range of environments. Niche breadth calculated as Levins' (B) and Roughgarden's (w²) indicated that flowering, and hence sexual reproduction, was limited to a much narrower range of environments than was vegetative growth. We also found significant genotype × environment interactions on both gradients, indicating differences in genetic response to the environment.     

The Adaptive Potential of the Middle Domain of Yeast Hsp90

The distribution of fitness effects (DFEs) of new mutations across different environments quantifies the potential for adaptation in a given environment and its cost in others. So far, results regarding the cost of adaptation across environments have been mixed, and most studies have sampled random mutations across different genes. Here, we quantify systematically how costs of adaptation vary along a large stretch of protein sequence by studying the distribution of fitness effects of the same ≈2,300 amino-acid changing mutations obtained from deep mutational scanning of 119 amino acids in the middle domain of the heat shock protein Hsp90 in five environments. This region is known to be important for client binding, stabilization of the Hsp90 dimer, stabilization of the N-terminal-Middle and Middle-C-terminal interdomains, and regulation of ATPase–chaperone activity. Interestingly, we find that fitness correlates well across diverse stressful environments, with the exception of one environment, diamide. Consistent with this result, we find little cost of adaptation; on average only one in seven beneficial mutations is deleterious in another environment. We identify a hotspot of beneficial mutations in a region of the protein that is located within an allosteric center. The identified protein regions that are enriched in beneficial, deleterious, and costly mutations coincide with residues that are involved in the stabilization of Hsp90 interdomains and stabilization of client-binding interfaces, or residues that are involved in ATPase–chaperone activity of Hsp90. Thus, our study yields information regarding the role and adaptive potential of a protein sequence that complements and extends known structural information.     

A genetic interpretation of ecologically dependent isolation

Hybrids may suffer a reduced fitness both because they fall between ecological niches (ecologically dependent isolation) and as a result of intrinsic genetic incompatibilities between the parental genomes (ecologically independent isolation). Whereas genetic incompatibilities are common to all theories of speciation, ecologically dependent isolation is a unique prediction of the ecological model of speciation. This prediction can be tested using reciprocal transplants in which the fitness of various genotypes is evaluated in both parental habitats. Here we expand a quantitative genetic model of Lynch (1991) to include two parental environments. We ask whether a sufficient experimental design exists for detecting ecologically dependent isolation. Analysis of the model reveals that by using both backcrosses in both parental environments, environment-specific additive genetic effects can be estimated while correcting for any intrinsic genetic isolation. Environment-specific dominance effects can also be estimated by including the F1 and F2 in the reciprocal transplant. In contrast, a reciprocal transplant comparing only F1s or F2s to the parental species cannot separate ecologically dependent from intrinsic genetic isolation. Thus, a reduced fitness of F1 or F2 hybrids relative to the parental species is not sufficient to demonstrate ecological speciation. The model highlights the importance of determining the contribution of genetic and ecological mechanisms to hybrid fitness if inferences concerning speciation mechanisms are to be made.     

Genetic diversity assessment of anoxygenic photosynthetic bacteria by distance-based grouping analysis of pufM sequences

AIM: To assess how completely the diversity of anoxygenic phototrophic bacteria (APB) was sampled in natural environments. METHODS AND RESULTS: All nucleotide sequences of the APB marker gene pufM from cultures and environmental clones were retrieved from the GenBank database. A set of cutoff values (sequence distances 0.06, 0.15 and 0.48 for species, genus, and (sub)phylum levels, respectively) was established using a distance-based grouping program. Analysis of the environmental clones revealed that current efforts on APB isolation and sampling in natural environments are largely inadequate. Analysis of the average distance between each identified genus and an uncultured environmental pufM sequence indicated that the majority of cultured APB genera lack environmental representatives. CONCLUSIONS: The distance-based grouping method is fast and efficient for bulk functional gene sequences analysis. The results clearly show that we are at a relatively early stage in sampling the global richness of APB species. Periodical assessment will undoubtedly facilitate in-depth analysis of potential biogeographical distribution pattern of APB. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first attempt to assess the present understanding of APB diversity in natural environments. The method used is also useful for assessing the diversity of other functional genes.