Heritability, correlations and in silico mapping of locomotor behavior and neurochemistry in inbred strains of mice

The midbrain dopamine system mediates normal and pathologic behaviors related to motor activity, attention, motivation/reward and cognition. These are complex, quantitative traits whose variation among individuals is modulated by genetic, epigenetic and environmental factors. Conventional genetic methods have identified several genes important to this system, but the majority of factors contributing to the variation remain unknown. To understand these genetic and environmental factors, we initiated a study measuring 21 behavioral and neurochemical traits in 15 common inbred mouse strains. We report trait data, heritabilities and genetic and non-genetic correlations between pheno-types. In general, the behavioral traits were more heritable than neurochemical traits, and both genetic and non-genetic correlations within these trait sets were high. Surprisingly, there were few significant correlations between the behavioral and the individual neurochemical traits. However, striatal serotonin and one measure of dopamine turnover (DOPAC/DA) were highly correlated with most behavioral measures. The variable accounting for the most variation in behavior was mouse strain and not a specific neurochemical measure, suggesting that additional genetic factors remain to be determined to account for these behavioral differences. We also report the prospective use of the in silico method of quantitative trait loci (QTL) analysis and demonstrate difficulties in the use of this method, which failed to detect significant QTLs for the majority of these traits. These data serve as a framework for further studies of correlations between different midbrain dopamine traits and as a guide for experimental cross designs to identify QTLs and genes that contribute to these traits.     

The ecology of differences: assessing community assembly with trait and evolutionary distances

Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait‐based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait‐phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients.     

Quantitative analysis of correlations among flower traits in Gerbera hybrida,Compositae

Summary A Mean Correlation Response (MCR) model was developed to estimate the relative effectiveness of direct selection when other traits also respond to the selection. A measure of the relative effects of mean correlated response and direct response (R) and a measure of the relative efficiency of direct selection (IE) were applied to a genetic correlation matrix of 38 traits. These were measurements of inflorescence, receptacle and involucre, scape, disk florets, ray florets, and trans florets in the Davis population of Gerbera hybrida, Compositae. Generally, traits with high heritability had high direct and mean correlated response; these were often traits measuring disk and trans florets. Traits with low heritability had low direct and mean correlated response; these were often traits measuring the inflorescence. Traits of the inflorescence had the lowest efficiency of direct to mean correlated response.     

Functional regularity: a neglected aspect of functional diversity

Functional diversity has been identified as a key to understanding ecosystem and community functioning. However, due to the lack of a sound definition its nature and measurement are still poorly understood. In the same way that species diversity can be split into species richness and species evenness, so functional diversity can be split into functional richness (i.e. the amount of functional trait/character/attribute space filled) and functional evenness (i.e. the evenness of abundance distribution in functional trait space). We propose a functional regularity index (FRO) as a measure of functional evenness for situations where species are represented only by a single functional trait value (e.g. mean, median or mode), and species abundances are known. This new index is based on the Bulla O index of species evenness. When dealing with functional types or categorical functional traits, the Bulla O or any other accepted species evenness index may be used directly to measure functional evenness. The advantage of FRO is that it supplies a measure of functional evenness for continuous trait data. The FRO index presented in this paper fulfils all the a priori criteria required. We demonstrate with two example datasets that a range of FRO values may be obtained for both plant and animal communities. Moreover, FRO was strongly related to ecosystem function as seen in photosynthetic biomass in plant communities, and was able to differentiate sampling stations in a lagoon based on the functional traits of fish. Thus, the FRO index is potentially a highly useful tool for measuring functional diversity in a variety of ecological situations.     

Exposure to natural pathogens reveals costly aphid response to fungi but not bacteria

Immune responses are costly, causing trade‐offs between defense and other host life history traits. Aphids present a special system to explore the costs associated with immune activation since they are missing several humoral and cellular mechanisms thought important for microbial resistance, and it is unknown whether they have alternative, novel immune responses to deal with microbial threat. Here we expose pea aphids to an array of heat‐killed natural pathogens, which should stimulate immune responses without pathogen virulence, and measure changes in life‐history traits. We find significant reduction in lifetime fecundity upon exposure to two fungal pathogens, but not to two bacterial pathogens. This finding complements recent genomic and immunological studies indicating that pea aphids are missing mechanisms important for bacterial resistance, which may have important implications for how aphids interact with their beneficial bacterial symbionts. In general, recent exploration of the immune systems of non‐model invertebrates has called into question the generality of our current picture of insect immunity. Our data highlight that taking an ecological approach and measuring life‐history traits to a broad array of pathogens provides valuable information that can complement traditional approaches.     

Functional composition trajectory: a resolution to the debate between Suganuma,Durigan, and Reid

The selection of ecological indicators is an important step toward more effective restoration monitoring. The debate between Reid (2015) and Durigan and Suganuma (2015) regarding the usefulness of species composition for monitoring restoration trajectory is timely and salient, but it lacks a middle way proposal to balance ecological relevance and practical viability. We propose a way forward to resolving this debate, namely using easily measurable functional traits, a type of compositional measure, as an indicator. Assessing functional composition trajectory may help overcome some limitations with taxonomic identification and provide more meaningful outcomes to evaluate restoration success.     

Separation of time scales, fixation probabilities and convergence to evolutionary stable states under isolation by distance

To a first order of approximation, selection is frequency independent in a wide range of family structured models and in populations following an island model of dispersal, provided the number of families or demes is large and the population is haploid or diploid but allelic effects on phenotype are semidominant. This result underlies the way the evolutionary stability of traits is computed in games with continuous strategy sets. In this paper similar results are derived under isolation by distance. The first-order effect on expected change in allele frequency is given in terms of a measure of local genetic diversity, and of measures of genetic structure which are almost independent of allele frequency in the total population when the number of demes is large. Hence, when the number of demes increases the response to selection becomes of constant sign. This result holds because the relevant neutral measures of population structure converge to equilibrium at a rate faster than the rate of allele frequency changes in the total population. In the same conditions and in the absence of demographic fluctuations, the results also provide a simple way to compute the fixation probability of mutants affecting various ecological traits, such as sex ratio, dispersal, life-history, or cooperation, under isolation by distance. This result is illustrated and tested against simulations for mutants affecting the dispersal probability under a stepping-stone model.     

Transfected Chinese hamster ovary cells as a model system for cytokine immunocytochemistry and in situ hybridisation.

The presence of cytokine producing cells is most easily revealed by techniques measuring the secreted cytokines in culture supernatants or body fluids. However, these techniques only measure the bulk cytokine release by a given, often mixed cell population. To demonstrate cytokine production at the single cell level, immunocytochemistry (ICC) and in situ hybridisation (ISH) are now widely used techniques. To establish these techniques, an easily accessible model system is needed which permits the evaluation of different ICC and ISH protocols. It can be used to demonstrate the specificity of the antibodies and may serve as a positive control for samples of unknown cytokine content. Here we propose the use of Chinese hamster ovary (CHO) cells transfected to express one specific cytokine as such a model system. Its usefulness is demonstrated by the characterisation of six monoclonal antibodies to human interleukin-4 and the establishment of two in situ hybridisation protocols.     

Transfected Chinese hamster ovary cells as model system for cytokine immunocytochemistry and in situ hybridisation.

The presence of cytokine producing cells is most easily revealed by techniques measuring the secreted cytokines in culture supernatants or body fluids. However, these techniques only measure the bulk cytokine release by a given, often mixed cell population. To demonstrate cytokine production at the single cell level, immunocytochemistry (ICC) and in situ hybridisation (ISH) are now widely used techniques. To establish these techniques, an easily accessible model system is needed which permits the evaluation of different ICC and ISH protocols. It can be used to demonstrate the specificity of the antibodies and may serve as a positive control for samples of unknown cytokine content. Here we propose the use of Chinese hamster ovary (CHO) cells transfected to express one specific cytokine as such a model system. Its usefulness is demonstrated by the characterisation of six monoclonal antibodies to human interleukin-4 and the establishment of two in situ hybridisation protocols.     

Separation of time scales, fixation probabilities and convergence to evolutionarily stable states under isolation by distance

To a first order of approximation, selection is frequency independent in a wide range of family structured models and in populations following an island model of dispersal, provided the number of families or demes is large and the population is haploid or diploid but allelic effects on phenotype are semidominant. This result underlies the way the evolutionary stability of traits is computed in games with continuous strategy sets. In this paper similar results are derived under isolation by distance. The first-order effect on expected change in allele frequency is given in terms of a measure of local genetic diversity, and of measures of genetic structure which are almost independent of allele frequency in the total population when the number of demes is large. Hence, when the number of demes increases the response to selection becomes of constant sign. This result holds because the relevant neutral measures of population structure converge to equilibrium at a rate faster than the rate of allele frequency changes in the total population. In the same conditions and in the absence of demographic fluctuations, the results also provide a simple way to compute the fixation probability of mutants affecting various ecological traits, such as sex ratio, dispersal, life-history, or cooperation, under isolation by distance. This result is illustrated and tested against simulations for mutants affecting the dispersal probability under a stepping-stone model.     

Two paradigms of mathematical population biology. Attempting to synthesise

Whatever popular the slogan of nonlinear ecological interactions has been in theory, practical ecology professes the projection matrix paradigm, which is essentially linear, i.e., the linear matrix model paradigm for discrete-structured population dynamics. The dominant eigenvalue lamda1, of the projection matrix L is considered as a growth potential of the population. It provides for a quantitative measure of the fitness at which the species is adapted to the given environment, the measure being adequate and accurate, given the data of"identified individuals" type. The case of"identified individuals with unknown parents" bears uncertainty in the status-specific reproduction rates, which eliminates in a unique way (for a broad class of structures and life cycle graphs) by maximizing lamda1(L) under the constraints ensuing from the data and knowledge of species biology. The paradigm of linearity gives way to nonlinear models when modeled are species interactions, such as competition for shared resources, and where the outcome of interaction depends on the population structure of the competitors. This circumstance dictates a need for the synthesis of two paradigms, which is achieved in nonlinear matrix operators as models of interaction between the species whose populations are discrete-structured.     

Breeding for Yield Potential and Stress Adaptation in Cereals

The need to accelerate breeding for increased yield potential and better adaptation to drought and other abiotic stresses is an issue of increasing urgency. As the population continues to grow rapidly, the pressure on resources (mainly untouched land and water) is also increasing, and potential climate change poses further challenges. We discuss ways to improve the efficiency of crop breeding through a better physiological understanding by both conventional and molecular methods. Thus the review highlights the physiological basis of crop yield and its response to stresses, with special emphasis on drought. This is not just because physiology forms the basis of proper phenotyping, one of the pillars of breeding, but because a full understanding of physiology is also needed, for example, to design the traits targeted by molecular breeding approaches such as marker-assisted selection (MAS) or plant transformation or the way these traits are evaluated. Most of the information in this review deals with cereals, since they include the world's main crops, however, examples from other crops are also included. Topics covered by the review include the conceptual framework for identifying secondary traits associated with yield potential and stress adaptation, and how to measure these secondary traits in practice. The second part of the review deals with the real role of molecular breeding for complex traits from a physiological perspective. This part examines current developments in MAS and quantitative trait loci (QTL) detection as well as plant transformation. Emphasis is placed on the current limitations of these molecular approaches to improving stress adaptation and yield potential. The essay ends by presenting some ideas regarding future avenues for crop breeding given the current and possible future challenges, and on a multidisciplinary approach where physiological knowledge and proper phenotyping play a major role.     

The concepts of ‘plant functional types’ and ‘functional diversity’ in lake phytoplankton – a new understanding of phytoplankton ecology?

1. This is a discussion of the applicability to the phytoplankton of the concepts of ‘plant functional types’ (PFTs) and ‘functional diversity’ (FD), which originated in terrestrial plant ecology. 2. Functional traits driving the performance of phytoplankton species reflect important processes such as growth, sedimentation, grazing losses and nutrient acquisition. 3. This paper presents an objective, mathematical way of assigning PFTs and measuring FD. Ecologists can use this new approach to investigate general hypotheses [e.g. the intermediate disturbance hypothesis (IDH), the insurance hypothesis and synchronicity phenomena] as, for example, in its original formulation the IDH makes its predictions based on FD rather than species diversity.     

Fluctuating asymmetry in the otoliths of larval fish as an indicator of condition: conceptual and methodological aspects

Developmental instability, measured as fluctuating asymmetry (FA) in bilateral traits, has been used widely as an indicator of genetic or environmental stress in a variety of plant and animal taxa. FA arises as small deviations from perfect bilateral symmetry which reflect 'mistakes' in developmental processes resulting from the inability of the genotype to buffer itself effectively against environmental perturbations. Recently, it has been proposed that FA in the otoliths can be used as an indicator of condition in larval fish. This paper reviews the conceptual and methodological aspects of FA relevant to its potential use as a measure of well-being. Its simplicity makes FA an attractive tool to measure developmental precision and condition. However, there are several pitfalls, such as measuring error or potentially size dependence. Subtle asymmetries, i.e. between sides variation of a trait at the individual level, may not always be indicative of condition and should be interpreted with caution. The past-growth record of otoliths may provide a powerful means of studying the development of asymmetries at the level of the individual.     

Interactive effects of nutrient and mechanical stresses on plant morphology

BACKGROUND AND AIMS: Plant species frequently encounter multiple stresses under natural conditions, and the way they cope with these stresses is a major determinant of their ecological breadth. The way mechanical (e.g. wind, current) and resource stresses act simultaneously on plant morphological traits has been poorly addressed, even if both stresses often interact. This paper aims to assess whether hydraulic stress affects plant morphology in the same way at different nutrient levels. METHODS: An examination was made of morphological variations of an aquatic plant species growing under four hydraulic stress (flow velocity) gradients located in four habitats distributed along a nutrient gradient. Morphological traits covering plant size, dry mass allocation, organ water content and foliage architecture were measured. KEY RESULTS: Significant interactive effects of flow velocity and nutrient level were observed for all morphological traits. In particular, increased flow velocity resulted in size reductions under low nutrient conditions, suggesting an adaptive response to flow stress (escape strategy). On the other hand, moderate increases in flow velocity resulted in increased size under high nutrient conditions, possibly related to an inevitable growth response to a higher nutrient supply induced by water renewal at the plant surface. For some traits (e.g. dry mass allocation), a consistent sense of variation as a result of increasing flow velocity was observed, but the amount of variation was either reduced or amplified under nutrient-rich compared with nutrient-poor conditions, depending on the traits considered. CONCLUSIONS: These results suggest that, for a given species, a stress factor may result, in contrasting patterns and hence strategies, depending on a second stress factor. Such results emphasize the relevance of studies on plant responses to multiple stresses for understanding the actual ecological breadth of species.     

Evolutionary genetics of sex-limited traits under fluctuating selection

Ultimately based on the different gamete size and the resulting sex roles, most animal species have acquired traits that occur only in one of the sexes. For those sex-limited traits the impact of a single selection event is reduced, because the genes coding for these traits also occur unexpressed in the other sex and are therefore partly hidden to selection. All sex-limited traits thus show a storage effect analogous to a seed bank. This storage effect has to be considered when measuring the effect of fluctuating selection on sex-limited traits. Here, I develop appropriate equations to measure the ability of an allele to invade a population when fluctuating selection acts on sex-limited traits. A comparison of the equations for X-chromosomal and autosomal traits gives the following result: the evolution of traits limited to the heterogametic sex should preferentially involve X-chromosomal genes and the evolution of traits limited to the homogametic sex should preferentially involve autosomal genes. This difference between the sexes may contribute to explain (1) the large effect of X-chromosomal genes in causing hybrid sterility in the heterogametic sex and (2) the large effect of X-chromosomal genes on sexually selected traits in heterogametic males.     

FITNESS SENSITIVITY AND THE CANALIZATION OF LIFE-HISTORY TRAITS

Canalization is an abstract term that describes unknown developmental mechanisms that reduce phenotypic variation. A trait can be canalized against environmental perturbations (e.g., changes in temperature or nutrient quality), or genetic perturbations (e.g., mutations or recombination); this paper is about genetic canalization. Stabilizing selection should improve the canalization of traits, and the degree of canalization should be positively correlated with the traits' impact on fitness. Experiments testing this idea should measure the canalization of a series of traits whose impact on fitness is known or can be inferred, exclude differences among traits in the number of loci and alleles segregating as an explanation for the pattern of variability found, and distinguish between canalization against genetic and environmental variation. These conditions were met by three experiments within which the variation of fitness components among Drosophila melanogaster lines was measured and among which the genetic contribution to the variation among lines was clearly different. The canalization of the traits increased with their impact on fitness and did not depend on the degree of genetic differences among lines. That the flies used had been transformed by a P-element insert suggests that canalization was also effective against novel genetic variation. The results reported here cannot be explained by the classical hypothesis of reduction in the number of loci segregating for traits with greater impact on fitness and confirm that traits with greater impact on fitness are more strongly canalized. This pattern of canalization reveals an underappreciated role for development in microevolution. There is differential genetic canalization of fitness components in D. melanogaster.     

A standardized approach to estimate life history tradeoffs in evolutionary ecology

As tradeoffs limit the maximum Darwinian fitness individuals can reach, measuring reliably the strength of tradeoffs using appropriate metrics is of prime importance to understand the evolution of traits under constraints. Tradeoffs involving phenotypic traits and fitness components, however, are difficult to quantify in free‐ranging populations because of confounding effects due to environmental variation and individual heterogeneity. Furthermore, although some methods have been used previously to quantify tradeoffs, these methods cannot be applied with respect to binary traits, which are common to describe life histories (e.g. probability of reproduction, nesting success, offspring survival). Here, we demonstrate how to measure reliably the strength of tradeoffs involving binary traits using (auto)correlation estimates obtained from generalized linear (mixed) models. We first propose a standardized approach that accounts for the variation in the nature of the tradeoffs being compared (e.g. continuous/binary traits, repeated/non‐repeated measures), and then apply this method to longitudinal data from two contrasting species of large herbivores. Empirical estimates of tradeoffs varied among traits, and between‐species comparisons suggested that reproductive tradeoffs between successive breeding attempts might only occur in capital breeders. The empirical results we obtained clearly demonstrate that the method we provide allows measuring reliably the strength of tradeoffs under most circumstances, including tradeoffs on binary traits. Our original approach therefore offers an important first step for comparing the strength and, hence, the relative importance of different tradeoffs, and opens the door to a better understanding of the evolution of life history traits in free‐ranging populations.     

植物功能性状与环境和生态系统功能

植物性状反映了植物对生长环境的响应和适应,将环境、植物个体和生态系统结构、过程与功能联系起来(所谓的“植物功能性状”)。该文介绍了植物功能性状的分类体系,综述了国内外植物功能性状与气候(包括气温、降水、光照)、地理空间变异(包括地形地貌、生态梯度、海拔)、营养、干扰(包括火灾、放牧、生物入侵、土地利用)等环境因素,以及与生态系统功能之间关系的研究进展,探讨了全球变化(气候变化和CO₂浓度升高)对个体和群落植物功能性状的影响。植物功能性状的研究已经取得很多成果,并应用于全球变化、古植被恢复和古气候定量重建、环境监测与评价、生态保护和恢复等研究中,但大尺度、多生境因子下的植物功能性状研究仍有待于加强,同时需要改进性状的测量手段;我国的植物功能性状研究还需要更加明朗化和系统化。     

Methods to predict transgressive segregation in barley and other self-pollinated crops

Most of agronomically important characters are biometric traits. An improvement of these traits in cultivated plants by deriving segregants superior to parents, which could be developed as cultivars, is a main goal in breeding of self-pollinated crops. Two problems need to be solved: when will the progeny be better than its parents and how can a genetic potential of a given pair of parental genotypes be predicted? In this paper, transgressive segregation in homozygous barley populations is shortly reviewed. Various approaches to choosing parental forms are shown, and a theoretical method for predicting the frequency of transgressive segregants in a homozygous population is presented. Additionally, relationships between parental diversity estimated with molecular markers and the progeny performance are discussed. Although the prediction of transgressive segregation is still a problem, it seems promising to apply an approach measuring the performance of the parental genotypes and estimating their genetic distance by molecular markers.