Unraveling the relative contribution of inter‐ and intrapopulation functional variability in wild populations of a tadpole species

Functional traits are increasingly recognized as an integrative approach by ecologists to quantify a key facet of biodiversity. And these traits are primarily expressed as species means in previous studies, based on the assumption that the effects of intraspecific variability can be overridden by interspecific variability when studying functional ecology at the community level. However, given that intraspecific variability could also have important effects on community dynamics and ecosystem functioning, empirical studies are needed to investigate the importance of intraspecific variability in functional traits. In this study, 256 Scutiger boulengeri tadpole individuals from four different populations are used to quantify the functional difference between populations within a species, and the relative contribution of inter‐ and intrapopulation variability in functional traits. Our results demonstrate that these four populations differ significantly in functional attributes (i.e., functional position, functional richness, and low functional overlap), indicating that individuals from different populations within a species should be explicitly accounted for in functional studies. We also find similar relative contribution of inter‐ (~56%) and intrapopulation (~44%) variation to the total variability between individuals, providing evidence that individuals within populations should also be incorporated in functional studies. Overall, our results support the recent claims that intraspecific variability cannot be ignored, as well as the general idea of “individual level” research in functional ecology.     

Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality

Viruses often encode proteins with multiple functions due to their compact genomes. Existing approaches to identify functional residues largely rely on sequence conservation analysis. Inferring functional residues from sequence conservation can produce false positives, in which the conserved residues are functionally silent, or false negatives, where functional residues are not identified since they are species-specific and therefore non-conserved. Furthermore, the tedious process of constructing and analyzing individual mutations limits the number of residues that can be examined in a single study. Here, we developed a systematic approach to identify the functional residues of a viral protein by coupling experimental fitness profiling with protein stability prediction using the influenza virus polymerase PA subunit as the target protein. We identified a significant number of functional residues that were influenza type-specific and were evolutionarily non-conserved among different influenza types. Our results indicate that type-specific functional residues are prevalent and may not otherwise be identified by sequence conservation analysis alone. More importantly, this technique can be adapted to any viral (and potentially non-viral) protein where structural information is available.     

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.     

Consumer functional response and competition in consumer-resource systems

This study investigates the effect of the functional response of resource consumers on the relationship between resource overlap and competition for some two-consumer, two-resource models. Two measures of competition are examined: α, the competition coefficient, and β, an index of the ease of invasion by the second consumer species when the first is at its carrying capacity. A comparison of systems with linear (type-1) and decelerating (type-2) functional responses shows that: (1) Competition coefficients are functions of the population densities of consumers or resources in systems with type-2 responses. (2) Competition coefficients may differ substantially in magnitude between systems with type-1 and type-2 functional responses. (3) The relative handling time of different resources is important in determining the relationship between overlap and competition. Positive correlations between capture rates (per unit resource) and handling times cause the system with type-2 functional responses to exhibit a higher level of competition for a given level of overlap than for the case of negative correlation. (4) If the functional response is type-2 it may be possible to obtain a priority effect in which either consumer species can exclude the other. (5) Invasion may be easier in a system with type-1 functional responses than in a similar system with type-2 functional responses, even when competition coefficients are larger in the former. Accelerating functional responses also affect the relationship between overlap and competition, but realistic models of such responses are likely to be very complex. Several currently accepted ideas in competition theory depend upon the assumption of a linear functional response, and are unlikely to be generally valid.     

Functional diversity: back to basics and looking forward

Functional diversity is a component of biodiversity that generally concerns the range of things that organisms do in communities and ecosystems. Here, we review how functional diversity can explain and predict the impact of organisms on ecosystems and thereby provide a mechanistic link between the two. Critical points in developing predictive measures of functional diversity are the choice of functional traits with which organisms are distinguished, how the diversity of that trait information is summarized into a measure of functional diversity, and that the measures of functional diversity are validated through quantitative analyses and experimental tests. There is a vast amount of trait information available for plant species and a substantial amount for animals. Choosing which traits to include in a particular measure of functional diversity will depend on the specific aims of a particular study. Quantitative methods for choosing traits and for assigning weighting to traits are being developed, but need much more work before we can be confident about trait choice. The number of ways of measuring functional diversity is growing rapidly. We divide them into four main groups. The first, the number of functional groups or types, has significant problems and researchers are more frequently using measures that do not require species to be grouped. Of these, some measure diversity by summarizing distances between species in trait space, some by estimating the size of the dendrogram required to describe the difference, and some include information about species' abundances. We show some new and important differences between these, as well as what they indicate about the responses of assemblages to loss of individuals. There is good experimental and analytical evidence that functional diversity can provide a link between organisms and ecosystems but greater validation of measures is required. We suggest that non-significant results have a range of alternate explanations that do not necessarily contradict positive effects of functional diversity. Finally, we suggest areas for development of techniques used to measure functional diversity, highlight some exciting questions that are being addressed using ideas about functional diversity, and suggest some directions for novel research.     

A comparison of fingers and hand in varanus, opossum and primates

A comparative analysis of hands constitutes the basis of an assessment of hand function in an evolutionary context. Terms as functional domain and functional options are instrumental to define the functional expansion, which can be seen when comparing reptiles, opossum and primates. In man the structural arrangement can be interpreted in functional terms only by terms as functional continuum or universe and by performance control. In the great apes knuckle walking and brachiation seems to interfere with a full-fledged pollical-digital interplay, the latter function being considered to constitute the structural base of optimalization collecting afferent information, requiring brain development, which opens up categories as abstraction, design and freedom.     

The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability

The number of functional traits of a wastewater treatment plant (WWTP) microbial community (i.e. functional richness) is thought to be an important determinant of its overall functional performance, but the ecological factors that determine functional richness remain unclear. The number of taxa within a community (i.e. taxonomic richness) is one ecological factor that might be important. Communities that contain more taxa are more likely to have more functional traits, and a positive association is therefore expected between functional and taxonomic richness. Empirical tests for this positive association among WWTP communities, however, are lacking. We address this knowledge gap by measuring the functional and taxonomic richness of 10 independent WWTP communities. We demonstrate that functional and taxonomic richness are positively associated with each other. We further demonstrate that functional and taxonomic richness are negatively associated with the effluent NH₄‐N and BOD₅ concentrations. This led us to hypothesize that correlated variation in functional and taxonomic richness is likely related to variation in ambient nitrogen and carbon availability. We finally demonstrate that this hypothesis is consistent with the functional and taxonomic attributes of the WWTP communities. Together, our results improve our basic understanding of the ecology and functioning of WWTP communities.     

Plant functional traits and diversity in sand dune ecosystems across different biogeographic regions

Plant species of a functional group respond similarly to environmental pressures and may be expected to act similarly on ecosystem processes and habitat properties. However, feasibility and applicability of functional groups in ecosystems across very different climatic regions have not yet been studied. In our approach we specified the functional groups in sand dune ecosystems of the Mediterranean, Hyrcanian and Irano-Turanian phytogeographic regions. We examined whether functional groups are more influenced by region or rather by habitat characteristics, and identified trait syndromes associated with common habitat types in sand dunes (mobile dunes, stabilized dunes, salt marshes, semi-wet sands, disturbed habitats). A database of 14 traits, 309 species and 314 relevés was examined and trait-species, trait-plot and species-plot matrices were built. Cluster analysis revealed similar plant functional groups in sand dune ecosystems across regions of very different species composition and climate. Specifically, our study showed that plant traits in sand dune ecosystems are grouped reflecting habitat affiliation rather than region and species pool. Environmental factors and constraints such as sand mobility, soil salinity, water availability, nutrient status and disturbance are more important for the occurrence and distribution of plant functional groups than regional belonging. Each habitat is shown to be equipped with specific functional groups and can be described by specific sets of traits. In restoration ecology the completeness of functional groups and traits in a site may serve as a guideline for maintaining or restoring the habitat.     

Functional redundancy in ecology and conservation

Multiple studies have shown that biodiversity loss can impair ecosystem processes, providing a sound basis for the general application of a precautionary approach to managing biodiversity. However, mechanistic details of species loss effects and the generality of impacts across ecosystem types are poorly understood. The functional niche is a useful conceptual tool for understanding redundancy, where the functional niche is defined as the area occupied by a species in an n-dimensional functional space. Experiments to assess redundancy based on a single functional attribute are biased towards finding redundancy, because species are more likely to have non-overlapping functional niches in a multi-dimensional functional space. The effect of species loss in any particular ecosystem will depend on i) the range of function and diversity of species within a functional group, ii) the relative partitioning of variance in functional space between and within functional groups, and iii) the potential for functional compensation (degree of functional niche overlap) of the species within a functional group. Future research on functional impairment with species loss should focus on identifying which species, functional groups, and ecosystems are most vulnerable to functional impairment from species loss, so that these can be prioritized for management activities directed at maintaining ecosystem function. This will require a better understanding of how the organization of diversity into discrete functional groups differs between different communities and ecosystems.     

Condition-dependent functional connectivity: syntax networks in bilinguals

This paper introduces a method to study the variation of brain functional connectivity networks with respect to experimental conditions in fMRI data. It is related to the psychophysiological interaction technique introduced by Friston et al. and extends to networks of correlation modulation (CM networks). Extended networks containing several dozens of nodes are determined in which the links correspond to consistent correlation modulation across subjects. In addition, we assess inter-subject variability and determine networks in which the condition-dependent functional interactions can be explained by a subject-dependent variable. We applied the technique to data from a study on syntactical production in bilinguals and analysed functional interactions differentially across tasks (word reading or sentence production) and across languages. We find an extended network of consistent functional interaction modulation across tasks, whereas the network comparing languages shows fewer links. Interestingly, there is evidence for a specific network in which the differences in functional interaction across subjects can be explained by differences in the subjects' syntactical proficiency. Specifically, we find that regions, including ones that have previously been shown to be involved in syntax and in language production, such as the left inferior frontal gyrus, putamen, insula, precentral gyrus, as well as the supplementary motor area, are more functionally linked during sentence production in the second, compared with the first, language in syntactically more proficient bilinguals than in syntactically less proficient ones. Our approach extends conventional activation analyses to the notion of networks, emphasizing functional interactions between regions independently of whether or not they are activated. On the one hand, it gives rise to testable hypotheses and allows an interpretation of the results in terms of the previous literature, and on the other hand, it provides a basis for studying the structure of functional interactions as a whole, and hence represents a further step towards the notion of large-scale networks in functional imaging.     

Detection of moments of operation of functional units in the human cortex using a new method of EEG analysis]

A new approach to EEG processing was proposed. The method allows the poorly predicted points on an EEG recording to be found, which are interpreted as the moments when certain functional units of the brain are engaged or disengaged. The functional units may be probably represented by columns or supercolumns. The method was tested in EEG recordings when the visual illusions were induced in a subject by a rhythmic photostimulation. The method seems to be rather promising.     

Inverse relationship between evolutionary rate and age of mammalian genes

A large number of genes is shared by all living organisms, whereas many others are unique to some specific lineages, indicating their different times of origin. The availability of a growing number of eukaryotic genomes allows us to estimate which mammalian genes are novel genes and, approximately, when they arose. In this article, we classify human genes into four different age groups and estimate evolutionary rates in human and mouse orthologs. We show that older genes tend to evolve more slowly than newer ones; that is, proteins that arose earlier in evolution currently have a larger proportion of sites subjected to negative selection. Interestingly, this property is maintained when a fraction of the fastest-evolving genes is excluded or when only genes belonging to a given functional class are considered. One way to explain this relationship is by assuming that genes maintain their functional constraints along all their evolutionary history, but the nature of more recent evolutionary innovations is such that the functional constraints operating on them are increasingly weaker. Alternatively, our results would also be consistent with a scenario in which the functional constraints acting on a gene would not need to be constant through evolution. Instead, starting from weak functional constraints near the time of origin of a gene-as supported by mechanisms proposed for the origin of orphan genes-there would be a gradual increase in selective pressures with time, resulting in fewer accepted mutations in older versus more novel genes.     

植物群落的生物多样性及其可入侵性关系的实验研究

 生物入侵已经成为一个普遍性的环境问题,并为许多学者所关注。尽管一些理论研究和观察表明生物多样性丰富的群落不容易受到外来种的入侵,但后来有些实验研究并没能证实两者的负相关性,多样性 可入侵性假说仍然是入侵生态学领域争论比较多的一个焦点。人为构建不同物种多样性和物种功能群多样性（C3 禾本科植物、C4植物、非禾本科草本植物和豆科植物）梯度的小尺度群落,把其它影响可入侵性的外在因子和多样性效应隔离开来,研究入侵种喜旱莲子草(Alternanthera philoxeroides)在不同群落里的入侵过程来验证多样性 可入侵性及其相关假说。研究结果显示,物种功能群丰富的群落可入侵程度较低,功能群数目相同而物种多样性不同的群落可入侵性没有显著性差异,功能群特征不同的群落也表现出可入侵性的差异,生活史周期短的单一物种群落和有着生物固氮功能的豆科植物群落可入侵程度较高,与喜旱莲子草属于同一功能群且有着相似生态位的土著种莲子草(A. sessilis)对入侵的抵抗力最强。实验结果表明,物种多样性和群落可入侵性并没有很显著的负相关,而是与物种特性基础上的物种功能群多样性呈负相关,群落中留给入侵种生态位的机会很可能是决定群落可入侵性的一个关键因子。     

Opinion: an integrated approach to classifying neuronal phenotypes

Characterizing the functional phenotypes of neurons is essential for understanding how genotypes can be related to the neural basis of behaviour. Traditional classifications of neurons by single features (such as morphology or firing behaviour) are increasingly inadequate for reflecting functional phenotypes, as they do not integrate functions across different neuronal types. Here, we describe a set of rules for identifying and predicting functional phenotypes that combine morphology, intrinsic ion channel species and their distributions in dendrites, and functional properties. This more comprehensive neuronal classification should be an improvement on traditional classifications for relating genotype to functional phenotype.     

Measuring the contribution of community members to functional diversity

Although the contribution of community members to functional diversity is a key question of conservation ecology, its measurement and interpretation are rather problematic. In this paper, we suggest a novel method for decomposing functional diversity. To do this we consider functional units (i.e. species or a group of species with identical traits) as the functional building blocks of communities. Then we propose the use of a recently developed measure of functional diversity (called modified functional attribute diversity or MFAD) and suggest additive decomposition of MFAD into functional values contributed by the functional units. We point out that functional values are related to changes in MFAD if the functional unit is removed from the community. This property of decomposition allows the quantification of the contribution of community members to functional diversity. By studying artificial and actual communities we compare the performance of our new method with other recently developed contribution measures, which are based on dendrograms and ordinations. Both theoretical considerations and analyses of artificial and actual data sets suggest that the proposed method of calculating functional values expresses more explicitly the contribution of community members to functional diversity and hereby can be used as a simple, yet efficient method for searching for functional keystones in ecological communities or for quantifying the contribution of community members to functional diversity.     

A Bayesian Hierarchical Model for Classification with Selection of Functional Predictors

Summary In functional data classification, functional observations are often contaminated by various systematic effects, such as random batch effects caused by device artifacts, or fixed effects caused by sample‐related factors. These effects may lead to classification bias and thus should not be neglected. Another issue of concern is the selection of functions when predictors consist of multiple functions, some of which may be redundant. The above issues arise in a real data application where we use fluorescence spectroscopy to detect cervical precancer. In this article, we propose a Bayesian hierarchical model that takes into account random batch effects and selects effective functions among multiple functional predictors. Fixed effects or predictors in nonfunctional form are also included in the model. The dimension of the functional data is reduced through orthonormal basis expansion or functional principal components. For posterior sampling, we use a hybrid Metropolis–Hastings/Gibbs sampler, which suffers slow mixing. An evolutionary Monte Carlo algorithm is applied to improve the mixing. Simulation and real data application show that the proposed model provides accurate selection of functional predictors as well as good classification.     

Competitive interactions between forest trees are driven by species' trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly

The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that interaction strengths are mainly driven by trait hierarchy and not by functional or phylogenetic similarity. On the basis of this result, we thus propose that functional and phylogenetic convergence in local tree community might be due to competition-sorting species with different competitive abilities and not only environmental filtering as commonly assumed. We then show a functional and phylogenetic convergence of forest structure with increasing plot age, which supports this view.     

A computational theory of visual surface interpolation

Computational theories of structure-from-motion and stereo vision only specify the computation of three-dimensional surface information at special points in the image. Yet the visual perception is clearly of complete surfaces. To account for this a computational theory of the interpolation of surfaces from visual information is presented. The problem is constrained by the fact that the surface must agree with the information from stereo or motion correspondence, and not vary radically between these points. Using the image irradiance equation, an explicit form of this surface consistency constraint can be derived. To determine which of two possible surfaces is more consistent with the surface consistency constraint, one must be able to compare the two surfaces. To do this, a functional from the space of possible functions to the real numbers is required. In this way, the surface most consistent with the visual information will be that which minimizes the functional. To ensure that the functional has a unique minimal surface, conditions on the form of the functional are derived. In particular, if the functional is a complete semi-norm that satisfies the parallelogram law, or the space of functions is a semi-Hilbert space and the functional is a semi-inner product, then there is a unique (to within possibly an element of the null space of the functional) surface that is most consistent with the visual information. It can be shown, based on the above conditions plus a condition of rotational symmetry, that there is a vector space of possible functionals that measure surface consistency, this vector space being spanned by the functional of quadratic variation and the functional of square Laplacian. Arguments based on the null spaces of the respective functionals are used to justify the choice of the quadratic variation as the optimal functional. Possible refinements to the theory, concerning the role of discontinuities in depth and the effects of applying the interpolation process to scenes containing more than one object, are discussed.