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.     

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.     

山西五鹿山森林群落木本植物功能多样性

通过选取群落中木本植物种子的扩散方式、传粉方式、植株高度和盖度等13个功能性状,计算出群落的6个功能多样性指数:功能性状距离、功能性状平均距离、功能体积、功能均匀度、功能分散指数和Rao二次熵指数,结合群落物种丰富度指数、Shannon-Wiener指数和物种均匀度指数对山西五鹿山森林群落木本植物功能多样性进行研究。结果表明:(1)功能性状距离、功能性状平均距离、功能体积与物种丰富度、Shannon-Wiener指数显著正相关;功能均匀度与Shannon-Wiener指数、物种均匀度指数显著正相关;功能分散指数、Rao二次熵指数与物种均匀度指数、Shannon-Wiener指数显著正相关;(2)功能多样性的差异很大程度上是由于物种差异所引起的;(3)6个功能多样性指数可分为三类:功能性状距离、功能性状平均距离、功能体积为功能丰富度指数;功能均匀度为功能均匀度指数;功能分散指数和Rao二次熵指数为功能离散度指数。该分类结果符合指数的计算方法和生态学意义,以及相互独立的标准。     

南亚热带森林常见种和偶见种的功能多样性特征

群落特征可能取决于物种在功能实体功能特征的独特组合（FE）中的分布。了解这些分布是保护生物多样性和维持生态系统功能的基础。鼎湖山南亚热带常绿阔叶林群落物种丰富,根据物种的多度来区分常见种（每hm²超过一个个体）和偶见种（每hm²少于一个个体）。基于功能实体,分别计算功能实体数量、功能冗余度、功能脆弱度和功能过度冗余度来描述每个样方中常见种和偶见种的功能多样性。采用Wilcoxon检验检测常见种和偶见种功能性状的差异,通过线性回归分析常见种和偶见种的功能多样性与物种数量的关系,采用冗余分析（RDA）影响常见种和偶见种的功能多样性的环境因子。研究结果表明：（1）鼎湖山南亚热带常绿阔叶林群落中功能性状在常见种和偶见种间差异显著。（2）群落中数量较低的偶见种保持着较高比例的功能实体数量。功能实体数量、功能冗余度与常见种和偶见种数量显著正相关,功能过度冗余度与偶见种数量显著正相关,功能脆弱度与常见种和偶见种的物种数量呈显著负相关。（3）海拔是影响常见种功能多样性最关键的地形因子,凹凸度是影响偶见种功能多样性最关键的地形因子。土壤含水量是影响常见种功能多样性最关键的土壤因子,速效钾是影响偶见种功能多样性最关键的环境因子。研究结果表明,尽管物种丰富的热带森林具有较高的功能冗余,但其提供的保险效应不能抵消生态系统的功能脆弱性。减少具有独特功能实体和偶见种的损失是避免热带森林生态系统功能损失的有效和必要的方法。     

功能多样性和功能冗余对高寒草甸群落稳定性的影响

功能多样性和功能冗余是影响群落稳定性的重要因素,但它们对稳定性影响的相对强弱尚有争论。通过在青藏高原高寒矮嵩草(Kobresia humilis)草甸为期6a的刈割(不刈割、留茬3cm、留茬1cm)和施肥(施肥、不施肥)控制实验对此进行了探讨。研究结果显示,群落稳定性随着功能多样性和功能冗余的增大而单调增加,但由于功能多样性的变异性大于功能冗余的变异性,功能多样性与物种多样性间的相关性强于功能冗余与物种多样性间的相关性,功能多样性与群落稳定性间的相关性也强于功能冗余与群落稳定性间的相关性,因此,尽管功能冗余产生的保险效应对维持群落稳定性具有促进作用,但功能多样性的互补效应对维持群落稳定性的作用更大。结果表明,功能多样性和功能冗余对群落稳定性的相对影响与其变化程度正相关,功能多样性与群落稳定性的变化具有更紧密的联系,能更好地预测生态系统稳定性的变化。研究为草原生态系统的可持续管理提供了重要启示。     

Distance-Based Functional Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers

Hill numbers (or the “effective number of species”) are increasingly used to characterize species diversity of an assemblage. This work extends Hill numbers to incorporate species pairwise functional distances calculated from species traits. We derive a parametric class of functional Hill numbers, which quantify “the effective number of equally abundant and (functionally) equally distinct species” in an assemblage. We also propose a class of mean functional diversity (per species), which quantifies the effective sum of functional distances between a fixed species to all other species. The product of the functional Hill number and the mean functional diversity thus quantifies the (total) functional diversity, i.e., the effective total distance between species of the assemblage. The three measures (functional Hill numbers, mean functional diversity and total functional diversity) quantify different aspects of species trait space, and all are based on species abundance and species pairwise functional distances. When all species are equally distinct, our functional Hill numbers reduce to ordinary Hill numbers. When species abundances are not considered or species are equally abundant, our total functional diversity reduces to the sum of all pairwise distances between species of an assemblage. The functional Hill numbers and the mean functional diversity both satisfy a replication principle, implying the total functional diversity satisfies a quadratic replication principle. When there are multiple assemblages defined by the investigator, each of the three measures of the pooled assemblage (gamma) can be multiplicatively decomposed into alpha and beta components, and the two components are independent. The resulting beta component measures pure functional differentiation among assemblages and can be further transformed to obtain several classes of normalized functional similarity (or differentiation) measures, including N-assemblage functional generalizations of the classic Jaccard, Sørensen, Horn and Morisita-Horn similarity indices. The proposed measures are applied to artificial and real data for illustration.     

Functional richness, functional evenness and functional divergence: the primary components of functional diversity

Functional diversity is hypothesised as being beneficial for ecosystem functions, such as productivity and resistance to invasion. However, a precise definition of functional diversity, and hence a framework for its quantification, have proved elusive. We present a definition based on the analogy of the components of species diversity – richness, evenness and divergence. These concepts are applied to functional characters to give three components of functional diversity – functional richness, functional evenness and functional divergence. We demonstrate how each of these components may be calculated. It is hoped that our definition of functional diversity and its components will aid in elucidation of the mechanisms behind diversity/ecosystem-function relationships.     

Testing Fox's assembly rule: does plant invasion depend on recipient community structure?

Fox's assembly rule, that relative dearth of certain functional groups in a community will facilitate invasion of that particular functional group, serves as the basis for investigation into the functional group effects of invasion resistance. We explored resistance to plant invaders by eliminating or decreasing the number of understory plant species in particular functional groups from plots at a riparian site in southwestern Virginia, USA. Our functional groups comprise combinations of aboveground biomass and rooting structure type. Manipulated plots were planted with 10 randomly chosen species from widespread native and introduced plants commonly found throughout the floodplains of Big Stony Creek. We assessed success of an invasion by plant survivorship and growth. We analyzed survivorship of functional groups with loglinear models for the analysis of categorical data in a 4-way table. There was a significant interaction between functional groups removed in a plot and survivorship in the functional groups added to that plot. However, survivorship of species in functional groups introduced into plots with their respective functional group removed did not differ from survivorship when any other functional group was removed. Additionally, growth of each of the most abundant species did not differ significantly among plots with different functional groups manipulated. Specifically, species did not fare better in those plots that had representatives of their own functional group removed. Fox's assembly rule does not hold for these functional groups in this plant community; however, composition of the recipient community is a significant factor in community assembly.     

Using the relationship between taxonomic and functional diversity to assess functional redundancy in streams of an altered tropical watershed

The relationship between taxonomic and functional diversity indices has been used to better describe and understand the structure of biological communities. Functional diversity is expected to have an asymptotic relationship with species richness because at some point, the addition of new species will increase some of the already established functional groups (functional redundancy). However, the asymptotic relationship may not be reached in intermediately disturbed systems once many intolerant species that would have played a redundant role or even represented some functional groups have been lost. This study aimed to address such a relationship (taxonomic and functional indices) and to evaluate the functional redundancy in intermediately disturbed streams in the Atlantic Rainforest domain. We expected a positive linear relationship between taxonomic and functional diversity; however, we did not expect to find an asymptotic relationship between richness and functional diversity because of the loss of many intolerant species caused by anthropogenic uses. The taxonomic diversity indices were Species Richness (SR) and Simpson’s Diversity (SD), while the functional diversity indices were the Functional Richness (FRic) and Functional Dispersion (FDisp). The two taxonomic and two functional diversity indices showed a significant positive relationship that never reached an asymptote, suggesting low functional redundancy in the fish communities. Our results indicate that care is needed in the management of the studied streams because assemblies with low functional redundancy are more susceptible to loss of functions in the case of species loss.     

鼎湖山南亚热带常绿阔叶林植物功能性状变异与不同垂直层次个体生长的关联

建立植物功能性状与群落动态之间的关联是功能生态学的核心问题之一。本文基于鼎湖山1.44 ha塔吊样地的两次调查数据, 通过采集样地内所有4,142株个体的6种植物功能性状, 对比分析了个体水平植物功能性状和物种水平功能性状均值对不同垂直层次(灌木层、亚冠层和林冠层)个体生长的影响差异。首先, 分析了不同垂直层次下各植物功能性状的变化趋势; 其次, 计算了不同垂直层次下各植物功能性状的种内和种间变异水平; 最后, 运用结构方程模型探讨了植物功能性状、光竞争以及地下竞争对不同垂直层次树木生长的影响。结果表明: (1)不同垂直层次下的植物功能性状表现出明显的分异, 由灌木层至林冠层, 叶面积、比叶面积和能量供求关系指数显著降低, 而叶片厚度和叶片干物质含量显著升高; (2)不同垂直层次下植物功能性状的种间变异均大于种内变异, 且林冠层的种内功能性状变异均大于灌木层和亚冠层; (3)基于个体水平植物功能性状的结构方程模型较物种水平功能性状均值对生长具有更高的解释程度, 且个体水平植物功能性状的引入更有利于提高对灌木层个体生长的预测能力; (4)光竞争和地下竞争主要通过影响功能性状间接影响植物生长。由灌木层至林冠层, 同种间的相互作用逐渐减弱, 异种间的相互作用逐渐增强。综上, 将个体水平植物功能性状纳入分析有助于更好地理解群落的结构和动态。     

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.     

Effects of habitat fragmentation on the functional diversity of insects in Thousand Island Lake,China

Due to habitat fragmentation, the loss of species diversity has been extensively studied. On the contrary, the effects of habitat fragmentation on functional diversity is still poorly understood. In the Thousand Island Lake, we conducted studies of insect functional diversity on a set of 29 isolated islands. We used 10 functional diversity indices from three aspects (functional richness, functional evenness and functional divergence) to respectively describe functional diversity of insects on sample islands. We found the following results: (i) The functional indices selected could reflect the functional diversity of sample islands and it is further proved that in general, three components of functional diversity were independent of each other; (ii) Sample islands could be divided into two categories, island JSD and the remaining islands; (iii) Functional richness increased with island area and shape index, but had no significant correlation with isolation. Likewise, both functional evenness and functional divergence had no significant correlation with island attributes. The conclusion to emphasize from our research is that: (i) habitat fragmentation reduced the biological functional diversity to some extent, further demonstrating the importance of habitat continuity in biodiversity protection; and (ii) for functional diversity protection of insects in a fragmented landscape, an island which has high approximate shape index values of at least hundred hectare magnitude order has a critical promoting effect.     

Functional coherence in domain interaction networks

MOTIVATION: Extracting functional information from protein-protein interactions (PPI) poses significant challenges arising from the noisy, incomplete, generic and static nature of data obtained from high-throughput screening. Typical proteins are composed of multiple domains, often regarded as their primary functional and structural units. Motivated by these considerations, domain-domain interactions (DDI) for network-based analyses have received significant recent attention. This article performs a formal comparative investigation of the relationship between functional coherence and topological proximity in PPI and DDI networks. Our investigation provides the necessary basis for continued and focused investigation of DDIs as abstractions for functional characterization and modularization of networks. RESULTS: We investigate the problem of assessing the functional coherence of two biomolecules (or segments thereof) in a formal framework. We establish essential attributes of admissible measures of functional coherence, and demonstrate that existing, well-accepted measures are ill-suited to comparative analyses involving different entities (i.e. domains versus proteins). We propose a statistically motivated functional similarity measure that takes into account functional specificity as well as the distribution of functional attributes across entity groups to assess functional similarity in a statistically meaningful and biologically interpretable manner. Results on diverse data, including high-throughput and computationally predicted PPIs, as well as structural and computationally inferred DDIs for different organisms show that: (i) the relationship between functional similarity and network proximity is captured in a much more (biologically) intuitive manner by our measure, compared to existing measures and (ii) network proximity and functional similarity are significantly more correlated in DDI networks than in PPI networks, and that structurally determined DDIs provide better functional relevance as compared to computationally inferred DDIs.     

Functional diversity (FD), species richness and community composition

Functional diversity is an important component of biodiversity, yet in comparison to taxonomic diversity, methods of quantifying functional diversity are less well developed. Here, we propose a means for quantifying functional diversity that may be particularly useful for determining how functional diversity is related to ecosystem functioning. This measure of functional diversity “FD” is defined as the total branch length of a functional dendrogram. Various characteristics of FD make it preferable to other measures of functional diversity, such as the number of functional groups in a community. Simulating species' trait values illustrates how the relative importance of richness and composition for FD depends on the effective dimensionality of the trait space in which species separate. Fewer dimensions increase the importance of community composition and functional redundancy. More dimensions increase the importance of species richness and decreases functional redundancy. Clumping of species in trait space increases the relative importance of community composition. Five natural communities show remarkably similar relationships between FD and species richness.     

Plant community resilience in the face of fire: experimental evidence from a semi‐arid shrubland

The ability of communities or ecosystems to recover their structure and function after a disturbance is known as resilience. According to different views, resilience can be influenced by the resource‐use strategies of the plant functional types that dominate the community or by the existence of functional redundancy within plant functional types. We investigated how the dominance of different plant functional types and species affected the resilience of a mountain shrubland after an intense fire. We took advantage from a pre‐existing long‐term removal experiment in which either whole plant functional types (deciduous shrubs, graminoids, perennial forbs and annual forbs) or the dominant species within each plant functional type were removed for 10 years. We sampled species and plant functional types cover during the first growing season after the fire. First, to test whether functional redundancy increased resilience, we analyzed the existence of functional compensation inside plant functional types. Second, to test whether the dominance of plant functional types with different resource‐use strategies affected recovery, we compared resilience at the levels of species, plant functional types and total cover, estimated on the basis of a change index and multivariate Euclidean distances. No compensation was observed in any of the plant functional types. At the level of species, we found that the assemblages dominated by conservative resource‐use strategies were the ones showing higher resilience. This was due to the high recovery of the dominant species of shrubs plant functional type. The opposite (lowest recovery of conservative resource‐use strategies) was found at the plant functional type and total cover‐levels. Our study did not support the hypothesis of resilience by functional redundancy. Instead, regeneration by buried meristems from the pre‐fire stage appeared to be the factor that most influenced recovery. Resource‐use strategies explained resilience of vegetation cover, but not of floristic composition. Regeneration traits, rather than vegetative traits or mechanism of functional compensation, appeared as the most relevant to explain the response of this system after fire.     

Loss of phylogenetic and functional originalities of woody cerrado species in simulated extinction scenarios

Originality measures how different a given species is from all other co‐occurring species regarding either their phylogenetic history or functional traits. Since it is important to preserve the various aspects of diversity and original species carry more phylogenetic or functional information, originality may be used to assign conservation priorities. Our goal was to evaluate the relationships between phylogenetic and functional originalities, and their simulated losses under extinction scenarios based on abundance, fire tolerance and habitat preference. We placed 100 plots in a cerrado reserve located in central Brazil, sampled all woody plants species within the plots, measured 14 functional traits and measured fire history. We assembled a phylogenetic tree and a functional dendrogram, with which we calculated the originalities. Phylogenetic‐ and functional‐based originalities were correlated. However, the loss of functional originality was different from random extinctions on the abundance and fire tolerance scenarios, whereas the loss of phylogenetic originality was not. When compared with phylogenetic originality, functional originality brought more information to be used in conservation strategies because it was sensitive to differences in species abundance and fire tolerance. Thus, the extinction of rare or fire‐sensitive species would result in important functional changes due to loss of distinctive traits.     

Rice functional genomics research in China

Rice functional genomics is a scientific approach that seeks to identify and define the function of rice genes, and uncover when and how genes work together to produce phenotypic traits. Rapid progress in rice genome sequencing has facilitated research in rice functional genomics in China. The Ministry of Science and Technology of China has funded two major rice functional genomics research programmes for building up the infrastructures of the functional genomics study such as developing rice functional genomics tools and resources. The programmes were also aimed at cloning and functional analyses of a number of genes controlling important agronomic traits from rice. National and international collaborations on rice functional genomics study are accelerating rice gene discovery and application.     

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.     

Hierarchical determinants of the functional richness, evenness and divergence of a vertebrate predator assemblage

Environmental factors are hypothesized to affect the functional diversity of assemblages hierarchically. First, ecological filters constrain the range of functional traits potentially displayed by an assemblage by determining its taxonomic composition. Second, some factors determine actual functional traits through the phenotypic plasticity of species. Little is known about the relative importance of each set of factors and, by using a priori functional information, most empirical studies report only the variability expected from species turnover and neglect that associated to phenotypic plasticity. Herein, we use structural equation models to assess the factors driving the functional richness, evenness, and divergence of a top‐predator assemblage faced with high variability in resource availability and assemblage structure (i.e. species richness and abundance). We measured actual functional traits (i.e. diet composition and predation pressure) in the field and contrasted the effects of environmental filters and phenotypic plasticity (i.e. behavioral responses) by controlling for species turnover and sample size with a null model. We found that a priori estimations (i.e. null‐model expectations) tended to significantly underestimate (richness and divergence) or overestimate (evenness) functional‐diversity components, explaining just a fraction (13–63%) of the variability in observed values. Furthermore, while species richness strongly affected functional richness (positively) and evenness (negatively), and resource availability slightly affected functional divergence, via compositional effects, changes in functional‐diversity components attributable to behavioral responses of predators showed little or no association with environmental variables. As a consequence, results indicated that in productive years, functionally‐distinctive species exerting relatively low predation pressure entered the assemblage, increasing functional richness and decreasing functional evenness. However, the strong behavioral responses of functionally dominant species buffered such compositional changes, affecting to different extents the three functional‐diversity components. Thus, we argue in favor of considering phenotypic plasticity in future studies of functional diversity.