Objective recognition of guilds: testing for statistically significant species clusters

Summary Presently, no standard protocol for objective guild recognition is consistently used by ecologists. Apart from intuitive designations of guild membership, four statistically-based protocols are currently available: those of Colwell (1977); Holmes (1979); Lawlor (1980); and Adams (1985). The first is based on nearest-neighbor variance in overlap, the second on multivariate statistics, the third on clustering techniques, and the fourth on psychometric analysis. We propose a fifth approach, first developed by Strauss (1982) for purposes other than guild recognition. We advocate the use of bootstrap procedures to resample any given empirical matrix of consumers by resources, within constraints set by either of four different randomization algorithms. Subsequently, pseudovalues of similarity in resource use between the consumers are computed and their frequency distribution is displayed in a histogram. The overlap pseudovalue that exceeds percentile 95 may be considered statistically significant and chosen as the cutoff point that identifies significant species clusters (guilds) in the original (empirical) similarity matrix. We exemplify use of this approach with the food-niche matrix obtained for a predatory assemblage in California, and discuss its implications for the general analysis of guild structure.     

Effects of functional constraints and opportunism on the functional structure of a vertebrate predator assemblage

1. Within mainstream ecological literature, functional structure has been viewed as resulting from the interplay of species interactions, resource levels and environmental variability. Classical models state that interspecific competition generates species segregation and guild formation in stable saturated environments, whereas opportunism causes species aggregation on abundant resources in variable unsaturated situations. 2. Nevertheless, intrinsic functional constraints may result in species-specific differences in resource-use capabilities. This could force some degree of functional structure without assuming other putative causes. However, the influence of such constraints has rarely been tested, and their relative contribution to observed patterns has not been quantified. 3. We used a multiple null-model approach to quantify the magnitude and direction (non-random aggregation or divergence) of the functional structure of a vertebrate predator assemblage exposed to variable prey abundance over an 18-year period. Observed trends were contrasted with predictions from null-models designed in an orthogonal fashion to account independently for the effects of functional constraints and opportunism. Subsequently, the unexplained variation was regressed against environmental variables to search for evidence of interspecific competition. 4. Overall, null-models accounting for functional constraints showed the best fit to the observed data, and suggested an effect of this factor in modulating predator opportunistic responses. However, regression models on residual variation indicated that such an effect was dependent on both total and relative abundance of principal (small mammals) and alternative (arthropods, birds, reptiles) prey categories. 5. In addition, no clear evidence for interspecific competition was found, but differential delays in predator functional responses could explain some of the unaccounted variation. Thus, we call for caution when interpreting empirical data in the context of classical models assuming synchronous responses of consumers to resource levels.     

Geographic variation in seed removal of a myrmecochorous herb: influence of variation in functional guild and species composition of the disperser assemblage through spatial and temporal scales

The ecological influence of changes in the functional guild and species composition of ant assemblages on ant‐dispersal mutualisms is still poorly known. Using a multi‐scale approach over an 800 km range within the Iberian Peninsula, we tested the hypothesis that variation in seed removal rate was related to functional guild rather than to species composition variations of disperser assemblages in the myrmecochore herb Helleborus foetidus. At least two premises must be confirmed to validate this hypothesis: 1) ant assemblages that are dissimilar in species composition but with similar functional guild composition will not differ significantly in seed removal, and 2) assemblages with different functional guild composition will render different seed removal services. We conducted 3328 ant‐visitor censuses on 462 individual plants to identify both the species composition and functional guild variation of the ant‐disperser assemblage, and the plant seed removal rate. Functional guild composition of the ant assemblage was determined by the proportion of visits of ants acting as legitimate dispersers, facultative dispersers or elaiosome predators. Results showed that ant‐seed dispersal success seemed to be more sensitive to species composition changes of the ant assemblage than to functional guild shifts. However, this sensitivity was scale‐dependent. Thus, at the fine, inter‐individual scale, seed removal covaried with the species and functional guild composition of the ant assemblages; at the inter‐populational scale, differences in seed removal tended to be related to the dissimilarity of the assemblage species composition rather than the assemblage functional guild; finally, inter‐regional differences in seed removal were unrelated to dissimilarities of the ant assemblage composition or functional guild. Though differences in seed removal and the relative frequency of the legitimate dispersers tended to be positively correlated, none of the above premises were fully confirmed in this study. Therefore, our results did not support in full the hypothesis that the variation in seed removal was explained by shifts in functional guild composition, rather than shifts in species composition.     

The structure and components of European estuarine fish assemblages

This paper discusses the structure of fish assemblages using information from 17 European estuarine areas (in the British Isles, Portugal, Belgium, France, the Netherlands, Germany, Norway and Spain). Binary (presence/absence) and quantitative data for each assemblage have been used to assess the assemblage structure according to taxonomy (i.e. species identity). Following this, a total of 29 functional guilds were created in order to describe the use made of an estuarine area for each taxon encountered: feeding preferences, reproduction type, substratum preferences (for bottom dwelling fish) and position within the water column (vertical preference guild). The paper focuses on the designation and determination of the proportions of the guild members of the fish assemblage within each estuary. Ecological guilds within the assemblage include estuarine residents, marine juvenile migrants, catadromous and anadromous migrants, marine seasonal users, and freshwater and marine adventitious species. Feeding guilds include detritivores, planktonic feeders, infaunal croppers and sediment ingesters, piscivores, and active predators of mobile crustaceans. Reproduction guilds include planktonic and demersal spawners and those using brood-protection. The substratum preference indicates the proportions of sand, mud, rock and vegetation dwellers, and the vertical preference denotes benthic, demersal or pelagic species. The analysis has allowed both the estuaries to be grouped according to taxonomic and guild similarity and the characterisation of a typical European estuarine fish assemblage. Within the limits posed by differing sampling methods, times of sampling and survey rationale, there is a high similarity between estuaries. The data indicate common patterns of estuarine usage irrespective of the differences between the estuaries although such patterns cannot be interpreted fully given the incomplete knowledge of their physical and anthropogenic characteristics.     

Feeding guild structure of a rocky intertidal fish assemblage in central Chile

The identification and analysis of the guild structure of vertebrate assemblages has played a fundamental role in the understanding of the underlying mechanisms responsible for their community organization and structuring. This approach generally has not been undertaken for temperate water intertidal fish assemblages. In central Chile, fishes are important components of the intertidal community, but no studies attempting to understand their organization and structuring have been done. In the present study, the diets of 13 of the most abundant species which inhabit tidepools in the rocky intertidal zone of central Chile were determined. A total of 660 fishes was collected at 5 sites: Los Molles, Con-Cón, Quintay, El Tabo, and Las Cruces. Dietary overlap between all species pairs was calculated and a phenogram of dietary similarity was constructed and analyzed using a bootstrapping technique to objectively determine guild membership. The results showed that the intertidal fish assemblage of central Chile can be divided into three feeding guilds: two guilds consisting of carnivorous species and one guild of omnivorous and herbivorous species. The possible causes and implications of the resulting guild structure and the potential effects of predation by these fishes on other components of the intertidal community are discussed.     

Generating and testing predictions about community structure: Which theory is relevant and can it be tested with observational data?

Three issues are discussed relevant to the controversy over using null models and observational data on guild structure to test community-level predictions based on limiting similarity theory. First, I argue that most limiting similarity theory is not based on reasonable assumptions for plants and that the theory that is relevant does not generate any predictions about expected guild proportionality on a small spatial scale. Therefore, regardless of adequacy of the statistical methods, the predictions being tested by the body of literature using null models to test for niche limitation are unlikely to be relevant in most plant comunities. Second, assuming that the predictions are after all worth being tested, I argue that most tests using the guild approach do not provide adequate explanations of how the defined guilds could lead to greater competition within vs. between guilds. If this is not true for the particular guilds used, the predictions of guild proportionality or size constancy will not be valid. Third, I address the controversy over whether field experiments can provide more solid evidence than observational data about the role of competition in determining community structure by (1) suggesting methods of dealing with potential drawbacks of field experiments, and (2) suggesting alternative experimental approaches for directly addressing issues about community structure.     

Associations between avian functional guild response and regional landscape properties for conservation planning

This project facilitates a regional approach to conservation planning in Pennsylvania based on avian breeding habitat selection. The objectives were to: (1) determine the sensitivity of spatial pattern in avian diversity to changing thresholds of intra-guild species richness and (2) relate change of spatial pattern in avian diversity with landscape characteristics of bird Atlas blocks. Two state-wide spatial data layers, based on Landsat satellite data were constructed for this study. These regional landscape data were compared to Breeding Bird Atlas data from 1983 to 1989 using a geographic information system. Breeding bird data were recorded from 4928 blocks that form a grid covering Pennsylvania. Correlation analysis reduced landscape variables to 12 originally derived from forest, urban, roads, streams, and topographic data.Avian functional response guilds were used to analyze associations between breeding bird data and landscape variables. Functional response guilds were created by grouping organisms based on shared habitat preferences or behavioral characteristics. Most of the 18 avian guilds identified for this study were based on shared structural resource characteristics of preferred breeding habitat. Preferred structural resources frequently included the amount and type of forest. For this study, guilds separate resource characteristics by: (1) primary habitat (i.e. forest interior, forest edge), (2) area sensitivity (i.e. forest and grassland), (3) migratory status (i.e. resident, temperate, and tropical), and (4) nest placement (i.e. canopy nester, forest ground nester). Wetland obligate species were treated as a separate guild. Breeding Bird Atlas blocks were tabulated with respect to the number of species present from each guild. For a given guild, the number of its species in a block is termed guild-specific species richness. Sample blocks having high species richness for a given guild often occur adjacent or in close proximity forming spatial clusters in the landscape. Spatial coherence (adjacency/proximity) among the blocks forming these islands is shared guild-specific richness. Spatial clustered blocks of each guild represent areas that presumably possess required resources for members of that guild. Blocks having high intra-guild richness were evaluated with a group of block-level continuous variables using multiple logistic regressions. Logistic regression results indicate that a convincing connection exists between landscape properties of Breeding Bird Atlas blocks and habitat selection characteristics of guild members. Percent of forest cover and mean elevation were the most important habitat characteristics influencing intra-guild richness for most of the guilds tested. Concordance values from logistic regression were used to determine the strength of each guild model. Concordance, the proportion that represents the percent of correct guild richness predictions versus incorrect predictions, suggests a relationship between guild-rich clusters and habitat resources required by each guild. The highest concordance was for the exotics guild at 76.3% and the next highest was 74.8% for the grassland area sensitive guild. This signifies a 75% certainty that landscape variables could predict occurrence of a guild-rich block. Eight more guilds had concordance values greater than 65%.By using a guild approach, this study goes beyond total diversity to the more informative structural and functional diversity of guilds. Spatially clustered blocks of high species richness for a particular guild are more indicative of habitat availability and quality than would be the case for overall species richness. Clusters of blocks having high intra-guild species richness become candidate areas for conservation efforts.     

Variation in the guild composition of herbivorous insect assemblages among co‐occurring plant species

Variation in plant traits among plant species may promote the development of a characteristic functional assemblage of insect herbivores associated with each plant species. However, only a small number of studies have detailed the representation of several herbivore guilds among co‐occurring plant species to determine whether the functional structure of herbivorous insect assemblages varies widely and consistently among plant species. The present study provides one of the few published data sets reporting on the density of several guilds of insect herbivores among numerous plant species. Variation in guild associations with plant phenology and season are also described. Insect herbivores were divided into 10 guilds, and the representation of these guilds was examined for 18 co‐occurring plant species. Guild densities and assemblage composition varied significantly among plant species, even when variation over time was taken into account. Variation in guild densities and assemblage composition were not strongly related to the taxonomic relationships of the plants. The highest densities of several guilds occurred in spring and summer, although other guilds were not strongly seasonal. Certain guilds were strongly associated with the presence of new leaves, whereas other guilds appeared to prefer mature leaves. This resulted in assemblage differences between samples containing new and mature leaves and samples containing mature leaves only. Even though the timing and duration of leaf and flower production varied among plant species, this did not explain all variation in guild densities among plant species. It is suggested that additional factors, including plant traits, are contributing to the wide and consistent variation in herbivore assemblage composition among plant species.     

Global patterns of guild composition and functional diversity of spiders

The objectives of this work are: (1) to define spider guilds for all extant families worldwide; (2) test if guilds defined at family level are good surrogates of species guilds; (3) compare the taxonomic and guild composition of spider assemblages from different parts of the world; (4) compare the taxonomic and functional diversity of spider assemblages and; (5) relate functional diversity with habitat structure. Data on foraging strategy, prey range, vertical stratification and circadian activity was collected for 108 families. Spider guilds were defined by hierarchical clustering. We searched for inconsistencies between family guild placement and the known guild of each species. Richness and abundance per guild before and after correcting guild placement were compared, as were the proportions of each guild and family between all possible pairs of sites. Functional diversity per site was calculated based on hierarchical clustering. Eight guilds were discriminated: (1) sensing, (2) sheet, (3) space, and (4) orb web weavers; (5) specialists; (6) ambush, (7) ground, and (8) other hunters. Sixteen percent of the species richness corresponding to 11% of all captured individuals was incorrectly attributed to a guild by family surrogacy; however, the correlation of uncorrected vs. corrected guilds was invariably high. The correlation of guild richness or abundances was generally higher than the correlation of family richness or abundances. Functional diversity was not always higher in the tropics than in temperate regions. Families may potentially serve as ecological surrogates for species. Different families may present similar roles in the ecosystems, with replacement of some taxa by other within the same guild. Spiders in tropical regions seem to have higher redundancy of functional roles and/or finer resource partitioning than in temperate regions. Although species and family diversity were higher in the tropics, functional diversity seems to be also influenced by altitude and habitat structure.     

Ecological background of diatom functional groups: Comparability of classification systems

Functional classification based on species traits brought a revolution in community ecology, and also boosted phytoplankton and in phytobenton (diatom) research. Several studies stressed the usefulness of phytoplankton functional groups in ecological status assessment, and there is also a strong emphasis to use combined traits in ecological assessments of diatom assemblages. The Combined Eco-Morphological Functional Groups (CEMFGs) help to reveal species-environmental correlations, which can be hidden, controlling traits separately. Nowadays, there are three types of functional guild classifications simultaneously used in the literature: (i) the original classification proposed by Passy (O); (ii) Passy’s classification complemented with a separated planktic guild (P); (iii) the refined guild classification by Rimet and Bouchez, also containing the planktic guild (RB). One of the most important criteria of the combined functional groups is the well-defined ecological frame of these combined groups; thus it is vital to harmonise the classification of the taxa into guild based combined eco-morphological functional groups (CEMFGs). In this study we tested the similarities and dissimilarities of the correlations between environmental factors and CEMFGs created in the (i)-(iii) classifications. Samples were collected in 138 sampling sites on lowland rivers and streams in the Hungarian Lowland Region. Strong correlations were anticipated between the functional groups and environmental factors due to the presence of common and/or abundant planktic taxa. Our results validated the necessity of a separated planktic guild in ecological assessments of diatom assemblages. Further relevant differences between the correlations of CEMFGs-P or CEMFGs-RB and abiotic factors were hypothesised in the case of those functional groups which contained reassigned taxa with high frequency and/or abundance. Our results confirmed this hypothesis. Furthermore, the present study also highlighted the relevance of well-defined trait classification. Abundant and/or frequent taxa, which are able to change their life forms, can modify significantly the relationship between the functional group containing them and environmental factors. In the future, both field and laboratory studies should focus on revealing the circumstances, which cause the mentioned changes in traits of diatoms.     

不同纬度植物群落系统发育与功能性状结构研究

研究植物群落系统发育和功能性状结构有助于了解植物多样性维持机制及物种间的亲缘关系。甘肃省地理环境复杂,显著而多变的气候梯度形成了区域植被和环境差异,丰富了栖息地类型,具有显著的纵向连通性和纬度隔离性,以甘肃省典型纬度梯度植物群落为研究对象,通过对其进行群落学调查和功能性状测定,计算净亲缘关系指数(Net relatedness index, NRI)和平均成对性状距离(Mean pairwise trait distance, PW)来分析植物群落系统发育结构和功能性状格局对不同纬度的响应。结果表明：(1) Shannon-Weiner多样性指数,物种丰富度,谱系α多样性指数表现出随纬度增加而显著降低的变化趋势(P<0.05),Pielou均匀度指数随纬度的升高没有显著的变化趋势;(2)系统发育结构在高、低纬度上趋于发散状态(NRI<0),在中纬度上又表现出聚集(NRI>0)的谱系结构,表明种间竞争作用减弱,环境过滤作用逐渐增强,随纬度继续升高相似性限制作用在物种聚集过程中占优势;而群落的功能性状结构随着纬度增加表现出与谱系结构相反的状态,因此植物群落的系统发育和功能...     

Shaping up: a geometric morphometric approach to assemblage ecomorphology

This study adopts an ecomorphological approach to test the utility of body shape as a predictor of niche relationships among a stream fish assemblage of the Tickfaw River (Lake Pontchartrain Basin) in southeastern Louisiana, U.S.A. To examine the potential influence of evolutionary constraints, analyses were performed with and without the influence of phylogeny. Fish assemblages were sampled throughout the year, and ecological data (habitat and tropic guild) and body shape (geometric morphometric) data were collected for each fish specimen. Multivariate analyses were performed to examine relationships and differences between body shape and ecological data. Results indicate that a relationship exists between body shape and trophic guild as well as flow regime, but no significant correlation between body shape and substratum was found. Body shape was a reliable indicator of position within assemblage niche space.     

Seasonal dynamics of guild structure in a bird assemblage of the central Monte desert

Most studies of ecological guilds consider guild membership as a fixed attribute of species, and the guild structure as a fixed attribute of a community. Consequently, almost no study tackled the examination of temporal changes in the guild structure of a particular assemblage. We used data on foraging patterns of central Monte desert birds to assess seasonal differences in resource use by resident species, and to examine seasonal changes in the guild structure of the assemblage. From 1993 until 1999, we quantified the use of foraging substrates, manoeuvres, and height strata, and the utilisation of plants by 18 bird species. Resident species showed different kinds of seasonal dynamics, from no noticeable to drastic changes in their foraging patterns. Seasonal changes in guild structure were remarkable. Only two guilds were present all year round (ground foragers and foliage foragers), although they suffered important species turnover. Three other guilds had a seasonal occurrence: graminivores (during the non-breeding season), arboreal herbivores, and aerial feeders (during the breeding season). Two species changed from one guild to another between seasons. Both presence–absence of migrant species, and changes in the feeding ecology of resident species had an influence on the temporal dynamics of guild structure. These factors appeared to be related with changing resource availability, especially with the birds’ ability for facing lean conditions through migration and with the opportunistic use of seasonally superabundant resources. Our results undermine the trust in studies in which guild structure was assessed irrespective of temporal variations. We show also that guild membership is not a fixed attribute of a species: we should rather evaluate the individuals’ resource use in a given moment to assign them to a guild, instead of obtaining a single measure purporting to represent a species’ fixed attribute.     

Persistence of community structure: what happens when you change taxonomic scale?

It is common in community ecology to use the species as the taxonomic category of interest, yet in rich tropical assemblages containing guilds of very similar species this may not be appropriate. Such assemblages may be organized at the level of guilds rather than at the finer species level. In a ten-year study of assemblages of fish at One Tree Reef, Great Barrier Reef, we found species composition and the number of fish on a given lagoonal patch reef vary greatly across time (Sale and Douglas 1984; Sale et al. in preparation). The mean average proportional similarity of a reef's assemblage to itself at different times (censuses) is usually low at a value of around 0.5. This apparent variability may be ecologically irrelevant noise if organization is at the higher guild level. We have recast our database at the guild level to test this possibility. Thirteen guilds were defined by the diets, foraging habitats and times of the individual species comprising them. Similarity of an assemblage to itself at successive censuses was re-calculated using the number of individuals in each guild instead of the numbers in each species. This analysis yielded significantly higher levels of similarity (P<0.01) among censuses. To test whether this increase in similarity was due solely to the smaller number of categories used to calculate the similarity indices, 5 sets of randomly generated guilds were constructed using a Monte Carlo approach. No significant difference (P>0.05) was found between the average similarity among censuses when assemblages were classified into these null guilds and when they were classified according to the real guilds. These results indicate that shifting to the larger taxonomic scale of guilds does not reveal a significantly more persistent assemblage structure than that revealed when analysis is at the smaller scale of species. There is no evidence of an underlying organization of these assemblages at the guild level.     

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins

Three-dimensional cluster analysis offers a method for the prediction of functional residue clusters in proteins. This method requires a representative structure and a multiple sequence alignment as input data. Individual residues are represented in terms of regional alignments that reflect both their structural environment and their evolutionary variation, as defined by the alignment of homologous sequences. From the overall (global) and the residue-specific (regional) alignments, we calculate the global and regional similarity matrices, containing scores for all pairwise sequence comparisons in the respective alignments. Comparing the matrices yields two scores for each residue. The regional conservation score (C(R)(x)) defines the conservation of each residue x and its neighbors in 3D space relative to the protein as a whole. The similarity deviation score (S(x)) detects residue clusters with sequence similarities that deviate from the similarities suggested by the full-length sequences. We evaluated 3D cluster analysis on a set of 35 families of proteins with available cocrystal structures, showing small ligand interfaces, nucleic acid interfaces and two types of protein-protein interfaces (transient and stable). We present two examples in detail: fructose-1,6-bisphosphate aldolase and the mitogen-activated protein kinase ERK2. We found that the regional conservation score (C(R)(x)) identifies functional residue clusters better than a scoring scheme that does not take 3D information into account. C(R)(x) is particularly useful for the prediction of poorly conserved, transient protein-protein interfaces. Many of the proteins studied contained residue clusters with elevated similarity deviation scores. These residue clusters correlate with specificity-conferring regions: 3D cluster analysis therefore represents an easily applied method for the prediction of functionally relevant spatial clusters of residues in proteins.     

Morphological diversity at different spatial scales in a Neotropical bat assemblage

The morphology of species can be used to represent their ecological position and infer potential processes determining the structure of species assemblages. This ecomorphological approach has been widely applied to the study of bat assemblages which mainly focuses on a single spatial scale and particular guilds. We extended such an ecomorphological approach to a multi-scale analysis of a Neotropical bat assemblage and its constituent guilds (aerial and gleaning insectivores, frugivores, and nectarivores) to describe their structure at different spatial scales and determine the relative importance of inter-specific competition, habitat filtering, or stochastic processes shaping such structures. We measured the occupied morphological space (size) defined by wing and skull morphology independently and the nearest-neighbour distance (structure) among species within these spaces at each spatial scale. Observed patterns were compared with random expectations derived from null models for statistical inference. When controlling for species richness and regional sampling effects in the null models, we did not find a significant effect of spatial scale in the morphological structure of the studied bat assemblage and guilds. Morphological structure followed the same patterns across scales as those expected from random drawings of sample size alone. Similar results were obtained regardless of morphological complex (wing and skull) and guilds. At both the assemblage and guild levels, bat morphological structure seems to be determined by regional, abiotic processes (e.g. habitat filtering) shaping the composition and organization of the species pool.     

Genetic variation and relationship among and within Withania species as revealed by AFLP markers.

Withania somnifera is an important medicinal plant, and its anticancerous properties have been attributed to various classes of withanolide compounds. The objective of the present study was to investigate the inter- and intraspecific genetic variation present in 35 individuals of W. somnifera and 5 individuals of W. coagulans using AFLP (amplified fragment length polymorphism) marker technique. The information about genetic variation determined from AFLP data for 40 individuals was employed to estimate similarity matrix value based on Jaccard's coefficient. The similarity values were further used to construct a phenetic dendrogram revealing the genetic relationships. The dendrogram generated by UPGMA (unweighted pair group method of arithmetic averages) distinguished W. somnifera from W. coagulans and formed two major clusters. These two main clusters shared a similarity coefficient of 0.3, correlating with the high level of polymorphism detected. The dendrogram further separated W. somnifera into three subclasses corresponding to Kashmiri and Nagori groups and an intermediate type. The AFLP profile of Kashmiri individuals was distinct from that of the Nagori group of plants. The intermediate genotype was distinct as it shared bands with both the Kashmiri and Nagori individuals, even though it was identified as a Kashmiri morphotype. Furthermore, the intermediate type shared a similarity coefficient of 0.8 with the Kashmiri individuals. The present work revealed low levels of variation within a population though high levels of polymorphism were detected between Nagori and Kashmiri populations. The ability of AFLP markers for efficient and rapid detection of genetic variations at the species as well as intraspecific level qualifies it as an efficient tool for estimating genetic similarity in plant species and effective management of genetic resources.     

Towards a consensus for calculating dendrogram-based functional diversity indices

The widely used FD index of functional diversity is based on the construction of a dendrogram. This index has been the subject of a strong debate concerning the choice of the distance and the clustering method to be used, since the method chosen may greatly affect the FD values obtained. Much of this debate has been centred around which method of dendrogram construction gives a faithful representation of species distribution in multidimensional functional trait space. From artificially generated datasets varying in species richness and correlations between traits, we test whether any single combination of clustering method(s) and distance consistently produces a dendrogram that most closely corresponds to the matrix of functional distances between pairs of species studied. We also test the ability of consensus trees, which incorporate features common to a range of different dendrograms, to summarize distance matrices. Our results show that no combination of clustering method(s) and distance constantly outperforms the others due to the complexity of interactions between correlations of traits, species richness, distance measures and clustering methods. Furthermore, the construction of a consensus tree from a range of dendrograms is often the best solution. Consequently, we recommend testing all combinations of distances and clustering methods (including consensus trees), then selecting the most reliable tree (with the lowest dissimilarity) to estimate FD value. Furthermore we suggest that any index that requires the construction of functional dendrograms potentially benefits from this new approach.     

Mass coral bleaching causes biotic homogenization of reef fish assemblages

Global climate change is altering community composition across many ecosystems due to nonrandom species turnover, typically characterized by the loss of specialist species and increasing similarity of biological communities across spatial scales. As anthropogenic disturbances continue to alter species composition globally, there is a growing need to identify how species responses influence the establishment of distinct assemblages, such that management actions may be appropriately assigned. Here, we use trait‐based analyses to compare temporal changes in five complementary indices of reef fish assemblage structure among six taxonomically distinct coral reef habitats exposed to a system‐wide thermal stress event. Our results revealed increased taxonomic and functional similarity of previously distinct reef fish assemblages following mass coral bleaching, with changes characterized by subtle, but significant, shifts toward predominance of small‐bodied, algal‐farming habitat generalists. Furthermore, while the taxonomic or functional richness of fish assemblages did not change across all habitats, an increase in functional originality indicated an overall loss of functional redundancy. We also found that prebleaching coral composition better predicted changes in fish assemblage structure than the magnitude of coral loss. These results emphasize how measures of alpha diversity can mask important changes in the structure and functioning of ecosystems as assemblages reorganize. Our findings also highlight the role of coral species composition in structuring communities and influencing the diversity of responses of reef fishes to disturbance. As new coral species configurations emerge, their desirability will hinge upon the composition of associated species and their capacity to maintain key ecological processes in spite of ongoing disturbances.