How should a dendrogram‐based measure of functional diversity function? A rejoinder to Petchey and Gaston

This paper is a response to Petchey and Gaston's criticism of our previous paper on the measurement of dendrogram-based functional diversity. In contrast to their suggestions, we insist that Euclidean distance is unsuitable to the analysis of variables with mixed scale types and maintain our earlier view that both the distance function and the clustering method can influence the dendrogram-based measure of functional diversity. We propose an extension of Gower's formula to accommodate nominal traits with non-exclusive categories and emphasize the necessity of the methodological standardization of functional diversity measures.     

On dendrogram-based measures of functional diversity

Euclidean distance is commonly involved in calculating functional diversity (FD), for example, in measures based on dendrogram branch lengths. We point out that this function is inappropriate in many cases and that the choice of clustering method is more crucial than earlier thought. Gower's formula and UPGMA clustering are suggested here as a standard combination of techniques for calculating FD. The advantage of Gower's measure is its suitability to a mixture of scale types and its tolerance to missing values. Examples demonstrate that UPGMA clustering is more robust and has a better goodness of fit to dissimilarities than complete and single linkage classifications. In addition, we propose that the effect of individual species on FD is best evaluated by species removals and subsequent comparisons of tree length values. The influence of each functional trait is optimally judged by considering both dendrogram length and topological changes.     

Variations in the dispersal curves of macroalgal propagules from a source

The process of dispersal is critical to marine benthic species (i.e. invertebrates and algae) as a fundamental element of population ecology and a crucial ecological process that maintains the diversity in communities. We simultaneously sampled the abundance of spores inhabiting the water column at different distances from known parent sources at 3 sites along the coast of central Chile. From these data we constructed 258 dispersal curves for common rocky intertidal macroalgae. Only 43.8% of these curves could be predicted by the expected model, which describes the spatial distribution of propagules to be dominated by a larger concentration near the parent individual or “source site”, followed by a marked decrease in abundance with increasing distance. The curves that departed from the expected model (56.2%) were grouped into three curve types, according to the number of propagule abundance maxima observed in space. This work suggests that macroalgal propagule dispersal patterns are more variable than previously thought. The existence of several alternative curves to the expected model, as well as the presence of one to several abundance maxima associated with the differential distribution of propagule patches in the water column, suggests the idea that propagules are released in pulses which can be transported variable distances from the source site.     

Systematic analysis of genomic organization and heterogeneities of miRNA cluster in vertebrates

The clustering propensity of microRNA genes is a common biological phenomenon in various animal and plant species. To gain novel insight into genomic organization and potential functional heterogeneities of miRNA clusters in vertebrates from a genome scale, we used large scale data and presented a comprehensive analysis to examine various features of genomic organization of miRNA clusters across seven vertebrates by a combination of comparative genomics and bioinformatics approaches. The results of pair-wise distance analysis of same-strand consecutive miRNAs suggested that the fractions of the miRNA gene pairs are higher at relatively short pair-wise distances than those of protein-coding genes and other non-coding RNA genes. Especially relatively small number of miRNAs is more clustered at very short pair-wise distances than expected at random. We further observed significant difference between real miRNA clusters and randomly organized clusters for different aspects, including higher overlap of target genes, fewer seed types and significant enrichment in diseases. However, the extent of these features of clustered miRNAs has a different tendency and largely depends on inter-miRNA distances because of diverse clustering propensity of miRNAs in vertebrates, suggesting that this cooperated function or cooperative effects between miRNAs in clusters perhaps be affected by inter-miRNA distances.     

The effect of human disturbance and flock composition on the flight distances of waterfowl species

Flocking bird species tolerate an approaching human up to a certain distance. We measured this distance, i.e., flight distance, to an approaching small boat for 11 waterfowl species. The flight distances correlated positively with flock size and species diversity (Shannon index H′) in species that showed relatively short flight distances when they were in a single-species flock. However, we did not observe such a correlation for single-species flocks that showed relatively long flight distances. Only pochards (Aythya ferina), a species with large individual variation in flight distances, showed a positive correlation between flight distance and flock size in both single- and multispecies flocks. Flight distance seemed to be affected by usage of the water area: flight distances tended to be longer for waterfowl species that use a water area for foraging than for those that use it primarily for resting. Thus, the behavior of actively foraging species may be more affected by human disturbances than that of resting species. Received: March 10, 2001 / Accepted: May 22, 2001     

Impact of habitat diversity on the sampling effort required for the assessment of river fish communities and IBI

The spatial variation in the fish communities of four small Belgian rivers with variable habitat diversity was investigated by electric fishing to define the minimum sampling distance required for optimal fish stock assessment and determination of the Index of Biotic Integrity. This study shows that the standardised sampling distance of 100 m was not always sufficient to collect most species present. The required minimum sampling distance seems to be correlated with habitat diversity. In homogeneous streams, a mean sample distance of 282, 452 and 572 m is necessary to capture 80, 90 and 95% of all species present, respectively. In heterogeneous streams, these sample distances decrease to 217, 380 and 503 m. Hence, at least 300 m should be sampled to catch most species present with a single-pass sampling method. However, our results show that a 100 m sampling distance as presently used in the Flemish monitoring programs is sufficient to accurately describe the ecological quality since differences in IBI evaluation between adjacent stretches could at least for some rivers be explained by differences in habitat heterogeneity.     

Explaining the saproxylic beetle diversity of a protected Mediterranean area

Saproxylic beetle diversity is high at the Cabañeros National Park (central Spain), where woodland habitats exhibit remarkable heterogeneity. Our aim was to explain the diversity of saproxylic beetles, focusing on species turnover among mature woodland types. We surveyed five woodland types that represented the heterogeneity of the park’s woodland habitats. Beetles were collected using window traps over a period of 20 months. The Jaccard Similarity Index was used as indirect value of beta diversity among woodlands and to test the relation between species turnover and geographical distance. We also identified the contribution of species turnover to landscape diversity by using a partitioning model. Moreover, the presence of mixed woodlands (more than one tree species) allowed us to attempt to valorise the effect of tree species (coupled with their historical management) on species turnover among woodlands. Finally, we looked for different saproxylic beetle preferences for habitat and tree species using an indicator value method. We found that saproxylic beetle species composition varied significantly among the studied woodlands. The variation in species turnover was independent from the distance among woodlands, which suggested that beetle dispersal abilities could not explain this high turnover. Tree species within woodlands were a key factor that increased diversity turnover in woodlands and, consequently, the diversity of the park. Moreover, we found saproxylic beetle species that had different habitat and tree species preferences. We conclude that woodland heterogeneity (highly affected by woodland composition) seems to be the driving force for saproxylic beetle diversity in this protected area.     

Dispersal and diversity – unifying scale‐dependent relationships within the neutral theory

The response of species diversity to dispersal capability is inherently scale‐dependent: increasing dispersal capability is expected to increase diversity at the local scale, while decreasing diversity at the metacommunity scale. However, these expectations are based on model formulations that neglect dispersal limitation and species segregation at the local scale. We developed a unifying framework of dispersal–diversity relationships and tested the generality of these expectations. For this purpose we used a spatially‐explicit neutral model with various combinations of survey area (local scale) and landscape size (metacommunity scale). Simulations were conducted using landscapes of finite and of conceptually infinite size. We analyzed the scale‐dependence of dispersal‐diversity relationships for exponentially‐bounded versus fat‐tailed dispersal kernels, several levels of speciation rate and contrasting assumptions on recruitment at short dispersal distances. We found that the ratio of survey area to landscape size is a major determinant of dispersal–diversity relationships. With increasing survey‐to‐landscape area ratio the dispersal–diversity relationship switches from monotonically increasing through a U‐shaped pattern (with a local minimum) to a monotonically decreasing pattern. Therefore, we provide a continuous set of dispersal–diversity relationships, which contains the response shapes reported previously as extreme cases. We suggest the mean dispersal distance with the minimum of species diversity (minimizing dispersal distance) for a certain scenario as a key characteristic of dispersal–diversity relationships. We show that not only increasing mean dispersal distances, but also increasing variances of dispersal can enhance diversity at the local scale, given a diverse species pool at the metacommunity scale. In conclusion, the response of diversity to variations of dispersal capability at spatial scales of interest, e.g. conservation areas, can differ more widely than expected previously. Therefore, land use and conservation activities, which manipulate dispersal capability, need to consider the landscape context and potential species pools carefully.     

Changes in the abundance and diversity of coastal wetland fauna from the open water/macrophyte edge towards shore

Great Lakes coastal wetlands are widely recognized as areas of concentrated biodiversity and productivity, but the factors that influence diversity and productivity within these systems are largely unknown. Several recent studies have suggested that the abundance and diversity of flora and fauna in coastal wetlands may be related to distance from the open water/macrophyte edge. We examined this possibility for three faunal groups inhabiting a coastal wetland in Saginaw Bay, Lake Huron. We sampled crustacean zooplankton and benthic macro-invertebrates at five distances from open water in the summer 1994, and fish at three distances from open water in 1994 and 1995. We found significant spatial trends in the total abundance and diversity of zooplankton and fish, as well as the diversity of benthic macro-invertebrates. Zooplankton abundance and taxa richness were highest at intermediate distances from open water in a transition zone between the well-mixed bayward portion of the wetland, and the non-circulating nearshore area. Benthic macro-invertebrate taxa richness increased linearly with distance from open water. In contrast, fish abundance and species richness declined linearly and substantially (abundance by 78%, species richness by 40%) with distance from open water. Of the 40 taxa examined in this study, 21 had significant horizontal trends in abundance. This led to notable differences in community composition throughout the wetland. Our results suggest that distance from open water may be a primary determinant of the spatial distributions of numerous organismal groups inhabiting this coastal wetland. Several possible reasons for these distributions are discussed.     

Effects of newly planted hedges on ground-beetle diversity (Coleoptera, Carabidae) in an agricultural landscape

The diversity of ground-beetle communities (Coleoptera. Carabidae) was studied to assess the short-term impact of new hedges planted in an intensive agro-ecosystem. Hedges represent a new and undisturbed habitat for those polyphagous predators and may provide increased prey availability. Carabids were sampled with pitfall traps in a hedge and an adjacent cultivated field during the whole activity period of these insects to assess the effect of distance from the hedge on species diversity. Fenced pitfall traps were also used to estimate absolute population densities. Several diversity indices were calculated at various sampling levels (total area, distance treatment, trap). Kendall's coefficient of rank correlation between communities at adjacent distances showed that the greatest changes in species relative abundances occurred close to the hedge. Indices of species richness, dominance concentration, equitability and Fisher's a all indicated a significant decrease in species diversity with increasing distance from the hedge. These trends are explained by two complementary factors. First, the number of species decreased significantly with distance from the centre of the hedge. Second, the various species had different spatial patterns of total capture and absolute density. Four groups of species can thus be distinguished: species restricted to the hedge, species preferring the hedge, species preferring the crop, and species unaffected by the hedge. The respective roles of small-scale abiotic changes in habitat structure and differences in prey availability are discussed.     

Genetic relationships among the oral streptococci.

Genetic relationships and species limits among the oral streptococci were determined by an analysis of electrophoretically demonstrable variation in 16 metabolic enzymes. Fifty isolates represented 40 electrophoretic types, among which the mean genetic diversity per locus was 0.857. Mannitol-1-phosphate dehydrogenase was not detected in isolates of the sanguis species complex, and glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase were absent in species of the mutans complex. Clustering from a matrix of Gower's coefficient of genetic similarity placed the 40 electrophoretic types in 10 well-defined groups corresponding to the Streptococcus species S. mutans, S. sobrinus, S. cricetus, S. rattus, S. ferus, S. oralis (mitior), two distinct assemblages of S. sanguis strains, and two subdivisions of "S. milleri." The assignments of isolates to these groups were the same as those indicated by DNA hybridization experiments, and the coefficient of correlation between genetic distance estimated by multilocus enzyme electrophoresis and genetic similarity indexed by DNA hybridization was -0.897 (P less than 0.001) for 50 pairwise combinations of isolates. S. ferus, which is widely believed to be a member of the mutans complex, was shown to be phylogenetically closer to species of the sanguis complex.     

Population structure and genetic diversity in four tropical tree species in Costa Rica

Despite intensified interest in conservation of tropical forests, knowledge of the population genetics of tropical forest trees remains limited. We used random amplified polymorphic DNA (RAPD) data to evaluate trends in genetic diversity and differentiation for four tropical tree species, Alchornea latifolia, Dendropanax arboreus, Inga thibaudiana and Protium glabrum . These species occur at contrasting population densities along an elevational gradient and we use RAPD and ecological data to examine natural levels of genetic diversity of each species, trends in genetic variability with population density and structure, genetic differentiation along the elevation gradient, and the relationship between genetic diversity and such factors as seed dispersal and pollination syndrome. At the distances we examined (plot distances ranging from 0.8 to 8.6 km) there was very little genetic structuring at any distance along the gradient. All four species exhibited levels of variation expected for spatial distribution, mating system and pollinator syndrome; greater than 96% of the genetic variation occurred within plots for Inga thibaudiana, Protium glabrum and Dendropanax arboreus. Alchornea latifolia only occurred in a single plot. The results of this study contribute to a growing database of genetic diversity data that can be utilized to make predictions about the effect of disturbance and subsequent reductions in population size on genetic variation and structure in tropical tree species.     

Predicting the similarity of parasite communities in freshwater fishes using the phylogeny,ecology and proximity of hosts

Parasite communities tend to be dissimilar in hosts that are geographically, phylogenetically, ecologically and developmentally distant from one another. The decay of community similarity is a powerful and increasingly common method of studying parasite beta diversity, but most studies have examined only a single type of distance. Here, we evaluate distances based on the phylogeny, ecology, spatial proximity and size of hosts, as predictors of the similarity of parasite communities in individual hosts, host populations and host species. We surveyed parasites in six species of fish collected simultaneously from six localities in the St. Lawrence River, Canada, and species in a common group of larval parasites were discriminated using DNA sequences from barcode region of cytochrome c oxidase I. Distances based on the habitat use patterns of host species were good predictors of short‐term, ecological similarity of parasite communities, such as that operating at the scale of the individual host. The genetic distance between host species was associated with almost all types of similarity at all scales, particularly qualitative and phylogenetic similarity of parasite communities at the level of populations and meta‐populations of hosts. The trophic level, diet, spatial proximity and size of hosts were poor predictors of parasite community similarity. The increased taxonomic resolution provided by molecular data increased the explanatory power of regression models, and different factors were implicated when parasite species were distinguished with DNA barcodes than when larval parasites were lumped into morphospecies, as is commonly practiced.     

The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic,Cirsium pitcheri (Asteraceae)

Narrow endemics are at risk from climate change because of their restricted habitat preferences, lower colonization ability and dispersal distances. Landscape genetics combines new tools and analyses that allow us to test how both past and present landscape features have facilitated or hindered previous range expansion and local migration patterns, and thereby identifying potential limitations to future range shifts. We have compared current and historic habitat corridors in Cirsium pitcheri, an endemic of the linear dune ecosystem of the Great Lakes, to determine the relative contributions of contemporary migration and post-glacial range expansion on genetic structure. We used seven microsatellite loci to characterize the genetic structure for 24 populations of Cirsium pitcheri, spanning the center to periphery of the range. We tested genetic distance against different measures of geographic distance and landscape permeability, based on contemporary and historic landscape features. We found moderate genetic structure (Fst=0.14), and a north–south pattern to the distribution of genetic diversity and inbreeding, with northern populations having the highest diversity and lowest levels of inbreeding. High allelic diversity, small average pairwise distances and mixed genetic clusters identified in Structure suggest that populations in the center of the range represent the point of entry to the Lake Michigan and a refugium of diversity for this species. A strong association between genetic distances and lake-level changes suggests that historic lake fluctuations best explain the broad geographic patterns, and sandy habitat best explains local patterns of movement.     

Population Genetic Diversity in the Australian ‘Seascape’: A Bioregion Approach

Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitude squared. Removing region as an explanatory variable greatly reduced model performance (delta DIC 23.4). Several bioregions were identified as possessing notably high genetic diversity. Genetic diversity increased towards the equator with a ‘hump’ in diversity across the range studied (−9.4 to −43.7°S). Our results suggest that factors correlated with both region and latitude play a role in shaping intra-specific genetic diversity, and that bioregion can be a useful management unit for intra-specific as well as species biodiversity. Our novel statistical model should prove useful for future analyses of within species genetic diversity at broad taxonomic and geographic scales.     

东灵山区阎甲物种多样性研究

本文研究了北京东灵山区阎甲科（Coleptera;Histeridae）特种多样性,野外设样地调查共获标本2224头,分属于6属17种,Saprinus niponicus、Onthophilus foueipennis、Margarinotus niponicus和M.reichardti的个体数量均大于总数的10%, 4种共占总体个数的88.22%,是本地区常见种。本研究采用4种采集方法分别统计,肉诱法捕获的种类和数量最多,共12种占总数的70.19%,杯诱法和堆草诱法都捕到8种,分别占总数的23.61%和4.81%,肉筛法采到的标本仅有2种占总数的1.39%,研究优势物种Onthophilus foueipennis的季节性变化发现,该种集中分布在小龙门林区的阔叶混交林内,个体数量在5月和9月呈现2个季节峰值,其中9月达到全年最高峰。对小龙门林区内肉诱捕获的阎甲类群的物种多样性分析表明,阔叶林中的阎甲多样性指数和均匀度指数较高,混交林的丰富度和个体数量较高,针叶林的多样性系数和个体数量较低,混交林的均匀度指数较低,而相似性分析表明,空间距离是决定小龙门林区内森林生境类型间腐生性阎甲群落相似性程度的因素,生境类型自身对相似性没有显著影响,梨园岭退耕区阎甲的物种多样性指数和均匀度指数高于小龙门林区,但物种个体平均数量低于小龙门林区。以上结果表明,东灵山地区阎甲群落的分布受生境保护程度,干扰程度以及空间距离等因素的影响,保护并提高该地区的森林植被环境对提高阎甲物种多样性有重要意义。     

Biological diversity: Distinct distributions can lead to the maximization of Rao’s quadratic entropy

Rao’s quadratic entropy (QE) is a diversity index that includes the abundances of categories (e.g. alleles, species) and distances between them. Here we show that, once the distances between categories are fixed, QE can be maximized with a reduced number of categories and by several different distributions of relative abundances of the categories. It is shown that Rao’s coefficient of distance (DISC), based on QE, can equal zero between two maximizing distributions, even if they have no categories in common. The consequences of these findings on the relevance of QE for understanding biological diversity are evaluated in three case studies. The behaviour of QE at its maximum is shown to be strongly dependent on the distance metric. We emphasize that the study of the maximization of a diversity index can bring clarity to what exactly is measured and enhance our understanding of biological diversity.     

Bat species richness and abundance in tropical rain forest fragments and in agricultural habitats at Los Tuxtlas, Mexico

Faced with the rapid and extensive conversion of tropical rain forests to pasture lands and agricultural fields and with the need to preserve the remaining mammalian fauna, it is imperative to determine how the different species that form the mammalian community have responded to the anthropogenic alterations of their natural habitats To provide data in this direction, we sampled bats m 45 forest islands, m 20 agricultural habitats representing five types of vegetation (cocoa, coffee, mixed, citrus and allspice), in four live-fence sites and in four pasture sites at Los Tuxtlas, Veracruz, Mexico Sampling effort resulted in the capture of 2587 bats representing 35 species In forest habitats we detected 32 species We did not capture any bats at the four pasture sites, but the at the other agricultural habitats studied, we captured 38% of the bats and 77% of the species recorded Thirty-four percent of the species recorded were present at the live-fence habitats Isolating distance was an important variable influencing species richness in forests and in agricultural habitats Only 10% of the species recorded occurred m all the habitats studied, but 77% of the species occurred m a habitat other than ram forest Recaptures of bats indicated inter habitat movements in the fragmented landscape We discuss the conservation value for the bat fauna of agricultural islands of vegetation as elements reducing isolating distances among forest fragments     

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.     

Landscape genetics of an early successional specialist in a disturbance‐prone environment

Species that specialize in disturbed habitats may have considerably different dispersal strategies than those adapted to more stable environments. However, little is known of the dispersal patterns and population structure of such species. This information is important for conservation because many postfire specialists are at risk from anthropogenic changes to natural disturbance regimes. We used microsatellite markers to assess the effect of landscape variation and recent disturbance history on dispersal by a small mammal species that occupies the early seral stage of vegetation regeneration in burnt environments. We predicted that a postfire specialist would be able to disperse over multiple habitat types (generalist) and not exhibit sex‐biased dispersal, as such strategies should enable effective colonization of spatially and temporally variable habitat. We found significant differentiation between sites that fitted an isolation‐by‐distance pattern and spatial autocorrelation of multilocus genotypes to a distance of 2–3 km. There was no consistent genetic evidence for sex‐biased dispersal. We tested the influence of different habitat‐ and fire‐specific landscape resistance scenarios on genetic distance between individuals and found a significant effect of fire. Our genetic data supported recently burned vegetation having greater conductance for gene flow than unburnt habitat, but variation in habitat quality between vegetation types and occupied patches had no effect on gene flow. Postfire specialists must evolve an effective dispersal ability to move over distances that would ensure access to early successional stage vegetation. Natural disturbance and natural heterogeneity may therefore not influence population genetic structure as negatively as expected.