A multiple-site similarity measure independent of richness

The Diserud–Ødegaard multiple-site similarity index makes use of data on species shared by two or more sites, but produces equal similarity values in two different circumstances: species loss and true species turnover. We developed a new multiple-site similarity measure, which is independent of richness and performs better than the Diserud–Ødegaard index under conditions of equal richness between sites, because it discriminates between situations in which shared species are distributed evenly among sites or concentrated in few pairs of sites. We conducted several simulations to assess the relative performance of both the indices. The use of the new measure is recommended, enabling the simultaneous analysis of turnover and richness gradients based on two independent measures.     

A multiple-site dissimilarity measure for species presence/absence data and its relationship with nestedness and turnover

Multiple-site dissimilarity may be caused by two opposite processes of meta-community organization, such as species nestedness and turnover. Therefore, discriminating among these contributions is necessary for linking multiple-site dissimilarity to ecosystem functioning. This paper introduces a measure of multiple-site dissimilarity or beta diversity for presence/absence data that is based on information on species absences from the species × sites matrix. It is also shown that the newly proposed dissimilarity index can be additively partitioned into species nestedness and turnover.     

Partitioning the turnover and nestedness components of beta diversity

Aim  Beta diversity (variation of the species composition of assemblages) may reflect two different phenomena, spatial species turnover and nestedness of assemblages, which result from two antithetic processes, namely species replacement and species loss, respectively. The aim of this paper is to provide a unified framework for the assessment of beta diversity, disentangling the contribution of spatial turnover and nestedness to beta-diversity patterns.
Innovation  I derive an additive partitioning of beta diversity that provides the two separate components of spatial turnover and nestedness underlying the total amount of beta diversity. I propose two families of measures of beta diversity for pairwise and multiple-site situations. Each family comprises one measure accounting for all aspects of beta diversity, which is additively decomposed into two measures accounting for the pure spatial turnover and nestedness components, respectively. Finally, I provide a case study using European longhorn beetles to exemplify the relevance of disentangling spatial turnover and nestedness patterns.
Main conclusion  Assigning the different beta-diversity patterns to their respective biological phenomena is essential for analysing the causality of the processes underlying biodiversity. Thus, the differentiation of the spatial turnover and nestedness components of beta diversity is crucial for our understanding of central biogeographic, ecological and conservation issues.     

Evidence for an independent radiation of endosymbiotic litostome ciliates within Australian marsupial herbivores

Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by tree-like bifurcating evolutionary models. These observations might result from processes of species diversification and/or processes of sequence evolution that are not tree-like. In these cases, bifurcating tree representations provide poor visualization of phylogenetic signals in sequence data. In this paper, we use median networks to study DNA sequence substitution patterns in plant nuclear and chloroplast markers. We describe how to prune median networks to obtain so called pruned median networks. These simpler networks may help to provide a useful framework for investigating the phylogenetic complexity of recently diverged taxa with hybrid origins.     

Global patterns in peatmoss biodiversity

DNA sequence data from the nuclear ribosomal internal transcribed spacers (ITS) and the trnL-trnF chloroplast DNA regions were used to quantify geographical partitioning of global biodiversity in peatmosses (Sphagnum), and to compare patterns of molecular diversity with patterns of species richness. Molecular diversity was estimated for boreal, tropical, Neotropical, nonboreal (tropical plus Southern Hemisphere), Old World and New World partitions, based on a total of 436 accessions. Diversity was partitioned among geographical regions in terms of combined nuclear and chloroplast sequence data and separately for the ITS and trnL-trnF data sets. Levels of variation were estimated using phylogenetic diversity (PD), which incorporates branch lengths from a phylogenetic tree, and the number of polymorphic nucleotide sites. Estimates of species richness suggest that peatmoss diversity is higher in New World than Old World regions, and that the Neotropics constitute a "hotspot" of diversity. Molecular estimates, in contrast, indicate that peatmoss biodiversity is almost evenly divided between New and Old World regions, and that the Neotropics account for only 20-35% of global peatmoss diversity. In general, levels of tropical and boreal peatmoss molecular diversity were comparable. Two species, S. sericeum from the Old World tropics and S. lapazense from Bolivia, are remarkably divergent in nucleotide sequences from all other Sphagna and together account for almost 20% of all peatmoss diversity, although they are represented by only three of the 436 accessions (0.7%). These species clearly demonstrate the nonequivalence of species biodiversity value.     

A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes

Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50‐km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free‐living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.     

Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

‘Key biodiversity areas'' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4, 326–337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site''s share of a threatened species'' population; expand these to include the proportion of the species'' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species'' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.     

Fate of epiphytes on phorophytes with different architectural characteristics along the perturbation gradient of Sabal mexicana forests in Veracruz,Mexico

Question: Vascular epiphytes and hemiepiphytes (E/HE) in neotropical forests account for a large fraction of plant richness, but little is known of how the interplay between phorophyte architectural characteristics and habitat perturbation affect communities of E/HE. Location: Sabal mexicana forests in a coastal area of Veracruz, Mexico. Methods: We compared communities of E/HE on phorophytes with different architectural characteristics – the palm S. mexicana and non‐palm phorophytes – in three environments: conserved sites, perturbed sites and small regenerated forest fragments. We combined traditional (abundance, species richness, similarity and complementarity indices) and more recent (phylogenetic diversity) metrics to describe the communities of E/HE. Results: Overall, we recorded 924 E/HE individuals (nine families, 16 genera and 21 species). The abundance and species richness of E/HE was higher on palms than on non‐palm phorophytes. Abundance‐based complementarities between phorophytes and sites were high. We detected clear changes in community structure of E/HE with habitat perturbation, but there were no effects on the phylogenetic diversity of the E/HE community. Palm phorophytes hosted a more phylogenetically diverse community of E/HE than did non‐palm phorophytes. Conclusions: Palm phorophytes are key elements supporting the conservation of resilient communities of E/HE in S. mexicana forest. Habitat fragmentation has a strong effect on the structure of the E/HE community in S. mexicana forests. Ferns are the group of epiphytes most severely affected by habitat perturbation, but we detected no significant effect on the phylogenetic diversity of the community.     

Mulga bird communities. I. Species composition and predictability across Australia

Abstract Data are presented from bird censuses at 20 mulga (Acacia aneura) sites across Australia. Null (binomial) models show that community composition is far more consistent among censuses than is expected by a random drawing from all candidate species. By denning and using the designations ‘core species’, ‘peripheral species’, and ‘casual species’, it was shown that 32% of the total 81 bird species censused constituted core species and core niches that account for nearly 75% of the bird density in mulga bird communities countrywide. A minor proportion of the variation in the mulga censuses was attributable to geographic variation in vegetation structure, related to the β-component of diversity. Some mulga niches have regional replacements that contribute to a species turnover among sites and to the γ-diversity of the species set; other species of sporadic occurrence are attributable to the geographic position of the mulga site in terms of adjacent habitats (mostly eucalypt woodland and mixed acacia scrub), a ‘spillover’ effect. Regional variations in the composition of some specific guilds, namely ‘crows’, ‘wrens’, ‘butcherbirds’, foliage insectivores, ground-foraging insectivores, perch-and-pounce foragers and mid-sized, ground-foraging omnivores, are analysed in some detail to illustrate factors that contribute to a large species total in mulga, despite the predominance of core species.     

Plant species coexistence in cliff habitats

An ecological analysis of the ledge and crevice vegetation of cliffs in north-east Ireland was carried out using a sampling programme based on multivariate land classification. The composition of the vegetation was shown to be determined primarily by distance from the sea, elevation and rock type. The chemical composition and physical structure of the cliffs, together with environmental gradients associated with aspect, elevation and nearness to the sea provide a wide range of habitats in which plants coexist. Certain types of cliff vegetation contained associations of species with a contrasting ecology, such as arctic–montane, maritime, woodland, calcicole and calcifuge plants. The positions of these species in ordination space were found to be unique but overlapping. A model is described to account for these observations. It proposes that species dominance in cliff habitats is prevented by factors such as physical disturbance and that plants are able to coexist in cliff habitats which meet their common environmental tolerances and preferences. The model predicts that cliff habitats with the greatest diversity of species are likely to be subject to less extremes of environmental variability. These habitats include inland sites with nutrient enrichment by sea spray, north-facing sites, seepage sites, base-rich sites, low elevation sites and sites with a heterogeneous physical structure.     

Spatial gradients in species diversity of microscopic animals: the case of bdelloid rotifers at high altitude

Aim Organisms smaller than 2 mm appear not to follow the spatial patterns in richness and diversity commonly observed in macroscopic organisms. We describe spatial patterns in species diversity in a group of microscopic organisms, bdelloid rotifers, living in moss and lichen patches, in order to test the hypotheses of no relationship between species richness and composition and spatial gradients, suggested by previously published patterns in microscopic organisms. Location Moss and lichen patches as habitats for bdelloids, on high‐elevation peaks at altitudes between 2984 and 4527 m a.s.l. across the Italian, French and Swiss Alps, with distances among sample sites ranging from 1 m to 420 km, in comparison with lower‐elevation samples at altitudes from 850 to 1810 m a.s.l. Methods We sampled species assemblages of bdelloid rotifers living in isolated moss and lichen patches in 47 sites. We described the observed α, β and γ diversities; the heterogeneity of species assemblages; and the estimated number of species (incidence‐based coverage estimator). Patterns in species distribution were analysed at three different levels: (1) habitat, comparing species richness on moss and lichen substrates, testing differences in α diversity and heterogeneity (anova ), species composition (analysis of similarities test), and γ diversity (rarefaction curves); (2) altitude, comparing the observed richness with previously published data from locations well below 2000 m; and (3) distances between sites, correlating the matrix of Jaccard dissimilarities and the matrix of geographical distances with a Mantel test. Results Both species richness and species composition of bdelloid rotifers differed significantly between mosses and lichens at high elevations, but no difference was found in the heterogeneity of species assemblages. Alpha diversity was significantly lower at high‐elevation than at low‐elevation sites, but the estimated number of species was not reduced when compared with sites at low elevations. Geographical distance between sites had no effect on species composition in either mosses or lichens. The distribution of species was highly heterogeneous, with a low similarity among assemblages. Main conclusions As expected, bdelloids appear to occupy habitats selectively. The altitudinal gradient in species richness for bdelloid rotifers is limited to a decrease in α diversity only; such a decrease is not caused by a lower number of species (low γ diversity) being able to tolerate harsh conditions, and high‐altitude species are not a subset of species living at lower elevations. The observed values of α, β and γ diversity at high altitudes in the Alps are compatible with the scenario of a very low number of available propagules because of the low density of patches of favourable habitat. Our results suggest that the geographical distribution of animals, and therefore biodiversity patterns, may be strongly influenced by animal size, as small organisms such as bdelloids appear to show spatial patterns that differ from those known in larger animals. Differences in body size should be taken into account carefully in future studies of biodiversity patterns.     

A direct and efficient PAGE-mediated overlap extension PCR method for gene multiple-site mutagenesis

A simple, two-step efficient method to perform multiple-site mutagenesis of a gene from bacterial genome was developed. The method was named polyacrylamide gel electrophoresis (PAGE)-mediated overlap extension polymerase chain reaction (PCR) (POEP). The first step involves synthesis of individual fragments containing mutant sites with 15- to 25-bp overlap between two adjacent fragments. Mutations were introduced into the overlapping oligonucleotide primers which ensured the particular primer-template annealing. PAGE was used to remove contaminating parental templates, mispriming fragments, and leftover primers. The second step involves synthesis of the mutant full-length fragment. All purified PCR products from the first step were combined and used as the template for a second PCR using high-fidelity DNA polymerase, with the two outermost flanking oligonucleotides as primers. Using the POEP method, we have successfully introduced eight EcoRI sites into the Escherichia coli β-galactosidase (Lac Z) gene. The overall rate of obtaining the multiple mutant sites was 100%. The POEP method is simple, involving only two steps, and reliable for multiple-site mutagenesis and is promising to be widely used in gene modification.     

Effectiveness of multiple-site EMG biofeedback in the reduction of arousal

During the training phase, 36 subjects received (a) EMG biofeedback from multiple muscle sites, (b) EMG biofeedback from the frontal site, or (c) no biofeedback. Results indicated that neither biofeedback procedure reduced self-reports of anxiety, but that multiple-site biofeedback was effective in reducing several indices of autonomic arousal (pulse rate, finger pulse volume, and skin temperature) while frontal biofeedback was not. During the generalization/stress phase, all subjects were threatened with and received electric shocks and were told to apply the relaxation techniques they learned during the training phase even though no additional biofeedback would be provided. Results indicated that multiple-site biofeedback was effective in reducing self-reports of anxiety and autonomic arousal but that frontal biofeedback was not. These results confirm previous data indicating that frontal biofeedback is not an effective procedure for controlling stress, but suggest that EMG biofeedback can be effective in reducing self-reported anxiety and autonomic arousal if a multiple muscle-site feedback procedure is employed.     

Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilisation

Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major forms of environmental change – fertilisation and herbivore loss – are affected by species pool size and spatial compositional heterogeneity. Fertilisation led to higher rates of local extinction, whereas turnover in herbivore exclusion plots was driven by species replacement. Overall, sites with more spatially heterogeneous composition showed significantly higher rates of annual turnover, independent of species pool size and treatment. Taking into account spatial biodiversity aspects will therefore improve our understanding of consequences of global and anthropogenic change on community dynamics.     

北京东灵山辽东栎林植物物种多样性的多尺度分析

多尺度分析物种多样性格局能够为有效保护生物多样性提供重要信息.利用物种多样性的加法分配法则分析了样方-坡位-坡面等级尺度系统辽东栎林植物物种多样性(gamma多样性)的alpha多样性和beta多样性在各尺度上的分配关系.结果表明以物种丰富度为指标的区域物种多样性的最大贡献来自坡面尺度,表明坡面尺度是维持辽东栎林物种多样性的有效尺度;而对Simpson多样性和Shannon多样性的最大贡献则来自样方内,这决定于群落物种优势度和稀有度格局;各尺度间beta多样性组分随尺度的增大而增大可能是环境异质性和扩散作用的综合结果.各尺度间Shannon多样性对总体多样性的贡献大于Simpson多样性的贡献是偶见种在各尺度间分配的结果.物种多样性分配的加法法则为物种多样性格局的多尺度分析提供了理论框架,是检验物种多样性格局形成机制的有效方法.     

An elementary,structural analysis of river phytoplankton

Summary A structural analysis of river phytoplankton has been carried out based upon published studies on 67 rivers. When available on a yearly basis to account for seasonal variability, five structural features have been chosen: species composition, species richness, species dominance, diversity and biomass (total and per taxonomic groups). Despite the high number of reported studies, most of them cover only some of the aforementioned features. As a result of the low amount of studies, tropical rivers are underepresented. No size distribution studies have been carried out on river phytoplankton. The average species richness amounts to 126, being higher in temperate rivers. Roughly one half of each flora is comprised of sporadic species. No statistically significant relationship between species richness and latitude has been found despite the fact that tropical rivers appear to house fewer species than temperate rivers. Also, one half of the support in the floras are either benthic or tychoplanktonic. Diatoms comprise the majority of species numbers in the whole data set but are substituted by desmids in tropical rivers and by green algae when benthic species are not taken into account. There appears to be lower biomass in river phytoplankton than in lakes. Diatoms are also the major taxonomic group comprising total biomass in rivers but they share clearly a lower fraction in tropical rivers. On an average basis, diatoms appear to be more dominant in rivers than in lakes. The time course of diatom dominance occurs close to the summer solstice in tropical rivers whereas is much more lagged in temperate sites. The diversity of river phytoplankton is highly scattered (0.40–4.40 bits ind^–1).     

Why is the Cape Peninsula so rich in plant species? An analysis of the independent diversity components

With 2285 species of higher plants crammed into 471 km², the flora of South Africa's Cape Peninsula is exceptionally rich. Similar sized areas in other Mediterranean-climate region biodiversity hot-spots support between 4.7 and 2.7 times fewer species. The high plant species richness of the Cape Peninsula is due to the exceptionally high turnover between moderately species-rich sites in different habitats (beta diversity) and between sites in similar habitats along geographical gradients (gamma diversity). Highest beta diversity, encompassing almost complete turnover, was recorded along soil fertility gradients. Although similar patterns for these independent components explain the richness of other regions in the Cape Floristic Region, it is the very long and steep habitat gradients of the Cape Peninsula that makes this region exceptionally rich. Furthermore, the flora is characterized by a high degree of rarity, a phenomenon that undoubtedly influences the turnover. Future research should focus on developing a biological and ecological understanding of the different forms of rarity and integrating this into management plans for the maintenance of biodiversity.     

The diversity field of New World leaf‐nosed bats (Phyllostomidae)

Aim To analyse how the patterns of species richness for the whole family Phyllostomidae determine the structure of diversity fields (sets of species‐richness values) within the ranges of individual bat species. Location The range of the family Phyllostomidae in North and South America. Methods We generated a database of the occurrence of 143 phyllostomid bat species in 6794 quadrats, analysing the species‐richness frequency distribution for all sites, and for subsets of sites defined by the geographic ranges of species. Range–diversity plots, depicting simultaneously the size and the mean species richness of ranges, were built to explore the patterns of co‐occurrence in widespread and restricted species. We compared the empirical patterns against two null models: (1) with scattered (non‐cohesive) ranges, and (2) with cohesive ranges modelled with the spreading‐dye algorithm. Diversity fields were analysed with richness maps for individual species and with comparisons of species‐richness frequency distributions. Results Overall richness frequency distribution showed a multimodal pattern, whereas simulated distributions showed lower values of variance, and were unimodal (for model 1) and bimodal (for model 2). Range–diversity plots for the empirical data and for the cohesive‐ranges simulation showed a strong tendency of species to co‐occur in high‐diversity sites. The scattered‐ranges simulation showed no such tendency. Diversity fields varied according to idiosyncratic features of species generating particular geographic patterns and richness frequency distributions. Main conclusions Phyllostomid bats show a higher level of co‐occurrence than expected from null models. That tendency in turn implies a higher variance in species richness among sites, generating a wider species‐richness frequency distribution. The diversity field of individual species results from the size, shape and location of ranges, but also depends on the general pattern of richness for the whole family.     

Disentangling biotic interactions,environmental filters,and dispersal limitation as drivers of species co‐occurrence

A key focus in ecology is to search for community assembly rules. Here we compare two community modelling frameworks that integrate a combination of environmental and spatial data to identify positive and negative species associations from presence–absence matrices, and incorporate an additional comparison using joint species distribution models (JSDM). The frameworks use a dichotomous logic tree that distinguishes dispersal limitation, environmental requirements, and interspecific interactions as causes of segregated or aggregated species pairs. The first framework is based on a classical null model analysis complemented by tests of spatial arrangement and environmental characteristics of the sites occupied by the members of each species pair (Classic framework). The second framework, (SDM framework) implemented here for the first time, builds on the application of environmentally‐constrained null models (or JSDMs) to partial out the influence of the environment, and includes an analysis of the geographical configuration of species ranges to account for dispersal effects. We applied these approaches to examine plot‐level species co‐occurrence in plant communities sampled along a wide elevation gradient in the Swiss Alps. According to the frameworks, the majority of species pairs were randomly associated, and most of the non‐random positive and negative species associations could be attributed to environmental filtering and/or dispersal limitation. These patterns were partly detected also with JSDM. Biotic interactions were detected more frequently in the SDM framework, and by JSDM, than in the Classic framework. All approaches detected species aggregation more often than segregation, perhaps reflecting the important role of facilitation in stressful high‐elevation environments. Differences between the frameworks may reflect the explicit incorporation of elevational segregation in the SDM framework and the sensitivity of JSDM to the environmental data. Nevertheless, all methods have the potential to reveal general patterns of species co‐occurrence for different taxa, spatial scales, and environmental conditions.