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.     

Eutrophication decreases distance decay of similarity in diatom communities

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Measuring beta‐diversity from taxonomic similarity

Question: The utility of beta (β‐) diversity measures that incorporate information about the degree of taxonomic (dis)similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of β‐diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot‐to‐plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher‐level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify β‐diversity from taxonomic dissimilarities is discussed. Results: The proposed measure of taxonomic β‐diversity incorporates not only species richness, but also information about the degree of higher‐order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of β‐di‐versity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80% of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher‐order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot‐to‐plot similarity is only needed if we are interested in the residual system's variation that is related to the higher‐order taxonomic structure of a pair of species plots.     

长白山牛皮杜鹃群落物种多样性的海拔梯度变化及相似性

采用样地调查法,研究了牛皮杜鹃群落物种组成、群落结构特征、物种多样性及其沿海拔梯度的变化规律,对不同海拔牛皮杜鹃群落进行相似性分析。结果表明:(1)牛皮杜鹃群落相同海拔高度,草本层的物种多样性普遍高于灌木层的物种多样性。自海拔1926—1986m,灌木层α多样性指数先降低后升高,1986m后再次降低,到达海拔2010m处达到最低点,适应高山苔原带特殊生境条件的物种逐渐增多,多样性指数开始回升。海拔2250m,生物多样性指数的变化趋于平缓,物种组成相对较为稳定。海拔2528m以上,生物多样性再次呈降低趋势。草本层的α多样性指数中,物种多样性指数SW、丰富度指数D和均匀度指数R沿海拔梯度的变化趋势大致相同。海拔1986m处时出现最小值,海拔2350m时达最大值。牛皮杜鹃群落α多样性指数间呈P0.01水平极显著正相关性,物种丰富度指数对群落的物种多样性贡献率最大,表现为丰富度指数(D1、D2)种间机遇指数(H)生态优势度指数(SN)群落均匀度指数(R)。(2)牛皮杜鹃群落β多样性沿海拔梯度基本呈波形变化,草本层β多样性指数普遍高于灌木层β多样性指数。在牛皮杜鹃群落物种沿海拔梯度的替换速率上,草本植物高于灌木物种。Routledge指数的变化趋势不显著。海拔1986m处和海拔2250m处,草本层Cody指数出现两处极值,海拔2250m以上群落灌木层之间差异和变化较小,Whittaker多样性指数和Cody指数逐渐趋于平稳。(3)海拔梯度间生境及群落结构差异性越大,生物多样性变化越明显。海拔高度接近的群落间相似性系数较高,海拔是影响牛皮杜鹃群落差异的主要因素。     

Limiting similarity and functional diversity along environmental gradients

Recent developments in community models emphasize the importance of incorporating stochastic processes (e.g. ecological drift) in models of niche‐structured community assembly. We constructed a finite, spatially explicit, lottery model to simulate the distribution of species in a one‐dimensional landscape with an underlying gradient in environmental conditions. Our framework combines the potential for ecological drift with environmentally‐mediated competition for space in a heterogeneous environment. We examined the influence of niche breadth, dispersal distances, community size (total number of individuals) and the breadth of the environmental gradient on levels of species and functional trait diversity (i.e. differences in niche optima). Three novel results emerge from this model: (1) niche differences between adjacent species (e.g. limiting similarity) increase in smaller communities, because of the interaction of competitive effects and finite population sizes; (2) immigration from a regional species pool, stochasticity and niche‐assembly generate a bimodal distribution of species residence times (‘transient’ and ‘resident’) under a heterogeneous environment; and (3) the magnitude of environmental heterogeneity has a U‐shaped effect on diversity, because of shifts in species richness of resident vs. transient species. These predictions illustrate the potential importance of stochastic (although not necessarily neutral) processes in community assembly.     

A two-stage probabilistic approach to multiple-community similarity indices

SUMMARY: A traditional approach for assessing similarity among N (N > 2) communities is to use multiple pairwise comparisons. However, pairwise similarity indices do not completely characterize multiple-community similarity because the information shared by at least three communities is ignored. We propose a new and intuitive two-stage probabilistic approach, which leads to a general framework to simultaneously compare multiple communities based on abundance data. The approach is specifically used to extend the commonly used Morisita index and NESS (normalized expected species shared) index to the case of N communities. For comparing N communities, a profile of N- 1 indices is proposed to characterize similarity of species composition across communities. Based on sample abundance data, nearly unbiased estimators of the proposed indices and their variances are obtained. These generalized NESS and Morisita indices are applied to comparison of three size classes of plant data (seedling, saplings, and trees) within old-growth and secondary rain forest plots in Costa Rica.     

东北地区6所高校校园种子植物属级相似性分析

校园植物能反映校园植物多样性水平。为了研究东北地区高校校园种子植物属组成的相似性,本研究以沈阳农业大学等6所位于东北地区的高校中的校园种子植物为研究对象,并选取北方极为常见的两个科：菊科（Asteraceae）和蔷薇科（Rosaceae）,研究其属组成的差异性与相似性。结果表明,6所高校校园种子植物属间相似性较高。菊科属的组成在各高校间差异性显著,蔷薇科属的组成在各高校相似性高。校园植物种类的多样性与差异性与校园面积、校园所处位置相关。本研究旨在为东北乃至其他地区高校校园生物多样性的进一步研究和其他高校校园植物调查提供基础。     

Abundance-based similarity indices and their estimation when there are unseen species in samples

A wide variety of similarity indices for comparing two assemblages based on species incidence (i.e., presence/absence) data have been proposed in the literature. These indices are generally based on three simple incidence counts: the number of species shared by two assemblages and the number of species unique to each of them. We provide a new probabilistic derivation for any incidence-based index that is symmetric (i.e., the index is not affected by the identity ordering of the two assemblages) and homogeneous (i.e., the index is unchanged if all counts are multiplied by a constant). The probabilistic approach is further extended to formulate abundance-based indices. Thus any symmetric and homogeneous incidence index can be easily modified to an abundance-type version. Applying the Laplace approximation formulas, we propose estimators that adjust for the effect of unseen shared species on our abundance-based indices. Simulation results show that the adjusted estimators significantly reduce the biases of the corresponding unadjusted ones when a substantial fraction of species is missing from samples. Data on successional vegetation in six tropical forests are used for illustration. Advantages and disadvantages of some commonly applied indices are briefly discussed.     

Genetic similarity and diversity of parthenogenetic and bisexual populations of the freshwater snail Melanoides tuberculata (Gastropoda: Prosobranchia)

Genetic variability and similarity were analysed in four parthenogenetic and five bisexual populations of the snail Melanoides tuberculata found in Israel. Electrophoretic studies of six enzymatic systems revealed 28 zones of activity. The average genetic identity between populations was low—0.725. A particularly low similarity (0.628) was obtained between parthenogenetic populations, compared to the average of 0.822 observed among the bisexual ones. The percentage of fixed electrophoretic bands in parthenogens was 53.9% compared to 12.5% observed in bisexual populations. The diversity of parthenogenetic populations was found to be lower than those of bisexual. The amount of electrophoretic diversity between populations of the parthenogenetic group was found to be 80%, whereas within the bisexual group the diversity between populations was only 42%.     

Environment, dispersal and patterns of species similarity

Aim The aim of this paper is to evaluate the combined effects of geographical distance and environmental distance on patterns of species similarity (similarity in species composition between sites), and to identify factors affecting the rate of decay in species similarity with each type of distance. Location Israel. Methods Data on species composition of land snails and land birds were recorded in 27 sites of 1 × 1 km scattered across a rainfall gradient in Israel. Matrices of similarity in species composition between all pairs of sites were computed and analysed with respect to corresponding matrices of geographical distance and rainfall distance (defined as the difference in mean annual rainfall between sites, and used as a measure of environmental distance). Mantel tests were applied to determine the correlation between species similarity and each type of distance. Factors affecting the decay in species similarity were investigated by comparing different subsets of the data using randomization tests. Results Both rainfall distance and geographical distance had negative effects on species similarity. The effect of rainfall distance was statistically significant even after controlling for differences in geographical distance, and vice versa. The per‐unit effect of rainfall distance on species similarity decreased with increasing geographical distance, indicating that the two types of distances interacted in determining the similarity in species composition. Snails showed a higher rate of decay in species similarity with geographical distance than birds, and large snails showed a higher rate of decay than small snails, which are better passive dispersers. The per‐unit effects of both rainfall distance and geographical distance on species similarity were higher in the desert region than in the Mediterranean region. Analyses focusing on a grain size of 10 × 10 m showed a lower similarity in species composition and a lower rate of decay in species similarity with rainfall distance than analyses carried out at a grain size of 1 × 1 km. Main conclusions Patterns of similarity in species composition are influenced by the combined effects of environmental variation, the position of the area along environmental gradients, the dispersal properties of the component species, and the scale (both spatial extent and grain size) at which the patterns are examined.     

Both facilitation and limiting similarity shape the species coexistence in dry alkali grasslands

Facilitation is an important driver of community assembly, and often overwhelms the effect of competition in stressed habitats. Thus, net effect of biotic interactions is often positive in stressed grasslands, where dominant species and litter can protect the subordinate species. Besides facilitation, niche partitioning can also support species coexistence leading to limiting similarity between subordinate species. Our aim was to provide a detailed analysis of fine-scale biotic interactions in stressed alkali grasslands. We supposed, that there are positive relationships between the main biomass fractions and species richness. We expected the expansion of trait ranges and the increase of trait dissimilarity with increasing biomass scores (total litter, green biomass of dominant species) and species richness. We studied the relationships between main biomass fractions, species richness, functional diversity and functional trait indices (ranges, weighted means and Rao indices). We used fine-scale biomass sampling in nine stands of dry alkali grasslands dominated by Festuca pseudovina. The detected relationships were always positive between the main biomass fractions (green biomass of dominant species, total litter and green biomass of subordinate species) and species richness. We found that the green biomass of dominant species and total litter increased ranges and dissimilarity of functional traits. Our results suggest that in dry alkali grasslands facilitation is crucial in shaping vegetation composition. The green biomass of dominant species and total litter increased the biomass production of subordinate species leading to overyielding. We found that mechanisms of facilitation and limiting similarity were jointly shaping the species coexistence in stressed grasslands, such as alkali grasslands.     

Forb diversity and community similarity of kopjes in the Serengeti National Park, Tanzania

The forb communities of kopjes (rock outcrops) in the Simba, Maasai and Loliondo areas of the Serengeti National Park were examined to determine differences in species composition from surrounding grassland communities, and among sites within kopje and grassland communities. Species diversity measures and multivariate ordination techniques were used to examine the community similarity and species turnover between sites. All measures of forb species diversity were higher on the kopje sites with the exception of one grassland site, and the community composition significantly differed between these two habitat types, with more species and families exclusive to the kopje habitat. Species turnover was very high in grassland habitats, with two of the three areas (Simba and Loliondo) exhibiting a complete change in species composition. Kopjes, on the other hand, had remarkably similar forb communities, suggesting that the populations of the species present on these rock outcrops form patch structures. The distinct flora and higher diversity of kopje forbs raise interesting questions regarding distribution, dispersal and patch dynamics.     

Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies

Clustering approaches are pivotal to handle the many sequence variants obtained in DNA metabarcoding data sets, and therefore they have become a key step of metabarcoding analysis pipelines. Clustering often relies on a sequence similarity threshold to gather sequences into molecular operational taxonomic units (MOTUs), each of which ideally represents a homogeneous taxonomic entity (e.g., a species or a genus). However, the choice of the clustering threshold is rarely justified, and its impact on MOTU over-splitting or over-merging even less tested. Here, we evaluated clustering threshold values for several metabarcoding markers under different criteria: limitation of MOTU over-merging, limitation of MOTU over-splitting, and trade-off between over-merging and over-splitting. We extracted sequences from a public database for nine markers, ranging from generalist markers targeting Bacteria or Eukaryota, to more specific markers targeting a class or a subclass (e.g., Insecta, Oligochaeta). Based on the distributions of pairwise sequence similarities within species and within genera, and on the rates of over-splitting and over-merging across different clustering thresholds, we were able to propose threshold values minimizing the risk of over-splitting, that of over-merging, or offering a trade-off between the two risks. For generalist markers, high similarity thresholds (0.96–0.99) are generally appropriate, while more specific markers require lower values (0.85–0.96). These results do not support the use of a fixed clustering threshold. Instead, we advocate careful examination of the most appropriate threshold based on the research objectives, the potential costs of over-splitting and over-merging, and the features of the studied markers.     

Upward shift of alpine plants increases floristic similarity of mountain summits

Question: Does the upward shift of species and accompanied increase in species richness, induced by climate change, lead to homogenization of Alpine summit vegetation? Location: Bernina region of the Swiss Alps. Methods: Based on a data set from previous literature we expand the analysis from species richness to beta‐diversity and spatial heterogeneity. Species compositions of mountain summits are compared using a two‐component heterogeneity concept including the mean and the variance of Sørensen similarities calculated between the summits. Non‐metric multidimensional scaling is applied to explore developments of single summits in detail. Results: Both heterogeneity components (mean dissimilarity and variance) decrease over time, indicating a trend towards more homogeneous vegetation among Alpine summits. However, the development on single summits is not strictly unidirectional. Conclusions: The upward shift of plant species leads to homogenization of alpine summit regions. Thus, increasing alpha‐diversity is accompanied by decreasing beta‐diversity. Beta‐diversity demands higher recognition by scientists as well as nature conservationists as it detects changes which cannot be described using species richness alone.     

Processes at multiple scales affect richness and similarity of non‐native plant species in mountains around the world

Aim To investigate how species richness and similarity of non‐native plants varies along gradients of elevation and human disturbance. Location Eight mountain regions on four continents and two oceanic islands. Methods We compared the distribution of non‐native plant species along roads in eight mountainous regions. Within each region, abundance of plant species was recorded at 41–84 sites along elevational gradients using 100‐m² plots located 0, 25 and 75 m from roadsides. We used mixed‐effects models to examine how local variation in species richness and similarity were affected by processes at three scales: among regions (global), along elevational gradients (regional) and with distance from the road (local). We used model selection and information criteria to choose best‐fit models of species richness along elevational gradients. We performed a hierarchical clustering of similarity to investigate human‐related factors and environmental filtering as potential drivers at the global scale. Results Species richness and similarity of non‐native plant species along elevational gradients were strongly influenced by factors operating at scales ranging from 100 m to 1000s of km. Non‐native species richness was highest in the New World regions, reflecting the effects of colonization from Europe. Similarity among regions was low and due mainly to certain Eurasian species, mostly native to temperate Europe, occurring in all New World regions. Elevation and distance from the road explained little of the variation in similarity. The elevational distribution of non‐native species richness varied, but was always greatest in the lower third of the range. In all regions, non‐native species richness declined away from roadsides. In three regions, this decline was steeper at higher elevations, and there was an interaction between distance and elevation. Main conclusions Because non‐native plant species are affected by processes operating at global, regional and local scales, a multi‐scale perspective is needed to understand their patterns of distribution. The processes involved include global dispersal, filtering along elevational gradients and differential establishment with distance from roadsides.     

Microturbellarian species richness and community similarity among temporary pools:relationships with habitat properties

Temporary water bodies exhibit a high level of biodiversity,much of which is unique tothese habitats.Studies of microturbellarian community ecology in temporary pools are scarce,eventhough turbellarians are potentially important in organizing community structure.Moreover,therehas been virtually no documentation of microturbellarians from Israel.We examined the re-lationships between several pool properties (surface area,water depth,permanence and sedimentdepth)and microturbellarian species richness among 52 temporary pools at a single site.A total of17 taxa of microturbellarians were identi ed,of which 14 were determined to genus or species level.Richness was positively related with surface area and with maximal sediment depth,togetherexplaining 54%of the variance.In more intensive sampling of a subset of 18 pools,surface areawas the only signi cant predictor,explaining 76%of the variance.Community dissimilarity waspositively related with di erences in both surface area and permanence.We identi ed three cate-gories of pool size,each characterized by di erent turbellarian species:large pools were dominatedbyCastrada viridis andGieysztoria cuspidata ,intermediate pools byDochmiotrema limicola ,and many of the small pools byGieysztoria ornata andOlisthanella obtusa .Large pools contributed themost to regional diversity,with 11 of the 17 observed taxa.However,some species were unique tosmall pools.Thus,in order to maintain maximal regional diversity of temporary water turbellar-ians,it is important to conserve habitats containing pools of various sizes.     

The impact of urbanization on taxonomic and functional similarity among bird communities

Aim To assess spatial relationships between avian community similarity and level of urbanization. We tested the following hypotheses for taxonomic similarity: Hypothesis A – the decline in taxonomic similarity with distance is stronger for the least urbanized locations compared to the most urbanized locations; Hypothesis B – the converse of Hypothesis A; and Hypothesis C – the decline in taxonomic similarity with distance is stronger for the most and least urbanized locations compared to locations with intermediate levels of urbanization. We also determined if increasing urbanization led to increased functional similarity within bird communities. Location South‐eastern Australia. Methods Bird species occurrence and density were sampled across 18 towns and 72 neighbourhoods occupying a spatial gradient of up to 882 km. We calculated pairwise values in taxonomic similarity among each town and neighbourhood using the Sørenson coefficient and a similarity measure that accounts for differences in species richness among locations. These values were plotted against pairwise distances among towns and neighbourhoods using linear regression to measure similarity–distance relationships. Neighbourhoods were categorized into four levels of urban development based on dwelling density, urban intensity, vegetation cover, or the density of native, nectar‐rich plants. Variation in bird species density across neighbourhoods and frequency of occurrence across broad habitat types (habitat specialization) was used to assess functional similarity of bird communities in each neighbourhood. Results Among the 18 towns, the decline in taxonomic similarity with distance was weak and significantly less than among regional bird communities that occurred within a 1° grid square around each town. Among the 72 neighbourhoods, similarity–distance relationships differed substantially depending on the level of urban development. Generally, the strongest decline in similarity with distance was for neighbourhoods with the highest and lowest dwelling density, urban intensity and vegetation cover, supporting Hypothesis C. The functional similarity of bird communities increased significantly with dwelling density, and decreased significantly with an increasing density of nectar plants. Main conclusions At the town level, urbanization appears to homogenize regional bird communities. Among neighbourhoods, similarity–distance relationships are substantially influenced by the level of urban development, and increasing urbanization leads to greater functional similarity within bird communities.