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.     

青藏高原高寒草甸物种多样性的海拔梯度分布格局及对地上生物量的影响

植物物种多样性在海拔梯度上的变化规律以及物种多样性与生产力的关系是生态学研究的热点, 至今还没有得出一般性规律。本文以青海省海南藏族自治州贵德县的拉脊山(36°21′ N, 101°27′ E, 海拔3,389-3,876 m)和果洛藏族自治州的玛沁县军牧场山体(34°22′ N, 100°30′ E, 海拔4,121-4,268 m)为研究对象, 对植物高度、盖度、地上生物量和物种多样性随海拔高度的变化进行调查和统计分析, 以探讨青藏高原高寒草甸的物种多样性和地上生物量在海拔梯度上的变化规律及两者的关系。结果表明: (1)两条山体样带上地上生物量与物种多样性随海拔的变化规律一致: 随着海拔的升高, 地上生物量线性降低; Shannon-Wiener指数、Simpson指数和物种丰富度都呈单峰曲线, 在中间海拔最大, 而Pielou指数随海拔的升高线性增加。结合目前针对青藏高原高寒草甸的研究数据, 发现物种丰富度随海拔高度的变化均呈单峰曲线, 说明随着海拔的升高物种多样性先升高后降低可能是青藏高原物种多样性分布的普遍规律。(2)地上生物量与物种多样性的关系在两条山体样带上表现一致: 地上生物量随Shannon- Wiener指数、Simpson指数和Pielou指数的升高而线性降低, 但与物种丰富度不相关。综合两条山体样带所有样方数据, 发现地上生物量与Shannon-Wiener指数、Simpson指数不相关, 而随物种丰富度的升高线性增加。结合目前在青藏高原的相关研究数据, 发现地上生物量与物种丰富度呈S型曲线(logistic model)。     

Optimising Drug Solubilisation in Amorphous Polymer Dispersions: Rational Selection of Hot-melt Extrusion Processing Parameters

The aim of this article was to construct a T–ϕ phase diagram for a model drug (FD) and amorphous polymer (Eudragit® EPO) and to use this information to understand the impact of how temperature–composition coordinates influenced the final properties of the extrudate. Defining process boundaries and understanding drug solubility in polymeric carriers is of utmost importance and will help in the successful manufacture of new delivery platforms for BCS class II drugs. Physically mixed felodipine (FD)–Eudragit^® EPO (EPO) binary mixtures with pre-determined weight fractions were analysed using DSC to measure the endset of melting and glass transition temperature. Extrudates of 10 wt% FD–EPO were processed using temperatures (110°C, 126°C, 140°C and 150°C) selected from the temperature–composition (T–ϕ) phase diagrams and processing screw speed of 20, 100 and 200rpm. Extrudates were characterised using powder X-ray diffraction (PXRD), optical, polarised light and Raman microscopy. To ensure formation of a binary amorphous drug dispersion (ADD) at a specific composition, HME processing temperatures should at least be equal to, or exceed, the corresponding temperature value on the liquid–solid curve in a F–H T–ϕ phase diagram. If extruded between the spinodal and liquid–solid curve, the lack of thermodynamic forces to attain complete drug amorphisation may be compensated for through the use of an increased screw speed. Constructing F–H T–ϕ phase diagrams are valuable not only in the understanding drug–polymer miscibility behaviour but also in rationalising the selection of important processing parameters for HME to ensure miscibility of drug and polymer.KEY WORDS: DSC, Flory–Huggins theory, hot-melt extrusion, thermal processing     

An illustrated key to the cuckoo wasps (Hymenoptera,Chrysididae) of the Nordic and Baltic countries,with description of a new species

The Chrysididae are a group of cleptoparasitic and parasitoid aculeate wasps with a large number of rare and endangered species. The taxonomy of this group has long been confusing due to the similarity of species and extensive intraspecific variation. We present for the first time a comprehensive dichotomous key for all 74 species found in the Nordic and Baltic countries. In addition to diagnostic characters, information on the distribution and biology of each species is also presented. A new species, Chrysis borealis Paukkunen, Ødegaard & Soon, sp. n. is described on the basis of specimens collected from Fennoscandia. Chrysis gracillima Förster, 1853 is recorded as new to the Nordic and Baltic countries.     

Are stacked species distribution models accurate at predicting multiple levels of diversity along a rainfall gradient?

We use observed patterns of species richness and composition of ant communities along a 1000 mm rainfall gradient in northern Australian savanna to assess the accuracy of species richness and turnover predictions derived from stacked species distribution models (S‐SDMs) and constrained by macroecological models (MEMs). We systematically sampled ants at 15 sites at 50 km intervals along the rainfall gradient in 2012 and 2013. Using the observed data, we created MEMs of species richness, composition and turnover. We built distribution models for 135 of the observed species using data from museum collections and online databases. We compared two approaches of stacking SDMs and three modelling algorithms to identify the most accurate way of predicting richness and composition. We then applied the same beta diversity metrics to compare the observed versus predicted patterns. Stacked SDMs consistently over‐predicted local species richness, and there was a mismatch between the observed pattern of richness estimated from the MEM, and the pattern predicted by S‐SDMs. The most accurate richness and turnover predictions occurred when the stacked models were rank‐ordered by their habitat suitability and constrained by the observed MEM richness predictions. In contrast with species richness, the predictions obtained by the MEM of community similarity, composition and turnover matched those predicted by the S‐SDMs. S‐SDMs regulated by MEMs may therefore be a useful tool in predicting compositional patterns despite being unreliable estimators of species richness. Our results highlight that the choice of species distribution model, the stacking method used, and underlying macroecological patterns all influence the accuracy of community assembly predictions derived from S‐SDMS.     

Patterns and drivers of Nothobranchius killifish diversity in lowland Tanzania

Temporary pools are seasonal wetland habitats with specifically adapted biota, including annual Nothobranchius killifishes that survive habitat desiccation as diapausing eggs encased in dry sediment. To understand the patterns in the structure of Nothobranchius assemblages and their potential in wetland conservation, we compared biodiversity components (alpha, beta, and gamma) between regions and estimated the role and sources of nestedness and turnover on their diversity. We sampled Nothobranchius assemblages from 127 pools across seven local regions in lowland Eastern Tanzania over 2 years, using dip net and seine nets. We estimated species composition and richness for each pool, and beta and gamma diversity for each region. We decomposed beta diversity into nestedness and turnover components. We tested nestedness in three main regions (Ruvu, Rufiji, and Mbezi) using the number of decreasing fills metric and compared the roles of pool area, isolation, and altitude on nestedness. A total of 15 species formed assemblages containing 1–6 species. Most Nothobranchius species were endemic to one or two adjacent regions. Regional diversity was highest in the Ruvu, Rufiji, and Mbezi regions. Nestedness was significant in Ruvu and Rufiji, with shared core (N. melanospilus, N. eggersi, and N. janpapi) and common (N. ocellatus and N. annectens) species, and distinctive rare species. Nestedness apparently resulted from selective colonization rather than selective extinction, and local species richness was negatively associated with altitude. The Nothobranchius assemblages in the Mbezi region were not nested, and had many endemic species and the highest beta diversity driven by species turnover. Overall, we found unexpected local variation in the sources of beta diversity (nestedness and turnover) within the study area. The Mbezi region contained the highest diversity and many endemic species, apparently due to repeated colonizations of the region rather than local diversification. We suggest that annual killifish can serve as a flagship taxon for small wetland conservation.     

The need for richness‐independent measures of turnover when delineating biogeographical regions

Delineating biogeographical regions is one of the primary steps when analysing biogeographical patterns. In their proposed quantitative framework, Kreft & Jetz (2010, Journal of Biogeography, 37 , 2029–2053) recommended the use of the β_sim index to delineate biogeographical regions because this turnover measure is weakly affected by differences in species richness between localities. A recent study by Carvalho et al. (2012, Global Ecology and Biogeography, 21 , 760–771) critiziced the use of β_sim in ecological and biogeographical studies, and proposed the β_‐3 index. Here we used simple numerical examples and an empirical case study (European freshwater fishes) to highlight potential pitfalls associated with the use of β_‐3 for bioregionalization. We show that β_‐3 is not a richness‐independent measure of species turnover. We also show that this index violates the ‘complementarity’ property, namely that localities without species in common have the largest dissimilarity, which is an essential prerequisite for beta diversity studies.     

Implications of species loss in freshwater fish assemblages

Freshwater systems are vulnerable to pollution and species loss often ensues. Are there additional implications for assemblage structure? Here we use Berger‐Parker d. Simpson's I/D and Simpson's F to measure the ecological diversity of pristine and perturbed freshwater fish assemblages in Trinidad. West Indies, and Oklahoma. USA. Although the impacted sites typically had fewer species than expected, they could not be distinguished from unperturbed ones of equivalent richness. Changes in the evenness of these assemblages are thus driven by changes in richness. One practical outcome is that diversity indices may not provide independent verification of the detrimental consequences of pollution. The similarity in structure of naturally and anthropogenically impoverished assemblages provides no grounds for complacency, however, since it ignores the evolutionary history of the species concerned. On the basis of our results we suggest that species provenance may be important in tests of ecological function. Moreover, these investigations should replicate natural patterns of evenness as well as richness.     

Elevational Patterns of Diversity and Abundance of Eusocial Paper Wasps (Vespidae) in Costa Rica

We used a standard sampling protocol to measure elevational patterns of species richness and abundance of eusocial paper wasps (Hymenoptera: Vespidae) in Costa Rica. The sample transect of six sites spanned approximately 2000 m in elevation from lowland to montane forest. Species accumulation curves and species richness estimates both document a low elevation peak in paper wasp species richness at 50 and 300 m asl, with a decline in species richness at higher elevations. Comparison of species composition among elevations revealed strong species turnover from a rich lowland fauna to a depauperate, but distinct, montane fauna. We also observed a general trend toward a greater abundance of paper wasps at higher elevations, a pattern not usually observed in eusocial insects. Army ant species that prey on paper wasps declined in abundance with elevation across the sample transect, a pattern that has been observed at other sites. We discuss the possibility that elevational changes in predation pressure affect variation in paper wasp abundance and species richness. Eusocial paper wasp species employ one of two modes of colony founding, independent and swarm founding. We found that the total abundance of individual swarm-founding wasps was higher at all elevations than the abundance of independent-founding wasps, supporting previous suggestions that Neotropical swarm founders are more successful ecologically.     

Coexpression network analysis in abdominal and gluteal adipose tissue reveals regulatory genetic loci for metabolic syndrome and related phenotypes

Metabolic Syndrome (MetS) is highly prevalent and has considerable public health impact, but its underlying genetic factors remain elusive. To identify gene networks involved in MetS, we conducted whole-genome expression and genotype profiling on abdominal (ABD) and gluteal (GLU) adipose tissue, and whole blood (WB), from 29 MetS cases and 44 controls. Co-expression network analysis for each tissue independently identified nine, six, and zero MetS–associated modules of coexpressed genes in ABD, GLU, and WB, respectively. Of 8,992 probesets expressed in ABD or GLU, 685 (7.6%) were expressed in ABD and 51 (0.6%) in GLU only. Differential eigengene network analysis of 8,256 shared probesets detected 22 shared modules with high preservation across adipose depots (D_ABD-GLU = 0.89), seven of which were associated with MetS (FDR P<0.01). The strongest associated module, significantly enriched for immune response–related processes, contained 94/620 (15%) genes with inter-depot differences. In an independent cohort of 145/141 twins with ABD and WB longitudinal expression data, median variability in ABD due to familiality was greater for MetS–associated versus un-associated modules (ABD: 0.48 versus 0.18, P = 0.08; GLU: 0.54 versus 0.20, P = 7.8×10⁻⁴). Cis-eQTL analysis of probesets associated with MetS (FDR P<0.01) and/or inter-depot differences (FDR P<0.01) provided evidence for 32 eQTLs. Corresponding eSNPs were tested for association with MetS–related phenotypes in two GWAS of >100,000 individuals; rs10282458, affecting expression of RARRES2 (encoding chemerin), was associated with body mass index (BMI) (P = 6.0×10⁻⁴); and rs2395185, affecting inter-depot differences of HLA-DRB1 expression, was associated with high-density lipoprotein (P = 8.7×10⁻⁴) and BMI–adjusted waist-to-hip ratio (P = 2.4×10⁻⁴). Since many genes and their interactions influence complex traits such as MetS, integrated analysis of genotypes and coexpression networks across multiple tissues relevant to clinical traits is an efficient strategy to identify novel associations.     

Spatial Variability in Species Composition in Birds and Insects

If spatial patterns of change within a habitat were similar for both vertebrates and insects, then vertebrates would provide useful surrogates for designing reserves for the conservation of invertebrates. Data from two eucalypt habitats were analysed to determine levels of habitat richness, site richness and species turnover in birds and insects. For birds the relatively low species richness and turnover indicated that sites within the habitat were similar in composition. In wet eucalypt forests Diptera were very speciose with over 1,000 morphospecies sorted. Species turnover was slightly higher than for birds, indicating a large number of species change from site to site. In dry eucalypt woodland, insects trapped through the winter months were not speciose but turnover between sites was very large. This suggests reserves designed to conserve insects may need to be larger than for birds in order to include the high site variability and richness of insect communities.Spatial patterns of birds and insects were investigated further, to determine if sites that were closer together were more similar for both birds and insects. No patterns were found for birds in either habitat suggesting birds are not responding to changes in the environment at this scale. Diptera in wet eucalypt forest showed higher similarity between close sites than distant sites, while for winter insects in dry eucalypt woodland the relationship was significant when two outlier points were removed. Overall, birds are not good surrogates for insects in either habitat as no relationship between birds and insects in site-to-site similarity was found.     

Distribution pattern, endemism, threat status and conservation measures of fishes in the Tunga and Bhadra rivers of Western Ghats, India

This study documents the distribution patterns, endemism and uniqueness (species richness) of fishes in the Tunga and Bhadra rivers of Western Ghats, India. We recorded 77 species represented by 7 orders, 16 families and 44 genera, of which 36 species are endemic to Western Ghats, 12 species endemic to India and 26 species endemic to the Indian Subcontinent. Based on our analysis on the distribution patterns, the Tunga River is richer in diversity and higher in endemism than the Bhadra. We calculated the similarity of the species composition among sites within these two rivers using the Jacquard index. The similarity index between the sampling sites of these rivers revealed that the similarity decreases with increasing distance between the sampling sites. Of the 77 fish species we collected, 8 species (11.1%) are in the Critical category, 10 species (13.8%) are in the High Risk category, 36 species (50%) are in the Moderate category and the remaining 18 species (25%) are at lower risk. The threat status of fishes found in the Tunga and Bhadra rivers strongly suggests the need for effective conservation measures to conserve the fish species richness of these rivers.     

Partitioning multiple-site tree-like beta diversity into turnover and nestedness components without pairwise comparisons

In this letter, I extend a species-level partitioning framework for a multiple-site dissimilarity index established by Ricotta and Pavoine (2015) to account for tree-like information (i.e., evolutionary history, taxonomic classification or functional divergence of species). This novel framework can be applied to evaluate the relative contribution of turnover versus nestedness to total multiple-site tree-like beta diversity in empirical settings. The feature of the framework is to account for expectedly and unexpectedly absence of species in the sites without pairwise comparisons between sites. Simple examples with step-by-step calculation details and corresponding R computing code are provided to better understand and apply the proposed framework.     

Evaluation of Forest Recovery over Time and Space Using Permanent Plots Monitored over 30 Years in a Jamaican Montane Rain Forest

Conservation of tropical forest biodiversity increasingly depends on its recovery following severe human disturbance. Our ability to measure recovery using current similarity indices suffers from two limitations: different sized individuals are treated as equal, and the indices are proportionate (a community with twice the individuals of every species as compared with the reference community would be assessed as identical). We define an alternative recovery index for trees – the Tanner index, as the mean of the quantitative Bray-Curtis similarity indices of species composition for stem density and for basal area. We used the new index to compare the original (pre-gap) and post-gap composition of five experimental gap plots (each 90–100 m²) and four control plots over 24–35 years in the Blue Mountains of Jamaica. After 24–35 years, these small gaps surrounded by undisturbed forest had recovered 68% of the sum of per species stem density and 29% of the sum of per species basal area, a recovery index of 47%. Four endemic species were especially reduced in density and basal area. With the incorporation of basal area and stem density, our index reduces over-estimations of forest recovery obtained using existing similarity indices (by 24%–41%), and thus yields more accurate estimates of forest conservation status. Finally, our study indicates that the two kinds of comparisons: 1) over time between pre-gap and post-gap composition and 2) over space between gap plots and spatial controls (space-for-time substitution) yield broadly similar results, which supports the value of using space-for-time substitutions in studying forest recovery, at least in this tropical montane forest.     

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.     

Application of an index of biological integrity (IBI) to fish assemblages of the rivers Khan and Kshipra (Madhya Pradesh), India

1. A multimetric index of fish assemblage integrity was developed and similarity analyses were conducted on fish species in two central Indian rivers and the effects of distance from municipal and industrial effluents on those indices then evaluated.
2. Five metrics from Karr et al . (1986 , Illinois Natural History Survey Special Publication 5 , Urbana, IL) were adopted: intolerant species richness, % omnivorous individuals, % top carnivore individuals, total number of individuals and % individuals with anomalies. Seven new metrics (native species richness, native family richness, benthic species richness, water column species richness, % non-native individuals, % tolerant individuals and % herbivorous individuals) were added.
3. Non-native individuals represented 1–55% of the assemblages at sampled sites which held fish.
4. Fish were present at eleven sites and not collected at two sites, despite heavy metal concentrations exceeding U.S. Environmental Protection Agency acute criteria at all sites.
5. Two types of metric scoring were examined. The traditional 5–3–1 method showed the same pattern as continuous scoring from 0 to 10, but produced a higher integrity class at one site.
6. Scores on our modified index of fish assemblage integrity increased with distance downstream from a major effluent source in each river. Jaccard similarity scores between the least disturbed downstream site and all other sites decreased with increasing distance and disturbance.
7. It was concluded that Karr's original index and its theoretical foundations are easily adaptable, even to an ichthyofauna containing no species, and only two families (Cyprinidae, Poeciliidae), in common with the midwestern United States.     

高原鼠兔干扰对高寒草甸β多样性的影响

β多样性反映生物群落沿某一环境梯度的物种周转速率, 该研究尝试采用β多样性揭示植物群落随小型啮齿草食动物干扰梯度变化的生态过程。该研究利用野外随机样地的采集数据, 分析了高原鼠兔(Ochotona curzoniae)不同干扰强度下Whittaker指数的变化特征, 并利用群落二元丰富度的方差分解法, 确定了单个物种(SCBD)和单个干扰位点(LCBD)对β多样性的贡献。主要结果: 随高原鼠兔干扰强度增加, 植物群落内物种周转速率呈先增加后降低的趋势; 占据位点数居中的物种对区域内的β多样性贡献较大, 其中冰草(Agropyron cristatum)、臭蒿(Artemisia hedinii)、小花草玉梅(Anemone rivularis var. flore-minore)等单个物种对整个区域内β多样性的贡献最为突出; 整个区域内干扰位点T₀ (高原鼠兔干扰强度为0)对区域β多样性贡献值最大, LCBD值和该位点的群落丰富度呈显著负相关关系, 但与高原鼠兔干扰强度无显著关联。说明重点保护LCBD值高的干扰位点所在的高寒草甸, 以及SCBD值较高的冰草、臭蒿、小花草玉梅, 对保护高原鼠兔存在时高寒草甸植物群落多样性具有重要意义。     

Patterns of ferns community assemblages in some Malaysian and Nigerian tropical forests

Research on fern ecology has gained attention in the last decade, yet there is a paucity of information on the comparison of ferns communities across continents. This study focused on comparing the ferns community assemblages in some tropical forests of Malaysia and Nigeria, thereby assessing the patterns of species richness (SR) and phylogenetic diversity (PD) in relation to the bioclimatic drivers across the continents. The diversity and taxonomic compositions of ferns were assessed using 180 plots of 10 m × 10 m in each country. The species richness and other diversity indices were determined using the combined forests data for each country and for the individual forests. Also, the phylogenetic diversity of the ferns was assessed using the genus‐based molecular sequences downloaded from the GeneBank. The patterns of the ferns SR and PD in the two countries as driven by some bioclimatic factors were evaluated using the regression analysis. The observed and rarefied–extrapolated fern species richness is significantly higher in Malaysian forests than in Nigerian forests. Also, the other diversity indices are significantly higher in Malaysian forests except for the Shannon index which showed no significant difference between the two biogeographic regions. There is a very low similarity (7.41%) in the taxonomic composition of ferns between the two biogeographic areas, although the similarity in composition increased with increasing taxonomic levels (species: 7.41%, genus: 12.77%, family: 70.96%). Terrestrial and epiphytic ferns are more dominant than the other life forms in the two countries. The precipitation variables drive the phylogenetic structure of ferns in Nigeria, whereas both precipitation and temperature variables drive the phylogenetic structure of ferns in Malaysia. This indicates that ferns assemblages in Nigeria and Malaysia are driven by both climatic variables. Besides, we also hypothesize that these observed differences could be due to other historical and evolutionary processes.