On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages

Bray-Curtis similarity is widely employed in multivariate analysis of assemblage data, for sound biological reasons. This paper discusses two problems, however, with its practical application: its behaviour is erratic (or even undefined) for the vanishingly sparse samples that may be found as an end-point to a severe impact gradient, or a start-point in colonisation studies; and, in common with all similarity measures on species-level data, it is sensitive to inconsistency of taxonomic identification through time. It is shown that the latter problem is ameliorated by application of ‘taxonomic dissimilarity’ coefficients, a natural extension of the concept of taxonomic distinctness indices. Two previous suggestions for use with presence/absence data, denoted here by Γ⁺ and Θ⁺, are noted to be simple generalisations of the Bray-Curtis and Kulczynski measures, respectively. Also seen is their ability to permit ordinations of assemblages from wide geographic scales, with no species in common, and for which Bray-Curtis would return zero similarity for all pairs of samples.The primary problem addressed, however, is that of denuded or entirely blank samples. Where it can be convincingly argued that impoverished samples are near-blank from the same cause, rather than by random occurrences from inadequate sample sizes (tow length, core diameter, transect or quadrat size etc.), a simple adjustment to the form of the Bray-Curtis coefficient can generate meaningful MDS displays which would otherwise collapse, and can improve values of the ANOSIM R statistic (increased separation of groups in multivariate space). It is also shown to have no effect at all on the normal functioning of a Bray-Curtis analysis when at least a modest amount of data is present for all samples.Examination of the properties of this ‘zero-adjusted’ Bray-Curtis measure goes hand-in-hand with a wider discussion of the efficacy of competing similarity, distance or dissimilarity coefficients (collectively: resemblance measures) in community ecology. The inherent biological guidelines underlying the ‘Bray-Curtis family’ of measures (including Kulczynski, Sorenson, Ochiai and Canberra dissimilarity) are made explicit. These and other commonly employed measures (e.g. Euclidean, Manhattan, Gower and chi-squared distances) are calculated for several ‘classic’ data sets of impact events or gradients in space and time. Behaviour of particular coefficients is judged against the interpretability of the resulting ordination plots and an objective measure of the ability to discriminate between a priori defined hypotheses, representing impact conditions. A second-stage MDS plot of a set of resemblance coefficients, based on the respective similarities of the multivariate patterns each generates (an MDS of MDS plots, in effect), is seen to be useful in determining which coefficients are extracting essentially different information from the same assemblage matrix. This suggests a mechanism for practical classification of the plethora of resemblance measures defined in the literature. Similarity-based ANOSIM R statistics and Spearman ρ correlations, whose non-parametric structure make them absolutely comparable across different resemblance measures, answer questions about whether the different information extracted by some coefficients is more, or less, helpful to the final biological interpretation.     

湖北八角莲属植物过氧化物酶同工酶分析

用聚丙烯酰胺凝胶电泳分离湖北八角莲属４种植物的过氧化物酶同工酶,并采用薄层扫描和排序分析法,对其亲缘关系进行了比较分析。结果表明,六角莲与八角莲、小八角莲、乌云伞的亲缘关系较远。小八角莲、八角莲与乌云伞亲缘关系较近,同时还为乌云伞作为一个独立种提供了佐证。     

Sequence diversity under the multispecies coalescent with Yule process and constant population size

The study of sequence diversity under phylogenetic models is now classic. Theoretical studies of diversity under the Kingman coalescent appeared shortly after the introduction of the coalescent. In this paper we revisit this topic under the multispecies coalescent, an extension of the single population model to multiple populations. We derive exact formulas for the sequence dissimilarity of two sequences drawn at random under a basic multispecies setup. The multispecies model uses three parameters—the species tree birth rate under the pure birth process (Yule), the species effective population size and the mutation rate. We also discuss the effects of relaxing some of the model assumptions.     

象山港浮游动物β多样性及其成分变化的环境因子解释

根据象山港24个站位浮游动物样品和配套环境数据,采用R语言的gdm工具包对浮游动物β多样性进行了广义非相似性模型(GDM)分析,并利用betapart工具包对β多样性进行了成分(周转和嵌套性)分解,探讨了环境因子与浮游动物β多样性及其成分间的关系。GDM模型分析结果表明,有10个环境变量(表层水温、溶解氧、水深、透明度、p H、叶绿素a、地理距离、电导率、盐度、悬浮颗粒物)对浮游动物β多样性有影响,解释了GDM模型偏差比例的75.2%。在这10个变量中,水温、溶解氧、水深是驱动β多样性变化重要因子,3个变量累计相对贡献比例占63.9%(以GDM模型偏差的可解释比例作为100%),其他7个变量占36.1%;3个变量中,又以水温最重要,相对贡献比例占到38.4%。从各预测变量的影响梯度看,地理距离、p H和盐度分别在约高于25 km、7.8和25,水温、叶绿素a含量分别在约低于22℃和0.5μg/L时,随着变量梯度的增加,β多样性增大;而溶解氧、电导率、透明度和水深则随着梯度增加β多样性一直增加,悬浮颗粒物含量对β多样性几乎无影响。据β多样性成分分解结果,象山港浮游动物在时空变化上总体以周转为主,嵌套性很低。在象山港,浮游动物嵌套性主要发生于大型浮游动物和幼体类群,尤其是幼体类群,嵌套性在时空上几乎都高于周转。进一步的Pearson相关性分析表明,与大型浮游动物嵌套性显著相关的环境因子是水温和溶解氧,而与幼体类嵌套性显著相关的环境因子除水温和溶解氧外,还有电导率和流速。     

Association of ecotones with relative elevation and fire in an upland Florida landscape

Question: What are the importance of elevation and fire in maintaining ecotones of Florida scrub assemblages along a gradual topographic gradient? Location: Archbold Biological Station (ABS), 12 km south of Lake Placid, Florida, USA. Methods: Vegetation cover of upland Florida shrublands was quantified using the line‐intercept method along 20 transects traversing similar elevation gradients, stratified by time since fire (TSF). We objectively identified shrubland ecotones using a split moving windows boundary analysis (SMW) with three different window widths. Non‐metric multidimensional scaling ordination was used to determine relationships among plant assemblages defined by SMW. Results: We located up to four ecotones per transect, the majority of which were wide, highly heterogeneous zones. Relative elevation controlled the distribution of plant assemblages in upland Florida shrublands. Ecotones in shrublands > 30 years TSF had relatively low dissimilarity values in SMW, indicating that previously discrete plant assemblages with longer TSF were becoming more similar with time. Conclusions Split Moving Windows (SMW) analysis identified ecotones relatively well although patches generated by oak clonal growth were sometimes identified as ecotones. Fire suppression caused ecotones to become more diffuse, suggesting that without fire at least every 30 years, discrete plant assemblages within upland Florida shrublands will be more continuous.     

广东鉴江水系底栖硅藻多样性与时空分布特征

为了解广东省鉴江水系底栖硅藻多样性和时空分布特征,对全流域进行了底栖硅藻采样调查。结果表明,从19个采样点4次采样中共检出底栖硅藻10科52属242种,其中舟形藻属(Navicula)、菱形藻属(Nitzschia)和异极藻属(Gomphonema)是优势类群,出现频次和相对丰度较高。硅藻多样性指数(丰富度、真香农多样性指数和真辛普森多样性指数)随河流等级呈现一定的空间分布特征,但它们季节变化不明显。底栖硅藻群落相异性在上游和下游河段较高,从一级到三级河流递减,四级河流又增加。底栖硅藻群落结构空间变化明显,季节变化显著。群落丰富度的稀疏曲线表明,热带河流底栖硅藻群落以400个体计数,不能完整反映底栖硅藻多样性。这些为鉴江水系河流健康监测和水生态保护奠定了基础。     

Distance-based tests for homogeneity of multivariate dispersions

Summary The traditional likelihood‐based test for differences in multivariate dispersions is known to be sensitive to nonnormality. It is also impossible to use when the number of variables exceeds the number of observations. Many biological and ecological data sets have many variables, are highly skewed, and are zero‐inflated. The traditional test and even some more robust alternatives are also unreasonable in many contexts where measures of dispersion based on a non‐Euclidean dissimilarity would be more appropriate. Distance‐based tests of homogeneity of multivariate dispersions, which can be based on any dissimilarity measure of choice, are proposed here. They rely on the rotational invariance of either the multivariate centroid or the spatial median to obtain measures of spread using principal coordinate axes. The tests are straightforward multivariate extensions of Levene's test, with P‐values obtained either using the traditional F‐distribution or using permutation of either least‐squares or LAD residuals. Examples illustrate the utility of the approach, including the analysis of stabilizing selection in sparrows, biodiversity of New Zealand fish assemblages, and the response of Indonesian reef corals to an El Niño. Monte Carlo simulations from the real data sets show that the distance‐based tests are robust and powerful for relevant alternative hypotheses of real differences in spread.     

A study on the community analysis using three-factorial data (time x site x species)

1. This study is to demonstrate that the analysis of biological communities using scaling unstandardized squared Euclidean distance is extremely effective to deal with data which are quite generally collected by 3 factors (time x site x species).
2. The main part of this study has been explained in detail byWilliams andStephenson (1973). We have conducted some discussion introducing mathematic complementary explanation as well as expansive interpretation.
3. The dissimilarity measure based on squared Euclidean distance is used to classify clusters from a dendrogram obtained by cluster analysis. The outline of the community structure can be known by comparing the values of mean variance per comparison and interaction.
4. The table of mutual comparison among clusters introduces dynamic pattern expression for community. Contributions by species to time and site are capable of expressing a concrete role of the species.
5. We apply the technique above to the demersal fish community in Shijiki Bay, Hirado Island, Nagasaki Pref. Number of individuals caught with Gochi trawls at 11 fixed stations in 1975–1984 are used as material for analysis. 84 species is accounted.

     

Resemblance in phylogenetic diversity among ecological assemblages

Questions: How can a resemblance (similarity or dissimilarity) measure be formulated to include information on both the evolutionary relationships and abundances of organisms, and how does it compare to measures lacking such information? Methods: We extend the family of Phylogenetic Diversity (PD) measures to include a generalized method for calculating pair‐wise resemblance of ecological assemblages. Building on previous work, we calculate the matching/mismatching components of the 2 × 2 contingency table so as to incorporate information on both phylogeny and abundance. We refer to the class of measures so defined as “PD resemblance” and use the term “SD resemblance” for the traditional class of measures based on species diversity alone. As an illustration, we employ data on the diversity and stem density of shrubs of Toohey Forest, Australia, to compare PD resemblance to its SD resemblance equivalent for both incidence and abundance data. Results: While highly correlated, PD resemblance consistently measures assemblages as more similar than does SD resemblance, and tends to “smooth out” the otherwise skewed and truncated distribution of pair‐wise resemblance indices of our high‐turnover data set, resulting in nMDS ordinations with lower stress. Randomization of species distributions across assemblages indicates that phylogeny has made a significant contribution to the ordination pattern. Conclusions: PD resemblance measures, in addition to providing an evolutionary perspective, have great potential to improve distance‐based analyses of community patterns, particularly if species responses to ecological gradients are unimodal and phylogenetically conserved.