缙云山常绿阔叶林的排序

排序概念由苏联学者拉孟斯基(1930)第一次提出并首先用环境梯度为坐标去排列植物群落。然而,这一方法在60年代电子计算技术的普遍应用和连续性学派(个体学派)兴旺发达起来以后,才迅速发展起来。排序是植物群落样本的一种空间排列,是揭示其空间连续变化的有效技术。至今方法很多,但一般分为两类,一类是用环境因子进行排列,称为直接排序,或称直接梯度分析,或者就叫梯度分析。另一类是用植物群落本身的特征(属性)来排序,称为间接排序,或间接     

A resemblance function based on probability: Applications to field and simulated data

A resemblance function (COCHIS) based on the probability of species association and correlation is proposed. It is a development of the underlying idea of association analysis and can serve to produce similarity matrices for polythetic classifications and ordinations. Examples are given utilizing field and simulated data.The work has been supported by the Italian Ministry of Education. We would like to thank the Profs. D W. Goodall, E. van der Maarel and I. Orlóci for comments.     

Factors affecting the character stability of classifications

The effect of six resemblance coefficients (taxonomic distance, Manhattan distance, correlations, cosines, and two new general dissimilarity coefficients) on the character stability of classifications based on six data sets was evaluated. The six data sets represent a variety of organisms, and of ratios of number of characters to number of OTUs, and were randomly bipartitioned 100 times. The results of matrix correlations, cophenetic correlations and two consensus measures indicate that no one resemblance coefficient is uniformly better than all others when evaluated in terms of the stability of a classification, although taxonomic distance and Manhattan distance produce relatively more stable classifications than the other resemblance coefficients. An index of dimensionality, the stemminess and cophenetic correlations of classifications were calculated for the six data sets and also for 20 data sets analyzed in an earlier study. Regression analysis of stability on the ratio of number of characters to the number of OTUs, dimensionality, stemminess, and cophenetic correlations explained more than 70% of the variance in stability. Of the four factors, the ratio was by far the most important. Stemminess and dimensionality contributed little when considered singly, and did not add appreciably to the variance explained by ratio and cophenetic correlations.Dedicated to the memory of Prof.J. S. L. Gilmour. His insightful wrightings on naturalness in classifications paved the way for the development of numerical phenetics.     

Braun‐Blanquet's legacy and data analysis in vegetation science

Abstract. This article investigates whether the Braun‐Blanquet abundance/dominance (AD) scores that commonly appear in phytosociological tables can properly be analysed by conventional multivariate analysis methods such as Principal Components Analysis and Correspondence Analysis. The answer is a definite NO. The source of problems is that the AD values express species performance on a scale, namely the ordinal scale, on which differences are not interpretable. There are several arguments suggesting that no matter which methods have been preferred in contemporary numerical syntaxonomy and why, ordinal data should be treated in an ordinal way. In addition to the inadmissibility of arithmetic operations with the AD scores, these arguments include interpretability of dissimilarities derived from ordinal data, consistency of all steps throughout the analysis and universality of the method which enables simultaneous treatment of various measurement scales. All the ordination methods that are commonly used, for example, Principal Components Analysis and all variants of Correspondence Analysis as well as standard cluster analyses such as Ward's method and group average clustering, are inappropriate when using AD data. Therefore, the application of ordinal clustering and scaling methods to traditional phytosociological data is advocated. Dissimilarities between relevés should be calculated using ordinal measures of resemblance, and ordination and clustering algorithms should also be ordinal in nature. A good ordination example is Non‐metric Multidimensional Scaling (NMDS) as long as it is calculated from an ordinal dissimilarity measure such as the Goodman & Kruskal γ coefficient, and for clustering the new OrdClAn‐H and OrdClAn‐N methods.     

Pluralism and diversity: trends in the use and application of ordination methods 1990‐2007

Question: What are the trends and patterns in the application of ordination techniques in vegetation science since 1990? Location: Worldwide literature analysis. Methods: Evaluation of five major journals of vegetation science; search of all ISI‐listed ecological journals. Data were analysed with ANCOVAs, Spearman rank correlations, GLMs, biodiversity indices and simple graphs. Results: The ISI search retrieved fewer papers that used ordinations than the manual evaluation of five selected journals. Both retrieval methods revealed a clear trend in increasing frequency of ordination applications from 1990 to the present. Canonical Correspondence Analysis was far more frequently detected by the ISI search than any other method. Applications such as Correspondence Analysis/Reciprocal Averaging and Detrended Correspondence Analysis have increasingly been used in studies published in “applied” journals, while Canonical Correspondence Analysis, Redundancy Analysis and Non‐Metric Multidimensional Scaling were more frequently used in journals focusing on more “basic” research. Overall, Detrended Correspondence Analysis was the most commonly applied method within the five major journals, although the number of publications slightly decreased over time. Use of Non‐Metric Multidimensional Scaling has increased over the last 10 years. Conclusion: The availability of suitable software packages has facilitated the application of certain techniques such as Non‐Metric Multidimensional Scaling. However, choices of ordination techniques are currently less driven by the constraints imposed by the software; there is also limited evidence that the choice of methods follows social considerations such as the need to use fashionable methods. Methodological diversity has been maintained or has even increased over time and reflects the researcher's need for diverse analytical tools suitable to address a wide range of questions.     

Diversity of tiger moths in a Neotropical hotspot: determinants of species composition and identification of biogeographic units

The Brazilian Atlantic Forest is a Biodiversity Hotspot, yet many biological groups in this biome are poorly known. We compiled information on the diversity of Atlantic Forest tiger moths (Arctiidae) and assessed the resemblance among localities, whether arctiid assemblages are concordant with major vegetation types, and the importance of environmental factors in structuring the variation among assemblages. Additionally, we developed a procedure composed of subsampling and procrustean analysis to assess the robustness of the results from community composition ordinations when localities differ in species richness. To do this, we built a database from specimens deposited in the ten most important Brazilian entomological collections, and mapped species richness in one-degree latitude/longitude grid cells. We employed Principal Coordinates Analysis to assess similarities among the best-sampled localities. We obtained 8,667 records including 1,193 species, representing 60 and 20% of the estimated Brazilian and Neotropical faunas, respectively. Our subsampling procedure indicated that the ordination was not greatly affected by differences in species richness, and was congruent with major vegetation types. Lowland localities on the seacoast were quite distinct in species composition. A second group included localities in montane areas in the southeast part of the biome. The last group included localities in the southern region and those with Araucaria forests, and was associated with long distances from the ocean, even distribution of precipitation throughout the year, and large annual temperature ranges.     

稻田田埂昆虫群落与田埂杂草关系的研究

为探索稻田田埂昆虫群落与田埂类型的关系,本文对田埂昆虫群落进行主分量分析和模糊聚类分析,结果表明:田埂昆虫群落类型与田埂类型有一定的联系。经典范分析,从定量上明确田埂昆虫群落与田埂类型的关系程度(r_1=0.8232),并得出田埂杂草高度是影响田埂昆虫群落的关键因子。     

Functional traits,convergent evolution,and periodic tables of niches

Ecology is often said to lack general theories sufficiently predictive for applications. Here, we examine the concept of a periodic table of niches and feasibility of niche classification schemes from functional trait and performance data. Niche differences and their influence on ecological patterns and processes could be revealed effectively by first performing data reduction/ordination analyses separately on matrices of trait and performance data compiled according to logical associations with five basic niche ‘dimensions’, or aspects: habitat, life history, trophic, defence and metabolic. Resultant patterns then are integrated to produce interpretable niche gradients, ordinations and classifications. Degree of scheme periodicity would depend on degrees of niche conservatism and convergence causing species clustering across multiple niche dimensions. We analysed a sample data set containing trait and performance data to contrast two approaches for producing niche schemes: species ordination within niche gradient space, and niche categorisation according to trait‐value thresholds. Creation of niche schemes useful for advancing ecological knowledge and its applications will depend on research that produces functional trait and performance datasets directly related to niche dimensions along with criteria for data standardisation and quality. As larger databases are compiled, opportunities will emerge to explore new methods for data reduction, ordination and classification.     

Comparisons of three ordination techniques

Summary Simulated coenoclines were used to test performance of several techniques for ordinating samples by species composition: Wisconsin polar or Bray-Curtis ordination with Euclidean distance (ED) and the complements of percentage similarity (PD) and coefficient of community (CD) as distance measures, Principal components analysis, and polar and non-polar or indirect use of Discriminant function analysis. In general the Bray-Curtis technique gave the best ordinations, and PD was the best distance measure. Euclidean distance gave greater distortion than PD in all tests; CD may be better than PD only for some sample sets of high alpha and beta diversity and high levels of noise or sample error. Principal components ordinations are increasingly distored as beta diversity increases, and are highly vulnerable to effects of both noise and sample clustering. Discriminant function analysis was found generally unsuitable for ordination of samples by species composition, but likely to be useful for sample classification.     

Traditional morphometrics in plant systematics and its role in palm systematics

A review is given of the role of traditional morphometrics in plant systematics. The three most commonly used techniques of data analysis – Cluster Analysis, Principal Component Analysis and Discriminant Analysis – are discussed. The kinds of data that can be taken from palm specimens and the problems of using specimens as data sources are outlined. Published systematic studies of palms using traditional morphometrics are reviewed. More recent studies indicate that: hybrid zones between species may be common; infraspecific diversity is greater than previously suspected; there may be more than double the currently accepted number of species; and our current knowledge of morphological variation in palms is superficial. A procedure for scientific systematics is given, which incorporates traditional morphometric methods.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 103–111.     

Biodiversity shortcuts in biomonitoring of novel ecosystems

Hydropower reservoirs are novel ecosystems that present different challenges for the design of biomonitoring programs. To ensure long-term programs and wide spatial coverage, it is important to test the reliability of different cost-saving strategies that have been widely evaluated among researchers, such as taxonomic sufficiency, numerical sufficiency and surrogate groups. Using data on zooplankton composition, our objective was to test whether these strategies could be applied to increase the efficiency of biomonitoring programs in reservoirs. Zooplankton data were collected at the Santo Antônio do Jari Hydroelectric Plant, which is located between the states of Pará and Amapá (Amazon region, Brazil), over 23 months between 2012 and 2015. The data were organized in different taxonomic groups (cladocerans, copepods, rotifers and testate amoebae) and matrices by decreasing the taxonomic resolution (from species to genera and families) and the numerical resolution (from species abundance to species presence/absence) of the data. The ordination patterns obtained with Principal Coordinate Analysis for the different matrices were compared using Procrustes analyses. Our results suggest that ordination patterns using genus-level data were similar to those obtained with species-level data. However, analyses based on family-level data were often unable to reproduce results based on species-level data. Ordination patterns using presence/absence data were similar to those obtained from abundance data. We also found that the strengths of the relationships between ordinations derived from different taxonomic groups (e.g., rotifers and cladocerans) were low and often not significant. We conclude that the use of zooplankton genera and presence/absence data may be a reliable strategy to monitor reservoirs. However, our results highlight the need to monitor different zooplankton groups, as the ordination patterns depicted by a given group were poorly related to those generated by a second zooplankton group.     

运用数学方法研究植物区系地理

本文对植物区系地理学中区系丰富性、区系相似性、区系成分划分及其区系区划等几个基本问题,在应用数学方法研究的现状进行了评述.本文指出了应用数学方法研究植物区系地理学中存在且亟待解决的几个重要的理论与实际问题.     

运用数学方法研究植物区系地理

本文对植物区系地理学中区系丰富性、区系相似性、区系成分划分及其区系区划等几个基本问题,在应用数学方法研究的现状进行了评述.本文指出了应用数学方法研究植物区系地理学中存在且亟待解决的几个重要的理论与实际问题.     

Sequence clustering threshold has little effect on the recovery of microbial community structure

Analysis of microbial community structure by multivariate ordination methods, using data obtained by high‐throughput sequencing of amplified markers (i.e., DNA metabarcoding), often requires clustering of DNA sequences into operational taxonomic units (OTUs). Parameters for the clustering procedure tend not to be justified but are set by tradition rather than being based on explicit knowledge. In this study, we explore the extent to which ordination results are affected by variation in parameter settings for the clustering procedure. Amplicon sequence data from nine microbial community studies, representing different sampling designs, spatial scales and ecosystems, were subjected to clustering into OTUs at seven different similarity thresholds (clustering thresholds) ranging from 87% to 99% sequence similarity. The 63 data sets thus obtained were subjected to parallel DCA and GNMDS ordinations. The resulting community structures were highly similar across all clustering thresholds. We explain this pattern by the existence of strong ecological structuring gradients and phylogenetically diverse sets of abundant OTUs that are highly stable across clustering thresholds. Removing low‐abundance, rare OTUs had negligible effects on community patterns. Our results indicate that microbial data sets with a clear gradient structure are highly robust to choice of sequence clustering threshold.     

The influences of habitat and seasonal sampling regimes on the ordination and classification of macroinvertebrate assemblages in the catchment of the River Wye,Wales

Assemblages of benthic macroinvertebrates were assessed in relation to environmental variables at 45 sites in the catchment of the Welsh River Wye in 1982.Samples were collected from three habitats (margins, riffles, flats) and in two seasons (Spring and Autumn), separated and combined data sets being ordinated by DECORANA and classified by TWINSPAN. Correlations between primary ordinations were high (p < 0.001) and always strongly related to total hardness or pH; secondary ordinations were also intercorrelated and were related to stream slope.In each instance, total hardness and slope were the strongest discriminants between site groupings produced by TWINSPAN. It is concluded that relationships between faunal assemblages, stream chemistry and stream physiography would be effectively detected in the Wye catchment in either Spring or Autumn and in each of the habitats sampled. However, the most precise categorization of assemblage type required a sampling strategy which combined habitat and seasonal data.     

Optimization based tumor classification from microarray gene expression data

Background

An important use of data obtained from microarray measurements is the classification of tumor types with respect to genes that are either up or down regulated in specific cancer types. A number of algorithms have been proposed to obtain such classifications. These algorithms usually require parameter optimization to obtain accurate results depending on the type of data. Additionally, it is highly critical to find an optimal set of markers among those up or down regulated genes that can be clinically utilized to build assays for the diagnosis or to follow progression of specific cancer types. In this paper, we employ a mixed integer programming based classification algorithm named hyper-box enclosure method (HBE) for the classification of some cancer types with a minimal set of predictor genes. This optimization based method which is a user friendly and efficient classifier may allow the clinicians to diagnose and follow progression of certain cancer types.

Methodology/Principal Findings

We apply HBE algorithm to some well known data sets such as leukemia, prostate cancer, diffuse large B-cell lymphoma (DLBCL), small round blue cell tumors (SRBCT) to find some predictor genes that can be utilized for diagnosis and prognosis in a robust manner with a high accuracy. Our approach does not require any modification or parameter optimization for each data set. Additionally, information gain attribute evaluator, relief attribute evaluator and correlation-based feature selection methods are employed for the gene selection. The results are compared with those from other studies and biological roles of selected genes in corresponding cancer type are described.

Conclusions/Significance

The performance of our algorithm overall was better than the other algorithms reported in the literature and classifiers found in WEKA data-mining package. Since it does not require a parameter optimization and it performs consistently very high prediction rate on different type of data sets, HBE method is an effective and consistent tool for cancer type prediction with a small number of gene markers.     

Pre-climax epiphyte communities of bryophytes and lichens in Mediterranean forests from the Central Plateau (Spain)

The pre-climax epiphytic communities of forests from the Spanish Mediterranean region (Central Plateau) were studied by numerical and traditional floristic methods. One hundred phytosociological relevés were analyzed through a classical numerical approach based on hard partitions improved by PCoA — Principal Coordinates Analysis — ordinations. Two groups easily related to two different suballiances included in Frullanion dilatatae Lecointe 1975, Ulotenion crispae (Barkman 1958) Lecointe 1975 and Fabronienion pusillae Barkman 1958 were detected. Two new syntaxa within the ass. Ortotrichetum lyellii (Allorge 1922) Lecointe 1975 are proposed. Phytogeography, syntaxonomy and ecology of these communities are discussed.     

Complex clines: the predictivity of complicated patterns of geographic variation portrayed by multivariate analysis

The stability of complex patterns of geographic variation was investigated by assessing the congruence between multivariate ordinations derived from randomly chosen real characters. Two series of populations were analysed representing two situations with complex patterns of geographic variation. The first, a ‘Eurasian’ series of populations, showed a strongly structured hierarchical pattern, the second, an ‘eastern’ series of populations, showed a more subtle complex pattern of smooth clines and steps. The characters were selected from a total of 81 (Eurasian) or 61 (eastern) within-population independent characters from six different systems. The congruence between ordinations of the geographical populations was measured by the rotational fit statistic, R². Three procedures were used to compare ordinations based on from two to up to 80 characters randomly chosen to give: A, completely independent character sets; B, subsets compared to the total set; and C, potentially overlapping sets. All three procedures showed that congruence between the ordinations was asymptotic in relation to character number. This relationship was described by one of two mathematical models (procedure B did not result in a hyperbolic model as found with simple patterns of geographic variation). Generally speaking, once a sufficient number of characters are used, the complex patterns of geographic variation are stable, reliable and predictive and not substantially influenced by character choice. The strongly structured hierarchical pattern required 15 or so characters to achieve reliability whilst the more subtle patterns required 20 or so characters. However, the addition of further characters does improve reliability in both cases. The greater percentage of variance portrayed by three-dimensional ordinations compared to two-dimensional ordinations is achieved at the cost of lower congruence when a sufficient number of characters are used. If case studies of geographic variation were to adopt these procedures (preferably using completely independent character sets; procedure A) the reliability of their results would be indicated).