排序和广义线性模型与广义可加模型在植物种与环境关系研究中的应用

排序和广义线性模型(Generalized Linear Model,GLM)与广义可加模型(Goneralized Additive Model,GAM)是研究植物种与环境间关系的重要方法。基于线性模型的排序方法应限定于环境梯度较短的植被数据。而基于单峰模型的排序方法更适用于梯度较长的情况。PCA、CA／RA系列和CCA系列是常用的排序方法。同时进行环境数据和植被数据分析的CCA系列,能清楚地得出植物种与环境间的关系。CCA改进后的DCCA和PCCA,是现今较理想的排序方法。GLM和GAM实质上是用环境变量的高阶多项式来拟合植物种与环境变量的关系。GLM和GAM扩展了植物种与环境变量之间的关系模型,能深入地探讨植物种与环境间的关系。GLM主要是模型决定的,而GAM主要取决于原始数据。一般来说,排序能得出研究区域的主要环境梯度,提供了物种聚集和植物群落的概略描述。GLM与GAM对于深入研究单个植物种与环境间的关系具有优势。在实际研究中,两种方法结合使用能互补不足。     

Species response curves along environmental gradients. A case study from SE Norwegian swamp forests

Abstract. Vegetation science has relied on untested paradigms relating to the shape of species response curves along environmental gradients. To advance in this field, we used the HOF approach to model response curves for 112 plant species along six environmental gradients and three ecoclines (as represented by DCA ordination axes) in SE Norwegian swamp forests. Response curve properties were summarized in three binary response variables: (1) model unimodal or monotonous (determinate) vs. indeterminate; (2) for determinate models, unimodal vs. monotonous and (3) for unimodal models, skewed vs. symmetric. We used logistic regression to test the influence, singly and jointly, of seven predictor variables on each of three response variables. Predictor variables included gradient type (environmental or ecocline) and length (compositional turnover); species category (vascular plant, moss, Sphagnum or hepatic), species frequency and richness, tolerance (the fraction of the gradient along which the species occurs) and position of species along each gradient. The probability for fitting a determinate model increased as the main occurrence of species approached gradient extremes and with increasing species tolerance and frequency and gradient length. Appearance of unimodal models was favoured by low species tolerance and disfavoured by closeness of species to gradient extremes. Appearance of skewed models was weakly related to predictors but was slightly favoured by species optima near gradient extremes. Contrary to the results of previous studies, species category, gradient type and variation in species richness along gradients did not contribute independently to model prediction. The overall best predictors of response curve shape were position along the gradient (relative to extremes) and tolerance; the latter also expressing gradient length in units of compositional turnover. This helps predicting species responses to gradients from gradient specific species properties. The low proportion of skewed response curves and the large variation of species response curves along all gradients indicate that skewed response curves is a smaller problem for the performance of ordination methods than often claimed. We find no evidence that DCA ordination increases the unimodality, or symmetry, of species response curves more than expected from the higher compositional turnover along ordination axes. Thus ordination axes may be appropriate proxies for ecoclines, applicable for use in species response modelling.     

Can we trust gradients extracted by Detrended Correspondence Analysis?

Abstract. In this study, data from dry temperate grassland vegetation in Denmark are used to compare the predictive power of gradients obtained by ordination. One of the problems of ordination methods based on weighted averaging, namely the assumption of symmetric, unimodal response curves, is investigated by smoothing species responses to simple and complex gradients respectively. It was found that species response types to a pH gradient are diverse and often deviate from a unimodal, symmetrical shape. Bimodal responses were also found, but they disappeared when more influential gradients were considered. Many species showed truncated responses with optima near gradient ends. In order to assess the impact of unrealistic response assumptions and reported problems with instability on the performance of DCA, the predictive potentials of measured variables and coenoclines extracted by DCA were compared. Despite field data violating the assumption of unimodal response, DCA was found to extract gradients predicting species abundance better than the environmental variables available. Shortcomings and advantages of indirect and direct methods in plant ecology are discussed.     

稀有种处理对RDA排序结果影响的比较研究

为了解稀有种对RDA排序结果的影响,该研究以北京东灵山华北落叶松林调查数据为例,在RDA排序的基础上,对比分析了未处理稀有种RDA与剔除频度5%、盖度5%的稀有种后RDA排序结果的差异,并用蒙特-卡罗拟合检验分析了二者物种变量和环境变量之间的相关关系,以及用Spearman秩相关系数检验了对应排序轴的相关性。结果表明:(1)蒙特-卡罗拟合检验结果显示未处理稀有种RDA与剔除稀有种RDA各自对应的物种变量和环境变量之间均呈极显著相关关系;(2)从排序轴特征值对物种数据方差以及物种—环境关系解释量来看,剔除稀有种RDA前两排序轴与前四排序轴均有较高的物种-环境关系累积解释量;(3)剔除稀有种前后对应排序轴的Spearman秩相关分析结果表明,尽管未处理稀有种RDA和剔除稀有种RDA在第三轴和第四轴间存在一定的交叉,但二者对应的前四排序轴均呈极显著的一一对应关系(P0.001),相似性极高。总之,结合物种-环境关系的累积解释量及对应排序轴的相关性可知,在环境因子个数较少、研究尺度较小时,使用RDA排序揭示植物种、植物群落和环境因子之间相互作用的生态关系时,剔除稀有种前后RDA排序具有较高吻合性,只是对环境因子的解释趋势稍有差异。     

Distribution of twelve moist forest canopy tree species in Liberia and Côte d'Ivoire: response curves to a climatic gradient

Abstract. The occurrence and abundance of 12 canopy tree species from the moist tropical forests of West Africa have been studied in relation to a climatic gradient. We focused on environmental factors related to water availability: annual amount of rainfall, the length of the dry season, and cumulative water deficit. Species occurrence and abundance data are used for 39 forest sites in Liberia and southwest Côte d'Ivoire. Species responses are modelled using a set of five increasingly complex models, ranging from a no-trend model to a skewed bell-shaped response curve. The study species show different distribution patterns. Most of them suggest a close relationship to climatic conditions. Fitting of species occurrence data to each of the three climatic factors results in most cases in simple models. In only one out of 36 cases a bell-shaped response curve is needed to describe the data. Four of the 12 species show no response to the climatic factors when only occurrence is evaluated. When abundance data are used, in 33 of the 36 cases significant response models are found. In general these are much more complex than in the cases of species occurrence data: in 10 of the 36 cases a bell-shaped response model is found to describe the data best. This is in contrast with the widespread belief that species response curves are bell-shaped: within the forest zone in the area studied this is not generally the case. The importance of the three climatic factors for the distribution of the species is evaluated: for four species mean annual rainfall is the most important variable, for four species the length of the dry period, and for one species cumulative water deficit. Consequently, the assumption that mean annual rainfall is the most important factor determining tree species distribution in West African forests is not correct. Species response models to climatic factors show where species have their geographical optima. Implications for forest management are briefly discussed.     

On non-linear species response models in ordination

Ordination techniques are plagued by the non-linearity of vegetation data. The purpose of ordination is discussed and considered to be the process of arranging samples (or species) in relation to one or more environmental gradients or abstract axes that may represent such gradients, the arrangement to be ecologically significant. The appropriateness of various models of vegetation to current ordination techniques is considered, particularly the gaussian species response curve. Two alternatives are suggested based on -functions and an ecological response curve model incorporating competition between species.     

Ordination methods and chironomid species in stony bottom streams

Stony bottom streams in Italy were sampled in 369 sites in different years, and 174 chironomid species (or species groups) were identified.The species by sites matrix was submitted to different ordination methods, with the aim of outlining the major factors that are responsible of the observed species composition.The methods considered were principal component analysis (PCA), detrended correspondence analysis (DCA) and non-metric multidimensional scaling (MDSCAL). These methods assume different models describing the species-responses to the environmental gradients.PCA gave poor results, the best species ordination was given by MDSCAL. DCA gave results in agreement with MDSCAL. DCA results were useful as a starting point to perform MDSCAL. MDSCAL was performed with different options. At last Procrustean analysis was carried out to have a single fitted configuration, that summarized the results given by the different MDSCAL methods.All multivariate analyses emphasized that the first ordination axis can be interpreted as a crenonrithron-potamon gradient, probably an oxygen availability and/or a water temperature gradient, whereas the second axis can be considered a water speed gradient, separating lotic from lentic sites.The 3rd and 4th ordination axes had apparently no ecological meaning.Separated clusters of species were never evident, so well defined chironomid species assemblages could not be outlined in this analysis.     

Measuring ecological niche overlap from occurrence and spatial environmental data

Aim Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data. Location Europe, North America and South America. Methods The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with pre‐defined distributions and amounts of niche overlap to evaluate several ordination and species distribution modelling techniques for quantifying niche overlap. We illustrate the approach with data on two well‐studied invasive species. Results We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographical space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results. Main conclusions The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate for studying niche differences between species, subspecies or intra‐specific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intra‐specific lineage has changed over time.     

Plant-environment relationships on the Montlake wildlife area,Seattle, Washington,USA

Grassland vegetation on the Montlake fill was analyzed using TWINSPAN. Eight herb communities were recognized. Moisture, proximity to gas vents, and disturbance are the main factors that control species and community distributions. Binary discriminant analysis (BDA) and detrended correspondence analysis (DCA) were used to study species-environment relationships. BDA revealed complex species response patterns and the resultant indicator values were used to interpret the ordination axes. Species distributions are controlled primarily by moisture, but also influenced by soil pH. Multiple regressions revealed little about plant-environment relationships not discovered by BDA. Before robust nonlinear methods are available, BDA, metric ordination with data stratification and nonmetric ordination are methods that can yield satisfactory results in exploratory plant-environment studies. BDA alone is an efficient, useful first approach where response patterns of species are initially unknown.Abbreviations BDA Binary Discriminant Analysis - DCA Detrended Correspondence Analysis     

Current problems of environmental gradients and species response curves in relation to continuum theory

Abstract. Comparisons of the positions of species on Grimes'C-S-R triangular ordination model with their responses to individual environmental gradients indicates that the C-S-R model does not necessarily predict species ecological behaviour. The importance of the stress, productivity and disturbance gradients relative to other environmental gradients needs to be determined. In studies of species behaviour along a biomass/productivity gradient the collective vegetation property, biomass, has been confused with the environmental factor, fertility. Patterns of responses to biomass gradients e.g. Keddy's centrifugal model, should be examined in a two-dimensional environmental space to avoid such confounding effects. Assumptions regarding the shapes of species responses to environmental gradients remain untested. A recent model of species response functions to environmental gradients suggested that skewed responses curves show a pattern in the direction of the skew, always with the tail towards the presumed most mesic position on the gradient. Further evidence is presented to support this model for a temperature gradient in eucalypt forest in south-eastern Australia. 21 out of 24 species tested conform to the model.     

Community pattern analysis: A method for quantifying community mosaic structure

A method of quantifying community spatial patterns, community pattern analysis, is described. It is proposed that ordination analysis is used to obtain an integrated score for each quadrat from transect data. For the data presented here, separate ordinations were made of both floristic and environmental (soils) data. The ordination axis scores are then analysed using two or three-term local variance analysis to quantify the scales of community pattern. Correlation analyses allow the relationship between the vegetation and soils data (as represented by ordination axis scores), and other environmental data to be investigated at defined scales. The advantages of this method, that employs the joint application of conventional methods, are that it includes the influence of all species in the analysis, and that multiple uncorrelated scales of pattern within a community are identified.     

Environmental correlates of species distributions in a saxicolous lichen community

Abstract. The importance of abiotic environmental factors in determining species distributions in a saxicolous lichen community at Jonas Rockslide, Jasper National Park, Alberta is assessed using Canonical Correspondence Analysis. This technique allows ordination of species on axes determined by measured environmental variables. The suitability of this technique for handling data which may not be normally distributed is confirmed by comparison with the results obtained using a non-parametric correlation coefficient. The variables found to be most highly correlated with species distributions are altitude on the rockslide and inclination from horizontal of the rockface (slope). These variables are thought to determine temperature and water availability at the rock surface. Using the first two ordination axes, species can be divided into groups, based on shared responses to the measured environmental variables.     

Analyzing floristic inventories with multiple maps

Spatial observations of plant occurrences contain a wealth of information on relations among species and on the relation between species and environmental conditions. Typically, inventory data of this kind are large co-occurrence matrices, and hence, direct ecological interpretations based on expert knowledge are often very difficult. Hitherto, ordination approaches have been used to construct a virtual ordination space (represented as one or multiple scatter plots) in which species that often co-occur are situated close together, whereas species that hardly co-occur are found far apart. In this study, we investigate a recently proposed ordination approach, multiple maps t-SNE, that constructs multiple, independent ordination spaces in order to reveal and visualize complementary structure in the data. We compare multiple maps t-SNE to several conventional ordination approaches, exploring a large inventory of vascular plant occurrences (FLORKART). Our results reveal that multiple maps t-SNE is well suited for the analysis of floristic inventories. In particular, multiple maps t-SNE uncovers the major dependencies of species co-occurrences on climate and soil biogeochemical preconditions.     

Studies of a vegetation transect through brigalow (Acacia harpophylla) forest in central Queensland

Vegetation and environmental data were collected in 182 contiguous plots along a belt transect, 3.7 km long, in central Queensland through a relatively undisturbed forest dominated by brigalow (Acacia harpophylla). A subset of eighty-nine plots using percentage cover of 128 species was classified using a polythetic agglomerative approach. Dual stand and species ordinations by principal component analysis and reciprocal averaging were also undertaken. The cluster analysis and ordination of unstandardized cover data, grouped stands on the basis of abundance of the predominant canopy species, but only where these species were true dominants such as Macropteranthes leichhardtii did these same groupings appear in the ordination of standardized data. The latter ordination was ecologically more satisfying, but the complementary species ordination was unsatisfactory. The vegetation-species complex was best explained by dual species and stand ordinations using presence-absence data. Reciprocal averaging appeared to produce a marginally better ordination than principal component analysis. An ordination of eleven environmental factors indicated soil profile and presence of gilgai were the most important environmental variables. The ordination was enhanced by varimax rotation which focused on a more homogeneous environmental gradient and coincided more closely with the vegetation ordinations. An ordination using both species and environmental factors substantiated the explanation of the vegetation-environmental complex derived from separate ordinations. The main gradient revealed from the ordinations appeared to be a mesic-xeric gradient stretching from Macropteranthes leichhardtii semi-evergreen vine thicket at the mesic end diverging through various A. harpophylla - dominant communities to A. harpophylla - Eucalyptus melanophloia woodland on duplex soils and Dichanthium affine grassland on clay soils. Six plant communities are defined and described and each related to a particular set of environmental conditions. These communities are bonewood (Macropteranthes leichhardtii) - semi-evergreen vine thicket, brigalow (Acacia harpophylla) - semi-evergreen vine thicket, brigalow (A. harpophylla) continuum (clay soils), Dichanthium affine grassland, brigalow (A. harpophylla) continuum (duplex soils) and brigalow (A. harpophylla) - silver-leaved ironbark (Eucalyptus melanophloia) woodland.     

Elements of metacommunity structure of Paraguayan bats: multiple gradients require analysis of multiple ordination axes

Techniques to evaluate elements of metacommunity structure (EMS; coherence, species turnover and range boundary clumping) have been available for several years. Such approaches are capable of determining which idealized pattern of species distribution best describes distributions in a metacommunity. Nonetheless, this approach rarely is employed and such aspects of metacommunity structure remain poorly understood. We expanded an extant method to better investigate metacommunity structure for systems that respond to multiple environmental gradients. We used data obtained from 26 sites throughout Paraguay as a model system to demonstrate application of this methodology. Using presence–absence data for bats, we evaluated coherence, species turnover and boundary clumping to distinguish among six idealized patterns of species distribution. Analyses were conducted for all bats as well as for each of three feeding ensembles (aerial insectivores, frugivores and molossid insectivores). For each group of bats, analyses were conducted separately for primary and secondary axes of ordination as defined by reciprocal averaging. The Paraguayan bat metacommunity evinced Clementsian distributions for primary and secondary ordination axes. Patterns of species distribution for aerial insectivores were dependent on ordination axis, showing Gleasonian distributions when ordinated according to the primary axis and Clementsian distributions when ordinated according to the secondary axis. Distribution patterns for frugivores and molossid insectivores were best described as random. Analysis of metacommunities using multiple ordination axes can provide a more complete picture of environmental variables that mold patterns of species distribution. Moreover, analysis of EMS along defined gradients (e.g., latitude, elevation and depth) or based on alternative ordination techniques may complement insights based on reciprocal averaging because the fundamental questions addressed in analyses are contingent on the ordination technique that is employed.     

Relationships between environmental variables and vegetation across mountain wetland sites,N. Iran

The mountain wetlands studied represent a unique habitat on the southern slopes of the Alborz mountain range, the second largest range in Iran. In comparison with other parts of this range the western section is ecologically and botanically unknown. Floristic and vegetation variation were assessed using diverse environmental variables along a broad altitudinal span (350 m to 3200 m a.s.l.). Using both statistical and ordination analyses floristic variation was assessed on three defined altitudinal belts which were delimited based on Alborz macro-climatic boundaries. The distribution of individual wetland plant species, of phytogeographic elements and of life-forms all differ among altitudinal belts. This result is also shown in both direct and indirect analyses of ordinations. The proportion of geophytes significantly increases with altitude and geophytes are very well represented in the upper altitudinal belt. The number of species of a narrow phytogeographical distribution (e.g. endemics) increases with altitude, soil pH and EC declined with altitude. The first axis of DCA ordination with passively projected environmental variables indicates that, organic matter and concentration of Fe²⁺ are increased toward higher altitude. The second axis of ordination is related to both soil texture and slope inclination. The distribution of species in the CCA species plot is also close to the distribution of those in the DCA ordination. This study indicates that altitude and slope together with other dependent environmental variables (pH, EC, Ca²⁺ and soil texture) are the main ecological factors controlling species distribution across the Western Alborz wetland sites.     

A new model for the continuum concept

A reformulation of the continuum concept is presented after considering the implications of the community/continuum controversy and current niche theory. Community is a spatial concept dependent on landscape pattern while the continuum is an environmental concept referring to an abstract space. When applying niche theory to plants, the mechanisms of competition are ill-defined and the assumption of bell-shaped response curves for species unrealistic.Eight testable propositions on the pattern of response of vegetation to environmental gradients are presented 1. Environmental gradients are of two types. a) resource gradients or b) direct physiological gradients. 2. The fundamental niche response of species to resource gradients is a series of similar nested response curves. 3. The fundamental niche response of species to direct gradients is a series of separate, independent, overlapping response curves. 4. Species fundamental response curves are such that they have a relative performance advantage in some part of the environmental space. 5. The shape of the realized niche is variable even bimodal but predictable from the fundamental response given the other species present. Propositions 6–8 describe the response shapes of emergent community properties to environmental gradient; species richness is bimodal, dominance trimodal and standing crop unimodal. Detailed comparisons of these propositions are made with the alternative theories of Ellenberg, Gauch and Whittaker, Grime, and Tilman. These theories are incomplete lacking several generally accepted properties of plants and vegetation.     

微生物生态研究中BIOLOG方法数据分析及R语言实现

微生物生态研究中,对微生物群落结构、群落特征以及其与环境因素的关系的揭示,一直受到广泛关注;适当的数据分析方法有助于更清晰地刻画微生物群落结构特征,明确其与环境因素的关系。结合实例,对微生物生态研究中基于BIOLOG微平板技术的数据分析方法进行梳理,分别介绍数据读取整理、特征指数计算、非限制性排序、限制性排序、聚类分析、环境向量拟合、蒙特尔检验等常用数据操作及生态分析方法;针对不同方法结论,结合研究目标和生态理论给出具有统计学意义的解释,并评价不同方法特点及适用场景;分析过程以R语言实现,并提供全部代码。结果表明,BIOLOG方法产生数据能从多个角度表征微生物群落功能特征,并结合环境指标梯度进行分析;但BIOLOG数据可能不满足正态性分布,在基于正态分布的分析前应提前进行检验;排序分析时应慎用主成分分析,可优先采用其他基于距离矩阵的排序方法;R语言能够简化BIOLOG数据读取及操作,易于完成各类统计分析。本研究能够对微生物生态研究者科学选择应用统计分析方法、提高数据处理效率提供直接参考。     

安太堡矿区人工植被在恢复过程中的生态关系

采用TWINSPAN、DCA和DCCA,从植物种、植物群落与环境因子关系方面对平朔安太堡矿区的人工植被在恢复过程中的生态关系进行了研究.结果表明,将63个样方划分为12个群落类型,反映了植物群落与环境梯度之间的关系,并列举了各群落的特征.DCA排序图明显反映出排序轴的生态意义,随着复垦时间的增加,土壤含水量也不断升高.DCCA排序进一步表明了土壤有机质含量是所有因子中对植物群落发展起决定性作用的主要环境因素.     

Two approaches using traits to assess ecological resilience: A case study on earthworm communities

The relation between biological diversity and ecosystem functioning is a central theme in ecology. Ecological traits of species are often regarded as a link between structure and function, and trait distributions in a community may change in response to environmental stressors. Likewise, resilience in a community may be derived from the diversity in traits and trait values relevant to a particular stressor. We combine two approaches to test this: a novel trait frequency analysis and a multivariate ordination approach. The two methods are applied on a case study of an earthworm community in a frequently flooded floodplain in the Netherlands. Periodic flooding in floodplains restricts population growth and recolonization of earthworms. The strategies employed by different earthworm species for coping with this stress can be described by a combination of ecological traits. From the literature we compiled 10 ecological traits for the earthworm species encountered along an inundation gradient in the Duursche Waarden floodplain area flanking the river IJssel. Trait frequency analysis showed a greater diversity at low elevation sites of traits considered to be associated to flood tolerance, suggesting greater community resilience to flooding. The ordination analysis using trait composition provided information on which trait classes in the community were related with the inundation stress. Results from both analyses showed that important traits in species to deal with flooding are active dispersal, high hydrophily, diapause and parthenogenetic reproduction. Thus, a further understanding of community resilience was gained by combining traditional ordination analysis with trait diversity analysis.