等位基因多态性群体遗传结构的多元非线性分析方法

长期以来,对于多维基因多态性数据的多元统计分析,如计算遗传距离时昕用的聚类分析、分析群体遗传结构时所用的主成分分析、因子分析和典型相关分析等,一直应用为无约束条件数据而设计的经典多元线性分析方法,并没有注意基因多态性数据的“闭合效应”所带来的问题。从分析基因多态性数据的分布和结构特征入手,文中指出了基因多态性分布具有“闭合数据”的特点,分析了由于“闭合效应”的影响,经典多元线性方法用于群体遗传结构分析昕面临的困难。根据成分数据统计分析的理论和方法,提出了基因多态性群体遗传结构的多元非线性分析基本方法。并以主成分分析为例,通过实例比较和分析了经典线性主成分分析和“对数比”非线性主成分分析的结果,证明“对数比”非线性主成分分析方法是研究基因多态性群体遗传结构的良好方法,具有特异、灵敏等优点,其结果符合群体遗传学规律。     

The Hindlimb Elements of the Maas (Aves,Dinornithidae): A Multivariate Assessment of Size and Shape

A multivariate morphometric analysis of size and shape was performed on the hindlimb skeletal elements of the extinct New Zealand moas (Dinornithidae). Investigations were undertaken of size-shape patterns within species and among moas as a group using principal components analysis; between species investigations used canonical analysis. In addition, standard allometric curve-fitting of six femur, seven tibiotarsus, and nine tarsometatarsus variables against body size was performed. Size was the major discriminator along the first principal component for all three bones in the intraspecific and whole-group analyses. Shape was the important discriminator along the second component: in the whole-group analysis of all three bones, separation was based on relative robustness of the shaft, whereas in the intraspecific analyses shaft robustness was only expressed in the analysis of the femur, there being little correspondence in the results between the intraspeci fic and whole-group analyses of the tibiotarsus and tarsometatarsus. Size was the major discriminator along the first canonical axis for the between-group investigations of the femur and tibiotarsus, but in the analysis of the tarsometatarsus shape influences were equally as important as those of size. The second canonical axis separated groups on the basis of shape differences in all three hindlimb elements. The genus Dinornis, which contains the largest species of moas, has evolved sizeshape patterns very different from those of other moas. The species of Dinornis did not follow size-dependent allometric trends and evolved proportionately thinner legs than might be expected for their body size. All other moas exhibit allometric increase in all hindlimb variables except bone lengths. Dinornis may have evolved a cursorial mode of locomotion as an adaptation for certain intraspecific behavioral interactions.     

人体冲击与人体代用品的研究──猕猴与人形体的相关特性

本文在实际测量数据的基础上,提出一种运用主成分分析的方法对数据进行筛选和匹配,进而对人体和猕猴作典型相关分析,从而得出这种替代是有意义的．     

Interspecific relations of African crocidurine shrews (Mammalia: Soricidae) based on multivariate analysis of mandibular data

Eighteen graded non-metric characters and 30 measurements of the mandible and lower dentition were used to investigate the grouping of African species of the genera Crocidura, Suncus and Sylvisorex. Seventy-seven taxa (species, subspecies and synonyms), including four European species, were represented by one to nine mandibles (147 mandibles in all), and the means of four Pleistocene African species were also included. The metric data were subjected to principal component and canonical variate analyses, and the non-metric data to principal component analysis. Grouping was detected by comparing the results of the three analyses. Six groups are recognized within the genus Crocidura , typified by C. fumosa, C. turba, C. russula, C. fuscomurina, C. hirta and C. flavescens. Sylvisorex is divisible into two groups, typified by S. lunaris and S. granti. The African species of Suncus (but not the introduced species, S. murinus ) form a single group, which is linked to the Sylvisorex granti group. Suncus is closely related to, or convergent with, the Crocidura fuscomurina group. The first non-metric principal component, the second metric principal component and the second canonical variate are significantly correlated. It is considered that these together represent a general trend of evolutionary advance. Phylogenetic relations are discussed in the light of this; Crocidura may be diphylefic.     

Ecomorphology of a size-structured tropical freshwater fish community

Among nine species of a tropical community ecomorphological correlates were sought throughout ontogeny. Ontogenetic changes were distinguished by establishing six pre-defined size-classes. Morphometric data associated with feeding were compared by canonical correspondence analysis to dietary data. This analysis revealed seven significant relationships, showing 71% of the morphological variance explained 77% of the variance in diet. Based on funtional ecomorphological relationships established in other studies and results of the canonical correspondence analysis, three food characters were selected: the size of the food particles, the type of food (vegetable versus animal) and the vertical position in the water column. The morphometric data were reduced using principal component analysis into three axis explaining 83% of the variation. The morphological characters with the highest loadings were: mouth gape on the first principal component axis, length of the intestine tract on the second and the orientation of the mouth together with the presence of barbels on the third. These axis were significantly correlated with, respectively, the size, the type and the vertical position of the food. The importance of morphological changes during ontogeny in explaining dietary changes was shown because 75% of the variation in the first, and most important, morphological principal component was accounted for by differences between size-classes. Assuming functional relationships, the potential niches of the species/size-classes were established, distinguishing herbivorous, omnivorous/molluscivorous and carnivorous species which, in turn, were segregated by their potential to feed on larger prey. This revised version was published online in July 2006 with corrections to the Cover Date.     

Choosing the number of principal coordinates when using CAP,the canonical analysis of principal coordinates

This study explores various options available for choosing the number of principal coordinates m in the canonical analysis of principal coordinates ‘CAP’, a useful procedure that has wide‐ranging application wherever multivariate data sets are collected or generated. Choosing too few coordinates (small m) in this constrained (i.e. hypothesis‐based) ordination procedure may lead to inadequate separation of the groups (when used as a canonical discriminant analysis) or to inadequate correlation between explanatory and response variables (when used as a canonical correlations analysis), whereas choosing too many (large m) may lead to overparameterization, resulting in overfitting of the data and spurious relationships. It is shown here that the optimum number of principal coordinates is simply the one that results in the smallest P value in the canonical analysis carried out using permutations. For data in which more than one m value results in the same minimum P value, m should be chosen from that set to be the number of principal coordinates that minimizes the leave‐one‐out residual sum of squares. This choice of m provides suitable solutions for each of the 17 case studies investigated here (which yielded 17 canonical discriminant analyses and 7 canonical correlation analyses).     

Beyond principal component analysis: Canonical component analysis for data reduction in classification of EPs

The authors tested a new procedure for the discrimination of EPs obtained in different stimulus situations. In contrast with principal component analysis (PCA) used so far for the purpose of data compression, the method referred to as canonical component analysis (CCA) is optimal for the purpose of discrimination. To illustrate this, the authors performed both PCA and CCA for the same material, then after carrying out discriminant analysis (SDWA) for the data transformed in this way, compared the performance of the two procedures in discrimination. In view of both the theoretical and practical considerations, the authors recommend that in the future researchers use CCA instead of PCA in EP studies for data reduction carried out for discrimination.     

辽宁省冰砬山森林立地分类的研究

森林立地的研究是人工林集约经营的基础,正确地选择宜林地,科学造林,真正做到适地适树,必须进行森林立地分类。森林立地分类应是以现代森林生态学和生态系统理论为依据,研究植被(立木、下木、地被物)和地形、植被与土壤以及地形和土壤的关系。在揭     

Multiple Linear Regression on Canonical Correlation Variables

When the explanatory variables of a linear model are split into two groups, two notions of collinearity are defined: a collinearity between the variables of each group, of which the mean is called residual collinearity, and a collinearity between the two groups called explained collinearity. Canonical correlation analysis provides information about the collinearity: large canonical correlation coefficients correspond to some small eigenvalues and eigenvectors of the correlation matrix and characterise the explained collinearity. Other small eigenvalues of this matrix correspond to the residual collinearity. A selection of predictors can be performed from the canonical correlation variables, according to their partial correlation coefficient with the explained variable. In the proposed application, the results obtained by the selection of canonical variables are better than those given by classical regression and by principal component regression.     

微生物生态研究中基于BIOLOG方法的数据分析

BIOLOG微平板法作为一种方便快速的微生物检验技术,已广泛应用于环境微生物检测,微生物生态研究等方面,发挥着越来越重要的作用。该方法可以获得关于微生物群落碳源利用能力的大量数据,反映出关于微生物活性的丰富信息。然而大量的数据也对解释和分析提出了挑战,分析了应用于BIOLOG产生数据的统计分析方法,对常用的AWCD值计算,多样性指数计算,主成分分析(PCA),聚类分析,相关、回归等方法深入探讨,阐述各自的功能、不足以及在应用中容易出现的问题。另外也对一些不常见的方法,如非参数多元分析(Non-Parametric version of MANOVA/Permutation version of MANOVA)、动力学参数分析、多元回归树、典范对应分析等也进行了讨论。通过对不同方法应用目标和原理的分析论述了各自优缺点,对微生物研究中基于BIOLOG方法数据分析的选择应用提供参考。     

不同寄主上桃粉大尾蚜的取食偏好及形态变异研究

【目的】桃粉大尾蚜Hyalopterus pruni Geoffroy是一种常见的农业害虫,分布广泛。本文对采自上海地区粘核毛桃Amygdalus persica L.var.scleropersica(Reich.)Yüet Lu、紫叶李Prunus cerasifera Ehrhar f.atropurpurea(Jacq.)Rehd.和芦苇Phragmites australis(Cav.)Trin.ex Steud.3种植物上桃粉大尾蚜的取食偏好和形态变异进行了研究。【方法】通过叶碟法观测桃粉大尾蚜对3种寄主叶片的取食偏好,同时测量体长、体宽、触角各节长、喙末端长和宽、各足节长等30个形态指标,基于对形态数据的统计分析,包括主成分分析、聚类分析和判别分析,研究不同寄主植物上桃粉大尾蚜的形态变异。【结果】饲以3种寄主植物叶片时,来自粘核毛桃和芦苇上的桃粉大尾蚜对各寄主叶片的总体喜食程度依次为芦苇>粘核毛桃>紫叶李,来源于紫叶李上的个体对3种叶片的喜食程度为芦苇>粘核毛桃=紫叶李;形态数据分析发现粘核毛桃和紫叶李上的桃粉大尾蚜各指标间均无显著差异(P>0.05),但二者与芦苇上的个体在触角节Ⅱ、触角末节鞭部长、喙末端长和中足胫节的长度间差异显著(P<0.05),紫叶李与芦苇上的个体前足跗节Ⅰ长这一指标差异显著(P<0.05),此外,主成分分析筛选的体长、头宽、触角各节和各足长度等特征构成的前四个主成分对总体方差的累计贡献率达到66.206%,其中贡献率较高的特征为触角和各足节长度,系统聚类和典型判别分析的结果显示采自芦苇上的桃粉大尾蚜区别于粘核毛桃和紫叶李上的,归为一类,同为蔷薇科植物的紫叶李和粘核毛桃上的桃粉大尾蚜克隆有小部分重叠。【结论】禾本科植物上的桃粉大尾蚜种群形态特征与蔷薇科植物上的相比,触角节Ⅱ和末节鞭部、喙末端长、中足胫节的长度存在一定的分化,初步推测造成桃粉大尾蚜形态分化的原因主要为寄主植物营养成分及其表面特征,其种内变异的具体机制仍需进一步探索。     

Associations between fish assemblages and environmental factors for Mediterranean-type rivers during summer

The structure of summer fish assemblages was examined along longitudinal gradients in 31 Mediterranean-type rivers of the middle Guadiana basin (south-west Iberian Peninsula), using data from 157 sites including small streams to deep rivers. An ordination analysis, based on 16 variables, was applied to species presence, using principal component and canonical correspondence analysis. The results for the habitat data were compared with those for the biological data using a Mantel analysis, and the agreement was highly significant. Spatial structure was considered by partitioning the total variability among the environmental and geographical variables. The fish assemblages showed longitudinal zoning during the summer, with species distributed over gradients of habitat size (depth), water quality (current and physico-chemical variables), and cover (substratum and vegetation), according to their adult size and life history. The size of the habitat that remained available in summer had the greatest biological effect, being the most important factor explaining fish species distribution and assemblage structure during this stressing season. Strictly spatial variation was low, but there was still a high residual variation. Habitat associations and life-history strategies are discussed for native and exotic species.     

Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis.

A comparison is made between a 200-ps molecular dynamics simulation in vacuum and a normal mode analysis on the protein bovine pancreatic trypsin inhibitor (BPTI) in order to elucidate the dual aspects of harmonicity and anharmonicity in the dynamics of proteins. The molecular dynamics trajectory is analyzed using principal component analysis, an effective harmonic analysis suited for comparison with the results from the normal mode analysis. The results suggest that the first principal component shows qualitatively different behavior from higher principal components and is associated with apparent barrier crossing events on an anharmonic conformational energy surface. The higher principal components appear to have probability distributions that are well approximated by Gaussians, indicating harmonicity. Eliminating the contribution from the first principal component reveals a great deal of correspondence between the 2 methods. This correspondence, however, involves a factor of 2, as the variances of the distribution of the higher principal components are, on average, roughly twice those found from the normal mode analysis. A model is proposed to reconcile these results with those from previous analyses.     

Climate in relation to deterioration of stored grain

Summary A hypothesis elucidating the basic relationship between abiotic climatic variates and the deterioration of stored grain by biotic agents was developed for the 41 crop districts in the Prairie Provinces of Canada. Principal component (7 variates measured) and canonical correlation (6 variates measured) analyses were applied to data from each of the 3 crop years (1967–1969), for each of the 3 principal component analyses and for each of the 3 canonical correlation analyses. The data consisted of crop district means of infestation reports from 2522 managers of grain elevators and also of representative meteorological observations from each crop district. The major variates measured were the number of reports of: hot spots, infestations of a) fungus beetles and mites, and b) Cryptolestes ferrugineus (Stephens), and grain fumigants. The climatic variates consisted of mean temperature, precipitation, and number of days above 20° C (68° F) for July, August and September. Three major components, which together explained 64–80% of the variation, indicated broadly similar trends in all analyses. The first component indicated that lower mean temperatures and larger numbers of cool days increased the incidence of fungus-induced hot spots in wet harvested grain. The second component indicated the extent of arthropod infestations: warmer weather increased C. ferrugineus infestation, whereas cooler weather increased infestation by mites and secondary insect species. The third component was a measure of precipitation. Canonical correlation analyses based on 1967 and 1969 data yielded canonical roots that were statistically insignificant at the 1% level. Analyses of 3 external abiotic and 3 biotic response variates based on 1968 data showed that only the first pair of canonical variates was significant, the degree of predictability (R _c ² ) being 56% (P<0.01). The analyses revealed that lower temperatures, a greater number of cool days, and higher precipitation increased the number of hot spots in 1968 confirming the findings of the principal component analyses. The pattern of hot spot development in relation to climatic characteristics was similar in all crop districts for all years examined. There was a linear relationship between climatic and biotic variates for all these crop districts but the degree of relationship varied geographically. The first and second principal component values for each crop district were ranked and plotted on a climatic map of the Prairie Provinces. The ranking showed that the incidence of hot spots and arthropod infestations was highest in the Sub-boreal and Humid southeastern regions, whereas the incidence was lowest in the Dry Belt region. C. ferrugineus was most common in the Humid southeastern region.Contribution No. 522 from Canada Department of Agriculture, Research Station, Winnipeg, Manitoba, R3T 2M9, Canada.     

The taxonomic status of the Tuva vole Alticola (A.) tuvinicus Ognev (Mammalia: Arvicolinae)]

Some forms united under species Alticola tuvinicus s. lato (4 samples), A. semicanus (1 sample), A. argentatus (8 samples) are compared by 16 characters by means of principal component method and canonical analysis. Species distinctness of A. semicanus is confirmed. Specific status of the form olchonensis is supposed. The results concerning tuvinicus s. str. and kosogol are not clear-cut: these forms may be well differentiated subspecies within either A. tuvinicus s. lato or A. argentatus.     

Environmental factors influence on chemical polymorphism of the essential oils of Lychnophora ericoides

Lychnophora ericoides is a Brazilian medicinal plant used in folk medicine as an anti-inflammatory and analgesic agent. The essential oils from leaves of two populations with and without scent, collected at 2-month intervals during an 1-year period, were analysed by GC-MS. The results were submitted to principal component and cluster analysis which allowed two groups of essential oils to be distinguished with respect to sampling site and scent: cluster I (Vianópolis site, with specimens exhibiting an aromatic scent) containing a high percentage of alpha-bisabolol (44.7-76.4%) and alpha-cadinol (10.9-23.5%), and cluster II (Cristalina site, with specimens without scent) characterised by a high content of (E)-nerolidol (31.3-47.1%) and ar-dihydro-turmerone (4.8-15.4%). The canonical discriminant analysis showed that using the data set of the seven sampling months and (E)-nerolidol and alpha-bisabolol as predictable variables, it was possible to distinguish between the samples harvested according to Cerrado seasons, dry winter (May-September) and humid summer (November-March). In addition, canonical correlation analysis between the soil sampling sites and the populations revealed a significant relationship between oil components and edaphic factors. Oxygenated sesquiterpenes and potential acidity, Al saturation, cationic exchange capacity, silt, and sand load as the first canonical variate were fairly strongly related to samples collected in Vianópolis site. On the other hand, monoterpenes and sesquiterpene hydrocarbons were strongly related to chemical balance in soils (organic matter, P and base saturation), which is related to samples at the Cristalina site. The chemovariation observed appears to be environmentally determined.     

Challenges in the presentation and analysis of plant-macrofossil stratigraphical data

Plant-macrofossil analysis is being increasingly used in Quaternary science, particularly palaeoecology and vegetation history. Although the techniques of macrofossil analysis are well-tried and relatively simple, the resulting data consisting of qualitative binary presences and absences, ordinal classes, and quantitative counts are not simple from the viewpoint of numerical data-analysis. This essay reviews the nature of macrofossil data and discusses the problem of zero and non-zero values. Problems in the presentation of macrofossil data are outlined and possible solutions are discussed. The handling of such data is discussed in terms of data summarisation, data analysis, and data interpretation. Newly developed numerical methods that take account of the mixed nature and the stratigraphical ordering of macrofossil data are outlined, such as (distance-based) multivariate regression trees, canonical analysis of principal coordinates, principal curves, cascade multivariate regression trees, and RLQ analysis. These and other techniques outlined have the potential to help exploit the full potential of macrofossil stratigraphical data in Quaternary palaeoecology.     

Resolution of batch variations in pyrolysis mass spectrometry of bacteria by the use of artificial neural network analysis

A simple, but stringent, three group model of bacterial interstrain identity (two cultures of the same strain ofEscherichia coli) and difference (a culture of a serologically distinct strain) was used in multiple serial weekly subcultures for five weeks to demonstrate the effect of both growth-related (phenotypic) and machine-related variation on pyrolysis mass spectra. An aliquot of serum from a single sample was included in each pyrolysis batch to distinguish machine drift from culture drift. Conventional principal component (PC) canonical variate (CV) analysis was successful within each pyrolysis batch but the variations between batches precluded the use of data from more than one batch in successful PCCV analysis. In contrast, artificial neural networks (ANNs) trained with data from one batch could be successfully used to identify groups in data from non-contemporaneous pyrolysis batches. Although the ANN method will require validation in more complex settings than this simple model, it is a promising approach to the problem of batch constraint in pyrolysis mass spectrometry.     

Characterization of exopolymers of aquatic bacteria by pyrolysis-mass spectrometry

Exopolymers from a diverse collection of marine and freshwater bacteria were characterized by pyrolysis-mass spectrometry (Py-MS). Py-MS provides spectra of pyrolysis fragments that are characteristic of the original material. Analysis of the spectra by multivariate statistical techniques (principal component and canonical variate analysis) separated these exopolymers into distinct groups. Py-MS clearly distinguished characteristic fragments, which may be derived from components responsible for functional differences between polymers. The importance of these distinctions and the relevance of pyrolysis information to exopolysaccharide function in aquatic bacteria is discussed.     

Multivariate patterns of geographic variation between the island and mainland populations of the Eastern grass snake (Natrix natrix natrix)

The substantial racial variation between the mainland and island populations of the Eastern grass snake ( Natrix natrix natrix ) is analysed by a range of multivariate methods, including principal component and canonical analysis. These techniques reveal a complex pattern of geographic variation which include sharp transition zones, gradual clines, a wide range of divergence of island populations and greater divergence per distance in the south than in the north. These patterns relate to the phylogenesis of this "incipient" species, and its post-Pleistocene range expansion as presented here and elsewhere. These racial patterns do not generally relate to physiographic features, conventional subspecies or CURRENT physical or biotic factors.