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.     

Mutation scanning methods for the analysis of parasite genes

Molecular variation is widespread in parasite populations, and its analysis has important implications for studying aspects relating to the function and organisation of genes, and the taxonomy, phylogeny and population genetics of parasites. This article reviews some PCR-based mutation scanning techniques that have advantages over currently used DNA methods for the analysis of genetic variation in parasites. The review is technical and describes briefly the principles of relevant techniques, examines some of their advantages and disadvantages and gives several examples for possible applications.     

Cytomorphometry. A methodologic study of preparation techniques, selection methods and sample sizes

The influence of methodologic aspects on cytomorphometric features was studied using preparations of hepatoma and/or mastocytoma cells. First, two preparation techniques (smear and oese) were compared. Second, four methods of selecting cells for cytomorphometric analysis (two conventional and two stratified methods) were tested for reproducibility. Third, heterogeneous cell populations were used to estimate the required sample size using the running coefficient of variation (CV), and the results were compared with expected (theoretical) values of the required sample size calculated using the standard error of the mean. The results showed significantly lower CVs for the smear preparation technique. The stratified methods appeared to be superior to the conventional methods for selecting cells for measurement. The experimentally assessed sample sizes were considerably lower than the corresponding theoretical calculations. These findings suggest that morphometric assessments in cytologic smears should utilize a stratified cell selection method. While experimentally assessed sample sizes are relatively small and therefore better routinely applicable, they may yield less reliable results in some cases. The need to test a sample for its reproducibility as well as its discriminatory power is emphasized.     

BIOMETRIC ANALYSIS OF GEOGRAPHIC VARIATION AND RACIAL AFFINITIES

1. The study of geographic variation and the racial affinities between populations is of central importance to systematics and evolutionary theory. When using phenotypic variation to measure the similarity between the populations of a species one should analyse the variation in several characters simultaneously. This is a statistical procedure and is known as multivariate analysis. Multivariate analysis of phenotypic variation, unlike some other methods, has the advantage of not being dependent on living specimens. 2. To obtain an adequate sample at each locality, and an adequate distribution of localities within a given geographic area, can be a major problem. The pooling of data from adjacent localities is discussed. 3. There are several sources of phenotypic variation within a species, e.g. sexual and ontogenetic variation. Failure to eliminate the non-geographic sources of variation can confuse the assessment of the similarity between populations. 4. Correlation between characters can reflect similar genetic control and/or similar patterns of geographic variation, the biological interpretation being influenced by whether the data come from one locality or many. 5. The influences of environmental induction and genetic control cannot easily be separated. Also, some characters may not be entirely homologous throughout the range of the species. 6. Most studies rely on far too few characters of a too restricted type to give an ‘overall’ assessment of the phenotypic similarity. This is one of the most neglected aspects of the study of geographic variation. 7. The various forms of clinal and categorical variation, the precise nature and position of sharp transition (hybrid) zones, the relationship between non-adjacent as well as adjacent populations and the phenotypic divergence between island populations, etc., all come under the heading of geographic variation. The ideal technique should be able to elucidate all types of geographic variation but some techniques can only be used effectively with a few of them. Moreover, techniques may be limited in their application because they require the data to conform to certain models, e.g. normal distribution. 8. The degree of phenotypic similarity between populations can be measured by a wide range of similarity coefficients. Comparison between even a small series of populations produces a large set (or matrix) of similarity coefficients that is difficult to interpret. However, the relationships between populations can be summarized in several ways and these may be loosely grouped into four categories; (i) network diagrams, (ii) contours and isometric plots, (iii) hierarchical clusters, and (iv) ordination methods. These methods are explained and their advantages and limitations discussed. 9. The hierarchical (dendritic) model of cluster analysis is unsuitable for analysing all but a few types of geographic variation. 10. There are several types of ordination technique. They all aim to summarize the variation of many characters in a reduced number of axes. One can either emphasize the biological interpretation of each separate axis, or treat the analysis as a classifying technique and assess the grouping of the populations in the space defined by the axes. Considerable care is needed in interpreting the results of both of these approaches. If correctly applied, ordination techniques generally can be used to analyse all the forms of geographical variation and are therefore recommended. Contrary to current practice they can be used with a large number of characters. The advantages and limitations of the various ordination techniques are discussed. 11. Contours and their three-dimensional isometric plots can be used to portray geographic variations in the information obtained from a multivariate analysis. However, contours and isometric plots are limited in their applicability and the amount of information they can convey. 12. The sophistication of some multivariate methods should not be allowed to cloak the scientific inadequacies of a study. The use of more than one technique and variety in the choice of pertinent parameters may be of value in indicating the reliability of the results.     

Within-species variation and measurement error in phylogenetic comparative methods

Most phylogenetically based statistical methods for the analysis of quantitative or continuously varying phenotypic traits assume that variation within species is absent or at least negligible, which is unrealistic for many traits. Within-species variation has several components. Differences among populations of the same species may represent either phylogenetic divergence or direct effects of environmental factors that differ among populations (phenotypic plasticity). Within-population variation also contributes to within-species variation and includes sampling variation, instrument-related error, low repeatability caused by fluctuations in behavioral or physiological state, variation related to age, sex, season, or time of day, and individual variation within such categories. Here we develop techniques for analyzing phylogenetically correlated data to include within-species variation, or "measurement error" as it is often termed in the statistical literature. We derive methods for (i) univariate analyses, including measurement of "phylogenetic signal," (ii) correlation and principal components analysis for multiple traits, (iii) multiple regression, and (iv) inference of "functional relations," such as reduced major axis (RMA) regression. The methods are capable of incorporating measurement error that differs for each data point (mean value for a species or population), but they can be modified for special cases in which less is known about measurement error (e.g., when one is willing to assume something about the ratio of measurement error in two traits). We show that failure to incorporate measurement error can lead to both biased and imprecise (unduly uncertain) parameter estimates. Even previous methods that are thought to account for measurement error, such as conventional RMA regression, can be improved by explicitly incorporating measurement error and phylogenetic correlation. We illustrate these methods with examples and simulations and provide Matlab programs.     

Microevolution in MioceneBrizalina (foraminifera) studied by canonical variate analysis and analysis of landmarks

A stratigraphically oriented series of the Miocene foraminiferal speciesBrizalina mandoroveensis from Ikang, Cameroon, was analyzed both by conventional multivariate morphometric procedures and by the tensor biometric method of Bookstein (1986;Statist. Sci. 1, 181–142), a method which analyzes sets of landmark points rather than specific variables of shape or size. The conventional analysis used five size-measures upon 170 specimens from five stratigraphic levels; the tensor analysis encompassed six landmarks (12 coordinates) upon 50 specimens. Whereas certain features appeared in both analyses, such as the separation between levels one and five, the techniques did not always agree with respect to the interpretation of those findings or about most details in the sequence of mean phenotypes. The canonical variate analysis bases its ordination upon a general size factor (the meaning of which is obscured by the foreshortening of within-group variation which is built into the technique). The tensor analysis locates a similar ordination using mainly features of shape.     

静止或缓流污染地表水微生物固定化修复技术研究进展

污染地表水体修复问题是最近几年才被广泛关注的环境保护课题,由于污染地表水体的特殊性,常规修复方法难以发挥高效作用,固定化微生物可以通过提供特殊的微环境,较好地保护优势菌不受土著菌恶性竞争,在保持高效修复能力的同时,可以将优势菌屏蔽于恶劣环境之外,在一定程度上克服了传统修复工艺的不足,具有较好的应用前景.本文概述了微生物固定化技术的特点,分析了利用固定化微生物修复污染环境介质存在的问题和可行性,针对城市静止或缓流污染地表水的特征,指出了将微生物固定化技术移植到污染地表水体修复领域需要解决的的关键技术.     

Variation in reaction norms: Statistical considerations and biological interpretation

Analysis of reaction norms, the functions by which the phenotype produced by a given genotype depends on the environment, is critical to studying many aspects of phenotypic evolution. Different techniques are available for quantifying different aspects of reaction norm variation. We examine what biological inferences can be drawn from some of the more readily applicable analyses for studying reaction norms. We adopt a strongly biologically motivated view, but draw on statistical theory to highlight strengths and drawbacks of different techniques. In particular, consideration of some formal statistical theory leads to revision of some recently, and forcefully, advocated opinions on reaction norm analysis. We clarify what simple analysis of the slope between mean phenotype in two environments can tell us about reaction norms, explore the conditions under which polynomial regression can provide robust inferences about reaction norm shape, and explore how different existing approaches may be used to draw inferences about variation in reaction norm shape. We show how mixed model‐based approaches can provide more robust inferences than more commonly used multistep statistical approaches, and derive new metrics of the relative importance of variation in reaction norm intercepts, slopes, and curvatures.     

Tissue culture of ornamental pot plant: a critical review on present scenario and future prospects

Recent modern techniques of propagation have been developed which could help growers to meet the demand of the horticultural industry in the next century. An overview on the in vitro propagation via thin cell layer, meristem culture, regeneration via organogenesis and somatic embryogenesis is presented. Available methods for the transfer of genes could significantly simplify the breeding procedures and overcome some of the agronomic and environmental problems, which other wise would not be achievable through conventional propagation methods. The development and remarkable achievements with biotechnology in ornamental pot plants made during the three decades have been reviewed. The usefulness of the pot plants in commercial industry as well as propagation techniques, screening for various useful characteristics and selection of somaclonal variation is also discussed.     

Pulsed EPR Determination of Water Accessibility to Spin-Labeled Amino Acid Residues in LHCIIb

Membrane proteins reside in a structured environment in which some of their residues are accessible to water, some are in contact with alkyl chains of lipid molecules, and some are buried in the protein. Water accessibility of residues may change during folding or function-related structural dynamics. Several techniques based on the combination of pulsed electron paramagnetic resonance (EPR) with site-directed spin labeling can be used to quantify such water accessibility. Accessibility parameters for different residues in major plant light-harvesting complex IIb are determined by electron spin echo envelope modulation spectroscopy in the presence of deuterated water, deuterium contrast in transversal relaxation rates, analysis of longitudinal relaxation rates, and line shape analysis of electron-spin-echo-detected EPR spectra as well as by the conventional techniques of measuring the maximum hyperfine splitting and progressive saturation in continuous-wave EPR. Systematic comparison of these parameters allows for a more detailed characterization of the environment of the spin-labeled residues. These techniques are applicable independently of protein size and require ∼10-20 nmol of singly spin-labeled protein per sample. For a residue close to the N-terminus, in a domain unresolved in the existing x-ray structures of light-harvesting complex IIb, all methods indicate high water accessibility.     

差异蛋白质组学的研究进展

差异蛋白质组是蛋白质组学研究的一个主要内容,其核心在于寻找某种特定臣寸素引起样本之间蛋白质组的差异,揭示并验证蛋白质组在生理或病理过程中的变化。进一步对蛋白质组差异信息分析后,理论上可以推断造成这种变化的原因。因此,对于临床上肿瘤预诊、药物靶标寻找、细胞调控分子的鉴别等有着极大的实际意义。差异蛋白质组研究要求可靠性和可重复性。因此,对于样本处理要求较高,激光微切割技术和高丰度蛋白去除技术的应用优化了样本处理方法。目前差异蛋白质组的主要研究方法仍是2-DE分离和MS鉴定联合应用,基于2-DE的2-DDIGE方法弥补了2-DE的弱点,更适用于差异蛋白质组研究。除2-DE技术外的其他几种技术手段,如多维液相色谱分离技术、ICAT技术、蛋白芯片技术等差异蛋白质组学研究技术可以作为2-DE技术的补充,甚至或替代技术。     

Where biology meets; or how science advances: Presidential Address to the Linnean Society delivered at the Anniversary Meeting, 24th May 1985

Major advances in 'unrestricted' sciences like biology commonly occur when individual scientists (or techniques) cross conventional discipline boundaries; intra-discipline studies are essential for the consolidation and progress of the science, but are less likely to produce significant insights. 'Restricted' (or exact) sciences ignore variation, and are probably less sensitive to warping from specialization. This generalization is illustrated by recent controversies in evolutionary biology, particularly the neutralism debates of the 1970s, where over-rigid adherence to theoretical models and unjustified assumptions about the effects of gene action were made. The consequence of some of these is shown by considering genetic changes in house mouse (Mus domesticus) populations which were used to demonstrate apparent drift operating on neutral traits, whereas longitudinal studies of closed populations proved that strong natural selection may operate; a proper understanding of genetical forces requires a knowledge both of the history of particular populations and of environmental pressures varying in time and space.     

Strain identification in Rhizobium trifolii using DNA restriction analysis, plasmid DNA profiles and intrinsic antibiotic resistances

Abstract Indigenous strains of R. trifolii , originating from different geographical regions, were compared using total DNA restriction analysis, plasmid DNA profiles and intrinsic antibiotic resistance patterns. The results of strain relatedness using 2 of these techniques (DNA restriction and antibiotic resistance patterns) were similar, and indicated that these strains formed a heterogeneous group. A large variation in plasmid DNA profiles was observed among the R. trifolii isolates investigated, indicating heterogeneity of plasmid DNA pools. This variation occurred even in some strains that were shown to be related on the basis of their antibiotic resistance patterns. The application of these techniques to differentiate indigenous R. trifolii strains is discussed in this report.     

Combining stable isotope analysis and conventional techniques to improve knowledge of the diet of the European Roller Coracias garrulus

Diet studies are crucial for understanding the ecology and evolution of species, as well as for establishing appropriate conservation and management strategies. However, they remain methodologically challenging due to variation between seasons, sites, sexes or age groups and even variation between individuals. Due to method‐specific characteristics and biases, a combination of existing techniques can overcome the inherent limitations of each technique and provide a more accurate and broad picture of species’ food preferences. Here, we examine diet information obtained using three different assessment methods to better understand the trophic ecology of the European Roller Coracias garrulus, a species targeted by conservation measures in Europe. First, we analysed regurgitated pellets and video‐recordings to report the diet composition of adult and nestling Rollers, respectively. Secondly, we used stable isotope analysis (SIA) to investigate adult sexual diet segregation as well as to confirm the main findings regarding adult and nestling diets obtained through conventional methods. Based on the analysis of pellets, the diet of adult Rollers was dominated by Coleoptera, whereas camera images revealed that the diet of nestlings was dominated by Orthoptera, mainly grasshoppers and bush crickets. Blood isotopic signatures of adult and nestling Rollers confirmed the results obtained through pellet and video‐recording techniques. Of the three methods, pellet analysis provided the most comprehensive trophic information regarding the detectable prey spectrum and prey species contribution, as well as basic diet information for the SIA. Our results also highlight the potential of SIA for assessing intraspecific variation in diet by sampling individuals of known age and sex, which is often unfeasible through conventional approaches. SIA analysis showed no differences in δ¹³C and δ¹⁵N ratios of blood between males and females and a high degree of overlap amongst isotopic niches, suggesting no sex‐specific partitioning in resource use. Overall, we showed that the combination of different methods could be used to gain new and clearer insights into avian trophic ecology that are essential for informing habitat management aiming to improve availability of foraging resources.     

Spatial Uncertainty and Ecological Models

Applied ecological models that are used to understand and manage natural systems often rely on spatial data as input. Spatial uncertainty in these data can propagate into model predictions. Uncertainty analysis, sensitivity analysis, error analysis, error budget analysis, spatial decision analysis, and hypothesis testing using neutral models are all techniques designed to explore the relationship between variation in model inputs and variation in model predictions. Although similar methods can be used to answer them, these approaches address different questions. These approaches differ in (a) whether the focus is forward or backward (forward to evaluate the magnitude of variation in model predictions propagated or backward to rank input parameters by their influence); (b) whether the question involves model robustness to large variations in spatial pattern or to small deviations from a reference map; and (c) whether processes that generate input uncertainty (for example, cartographic error) are of interest. In this commentary, we propose a taxonomy of approaches, all of which clarify the relationship between spatial uncertainty and the predictions of ecological models. We describe existing techniques and indicate a few areas where research is needed.     

分子水平的遗传多样性及其测量方法

遗传多样性水平是一项很重要的数据。目前从分子水平量化遗传多样性的方法以等位酶分析、ＲＦＬＰ分析和ＲＡＰＤ分析为代表。遗传变异在基因组中并非随机分布,所以取样方式对分析结果的影响不容忽视。本文叙述了遗传变异的产生和分布,并以此为基础比较了上述３种分析方法的理论与实践。     

Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex

Interest in cryptic species has increased significantly with current progress in genetic methods. The large number of cryptic species suggests that the resolution of traditional morphological techniques may be insufficient for taxonomical research. However, some species now considered to be cryptic may, in fact, be designated pseudocryptic after close morphological examination. Thus the “cryptic or pseudocryptic” dilemma speaks to the resolution of morphological analysis and its utility for identifying species. We address this dilemma first by systematically reviewing data published from 1980 to 2013 on cryptic species of Copepoda and then by performing an in‐depth morphological study of the former Eurytemora affinis complex of cryptic species. Analyzing the published data showed that, in 5 of 24 revisions eligible for systematic review, cryptic species assignment was based solely on the genetic variation of forms without detailed morphological analysis to confirm the assignment. Therefore, some newly described cryptic species might be designated pseudocryptic under more detailed morphological analysis as happened with Eurytemora affinis complex. Recent genetic analyses of the complex found high levels of heterogeneity without morphological differences; it is argued to be cryptic. However, next detailed morphological analyses allowed to describe a number of valid species. Our study, using deep statistical analyses usually not applied for new species describing, of this species complex confirmed considerable differences between former cryptic species. In particular, fluctuating asymmetry (FA), the random variation of left and right structures, was significantly different between forms and provided independent information about their status. Our work showed that multivariate statistical approaches, such as principal component analysis, can be powerful techniques for the morphological discrimination of cryptic taxons. Despite increasing cryptic species designations, morphological techniques have great potential in determining copepod taxonomy.     

Multiple fetal and adult hemoglobins in Malaysian Macaca nemestrina: consequences of a-chain variation

The hemoglobins of fetal and adult Macaca nemestrina were investigated electrophoretically and chromatographically. Standard electrophoretic techniques failed to reveal variation in either fetal or adult hemoglobins beyond that previously attributed to the presence of the duplicate γ-chain loci characteristic of this species. However, column chromatography of whole hemolysates on CM-Sephadex or of globin chains on CM-cellulose in 8 M urea revealed that some fetuses had four major hemoglobins and some adults had two major hemoglobin components. All animals examined were of Malaysian origin; the variation described is a consequence of variation in α-chain structure in Malaysian populations of this species, and of the interaction of different α chains with the products of the duplicate γ-chain loci.     

Developments in stallion semen evaluation

The conventional approach to evaluation of stallion semen dates back several decades, and includes evaluation of spermatozoal concentration, semen volume, spermatozoon morphological characteristics, and spermatozoal motility patterns initially and following in-vitro storage. While an analysis performed in this manner does have predictive value, incorporation of some more newly developed techniques may improve the predictive value of the examination. This communication addresses some newer tests that can be applied today for evaluation of semen, as well some tests that may be available in the coming years.     

Taking the stress out of blood collection: comparison of field blood‐sampling techniques for analysis of baseline corticosterone

Many ecological studies use stress hormones to assess the condition, health or disturbance levels of wild organisms. Common blood sampling protocols for this research involve trapping individuals and taking blood within three minutes to obtain a “baseline” for analysis of stress hormones (“conventional method”). In some situations it may be difficult to get an accurate measure of baseline values; therefore, alternative sampling techniques may be preferable. We compared corticosterone levels in samples taken via a newly developed, minimally invasive blood sampling technique with corticosterone levels in blood taken via the conventional method. We collected samples from incubating adult common terns Sterna hirundo via blood sucking bugs (Heteroptera, Triatominae) contained in “dummy eggs” (“bug method”) and compared measured corticosterone concentrations to concentrations in blood taken from the same birds using the conventional method. We found no significant differences in mean or variance of baseline corticosterone levels between samples collected via the different methods. This suggests that the bug method offers a viable alternative for hormone sampling.