Quantitative handling of characters useful in snake systematics with particular reference to intraspecific variation in the Ringed Snake Natrix natrix (L.)

This paper is based on the numerous characters used in a biometric study of the intraspecific variation of Natrix natrix (L.). These characters are drawn from the internal morphology, scalation, colour pattern, body proportions, dentition and dermal sense organs. The criteria involved in selecting these characters for taxonomic work are considered.
The alternative methods for quantifying the above features are discussed and so are the theoretical problems involved in coding the continuous characters.
The value of the characters in studying the geographic variation, ontogenetic variation and sexual dimorphism in N. natrix is indicated.
The use of a wider range of characters than just the scalation and colour pattern is urged when diagnosing the lower taxonomic levels of ophidians. The neglected internal morphology may well be able to supply characters to this end.     

Palynological richness and evenness: insights from the taxa accumulation curve

Palynology provides the opportunity to make inferences on changes in diversity of terrestrial vegetation over long time scales. The often coarse taxonomic level achievable in pollen analysis, differences in pollen production and dispersal, and the lack of pollen source boundaries hamper the application of diversity indices to palynology. Palynological richness, the number of pollen types at a constant pollen count, is the most robust and widely used diversity indicator for pollen data. However, this index is also influenced by the abundance distribution of pollen types in sediments. In particular, where the index is calculated by rarefaction analysis, information on taxonomic richness at low abundance may be lost. Here we explore information that can be extracted from the accumulation of taxa over consecutive samples. The log-transformed taxa accumulation curve can be broken up into linear sections with different slope and intersect parameters, describing the accumulation of new taxa within the section. The breaking points may indicate changes in the species pool or in the abundance of high versus low pollen producers. Testing this concept on three pollen diagrams from different landscapes, we find that the break points in the taxa accumulation curves provide convenient zones for identifying changes in richness and evenness. The linear regressions over consecutive samples can be used to inter- and extrapolate to low or extremely high pollen counts, indicating evenness and richness in taxonomic composition within these zones. An evenness indicator, based on the rank-order-abundance is used to assist in the evaluation of the results and the interpretation of the fossil records. Two central European pollen diagrams show major changes in the taxa accumulation curves for the Lateglacial period and the time of human induced land-use changes, while they do not indicate strong changes in the species pool with the onset of the Holocene. In contrast, a central Swedish pollen diagram shows comparatively little change, but high richness during the early Holocene forest establishment. Evenness and palynological richness are related for most periods in the three diagrams, however, sections before forest establishment and after forest clearance show high evenness, which is not necessarily accompanied by high palynological richness, encouraging efforts to separate the two.     

The assembly of ionic currents in a thalamic neuron. III. The seven-dimensional model

We replace our earlier three-dimensional ha-model of a thalamic neuron (Rose & Hindmarsh, Proc. R. Soc. Lond. B 237, 289-312 (1989b)) by a seven-dimensional ha-model. The stability and state diagrams for this seven-dimensional model are shown to be similar to those of the three-dimensional system with which it is compared. Two examples that illustrate how the seven-dimensional model can be related to experimental recordings are then discussed in detail. In each case we show the state and stability diagrams and the time courses of the different ionic currents during the burst response. We discuss how the various components of the state diagram could be determined experimentally. These experiments are illustrated by using our model to simulate the results of actual experiments. Finally the state and stability diagrams are transferred to a current-voltage diagram. This shows the advantage of the state diagram compared with the current-voltage diagram for representing the dynamics of the firing of a thalamic neuron.     

A universal bifurcation diagram for seasonally perturbed predator-prey models

The bifurcations of a periodically forced predator-prey model (the chemostat model), with a prey feeding on a limiting nutrient, are numerically detected with a continuation technique. Eight bifurcation diagrams are produced (one for each parameter in the model) and shown to be topologically equivalent. These diagrams are also equivalent to those of the most commonly used predator-prey model (the Rosenzweig-McArthur model). Thus, all basic modes of behavior of the two main predator-prey models can be explained by means of a single bifurcation diagram.     

A Reexamination of Roper’S Trend-Surface Analysis of Central Plains Radiocarbon Dates

Abstract

A reexamination of Roper’s (1976) trend-surface analysis of Central Plains radiocarbon dates indicates that 1) a nonlinear trend in the data was not recognized, and 2) the dates of the trend-surface contours given in her map of the Central Plains are in error. A revised trend-surface model is presented which better describes the site data and more closely agrees with the Central Plains cultural sequence.     

Phase diagrams for DNA crystallization systems

Phase diagrams for several oligonucleotide duplex-spermine systems have been constructed. These diagrams characterize the duplex and spermine concentrations ranges in which crystalline precipitates are formed. All of them are wedge-like form. The slope of the upper branch of the diagram is determined by the oligonucleotide length. The position of the lower branch depends on both the nucleotide sequence and its length. The position of the lower branch depends on both the nucleotide sequence and its length. It has been shown that the addition to the system of MgCl2 and NaCl salts and MPD results in specific changes in the diagrams. A model for oligonucleotide duplex-spermine system has been suggested which explains the main characteristic features of the obtained phase diagrams. The experimental phase diagrams for the (pGpT)n (pApC)n-spermine system (n = 2,3,4) have been analyzed ion terms of this model and the values of the binding constants of spermine and Mg2+ ions binding to duplexes have been determined. It permitted to identify the complexes that precipitated in different regions of the phase diagrams under various conditions. The diagram obtained in the presence of a cobalt hexammine counterion is also considered. It has been shown that this phase diagram, in general, is similar to those obtained for the oligonucleotide duplex-spermine system.     

Effects of molecular structure on two-dimensional phase diagram and thermodynamic quantities of mixed monolayers

Many kinds of two-component mixed monolayer systems were investigated to clarify the effect of molecular structures on the monolayer state. Two-dimensional phase diagrams and thermodynamic quantities were evaluated by correct thermodynamic analysis. The diagrams were classified into the following six types: (1) cigar type; (2) modified cigar type; (3) positive azeotropic type; (4) negative azeotropic type; (5) eutectic type; (6) complicated type. Phase diagram analysis and thermodynamic quantities, such as entropy, enthalpy and energy changes, were in good agreement with each other.     

G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots

The use of time-resolved fluorescence measurements in studies of telomeric G-quadruplex folding and stability has been hampered by the complexity of fluorescence lifetime distributions in solution. The application of phasor diagrams to the analysis of time-resolved fluorescence measurements, collected from either frequency-domain or time-domain instrumentation, allows for rapid characterization of complex lifetime distributions. Phasor diagrams are model-free graphical representations of transformed time-resolved fluorescence results. Simplification of complex fluorescent decays by phasor diagrams is demonstrated here using a 2-aminopurine substituted telomeric G-quadruplex sequence. The application of phasor diagrams to complex systems is discussed with comparisons to traditional non-linear regression model fitting. Phasor diagrams allow for the folding and stability of the telomeric G-quadruplex to be monitored in the presence of either sodium or potassium. Fluorescence lifetime measurements revealed multiple transitions upon folding of the telomeric G-quadruplex through the addition of potassium. Enzymatic digestion of the telomeric G-quadruplex structure, fluorescence quenching and Förster resonance energy transfer were also monitored through phasor diagrams. This work demonstrates the sensitivity of time-resolved methods for monitoring changes to the telomeric G-quadruplex and outlines the phasor diagram approach for analysis of complex time-resolved results that can be extended to other G-quadruplex and nucleic acid systems.     

Phase Diagrams for DNA Crystallization Systems

Abstract

Phase diagrams for several oligonucleotide duplex -spermine systems have been constructed. These diagrams characterize the duplex and spermine concentrations ranges in which crystalline precipitates are formed. All of them are wedge-like form. The slope of the upper branch of the diagram is determined by the oligonucleotide length. The position of the lower branch depends on both the nucleotide sequence and its length. The position of the lower branch depends on both the nucleotide sequence and its length. It has been shown that the addition to the system ofMgCl₂ and NaCl salts and MPD results in specific changes in the diagrams. A model for oligonucleotide duplex-spermine system has been suggested which explains the main characteristic features of the obtained phase diagrams. The experimental phase diagrams for the (pGpT)_n · (pApC)_n-spermine system (n = 2,3,4) have been analyzed ion terms of this model and the values of the binding constants of spermine and Mg²⁺ions binding to duplexes have been determined. It permitted to identify the complexes that precipitated in different regions of the phase diagrams under various conditions. The diagram obtained in the presence of a cobalt hexammine counterion is also considered. It has been shown that this phase diagram, in general, is similar to those obtained for the oligonucleotide duplex-spermine system.     

基于30个形态性状的中国杏属（Armeniaca Scop.）植物分类学研究

基于与叶和果实相关的30个形态性状(包括20个定性性状和10个定量性状)对中国杏属( Armeniaca Scop.)11种3变种进行了UPGMA聚类分析和主成分分析;在主成分分析基础上,构建了中国杏属植物的OTU散点图;并且,结合降水量分布图绘制了中国杏属植物分布图。聚类分析结果显示：供试杏属植物被分成2支。若包含毛叶梅( A. mume var. goethartiana Koehne),则毛叶梅、梅( A. mume Sieb.)、洪平杏( A. hongpingensis C. L. Li)以及政和杏( A. zhengheensis J. Y. Zhang et M. N. Lu)聚为一支,其余8种2变种聚为另一支;若不包含毛叶梅,梅则被划分在后一个分支中。主成分分析结果显示：前3个主成分的累计贡献率仅60.3180%,说明中国杏属植物的形态性状具有较大的遗传变异;在前3个主成分中,树高、叶片下表面被毛情况、叶长/叶柄长比值、叶长/叶宽比值、果核形状、叶宽、果核宽、叶柄长、果柄长和叶缘锯齿形状的绝对权重值均在0.7以上,表明这10个性状在中国杏属植物的分类学研究中具有重要作用。 OTU散点图显示：中国杏属植物在二维散点图上的分类结果与其聚类结果基本一致,并且,其聚类结果中的各分支在三维散点图上也能够明显区分,说明可以采用前3个主成分中绝对权重值较高的性状对中国杏属植物进行分类。分布图显示：杏属植物遍布中国各省(区),且主要集中分布在400和800 mm等降水量线之间的区域。结合上述研究结果及他人的研究成果,支持“将藏杏﹝A. holosericea ( Batal.) Kost.〕作为杏( A. vulgaris Lam.)的1个变种”以及“将政和杏作为梅的1个变种”的分类处理,并支持“将洪平杏作为独立种”的分类处理。此外,建议将仙居杏( A. xianjuxing J. Y. Zhang et X. Z. Wu)和华仁杏( A. cathayana D. L. Fu et al)作为杏属的栽培种。     

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Background

Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited.

Results

We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.

Conclusions

InteractiVenn allows set unions in Venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets. InteractiVenn is freely available online at: www.interactivenn.net.     

A complete graphical criterion for the adjustment formula in mediation analysis

Various assumptions have been used in the literature to identify natural direct and indirect effects in mediation analysis. These effects are of interest because they allow for effect decomposition of a total effect into a direct and indirect effect even in the presence of interactions or non-linear models. In this paper, we consider the relation and interpretation of various identification assumptions in terms of causal diagrams interpreted as a set of non-parametric structural equations. We show that for such causal diagrams, two sets of assumptions for identification that have been described in the literature are in fact equivalent in the sense that if either set of assumptions holds for all models inducing a particular causal diagram, then the other set of assumptions will also hold for all models inducing that diagram. We moreover build on prior work concerning a complete graphical identification criterion for covariate adjustment for total effects to provide a complete graphical criterion for using covariate adjustment to identify natural direct and indirect effects. Finally, we show that this criterion is equivalent to the two sets of independence assumptions used previously for mediation analysis.     

Explanation in Two Dimensions: Diagrams and Biological Explanation

Molecular biologists and biochemists often use diagrams to present hypotheses. Analysis of diagrams shows that their content can be expressed with linguistic representations. Why do biologists use visual representations instead? One reason is simple comprehensibility: some diagrams present information which is readily understood from the diagram format, but which would not be comprehensible if the same information was expressed linguistically. But often diagrams are used even when concise, comprehensible linguistic alternatives are available. I explain this phenomenon by showing why diagrammatic representation is especially well suited for a particular kind of explanation common in molecular biology and biochemistry: namely, functional analysis, in which a capacity of the system is explained in terms of capacities of its component parts.     

Palaeoenvironments of vertebrates on the southern shore of Tethys: The nonmarine Early Cretaceous of Tunisia

Through the Late Jurassic and Early Cretaceous, the southern shore of the Tethys Ocean migrated north and south over short distances. These vicissitudes are documented in the ‘continental intercalaire’, a long series of mainly non-marine sediments deposited across North Africa. A combined taxonomic, physical and chemical taphonomic study provides independent lines of evidence for reconstruction of palaeoenvironments within this marginal marine setting.The Douiret, Chenini and Oum ed Diab formations from the Tataouine basin of southern Tunisia span the later part of the Early Cretaceous. Microvertebrates from four sites in these formations show different modes of physical abrasion, time averaging, and mixing, based on a taphonomic analysis using a combination of physical and chemical methods. The taxonomic composition of each assemblage, and trends in rare earth element (REE) compositions of bones, from each locality were used as independent lines of evidence to indicate differences in early depositional environments. The Jebel Boulouha assemblage (Douiret Formation) is interpreted as a terrestrial carbonate-rich environment with relatively little mixing. The Touil el Mra assemblage (Oum ed Diab Formation) suggests a marginal marine environment with some mixing of previously interred bones. The Oued el Khil assemblage (Chenini Formation) and the Oum ed Diab assemblage (Oum Ed Diab Formation) are more equivocal, suggesting mixed freshwater and marine influences. Interpreting salinity in marginal marine settings is difficult, and best attempted from multiple, independent lines of evidence. We suggest that REE geochemistry can contribute to palaeoenvironmental reconstruction when used in combination with other, independent physical, palaeontological and /or geochemical methods.     

Determination of the quaternary phase diagram of the water-ethylene glycol-sucrose-NaCl system and a comparison between two theoretical methods for synthetic phase diagrams

Characterization of the thermodynamic properties of multi-solute aqueous solutions is of critical importance for biological and biochemical research. For example, the phase diagrams of aqueous systems, containing salts, saccharides, and plasma membrane permeating solutes, are indispensible in the field of cryobiology and pharmacology. However, only a few ternary phase diagrams are currently available for these systems. In this study, an auto-sampler differential scanning calorimeter (DSC) was used to determine the quaternary phase diagram of the water-ethylene glycol-sucrose-NaCl system. To improve the accuracy of melting point measurement, a “mass-redemption” method was also applied for the DSC technique. Base on the analyses of these experimental data, a comparison was made between the two practical approaches to generate phase diagrams of multi-solute solutions from those of single-solute solutions: the summation of cubic polynomial melting point equations versus the use of osmotic virial equations with cross coefficients. The calculated values of the model standard deviations suggested that both methods are satisfactory for characterizing this quaternary system.     

Pressure-temperature phase diagrams of biomolecules

The pressure-temperature phase diagram of various biomolecules is reviewed. Special attention is focused on the elliptic phase diagram of proteins. The phenomenological thermodynamic theory describing this diagram explains the heat, cold and pressure denaturations in a unified picture. The limitations and possible developments of this theory are discussed as well. It is pointed out that a more complex diagram can be obtained when the intermolecular interactions are also taken into account. In this case metastable states appear on the pressure-temperature (p-T) diagram due to intermolecular interactions. Pressure-temperature phase diagrams of other biopolymers are also discussed. While the p-T diagrams of helix-coil transition of nucleic acids and of gel-liquid crystal transition of lipid bilayers are non-elliptical, those of gelatinization of starch and of phase separation of some synthetic polymers show an elliptic profile, similar to that of proteins. Finally, the p-T diagram of bacterial inactivation is shown to be elliptic. From the point of view of basic science, this fact shows that the key factor of inactivation should be the protein type, and from the viewpoint of practical applications, it serves as the theoretical basis of pressure treatment of biosystems.     

A NUMERICAL TAXONOMIC STUDY OF THE GENUS PLATANUS BASED ON MORPHOLOGICAL AND PHENOLIC CHARACTERS

Forty-two morphological and eighty chemical (phenolic) characters were employed on a numerical taxonomic study of the genus Platanus. Ten taxa were used for morphological study, and nine were available for chemical study. UPGA was employed for cluster analysis; correlation coefficients served as a measurement of the similarity between each OTU-pair. Comparison was made for phenograms and graph diagrams of nine taxa based on morphological characters with those based on chemical characters. It has been found that the two agree with each other in many respects. Correlation coefficient between similarity matrices based on morphological and chemical characters is 0.573. The result generally supports the belief that taxa closely related on morphological grounds are similar biochemically. A systematic consideration of the genus has been made, based on the information available.     

A taxonomic reappraisal of the Daphnia hyalina complex (Crustacea: Cladocera): an experimental and ecological approach

The paper is a taxonomic study of the limnetic Daphnia populations of the English Lake District, the populations upon which the most popular taxonomic scheme is based (Johnson, 1952).
Johnson treats these populations as three varieties of the species D. hyalina, namely D. hyalina s. str., D.h. var. galeata and D.h. var. lacustris .
Careful examination of the populations of Esthwaite reveals that what has previously been regarded as a population of a single variety of D. hyalina. includes three distinct forms. Experimental work confirms that these are genetically distinct. One of these forms corresponds to D. hyalina var. galeata , whilst the other two are designated the "toothed" and "round-headed" forms.
The first part of the paper is concerned with the taxonomic status of var. galeata . Brooks (1957) and some later workers treat this as a separate species (D. galeata) on morphological grounds. This is fully supported by the present work. Differences between var. galeata and co-existing forms in incidence of sexual reproduction, in vertical distribution and in seasonal abundance and average brood-size provide further support for the separation of D. galeata.
The second part of the paper is concerned with D. hyalina s.str. which, on the basis of morphology, ecology and reproductive behaviour, is shown to be at least as distinct from other members of the complex as is D. galeata . It is argued that other forms should therefore to be removed from D. hyalina . The taxonomic status and affinities of the remaining "toothed" and "round-headed" forms are discussed.     

斑叶堇菜种宗性状变异式样的定量分析

斑叶堇菜与近缘种细距堇莱之间有许多过渡类型存在, 很难依据少数几个关键性特征对它们进行明确的划分。本文运用形象化散点图和柱状图的方法, 对从不同地点、不同居群收集的80份标本进行分析, 测量若干性状上的数量变异, 分析这些性状之间变异的相关程度, 结果表明:斑叶堇菜和细距堇菜各自应为独立的种, 支持W.Beck.1916年所作的成立细距堇菜的毛萼亚种的处理。