Species ordering on a variance criterion

Summary A technique for ordering, to identify diagnostic species, based on variance ratios has been described. The method was illustrated with river terrace data.The author would like to thank Dr. László Orlóci for permission to use the vegetation data employed in the illustration of the algorithm. This work was supported by a grant from the National Research Council of Canada.     

Ranking species based on sensitivity to perturbations under non-equilibrium community dynamics

Managing ecological communities requires fast detection of species that are sensitive to perturbations. Yet, the focus on recovery to equilibrium has prevented us from assessing species responses to perturbations when abundances fluctuate over time. Here, we introduce two data-driven approaches (expected sensitivity and eigenvector rankings) based on the time-varying Jacobian matrix to rank species over time according to their sensitivity to perturbations on abundances. Using several population dynamics models, we demonstrate that we can infer these rankings from time-series data to predict the order of species sensitivities. We find that the most sensitive species are not always the ones with the most rapidly changing or lowest abundance, which are typical criteria used to monitor populations. Finally, using two empirical time series, we show that sensitive species tend to be harder to forecast. Our results suggest that incorporating information on species interactions can improve how we manage communities out of equilibrium.     

A comparative measure of biodiversity based on species composition

In conservation planning, species richness and species endemism are the most often used metrics for describing the biodiversity importance of areas. However, when it comes to prioritizing regions for conservation actions these measures alone are insufficient because they do not reveal how similar or different the actual composition of species may be from one area to another. For comparative analysis an additional useful metric would be one that indicates the degree to which the species assemblage in one area is also represented in—or is distinct from—species assemblages of other areas. Here we describe a method for quantifying the compositional representativeness of species assemblages among geographic regions. The method generates asymmetric pairwise similarity coefficients that are then used to calculate separate measures for the representativeness and the distinctiveness of species assemblages in the regions being compared. We demonstrate the method by comparing fish communities among freshwater ecoregions of the Mississippi Basin, and then among smaller hydrological units within two individual freshwater ecoregions. At both scales of analysis, our measures of representativeness and distinctiveness reveal patterns of fish species composition that differ from patterns of species richness. This information can enhance conservation planning processes by ensuring that priority-setting explicitly consider the most representative and distinctive species assemblages.     

Efficient Evaluation of Ranking Procedures when the Number of Units is Large,with Application to SNP Identification

Simulation‐based assessment is a popular and frequently necessary approach for evaluating statistical procedures. Sometimes overlooked is the ability to take advantage of underlying mathematical relations and we focus on this aspect. We show how to take advantage of large‐sample theory when conducting a simulation using the analysis of genomic data as a motivating example. The approach uses convergence results to provide an approximation to smaller‐sample results, results that are available only by simulation. We consider evaluating and comparing various ranking‐based methods for identifying the most highly associated SNPs in a genome‐wide association study, derive integral equation representations of the pre‐posterior distribution of percentiles produced by three ranking methods, and provide examples comparing performance. These results are of interest in their own right and set the framework for a more extensive set of comparisons.     

基于几何形态测量学的植物鉴定方法

物种鉴定是植物研究中的一个重要环节,尤其对近缘种的鉴定是个难点。野外调查和采样时通常使用直接观察形态特征的方法来鉴定物种,容易产生鉴定误差。本文以同域分布的两个近缘种槲树（Quercus dentata Thunb.）和槲栎（Q.aliena Blume）为研究对象,通过叶片形态研究,探讨几何形态测量学方法,并对该方法的植物物种鉴定能力进行总结。该方法除了具备操作简单和分析准确的优势外,还弥补了传统物种鉴定方法的不足,可显著提高植物物种的鉴定能力。     

基于结构的单绕蛋白聚类图构建与分析

蛋白质分子进化规律研究是分子进化研究的重点,对揭示生命起源与进化机制有重要意义。本文对已知空间结构及物种信息的单绕蛋白,利用结构比对信息,构建了不同层次单绕样本系统聚类图。分析发现:功能相似蛋白存在明显聚集现象,同一超家族样本基本聚在一个大支中,同一家族样本集中在所属超家族下的小支中,功能约束下单绕样本聚类图与物种进化图有较好对应关系。结果表明:单绕蛋白的结构演化反映了蛋白质功能的约束,特定功能单绕样本的结构差异具有种属特异性,结构演化包含了物种进化信息。     

Fish Karyome: A karyological information network database of Indian Fishes

'Fish Karyome', a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.     

Effects of site and species characteristics on nested patterns of species composition in sedge meadows

Biotas of both geographical islands and habitat islands are often nested subsets of the biotas of successively more species-rich islands within the same system. The life history characteristics of a species may determine how that species contributes to the general pattern of species nestedness. Here, I investigate the floras of 56 sedge meadow wetlands in northern Illinois (USA) in order to characterize the degree of nestedness in these communities, determine which individual plant species contribute to the nested pattern, and investigate species characteristics that might be related to nonrandom patterns of distribution in individual plant species. The entire assemblage of species at all sedge meadows was significantly nested. Species richness and area were significantly correlated, and the nested pattern was closely related to site area, suggesting that species drop out of the assemblage in a predictable order as site area decreases. Some individual species exhibited nonrandom distributions across the sites, occurring more often in large, species-rich sites. Large sites were more likely than smaller sites to contain conservative species, i.e., those typical of pristine natural habitat, whereas nonconservative species were distributed more randomly among sites. Nested patterns of distribution of conservative species with respect to site area may result from their high probability of extinction on small sites or from a tendency for required habitats to co-occur on the same large sites. This revised version was published online in June 2006 with corrections to the Cover Date.     

中国葡萄属植物形态学聚类分组研究

对《中国葡萄志》描述的38个中国葡萄属野生种和1个栽培种,按照《葡萄种质资源描述规范和数据标准》的要求,对18个描述符用代码数量化并进行聚类分析,根据形态特征的相似程度,将我国葡萄属野生种和欧亚种划分为8个组和5个亚组。第1组包含毛葡萄、腺枝葡萄、龙泉葡萄、美丽葡萄和庐山葡萄,第2组包含麦黄葡萄和小叶葡萄,第3组包含5个亚组21个种类,其中亚组1包含山葡萄、陕西葡萄、浙江蘡薁、蘡薁和湖北葡萄,亚组2包含绵毛葡萄和勐海葡萄,亚组3包含小果葡萄、云南葡萄和葛藟葡萄,亚组4包含毛脉葡萄、华东葡萄、武汉葡萄和井冈葡萄,亚组5包含刺葡萄、秋葡萄、桦叶葡萄、网脉葡萄、蒙自葡萄、凤庆葡萄和河口葡萄,第4组仅包含欧洲葡萄,第5组包含温州葡萄、红叶葡萄、复叶葡萄、乳源葡萄和狭叶葡萄,第6组包含东南葡萄、罗城葡萄和闽赣葡萄,第7组仅包含菱叶葡萄,第8组仅包含鸡足葡萄一个种。     

基于信息网络模型的生态风险评价

人类开发活动造成剧烈的生态系统自然条件变化,生态风险评价可以对受到人为干扰下生态系统(包括物种和群落等)的潜在影响进行模拟和量化。通过对信息流量的概念和网络控制分析,综合考虑生态系统组分间的直接和间接作用,提出一种能实现全局风险模拟的生态网络模型,即信息网络模型。在该模型基础上,建立了面向整体生态系统的生态风险评价框架,同时实现兼容多胁迫因子统一模拟和多风险受体间的风险追踪。以澜沧江漫湾水库为例,在估算重金属Hg、Pb和Cd初始环境风险后,利用信息网络模型追踪分析生态系统中不同生态功能组分之间的风险传递路径,评估各生态组分和整体系统的危险程度。结果表明,在累积效应作用下,对于生态系统和部分群落,整合网络风险值与初始环境风险值之间有着显著差别;在发生环境胁迫时,虽然处于食物网底层的生物类群可能最先受险,但在控制信息作用下食物网上层类群也会受险,甚至其最终受到的潜在威胁比前者更大。信息网络模型可识别出复杂的风险流动路径和群落间的风险累积,从而为生态系统风险评价和管理提供更为系统综合的理论依据。     

A commentary on Ridley's cladistic solution to the species problem

The cladistic species concept proposed by Ridley (1989) rests on an undefined notion of speciation and its meaning is thus indeterminate. If the cladistic concept is made determinate through the definition of speciation, then it reduces to a form of whatever species concept is implicit in the definition of speciation and fails to be a truly alternative species concept. The cladistic formalism advocated by Ridley is designed to ensure that species are monophyletic, that they are objectively real entities, and that they are individuals. It is argued that species need not be monophyletic in order to be real entities, and that ancestor-descendant relations are not the only relations that confer individuality on entities. The species problem is recast in terms of a futile quest for a definition of that single kind of entity to which the term species should uniquely apply.     

Study on biogeographical divisions of China

On the basis of comprehensive natural factors (including altitude, landform, climate, vegetation, water system, farm belt, and so on), we first divide China's territory into 124 basic units by applying GIS techniques. Then 171 species of mammals and 509 of plants are selected for analysis on the basis of taxa with many representative species, wide distributions across China or thought to reveal biogeographic divisions in less well known parts of the country. We collected distribution data of these species through the China Species Information System, and utilized the GIS technique to identify in which of the 124 units each species has been recorded. The resulting data matrix was then arranged into dendrograms, aggregating the units at various levels on the basis of the mammal and plant distributions by application of similarity cluster analysis using both the Sørensen comparability index formula, and the Ward method to calculate correlation matrices. Finally, we summarize the different distribution characteristics of the aggregated units and their reasons of the two categories from these cluster dendrograms, and reach some important conclusions on the biogeographical regionalization of China. This research adopts a study method of starting from minimal basic units and then aggregating up to higher-level divisions, which is a new methodological attempt in the biogeographic division research field within China. By this method, the division boundaries can be determined by the cluster results of species distribution comparability rather than the limited species and ecology knowledge of an individual researcher as has been done in the past. This makes the resulting classification more objective and broader based. This method is also applicable to other biological taxa.     

Bayesian estimation of species richness from quadrat sampling data in the presence of prior information

We consider the problem of estimating the number of species of an animal community. It is assumed that it is possible to draw up a list of species liable to be present in this community. Data are collected from quadrat sampling. Models considered in this article separate the assumptions related to the experimental protocol and those related to the spatial distribution of species in the quadrats. Our parameterization enables us to incorporate prior information on the presence, detectability, and spatial density of species. Moreover, we elaborate procedures to build the prior distributions on these parameters from information furnished by external data. A simulation study is carried out to examine the influence of different priors on the performances of our estimator. We illustrate our approach by estimating the number of nesting bird species in a forest.     

Identification of cryptic species within liverwort Conocephalum conicum based on the volatile components

Cryptic speciation refers to cases where species are clearly genetically differentiated, but show little or no morphological differences. This study investigated whether volatile components can be used to distinguish the cryptic species within the Conocephalum conicum complex. Thirteen samples were included in this study representing four cryptic species (A, F, J, L) and the recently described Conocephalum salebrosum (formerly cryptic species S) detected in a worldwide collection. Results received from GC–MS analyses showed some differences between samples, indicating the existence of chemical polymorphism. It is evident from both statistical analyses (CA and PCA), that cryptic species L appears to be the most differentiated species, with the volatile components not significantly shared with the rest of the types. The most characteristic compound of this type is the sesquiterpene alcohol, conocephalenol. Distinction between other examined cryptic species were also indicated. However species F and J, as well as species A and C. salebrosum, share a great similarity in their volatile composition and are grouped together in both CA and PCA. Despite their similarities, we were able to find chemical markers which can describe each species. Cubebol is characteristic for C. salebrosum, while cryptic species A produces (E)-methylcinnamate. The presence of a large amount of the monoterpene hydrocarbon, sabinene, is characteristic for cryptic species J. In one of the analyzed specimens belonging to the cryptic species F, a large amount of cyclocolorenone was detected. Chemical differentiation was correlated with the geographical distribution of the analyzed samples.     

Releve ranking based on a sum of squares criterion

Summary When a very large number of phytosociological types have to be compared, a reduction of the number of relevés is desirable. In this paper a method of relevé selection from given phytosociological tables is suggested. The method is based on a sum of squares criterion. The advantage, in comparison with other selection procedures, is that this method provides a means on the basis of which the efficiency of a relevé selection can be objectively measured.Contribution from the Working Group for Data-Processing in Phytosociology, International Society for Vegetation Science.The work was completed at the Department of Plant Sciences of the University of Western Ontario, London, Canada. We wish to thank Prof. L. Orlóci for the hospitality and the helpful discussions. The work was supported by Italian C.N.R., within the project Promozione qualità dell'ambiente subproject Metodologie matematiche e basi di dati.     

Molecular identification and allopatric divergence of the white pine species in China based on the cytoplasmic DNA variation

Molecular identification of plant species may be highly related to the geographic isolation and speciation stages among species. In this study, we examined these possibilities in a group of white pines in China. We sampled 449 individuals from 60 natural populations of seven species from sect. Quinquefoliae subsect. Strobus. We sequenced four chloroplast DNA regions (around 3100 bp in length) and two mitochondrial DNAs (around 1000 bp in length). We identified 21 chlorotypes and 10 mitotypes. Both chlorotypes and mitotypes recovered from four species with long disjunction and restricted distributions in northern or northwestern China, Pinus sibirica, Pinus koraiensis, Pinus wallichiana and Pinus pumila are species-specific, suggesting that these cytoplasmic DNAs can distinguish them from the close relatives. Allopatric isolations should have contributed greatly to their genetic divergences. However, both chlorotypes and mitotypes recovered for Pinus dabeshanensis and Pinus fenzeliana distributed in southeastern and southern China are shared or closely related to those found in the widely distributed Pinus armandii. These two species may have diverged or derived from P. armandii recently. All of our findings together suggest that the discrimination power of the molecular identifications based on the cytoplasmic DNA barcodes may show variable discriminability depending on geographic isolation and speciation stages among the sampled species.     

An information theory based framework for the measurement of population health

This paper proposes a new framework for the measurement of population health and the ranking of the health of different geographies. Since population health is a latent variable, studies which measure and rank the health of different geographies must aggregate observable health attributes into one summary measure. We show that the methods used in nearly all the literature to date implicitly assume that all attributes are infinitely substitutable. Our method, based on the measurement of multidimensional welfare and inequality, minimizes the entropic distance between the summary measure of population health and the distribution of the underlying attributes. This summary function coincides with the constant elasticity of substitution and Cobb–Douglas production functions and naturally allows different assumptions regarding attribute substitutability or complementarity. To compare methodologies, we examine a well-known ranking of the population health of U.S. states, America's Health Rankings. We find that states’ rankings are somewhat sensitive to changes in the weight given to each attribute, but very sensitive to changes in aggregation methodology. Our results have broad implications for well-known health rankings such as the 2000 World Health Report, as well as other measurements of population and individual health levels and the measurement and decomposition of health inequality.