A Comparison of Predictive Methods in Extinction Risk Studies: Contrasts and Decision Trees

Over the last two decades an increasing emphasis has been placed on the importance of controlling for phylogeny when examining cross-species data; so-called comparative methods. These methods are appropriate for testing hypotheses about correlations between evolutionary events in the history of a clade and adaptive responses to those changes. When this approach is applied to extinction risk, possible correlations between evolutionary changes in, for example, body size or habitat specialisation and some measure(s) of current threat status are examined. However, there may be a mismatch here between the results of such studies, and the real, pragmatic needs of species conservation. This kind of approach certainly adds to our knowledge of some fundamental processes, but it is more difficult to see how this can be applied to conservation decision-making. For more practical purposes a decision-tree approach can be extremely useful. This paper illustrates the use of a contrasts based analysis of extinction risk compared with a decision-tree analysis for Galliformes (Aves). While the contrasts analyses concur with some general macroecological trends found in other studies, the decision-tree models provide lists of species predicted to be more at risk than current assessments would suggest. We argue that in practical terms, decision tree models might be more useful than a macroecological linear model-based approach.     

Extinction Risk: A Comparative Analysis of Central Asian Vertebrates

In 2004, IUCN listed 20% of all mammals, 12% of birds and 4% of reptiles as threatened with extinction. Why are these species, but not the others in their clades, at risk? Most comparative studies of Red List status to date have investigated the relationship between status and life history or ecology, either at a local level where species face a given situation which may be known in detail, or at a global level where threats are much more heterogeneous. The use of data at a sub-global level raises several issues, including the need to assess populations across geopolitical borders and how best to treat non-breeding phases of populations. However, regional-level data provide the opportunity to look in more detail at how threatening processes operate. We employ comparative analysis using phylogenetically independent contrasts and multiple regression to control for inter-related and confounding independent variables, to evaluate correlates of regional threat for three groups of central Asian vertebrates. We find that aspects of dispersal, area of occupancy, body mass and generation time are important in predicting the perceived risk of regional extinction.     

林木全同胞群体的多位点连锁分析

多位点连锁分析是构建人类以及动植物的遗传连锁图谱的关键步骤之一。但是由于林木遗传背景的复杂性,多位点连锁分析在林木的全同胞群体中还没有得到应用．本文将多位点连锁分析应用到林木的F1代全同胞群体中．对于全同胞群体的任意分离比的两个位点,给出了在不同的连锁相下从一个位点到另一个位点的转移概率矩阵．对于给定的一列标记位点,考虑了不同分离比位点以及两位点间的连锁相信息,采用隐马尔可夫链模型计算极大似然函数和相邻位点间的重组率．本文的方法有助于构建完整的高密度的林木遗传连锁图谱．     

Combining Population Viability Analysis with Decision Analysis

Management of endangered species requires methods to assess the effects of strategies, providing a basis for deciding on a best course of action. An important component of assessment is population viability analysis (PVA). The latter may be formally implemented through decision analysis (DA). These methods are most useful for conservation when used in conjunction. In this paper we outline the objectives and the potential of both frameworks and their overlaps. Both are particularly helpful when dealing with uncertainty. A major problem for conservation decision-making is the interpretation of observations and scientific measurements. This paper considers probabilistic and non-probabilistic approaches to assessment and decision-making and recommends appropriate contexts for alternative approaches.     

Model-based Conservation Decision Aiding in the Presence of Goal Conflicts and Uncertainty

Goal conflicts and uncertainty are two major problems in decision-making for conservation and species protection. Conflicts can often be found between ecological goals on the one hand and socio-economic goals on the other, but also among different ecological goals. They can be formally analysed by methods of multi-criteria analysis. As the solution of a multi-criteria decision problem usually depends on the weights put on the individual criteria (objectives), sensitivity and robustness analyses are necessary to understand the decision problem, concentrate on the essential aspects, and support actual decision processes fully. Uncertainty in the decision problem is often caused by scarcity of information needed to predict the consequences of management actions. The so-called outranking concept proved very useful in the consideration of such uncertainty. Based on a simple fictitious case study the paper demonstrates how multi-criteria decision analysis (in particular the PROMETHEE outranking method) in combination with population model analysis can assist in conservation biological decision-making.     

果树花芽孕育的研究概况

果树花芽孕育是一个成花因素积累的过程 ,也是芽顶端花原基形成前所必要的活动。随着研究手段的改进和水平的提高 ,近年来人们逐渐弄清了果树花芽孕育的概念、花芽孕育期间的重要生理生化变化以及外界因素调控花芽孕育的可能方式 ,而对果树花芽孕育调控基因的研究处于起步阶段。     

林木基因克隆研究进展

林木种质资源丰富, 种质间遗传差异大, 控制林木重要性状的基因克隆及转化对培育优良林木新品种具有很强的实用价值, 但许多具有潜在应用价值的林木基因未得到充分发掘和有效分离。近年来, 随着各种不同林木cDNA文库的建立, 大规模随机EST测序技术的运用以及克隆技术的不断完善, 特别是毛果杨(Populus trichocarpa)基因组测序计划的完成, 大量与林木重要性状相关的基因被分离和鉴定。这些重要基因的获得为利用转基因技术培育高产、优质、抗逆、抗病虫害的林木新品种奠定了一定的基础。该文综述了20多年来国内外林木基因克隆的研究进展, 对基因克隆及其应用过程中亟待解决的问题进行了讨论, 并对其发展趋势进行展望。     

Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model

Understanding the mechanism of the protein stability change is one of the most challenging tasks. Recently, the prediction of protein stability change affected by single point mutations has become an interesting topic in molecular biology. However, it is desirable to further acquire knowledge from large databases to provide new insights into the nature of them. This paper presents an interpretable prediction tree method (named iPTREE-2) that can accurately predict changes of protein stability upon mutations from sequence based information and analyze sequence characteristics from the viewpoint of composition and order. Therefore, iPTREE-2 based on a regression tree algorithm exhibits the ability of finding important factors and developing rules for the purpose of data mining. On a dataset of 1859 different single point mutations from thermodynamic database, ProTherm, iPTREE-2 yields a correlation coefficient of 0.70 between predicted and experimental values. In the task of data mining, detailed analysis of sequences reveals the possibility of the compositional specificity of residues in different ranges of stability change and implies the existence of certain patterns. As building rules, we found that the mutation residues in wild type and in mutant protein play an important role. The present study demonstrates that iPTREE-2 can serve the purpose of predicting protein stability change, especially when one requires more understandable knowledge.     

林木基因克隆研究进展

林木种质资源丰富,种质间遗传差异大,控制林木重要性状的基因克隆及转化对培育优良林木新品种具有很强的实用价值,但许多具有潜在应用价值的林木基因未得到充分发掘和有效分离。近年来,随着各种不同林木cDNA文库的建立,大规模随机EST测序技术的运用以及克隆技术的不断完善,特别是毛果杨（Populustrichocarpa）基因组测序计划的完成,大量与林木重要性状相关的基因被分离和鉴定。这些重要基因的获得为利用转基因技术培育高产、优质、抗逆、抗病虫害的林木新品种奠定了一定的基础。该文综述了20多年来国内外林木基因克隆的研究进展,对基因克隆及其应用过程中亟待解决的问题进行了讨论,并对其发展趋势进行展望。     

Modeling process and material alternatives in life cycle assessments

Background, Aims and Scope  Although LCA is frequently used in product comparison, many practitioners are interested in identifying and assessing improvements within a life cycle. Thus, the goals of this work are to provide guidelines for scenario formulation for process and material alternatives within a life cycle inventory and to evaluate the usefulness of decision tree and matrix computational structures in the assessment of material and process alternatives. We assume that if the analysis goal is to guide the selection among alternatives towards reduced life cycle environmental impacts, then the analysis should estimate the inventory results in a manner that: (1) reveals the optimal set of processes with respect to minimization of each impact of interest, and (2) minimizes and organizes computational and data collection needs. Methods  A sample industrial system is used to reveal the complexities of scenario formulation for process and material alternatives in an LCI. The system includes 4 processes, each executable in 2 different ways, as well as 1 process able to use 2 different materials interchangeably. We formulate and evaluate scenarios for this system using three different methods and find advantages and disadvantages with each. First, the single branch decision tree method stays true to the typical construction of decision trees such that each branch of the tree represents a single scenario. Next, the process flow decision tree method strays from the typical construction of decision trees by following the process flow of the product system, such that multiple branches are needed to represent a single scenario. In the final method, disaggregating the demand vector, each scenario is represented by separate vectors which are combined into a matrix to allow the simultaneous solution of the inventory problem for all scenarios. Results  For both decision tree and matrix methods, scenario formulation, data collection, and scenario analysis are facilitated in two ways. First, process alternatives that cannot actually be chosen should be modeled as sub-inventories (or as a complete LCI within an LCI). Second, material alternatives (e.g., a choice between structural materials) must be maintained within the analysis to avoid the creation of artificial multi-functional processes. Further, in the same manner that decision trees can be used to estimate ‘expected value’ (the sum of the probability of each scenario multiplied by its ‘value’), we find that expected inventory and impact results can be defined for both decision tree and matrix methods. Discussion  For scenario formulation, naming scenarios in a way that differentiate them from other scenarios is complex and important in the continuing development of LCI data for use in databases or LCA software. In the formulation and assessment of scenarios, decision tree methods offer some level of visual appeal and the potential for using commercially available software/ traditional decision tree solution constructs for estimating expected values (for relatively small or highly aggregated product systems). However, solving decision tree systems requires the use of sequential process scaling which is difficult to formalize with mathematical notation. In contrast, preparation of a demand matrix does not require use of the sequential method to solve the inventory problem but requires careful scenario tracking efforts. Conclusions  Here, we recognize that improvements can be made within a product system. This recognition supports the greater use of LCA in supply chain formation and product research, development, and design. We further conclude that although both decision tree and matrix methods are formulated herein to reveal optimal life cycle scenarios, the use of demand matrices is preferred in the preparation of a formal mathematical construct. Further, for both methods, data collection and assessment are facilitated by the use of sub-inventories (or as a complete LCI within an LCI) for process alternatives and the full consideration of material alternatives to avoid the creation of artificial multi-functional processes. Recommendations and Perspectives  The methods described here are used in the assessment of forest management alternatives and are being further developed to form national commodity models considering technology alternatives, national production mixes and imports, and point-to-point transportation models. ESS-Submission Editor: Thomas Gloria, PhD (t.gloria@fivewinds.com)     

紫丁香195个实生单株花表型性状变异分析

为了准确掌握紫丁香资源花部性状的变异程度及表型多样性水平,为紫丁香优良品种的选育提供理论依据。本研究以195株紫丁香实生单株为材料,对其5个数量性状和4个质量性状的变异、性状间相关性和聚类关系等进行了分析。结果表明,5个数量性状在群体内表现出极显著差异(P<0.01),且符合正态分布,变异系数为19.72%~30.22%,平均24.97%,其中花序长变异最大;根据ISCC-NBS色彩名称表示法将群体花色划分为白色系、浅粉色系、紫色系、紫红色系、紫粉色系和蓝紫色系等6个色系,其中紫色系(54.35%)和紫红色系(32.31%)所占比例最大;4个质量性状的多样性指数为0.36~1.09,平均0.86,其中花冠裂片(状态)最大,表明群体中质量性状变异类型丰富。相关性分析表明,5个数量性状之间均呈现极显著正相关,其中花序长与花序宽相关系数最大,为0.767。聚类分析表明,195株紫丁香基于欧氏距离可分为3大类,第一类群主要性状表现为花冠筒长;第二类群表现为花序长;第三类群表现为花冠裂片长。参试紫丁香资源花部性状表型变异丰富。     

沈阳市建成区行道树的结构与功能研究

城市森林不仅可以减少城市中的裸露地面 ,更是大气污染的天然净化器。它可以促使大气中Ｏ2和ＣＯ2 的平衡 ,降低多种有害气体浓度 ,吸附空气中的灰尘[3] 。沈阳市是一个重工业城市 ,由于历史和现实的原因 ,以工矿企业污染物排放为主要污染源的大气污染日益严重。因此 ,城市森林的建设对于减轻城市大气污染至关重要。行道树是城市森林的重要组成部分 ,是连接城市分段隔离绿地的纽带 ,同时又为野生动物提供了栖息地及迁移通道 ,被认为是城市自然恢复的重要手段 ,其功能越来越受到人们的重视[8] 。怎样合理配置行道树的结构 ,发挥其最大生态效…     

基于花粉形态数量分类的核果类系统关系研究

运用扫描电子显微镜(SEM)观察了李属、杏属、樱桃属和桃属的花粉形态,观察结果表明:核果类果树的花粉均为近扁球形,等极,辐射对称,极面观为三角形或钝三角形,赤面观均为椭圆形,花粉粒大小在各属间差异明显。核果类果树花粉属N3P4C5类型,3条孔沟沿极轴方向在赤道面上等间距环状分布,内孔位于沟的中央,完全独立于外壁,孔盖覆不规则的拟网状或脑纹状纹饰。供试核果类果树花粉的表面纹饰由平行条纹或不规则条脊及散落于条脊间的穿孔组成,各属间条脊的排列方式、宽窄、脊洼深浅及穿孔有无等性状上存在明显差异。根据花粉大小、表面纹饰及覆盖层穿孔等的一般演化规律,推测核果类果树由低到高的演化顺序为李属→杏属→樱桃属→桃属,并在聚类分析的基础上对属间亲缘关系进行了探讨,旨在为核果类系统关系的研究提供孢粉证据。     

八种针阔叶幼树清晨叶水势与土壤含水量的关系及其抗旱性研究

一、前言土壤是植物根系的生活环境,是供给植物赖以生存的水分和养分的源泉。干旱区的植物尤其是树木常常由于土壤供水不足而限制其自然分布和生长。根据土壤-植物-大气连续体系     

Pollen Dispersal Between Isolated Trees in the Brazilian Savannah: A Case Study of the Neotropical Tree Hymenaea stigonocarpa

This case study examines the pollen dispersal distance, pollen dispersal patterns and intra‐family genetic structure for isolated trees in pastures of the bat‐pollinated Neotropical tree species Hymenaea stigonocarpa using six microsatellite loci and parentage analysis. The sampling included 28 grouped trees (referred to as the population) and six isolated trees in pastureland along a highway in Mato Grosso do Sul State, Brazil. From the population, we sampled 137 seeds from 12 seed‐trees, and from the isolated trees, we sampled 34 seeds from two seed‐trees. The results showed that pollen was dispersed over long distances (reaching 7353 m) and therefore the spatially isolated trees were not reproductively isolated. The pollen immigration rate in the population was also high (31%). Isolated trees presented a higher selfing rate (s=26%) than trees in the population (s=12%), suggesting that the spatial isolation of the trees increased selfing. However, selfing was responsible for only 30 percent of the inbreeding in offspring and mating among relatives was 70 percent. In the population, excluding selfing, ca 72 percent of the pollen was dispersed over distances <1000 m (average: 860 m). For the two isolated seed‐trees, excluding selfing, the average pollen dispersal distance was 5229 m. The results demonstrate that although pollen can be dispersed over long distances for H. stigonocarpa isolated trees, a high percentage of pollen comes from the same tree (selfing) and mating was correlated. Consequently, seeds must be collected from a large number of seed‐trees for conservation purposes.     

福州市居住区景观树木多样性分析

对福州市辖区内自1995年建成的36个居住区景观树木构成和物种多样性进行调查,并根据建成年代和相对城市环线位置进行分析。结果表明,36个居住区共有155种12 694株景观树木,隶属于42科和97属。在树种构成分析中,将树种按常见程度分为6个组,标志组有20种,共7560株,优势组、常见组、少见组、稀有组以及孤生组分别有17、19、49、38、12种和2383、1297、1269、173、12株。多样性分析表明,福州市居住区景观树木多样性与发达城市比较还存在差距,尤其是旧居住区的景观树木物种多样性更低,树种选择也更为单一。此外,取样居住区中部分安置房居住区的景观树种多样性低于同时期非安置房居住区。     

核果类果树自交不亲和性研究进展

综述了核果类果树甜樱桃(PFunus avium L.)、杏(P.armeniaca L.)、扁桃(P.dulcis(Mill.)D.A.Webb)和梅(P.mume Sieb)等自交不亲和性的研究进展.着重讨论了S-RNase基因(s基因)和SLF基因(S-locus F-box基因,或称SFB基因),S基因在杂交后代群体中的遗传规律,利用S基因的遗传特性选育自交亲和品种和确定S基因型的主要方法及其特点以及自交亲和机制的几种可能的类型.     

Biological Dinitrogen Fixation in Gramineae and Palm Trees

Biological nitrogen fixation (BNF) in the Gramineae family has been well documented, but a complete understanding of this issue is needed to turn the research into a practical approach. The literature has a long and diverse list of diazotrophic bacteria found colonizing several plant tissues, such as roots, stems, leaves, and trash as well as the rhizosphere. However, only a limited amount of research has focussed on existing associations of N₂-fixing microorganisms with grasses or cereal, especially for BNF inputs and ecological studies under field conditions. The recent discovery of the endophytic diazotroph bacteria such as Acetobacter diazotrophicus, Herbaspirillum spp. and Azoarcus spp. colonizing the interior of sugarcane, rice, Kallar grass (Leptochloa fusca (L.) Kunth), respectively, and other species of grasses as well as cereals has led to a considerable interest in exploring these novel associations. There is a general consensus that plant genotype is a key factor to higher contributions of BNF together with the selection of more efficient bacterial strains. This review summarizes the present data on this field and introduces the discovery of a new group of diazotrophic bacteria colonizing palm trees and therefore opening a future perspective for using these plants, especially African oil palm, to replace diesel as a fuel.     

牛科(哺乳纲:偶蹄目)动物与生境利用有关的适应形态模式

对广义牛科动物颅后骨骼的多元变量分析揭示了牛科生境利用和体型之间的骨学特征。利用逐步分辨分析方法和一个基于机器学习的决策树方法鉴别了每种生境中牛科动物颅后解剖结构的形态特征。从110个广义牛科动物测量了43个指标进行了这项分析。利用所有主要肢骨测量值和以单根肢骨测量为主的测量值获得的分辨函数和决策树可以完美地区分适应开阔生境、森林和山地的牛科动物(在所有分析中得到了100 %正确的再分类)。由于调整的函数仅涉及到很小的颅后骨骼测量集,这些函数可以应用于研究考古学和古生物学发掘物中保存的不完整标本。这些表征生境利用的生态适应函数与那些用颅齿部性状建立、用于推测牛科动物食物选择的函数结合,具有刻画已灭绝的分类类群的古个体生态学和重建古环境的潜力。我们还分析了多元回归是否较单一因子回归表现出较高的预测能力,并提出了从每一种单根主要肢骨测量的颅后形态变量得到的最好代数函数     

Morphology of the Respiratory Trees in the Holothurians Apostichopus japonicus and Cucumaria japonica

The morphology of the respiratory trees in the holothurians Apostichopus japonicus and Cucumaria japonica was studied using histochemical and electron microscopic techniques. The epithelium of the respiratory tree cavity in A. japonicus consists of columnar cells about 17–20 m high. In C. japonica, this epithelium is composed of two cell types: bulbous cells embedded in the connective tissue layer and secretory cells; cells are 1–12 m high. A characteristic feature of cells of the respiratory tree cavity epithelium in these species is the presence of numerous phagosomes and coated vesicles in the apical cytoplasm. The cell surface has many microvilli and a single cilium. Cells of the coelomic epithelium contain vacuoles in the apical part and myofibrils in the basal region; the thickness of this epithelium in A. japonicus and C. japonica is 9–16 and 10–30 m, respectively. Based on the different structure of the respiratory trees and the absence of hemocytes in A. japonicus, it is suggested that the holothurian species studied have different routes of oxygen transport from the environment to the internal organs.