李氏方法与Farris氏方法产生的分支系统树的比较

中值淘汰法的主要目的是为了打破现代分支系统学中采用最简原理所带来的不确定性僵局。然而,在两个或两个以上分类单元都具有相同衍进指数的情况下,该方法也能不止产生一个分支系统树,因为没有一个客观标准来确定应该先连接哪一个分类单元,而连接的先后顺序不同,就会产生不同的分支系统树。中值淘汰法的作者认为,该法产生的结果不用简约性来判定。但是,该法也能构成最简约的分支系统树。本文还对应用中值淘汰法所面临的问题作了讨论。     

简约性，极性分析及中值淘汰法——与李朝銮先生商榷

无论是从理论基础上还是具体步骤上,中值淘汰法与分支学家常用的方法都不相同。在构建分支图之前识别祖征与反向进化,直接衍征与环极向衍征有悖于分支学的基本原则;而在具体运算过程中仅以2个分类单元求取中值又会掩盖反向进化;新的中值必须全部包括分支图上下面的中值的原则事实上是不承认反向进化。中值淘汰法产生的分支图不及Farris方法产生的分支图简约。     

分支系统学当前的理论和方法概述及华东地区山胡椒属十二个种的分支系统学研究

本文概述了当前分支系统学研究中涉及的主要理论和方法,包括性状的选取、性状状态和极性的确定、数据矩阵的分析计算、结果分支图的处理、分支图可靠性的评价及分支图的应用。本文同时以华东地区樟科山胡椒属Linderal2个种的分支系统学研究为例,讨论了用形态性状进行分支系统学研究中可能遇到的问题,也揭示了一些分支系统学与传统的系统学在应用性状推导进化关系上的不同点。对这12个种的分支系统学研究得出了一些不同于传统系统学方法所推测的山胡椒属内的系统发育关系,如分支系统学研究显示山胡椒组和球果组很近缘。在严格一致性分支图上,杯托组的黑壳楠和江浙山胡椒分别位于最原始和最进化的分支,表明这个组是复系类群。分支图也显示山胡椒组可能是复系类群。     

分支系统学当前的理论和方法概述及华东地区山胡椒属十二个种的…

本概述了当前分支系统学研究中涉及的主要理论和方法,包括性状的选取、性状状态和极性的确定、数据矩阵的分析计算、结果分支图的处理、分支图可靠性的评价及分支图的应用。本同时以华东地区樟科山胡椒属Ｌｉｎｄｅｒａ１２个种的分支系统学研究为例,讨论了用形态性状进行分支系统学研究中可能遇到的问题,也揭示了一些分支系统学与传统的系统学在应用性状推导进化关系上的不同点。对这１２个种的分支系统学研究得出了一些不同     

一个新的分支系统分析方法，中值淘汰法

本文评述了分支系统分析中最简原理或简约性在系统发育推论中的应用和存在的问题。在系统发育推论中使用简约性存在的主要问题在于,既无法获得最简约的系统树也不一定得到一个单一的解决办法。基于此,本文作者接受了Hennig用衍生性状来判断生物之间相似性的同时,用近代大多数生物系统学家接受的进化论各项原理代替Popper的简约性原理,以寻求单一的解决办法和获得确定性的结果为目标,提出了一个新的分支系统分析方法——中值淘汰法,用以研究系统发育。这个方法除了使用衍生性状来判断生物类群之间的亲缘关系外,还强调包括原始的也包括衍生性状在内的性状镶嵌组合在决定分支和辨别分类群过程中的作用。     

分支系统学简介

分支系统学是本世纪70年代以来发展起来的一个新的系统学派。本文扼要地介绍了分支系统学的创立、历史和发展,分支系统学的基本概念、特征分析法以及分支系统学的广泛应用给现代生物系统学所带来的广泛影响和冲击。     

分支系统学简介

分支系统学是本世纪70年代以来发展起来的一个新的系统学派。本文扼要地介绍了分支系统学的创立、历史和发展,分支系统学的基本概念、特征分析法以及分支系统学的广泛应用给现代生物系统学所带来广泛影响和冲击。     

分支系统学简介

分支系统学简介樊晋江（浙江省医学科学院寄生虫病研究所杭州３１００１３），关键词分支系统学，分支分类，系统发育１９５０年诞生的分支系统学，现在已经发展成为探索生物系统发育的有效工具之一。分支系统学与现代计算机技术的结合形成了新的分支学科─—数值分支系统...     

胎盘亚纲目间关系和分支分类问题

主要根据近两年的文献,从分支系统学观点综述了现生胎盘类哺乳动物的目变动,目上组群和目间种系发生关系,给出了其19目的分支图,讨论了目上水平分支分类的几个问题。     

锦鸡儿属种系发生关系重建的探讨

基于形态学、染色体、花粉形态24个特征,采用分支系统学方法研究锦鸡儿属（Caragana）的种系发生关系。根据分支图结果,将锦鸡儿属72种排列成12系5组。分支图也表达出分类群演化关系,对Moore(1968)种系发生方案提出了修改,重建了本属的种系发生关系。     

Comparison of the Cladograms Produced by Li's Method and Farris' Method

In order to avoid producing many equally most parsimonious trees, Li (1990) developed a new cladistic method, the Median Elimination Series (MES), to construct a single cladogram for a given data set. However, we found that Li's method can produce more than one tree if two or more taxa have the same advancement index (which is the total number of apomorphies for a taxon in a given data set), because there is no objective method to decide which taxon should be connected first and different orders of connection can produce different trees. Li claimed that the result produced by his method did not apply the principle of simplicity (parsimony). Nevertheless, Zhang (1991) recognised that Li's method actually accepted the principle of parsimony. Here we demonstrated that Li's method also can produce the minimum-length trees. We conclude that Li's method could produce more than one tree and the tree(s) may be the minimum-length possible. However, the length of tree(s) depends on the order of connection of the taxa. The major problems in using Li's methodare discussed.     

Cladistic Patterns,Component Analysis and Median Elimination Series

The principle of cladistic patterns and the method of component analysis (MCA) are introduced concisely with a hypothetic example and then applied to the cladistic analysis of the data on Chinese plants of the genus Cissus L. from Li (1990, Tab. 2). Thirteen resulted possible dichotomous cladograms are illustrated with characters, and they are the most parsimonious ones, all with a length of 41 steps. Comparison between them and the one byLi (1990, Fig. 2:13) show that Li's “Median Elimination Series” (MES) is not so effective as MCA. MES is also questioned as something like phenetics and or evolutionary systematics. Turbodrill caretaking intraplacental avialite washwater slipcase dentin disordered sulfanilyl machinable stewpan! Netherward pressbodies horror abscissa, keratosis frieze. 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小腹茧蜂亚科的雄外生殖器及族级单元系统发育的研究

对分布在东洋区和古北区的小腹茧蜂亚科 (膜翅目: 茧蜂科)21个属的67个种及外群折脉茧蜂属 (膜翅目: 茧蜂科) 2个种的雄外生殖器的5个性状进行了比较研究。在形态学研究的基础上,通过选用头部、胸部和腹部(包括雌雄外生殖器的性状) 等34个性状,运用支序分析的方法探讨了分布在东洋区和古北区的小腹茧蜂亚科21个属以及它们所属的族间的系统发育关系,并对Mason (1981) 的分类系统进行了重新评价。雄外生殖器和支序分析基本上证实并恢复了由Mason (1981) 确定的2个主要分支,即绒茧蜂族Apantelini+小腹茧蜂族Microgastrini和拱茧蜂族Fornicini+盘绒茧蜂族Cotesiini+侧沟茧蜂族MicroplitinI。绒茧蜂族Apantelini、拱茧蜂族Fornicini和侧沟茧蜂族Microplitini为单系群也被支持,但小腹茧蜂族Microgastrini和盘绒茧蜂族Cotesiini是否为单系群尚难于在树形图中体现,而且族内各属间的分支关系有变动。因此,尽管Mason的族级分类单元有一些欠缺,但仍是可信、实用的,不同意Walker等 (1990) 认为不应再使用Mason分族系统的观点。     

Optimization-based metabolic control analysis

In this work, a novel optimization-based metabolic control analysis (OMCA) method is introduced for reducing data requirement for metabolic control analysis (MCA). It is postulated that using the optimal control approach, the fluxes in a metabolic network are correlated to metabolite concentrations and enzyme activities as a state-feedback control system that is optimal with respect to a homeostasis objective. It is then shown that the optimal feedback gains are directly related to the elasticity coefficients (ECs) of MCA. This approach requires determination of the relative "importance" of metabolites and fluxes for the system, which is possible with significantly reduced experimental data, as compared with typical MCA requirements. The OMCA approach is applied to a top-down control model of glycolysis in hepatocytes. It is statistically demonstrated that the OMCA model is capable of predicting the ECs observed experimentally with few exceptions. Further, an OMCA-based model reconciliation study shows that the modification of four assumed stoichiometric coefficients in the model can explain most of the discrepancies, with the exception of elasticities with respect to the NADH/NAD ratio.     

Incorporating single-locus tests into haplotype cladistic analysis in case-control studies

In case-control studies, genetic associations for complex diseases may be probed either with single-locus tests or with haplotype-based tests. Although there are different views on the relative merits and preferences of the two test strategies, haplotype-based analyses are generally believed to be more powerful to detect genes with modest effects. However, a main drawback of haplotype-based association tests is the large number of distinct haplotypes, which increases the degrees of freedom for corresponding test statistics and thus reduces the statistical power. To decrease the degrees of freedom and enhance the efficiency and power of haplotype analysis, we propose an improved haplotype clustering method that is based on the haplotype cladistic analysis developed by Durrant et al. In our method, we attempt to combine the strengths of single-locus analysis and haplotype-based analysis into one single test framework. Novel in our method is that we develop a more informative haplotype similarity measurement by using p-values obtained from single-locus association tests to construct a measure of weight, which to some extent incorporates the information of disease outcomes. The weights are then used in computation of similarity measures to construct distance metrics between haplotype pairs in haplotype cladistic analysis. To assess our proposed new method, we performed simulation analyses to compare the relative performances of (1) conventional haplotype-based analysis using original haplotype, (2) single-locus allele-based analysis, (3) original haplotype cladistic analysis (CLADHC) by Durrant et al., and (4) our weighted haplotype cladistic analysis method, under different scenarios. Our weighted cladistic analysis method shows an increased statistical power and robustness, compared with the methods of haplotype cladistic analysis, single-locus test, and the traditional haplotype-based analyses. The real data analyses also show that our proposed method has practical significance in the human genetics field.     

THE HOLY GRAIL OF THE PERFECT CHARACTER: THE CLADISTIC TREATMENT OF MORPHOMETRIC DATA

Abstract— Data scored for cladistic analyses may be quantitative or qualitative, continuous or discrete, and show overlapping or non-overlapping values between taxa. Quantitative and qualitative are modes of expression of data, while continuous or discrete refer to properties of the set of numbers that express the data; both these pairs of terms have been confused with overlapping and non-overlapping. The degree of overlap of values between taxa is often used to filter characters in cladistic analyses: if a minimum amount of overlap is exceeded, or a minimum amount of disjunction not reached, characters are rejected as "not cladistic". However, this rests on a confusion between features of taxa and features of individual organisms (attributes). Cladistic characters are features of taxa, and comprise frequency distributions of attribute values over individuals of a taxon. Cladistic characters logically cannot overlap, although taxa may have overlapping attribute values. Thus, a priori rejection of characters that have overlapping attribute values is non-sensical. Such data may still be rejected from consideration for cladistic analysis if it could be demonstrated that they contain little recoverable phylogenetic signal. Few published analyses have empirically tested this. An analysis of overlapping morphometric data from three series of Banksia suggests that, at least in these cases, they map phylogeny almost as accurately as more conventional, qualitative morphological data. While more such tests are required, morphometric data should not be rejected a priori from cladistic analyses.     

螟黄足盘绒茧蜂复合群支序系统学研究（膜翅目：茧蜂科：小腹茧蜂亚科）

对螟黄足盘绒茧蜂复合群Cotesia flavipes complex (膜翅目：茧蜂科：小腹茧蜂亚科)分布全世界的5个种和外群侧沟茧蜂Microplitis 及荻茧蜂Diolcogaster 的25个性状,以及复合群5个种和外群螟蛉盘绒茧蜂Cotesia ruficrus、粘虫盘绒茧蜂Cotesia kariyai、粉蝶盘绒茧蜂Cotesia glomerata 的24个性状,分别进行比较研究,并运用支序分析的方法探讨该复合群内5个种种间的系统发育关系。支序分析表明螟黄足盘绒茧蜂复合群是一单系群,二化螟盘绒茧蜂C. chilonis 和大螟盘绒茧蜂C. sesamiae 近缘,芦螟盘绒茧蜂C. chiloluteelli 和汉寿盘绒茧蜂C. hanshouensis 近缘,螟黄足盘绒茧蜂C. flavipes相对独立。 以上研究表明无论是以近缘属作外群还是以同属其它种作外群,所得结果基本上都能反映螟黄足盘绒茧蜂复合群各种之间的分类地位。     

Taxic and Transformational Homology: Different Ways of Seeing

Hypotheses of taxic homology are hypotheses of taxa (groups). Hypotheses of transformational homology are hypotheses of transformations between character states within the context of an explicit model of character evolution. Taxic and transformational homology are discussed with respect to secondary loss and reversal in the context of three-taxon statement analysis and standard cladistic analysis. We argue that it is important to distinguish complement relation homologies from those that we term paired homologues. This distinction means that the implementation of three-taxon statement analysis needs modification if all data are to be considered potentially informative. Modified three-taxon statement analysis and standard cladistic analysis yield different results for the example of character reversal provided by Kluge (1994) for both complement relation data and paired homologues. We argue that these different results reflect the different approaches of standard cladistic analysis and modified t.t.s. analysis. In the standard cladistic approach, absence, as secondary loss, can provide evidence for a group. This is because the standard cladistic approach implements a transformational view of homology. In the t.t.s approach discussed in this paper, absence can only be interpreted as secondary loss by congruence with other data; absence alone can never provide evidence for a group. In this respect, the modified t.t.s. approach is compatible with a taxic view of homology.     

Long-Term Risk of Cardiovascular Disease among Type 2 Diabetic Patients with Asymptomatic Intracranial Atherosclerosis: A Prospective Cohort Study

Objective

To investigate whether asymptomatic middle cerebral artery (MCA) stenosis is associated with risk of cardiovascular disease (CVD) in Chinese with type 2 diabetes.

Methods

In this prospective cohort study, 2,144 Hong Kong Chinese with type 2 diabetes and without history of stroke or atrial fibrillation were recruited in 1994–1996 and followed up for a median of 14.51 years. Participants were assessed at baseline for MCA stenosis using transcranial Doppler. We performed survival analysis to assess the association between asymptomatic MCA stenosis and first CVD event, defined as ischemic stroke, acute coronary syndrome (ACS) or cardiovascular death.

Results

Of the 2,144 subjects, MCA stenosis at baseline was detected in 264 (12.3%). Rates of stroke, ACS and cardiovascular death per 100 were, respectively, 2.24, 2.92 and 1.11 among participants with stenosis, higher than among those without stenosis. Ten-year cumulative occurrence of stroke, ACS and cardiovascular death in subjects with MCA stenosis was 20%, 24% and 10%, respectively, higher than the corresponding values for subjects without stenosis(all P<0.001). After adjusting for covariates, MCA stenosis was found to be an independent predictor of stroke [hazard ratio (HR) 1.40, 95%CI 1.05–1.86; P = 0.02], ACS (HR 1.35, 95%CI 1.04–1.75; P = 0.02) and cardiovascular death(HR 1.56, 95%CI 1.04–2.33; P = 0.03).

Conclusions

Asymptomatic MCA stenosis is a risk factor for CVD in Chinese with type 2 diabetes, and detection of asymptomatic MCA stenosis by transcranial Doppler can identify diabetic individuals at high risk of future CVD. This finding is particularly important for diabetic individuals in Asia, where intracranial atherosclerosis is common.