分支格局、组份分析与中值淘汰法

文章简明介绍了现代分支系统学的分支格局原理和组份分析方法,并应用于李朝銮(1990,表2)的中国白粉藤属14种植物数据的分支分析。得出13个可能的最简约的二歧分支图,图长41步。这些分支图与李(1990)图2：13的比较表明,中值淘汰法不如组份分析方法有效,而且中值淘汰法有表相学和(或)进化系统学的疑问。     

A New Method for Cladistic Analysis—Median Elimination Series (MES)

The use of parsimony (or the principle of simplicity) in phylogenetic inference is reviewed. The major problem in using parsimony for phylogenetic reconstruction is that neither a single solution for a given set of data nor the most parsimonious tree could be provided. Therefore, based on recognition and judgement of similarity of organisms by Hennig's advanced character (1965) and some particular principles from evolutionary theory of Darwinism accepted by many systematists as general truths (Bonde 1977; Wiley 1975; Gaffrey 1979), the author has developed a new method, Elimination Series through Median Selection (Median Elimination Series, MES for short), for phylogenetic analysis. In addition to using the advanced characters for understanding the relationships between taxa, MES emphasizes that the mosaic characters including both primitive and advanced in an array of characters play an important part in determining the nodes or branches and distinguishing the taxa.The author considers median units as ancestors in a phylogenetic tree like Farris, but the concept and algorithm of “median” differ from Farris' (1970) in: (1) The author's median involves the top taxon and unplaced one, but Farris' median does the top taxon, its ancestor as well as unplaced one; (2) The median taken by the author is of common value or the least one among the associated characters of two taxa. However, the median taken by Farris is median numerical value among the three (3) The median or median unit called by the author is the numerical value of the relatively primitive character or taxon between the advanced characters or the taxa stood apart from the original position. Farris' one is the median position or number in the center of three taxa or its associated characters. The author recognizes that reversion of characters is possible and obtains the knowledge of it from observation and analysis of characters of organisms or scientific experiment and distinguished through analysis of morphocline and co-variation in a series of taxa, but not from induction only by mathematical model based on the principle of simplicity. The author divides co-variation into 4 types: 1. Progressive co-variation. Transformation series of characters A and a is as follows: A → A' a → a' reversed co-variation. Transformation series of characters A and a is as follows: A ← A' a ← a' 3. Progression-reversion co-variation. Transformation series of characters A and a is follows: A → A' a ← a' 4. Reversion-progression co-variation. Transformation series of characters A and a is as follows: A ← A' a → a' The characters next to the arrows should be advanced. Co-variation for most of the species of Cissus from China belongs to the type 1 and that for C. repanda Vahl. to the type 3, without types 2 and 4. In determining the progressive co-variation, reverse evolution of character could be distinguished through the analysis of morphocline and co-variation. The author has recognized two types of cyclic polarity, including unidirectional and bidirectional ones. For the former, the character may return back to the original state through more than one step. In fact, this is a complex reversion. For the latter, the character may reach a advanced state from the original one via two different ways. In fact, this is special progressive transformation series and it may often occur in complex reticulate evolution as a small net, for example, in evolution of leaf fragment and others of angiosperms (Meyen 1973). The cyclic polarity in C. repanda Vahl. is bidirectional (see transformation series 11 of the characters in Cissus). Transformation series of All the characters have been determined on the basis of analysis of morphocline, co-variation and cyclic polarity. In this paper, the three steps of understanding phylogenetic system are developed: (1) recognition of homologous characters; (2) discovery of internal relationships between homologous characters in order to obtain transformation series or phylogeny of homologous characters; (3) discovery of internal relationships between phylogenies of homologous characters in order to get a phylogenetic system of organisms or approaching understanding essence of evolution. The result inferred by MES is based on some principles of evolution from Darwin and Hennig but not judged by the principle of simplicity or parsimony from Popper (1960, 1968). The statement in this paper attempts to show that if a dilemma in modern cladistics could be solved, its principles must be reconsidered. Decontaminated thianthrene disproportion. 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中国柽柳属植物的分支分类研究

选取生长习性、植物形态、解剖结构、花粉特征以及种子微形态特征等共66个性状,采用简约法对国产柽柳属16种植物及外类群红砂Hololachne songarica进行分支分析,并用靴带检验法(Bootstrap)计算内部分支的支持率。分支图表明,国产柽柳属植物分为4个分支,分别属于Baum(1978)所划分的组Ⅰ及组Ⅱ中不同的系,从一个侧面说明基于经典分类所划分的组是比较自然的,同意Baum的属下分类系统。同时,基于分支分类结果并结合分子证据,对国产柽柳属属间亲缘关系及有争议种的分类学地位进行了探讨,认为甘蒙柽柳是独立于中国柽柳的种,多花柽柳是独立于多枝柽柳的种,盐地柽柳是刚毛柽柳的变种,而叶抱茎呈鞘状的沙生柽柳和莎车柽柳系统学关系很近,是较为原始的一类柽柳。     

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.     

中国灵猫科的支序系统学分析

选取分布于中国境内的8属9种灵猫科动物的88个骨骼性状、31个外部形态性状和1个行为性状,运用替代外群法分别以赤狐(犬科狐属)和青鼬(鼬科貂属)共同或单独作为外群进行支序分析,得出10个支序图,其步长(TL)为：106～136,一致性指数(CI)为0．581—0．660,保留指数(RI)为0．610—0．714。经合意分析得到4个相似的支序图,其TL为41—136,CI为0．581—0．732,RI为0．610—0．818,结果支持：①斑灵狸、大灵猫、小灵猫构成一个单系群,与传统分类一致(均属灵猫亚科);②椰子狸、花面狸、熊狸构成一个单系群,与传统分类一致(均属长尾狸亚科);③红颊獴、食蟹獴与灵猫科其他种为姐妹群关系(Bootstrap检验支持率100％),建议獴类为一亚科;④长颌带狸拥有较多自近裔性状如三个门齿孔,是一个高度特化的种类,其系统地位有待进一步研究。     

中国栎属(壳斗科)基于叶表皮及叶结构特征的分支分析

以三棱栎为外类群,基于叶表皮及叶结构特征对中国栎属进行初步的分支分析,结果显示了栎属内稳定的“支”结构及其种间关系。栎亚属可划分为5个组,分别为巴东栎组,高山栎组,Jiang子栎组,麻栎组和槲栎组,Jiang子栎组是栎亚属常绿栎类与落叶栎类之间的过渡类群;高山栎组应为栎亚属常绿栎类中的特化类群,而非最原始类群,5个组中,仅巴东栎组不是单系类群,而是一个多系类群,青冈亚属较栎亚属早分支,可划分为3大类;无毛类,简单被毛类和复杂被毛类;无毛类最原始,复杂被毛类与栎亚属关系最近,因此,叶表皮及叶结构特征对解决栎亚属组间亲缘关系有重要的分类学意义。     

分支系统学和种系发生种

简要评述进化系统学和分支系统学的物种概念问题。介绍了关系物种问题研究的一些新进展,特别是种系发生种概念和种系发生种的划定方法－居群聚合分析和分支单型聚合。     

旌节花科及其相关类群的分支分析

选取生长习性、植物形态、木材解剖、花的形态结构、花粉特征以及胚胎学和染色体数目等共72个性状,采用最大简约法（Maximum Parsimony,MP)对旌节花科及其相关类群五桠果科、猕猴桃科、山茶科、金莲木科和省沽油科等进行分支分析。并用靴带检验法（Bootstrap)计算内部分支的支持率。分支图表明,旌节花科与省沽油科组成姊妹群,靴带支持率为79％,表明旌节花科与省沽油科具有最为密切的关系。旌节花科与猕猴桃科的关系次之,旌节花科和省沽油科与猕猴桃科关系的靴带支持率为58％。然后是山茶科。而旌节花科与金莲木科和五桠果科的关系则依次疏远。这与我们在孢粉学和胚胎学研究中所得的结论在某些方面是基本一致的。与Nandi等人用形态学数据和分子数据分析得到的结论也比较吻合,他们的结论也认为旌节花科与省沽油科具有比较密切的关系。只是他们把五桠果科和金莲木科摆在更近的位置,而山茶科和猕猴桃科则放在较疏远的位置上。     

寄生红蜡蚧的扁角跳小蜂属6个种(膜翅目:跳小蜂科)的系统发育支序分析

选用寄生红蜡蚧的扁角跳小蜂属(Anicetus)6个种的14个形态特征和2个其他特征(寄主种数和是否寄生软蚧)作为内群性状,以柯氏花翅跳小蜂(Microterys clauseni)作为外群,运用PAUP(Version 4．0b10)程序做了支序分析。所得支序树状图有如下参数：树长=28;一致性指数=0．6786;稳定性指数=0.4375。6种扁角跳小蜂中,亲缘关系表示为：(A．annulatus,((A．rubensi,(A．beneficus,A．rarisetus)),(A．howardi,A.ohgushii)))。软蚧扁角跳小蜂(A.annulatus)与其他5个种的亲缘关系相对较远,与传统分类学观点一致。     

Phylogeny of Plastids Based on Cladistic Analysis of Gene Loss Inferred from Complete Plastid Genome Sequences

Based on the recent hypothesis on the origin of eukaryotic phototrophs, red algae, green plants, and glaucophytes constitute the primary photosynthetic eukaryotes (whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis), whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary or tertiary endosymbiotic events (involving a phototrophic eukaryote and a host cell). Although phylogenetic analyses using multiple plastid genes from a wide range of eukaryotic lineages have been carried out, some of the major phylogenetic relationships of plastids remain ambiguous or conflict between different phylogenetic methods used for nucleotide or amino acid substitutions. Therefore, an alternative methodology to infer the plastid phylogeny is needed. Here, we carried out a cladistic analysis of the loss of plastid genes after primary endosymbiosis using complete plastid genome sequences from a wide range of eukaryotic phototrophs. Since it is extremely unlikely that plastid genes are regained during plastid evolution, we used the irreversible Camin-Sokal model for our cladistic analysis of the loss of plastid genes. The cladistic analysis of the 274 plastid protein-coding genes resolved the 20 operational taxonomic units representing a wide range of eukaryotic lineages (including three secondary plastid-containing groups) into two large monophyletic groups with high bootstrap values: one corresponded to the red lineage and the other consisted of a large clade composed of the green lineage (green plants and Euglena) and the basal glaucophyte plastid. Although the sister relationship between the green lineage and the Glaucophyta was not resolved in recent phylogenetic studies using amino acid substitutions from multiple plastid genes, it is consistent with the rbcL gene phylogeny and with a recent phylogenetic study using multiple nuclear genes. In addition, our analysis robustly resolved the conflicting/ambiguous phylogenetic positions of secondary plastids in previous phylogenetic studies: the Euglena plastid was sister to the chlorophycean (Chlamydomonas) lineage, and the secondary plastids from the diatom (Odontiella) and cryptophyte (Guillardia) were monophyletic within the red lineage.     

Using Median Lines in Robust Bivariate Data Analysis

Methods for robust comparison of bivariate errors-in-variables are considered. The concept of median lines is introduced for the robust estimation of principal components. Median lines separate the bivariate sample space into two equally sized parts. Statistical properties of the model parameters are derived. Robust residual analysis assesses linear relationships as well as goodness of fit and allows for the detection of potential outliers. Special emphasis is laid on graphical methods. A bivariate box-plot is proposed for exploratory data analysis. The median lines procedure is illustrated by a real example.     

Cladistic and phenetic analyses of relationships among Fusarium spp. in Dongtan wetland by morphology and isozymes

Variations of 12 morphological characters and 78 isozymic bands among 78 isolates of five Fusarium spp. from Dongtan wetland were described and analysed with cladistic parsimony and phenetic UPGMA methods. Hierarchical cluster analysis of 12 morphological characters grouped 78 strains into five defined species with a high overlap between isolates. Hierarchical cluster analysis of isozyme patterns showed a higher degree of relationship among five Fusarium spp., in which Fusarium nivale, Fusarium semitectum and Fusarium oxysporum clustered as one group, and F. semitectum was closer to F. nivale than to F. oxysporum; Fusarium graminearum and Fusarium moniliforme formed one group and showed clearly distinct from the first group. Groups of individual isolates indicated by a plot of principal component analysis were consistent with these findings. The comparison of two different data sets revealed that isozyme patterns showed higher variations between species and among individual isolates than morphological characters. Parsimony analysis of morphological characters yielded unresolved cladograms. Parsimony analysis of isozymes as presence/absence characters revealed the same five species in general as the results indicated by phenetic analysis, differing in the relative position of species in subclusters.     

联合使用PAUP和 MacClade 程序进行支序分析

针对一组数据,同时利用MacClade和PAUP两个软件进行系统发育分析,是支序系统学前沿学者广泛使用的研究方法。本文主要介绍了PAUP^*4.0,MacClade4.0以及两者联合使用的优势,同时介绍了具体的操作方法。     

北美车前(Plantago Virginica)和车前(P.asiatica)分布格局的分形分析

北美车前 (ＰｌａｎｔａｇｏｖｒｉｇｉｎｉｃａＬ .)是我国东南地区的一种外来杂草 ,该杂草在浙江、江苏、上海、江西等省区有分布 ,多见于田梗路边、住宅四周、抛荒地、公路两侧等人畜出没频繁的地段 ,其种群生长迅速 ,呈现出生态爆发态势 ,是一种典型的生态入侵种。分形理论已被广泛地应用于自然科学、社会科学中的众多领域。在生态学领域 ,应用分形维数能够客观地表达种群的分布式样 ,同时也能反映种群占有空间、资源利用的能力[1～ 6 ] 。本研究以新入侵种北美车前为对象 ,并与我国境内分布较广的杂草车前 (Ｐ .ａｓｉａｔｉｃａ)作比…     

The Origin and Evolution of tRNA Inferred from Phylogenetic Analysis of Structure

The evolutionary history of the two structural and functional domains of tRNA is controversial but harbors the secrets of early translation and the genetic code. To explore the origin and evolution of tRNA, we reconstructed phylogenetic trees directly from molecular structure. Forty-two structural characters describing the geometry of 571 tRNAs and three statistical parameters describing thermodynamic and mechanical features of molecules quantitatively were used to derive phylogenetic trees of molecules and molecular substructures. Trees of molecules failed to group tRNA according to amino acid specificity and did not reveal the tripartite nature of life, probably due to loss of phylogenetic signal or because tRNA diversification predated organismal diversification. Trees of substructures derived from both structural and statistical characters support the origin of tRNA in the acceptor arm and the hypothesis that the top half domain composed of acceptor and pseudouridine (TΨC) arms is more ancient than the bottom half domain composed of dihydrouridine (DHU) and anticodon arms. This constitutes the cornerstone of the genomic tag hypothesis that postulates tRNAs were ancient telomeres in the RNA world. The trees of substructures suggest a model for the evolution of the major functional and structural components of tRNA. In this model, short RNA hairpins with stems homologous to the acceptor arm of present day tRNAs were extended with regions homologous to TΨC and anticodon arms. The DHU arm was then incorporated into the resulting three-stemmed structure to form a proto-cloverleaf structure. The variable region was the last structural addition to the molecular repertoire of evolving tRNA substructures. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

土壤中抗性基因的产生,扩散传播以及消减的研究进展

近年来,土壤中残留的大量抗生素不可避免的导致耐药微生物和抗性基因的增加和扩散,引起一系列土壤污染和生态风险。作为一类新兴污染物,抗性基因的污染水平已经远远超出我们的预想,因此对土壤中抗性基因的分布水平、扩散传播及消减技术的研究刻不容缓。本文对国内外土壤中抗生素和抗性基因残留水平进行了总结分析,探讨了土壤中抗性基因的产生、扩散的内在动力和机制。同时,分析了土壤中抗性基因分布和扩散的影响因素,如:抗生素残留水平,土壤理化性质和环境条件等。在此基础上,探讨了土壤抗性基因阻隔和消减技术,包括传统降解方法:高温,光照催化、微波-H2O2-微生物联合处理技术等,并提出新型消解技术:取代活性基团、靶位修饰以及改变外排泵的通透性等。讨论未来在控制抗性基因生态风险,降低其在土壤中的丰度,有效阻截技术的发展趋势。     

马铃薯StCRKs基因家族的鉴定分析及响应逆境信号的表达

为鉴定马铃薯（Solanum tuberosum）中富含半胱氨酸的类受体激酶（cysteine-rich receptor-like kinase,CRKs）,利用Pfam等工具对马铃薯蛋白质组和基因组序列进行分析,共鉴定到18个新的马铃薯StCRKs家族基因,这些基因分布在1、2、11和12号染色体上,均具有典型保守的CRK结构域。StCRKs基因的启动子区具有响应5种植物激素、昼夜节律、生物胁迫、非生物胁迫及种子特异性的响应元件。利用qRT-PCR方法对马铃薯盆栽苗开花期的根、茎、叶和花中的18个StCRKs基因进行组织特异性表达分析,结果显示不同基因的表达部位不同。分别用水杨酸类似物BTH和4 ℃低温处理马铃薯,有13个StCRKs基因能够响应低温信号,10个StCRKs基因能够被水杨酸类似物BTH诱导。为进一步深入研究StCRKs在生物胁迫及非生物胁迫中的功能提供了线索。     

Nonparametric Comparison of Longitudinal Response Patterns from Unpaired Samples Using Configural Frequency Analysis

Nonparametric methods of Configural Frequency Analysis (CFA) for the comparison of longitudinal response patterns are discussed. In particular, methods of transforming response patterns into profiles that can be analyzed using CFA are presented. When two independent samples are given, two sample CFA can be applied to perform local testing. An example is given from research on obesity. Two sample CFA of response pattern is compared to methods of global testing.     

Nonparametric Comparison of Longitudinal Response Patterns from Paired Samples Using Configural Frequency Analysis

Nonparametric methods of Configural Frequency Analysis (CFA) for comparing longitudinal response patterns are discussed. Characteristics of diagonally symmetric frequency distributions are mapped with hypotheses on the locus of treatment effects. Test statistics for the analysis of local dependencies are discussed. In particular, applications to paired samples are considered. A biomedical example is given from research on the effects of spasmolytic drugs. Local CFA-testing is compared with global testing. Alternative strategies of testing and the respective underlying assumptions are discussed.