简单INDEL编码与其它空位编码方法的比较

不同的系统发育重建算法以不同的方式编码空位,但是不同的编码方式对系统发育分析结果的影响并不清楚.介绍了一种新的空位编码方式--简单indel编码,并将它与将空位编码成丢失的数据和编码成第5性状作了比较.统计分析表明,简单indel编码的确比将空位编码成丢失的数据更有效,但是与将空位编码成第5性状相比两者结果差异不大.而且,随着空位含量的降低,简单indel编码发挥的作用也减少.     

天南星属的系统发育分析

运用分支分类学方法对天南星属进行了系统发育分析,以天南星属13个组为13个分支分类单位,选择菖蒲属作为外类群,从天南星属植物特征中选取13个性状作为建立数据矩阵的基本资料,并以外类群比较和通行的形态演化规律为依据这些性状进行极化,采用改进后的最大同步法和最小平行进化法进行分类运算,按照最简约的原则,选出演化长度较短的最大同步法谱分支图,作为本文讨论的基础,并在此基础上,探讨了天南星属各组的系统关系。     

鸡传染性支气管炎病毒(IBV)广西流行株3'端非编码区序列分析

本研究应用RT-PCR方法扩增出分离自广西的26株鸡传染性支气管炎病毒(IBV)以及参考株M41和疫苗株H120、Ma5和4/91的3'端非编码区(3'UTR)的cDNA,并对其进行了克隆、序列测定、比较及其系统进化分析。序列分析结果表明,与Beaudette株的3'UTR序列相比较,26株分离的IBV中有1株和3株的分离株3'UTR序列分别插入了23个和2个碱基,另外有12株、6株、1株、2株和1株的分离株3'UTR序列分别缺失了1个、2个、22个、29个和84个碱基,不同毒株之间碱基数量最大相差达107个碱基。系统进化分析结果表明,26株分离株可分为4群,其中21株属于第Ⅰ群,与经典疫苗株H120的核苷酸同源性均较低(54.4%～75.5%);3株与4/91同属于第Ⅱ群;1株与H120同属于第Ⅲ群;另外1株单独属于Ⅴ群。综上所述,广西流行IBV的绝大部分毒株在3'UTR序列上与目前常用的疫苗株相比都发生了很大的变异,而且存在多种形式的碱基缺失和插入现象。由此,我们认为流行株的变异可能是疫苗不能提供有效保护的主要原因。     

介绍系统发育分析计算机程序HENNIG86（1.5版）

Hennig86(1.5版)是一个适用于MS-DOS、IBM-PC及其各类兼容机的全交互式系统发育分析程序。该程序由著名的支序分类学理论家 James S. Farris博士编写,1988年正式问世。与现有的其它几个系统发育分析程序包如PHYLIP、PAUP等相比,Hennig86 具有体积小(49K),容量大,功能齐全,操     

低等鲤科鱼类RAPD分析及系统发育研究

通过对鲤科鱼类３０个个体所代表的１８个种的随机扩增,作者得到了大量有系统发育信息的ＤＮＡ多态片段。通过Ｒａｐｄｐｌｏｔ程序将ＤＮＡ的多态片段转换成遗传距离（ｄ＝１－Ｓ,Ｓ＝２ＮｘＮｙ／Ｎｘ＋Ｎｙ）。该遗传距离的矩阵经ＰＨＹＬＩＰ软件包中的Ｎｅｉｇｈｂｏｒ（ｏｐｔｉｏｎ＝ＮＪ）程序处理后,生成了低等鲤科鱼类代表属种的分支系统图。从该系统图中以看出：ＲＡＰＤ分析方法在鲤科鱼类的系统发育研究中有一定的局     

龙胆属的系统发育分析

本文运用支序分类的原理和方法,对龙胆科龙胆属的属下等级进行了重新归类和系统发育分析。龙胆属是一个单系群,以3项近裔共性为归类依据。性状分析作了性状同源性分析和性状极性分析。性状极化主要以外类群比较、性状相关性及染色体资料为依据,其它方法,如生物重演律原则、地理递进原则以及孢粉形态等也被结合使用。分析结果,双蝴蝶属和蔓龙胆属被选择为外类群,71个性状被选择作为建立数据矩阵的基本资料。使用PAUP程序对矩阵进行了运算,得到4个最简约的谱系分支图,它们均具一致性系数0.637,支序长度为160步,f-比值范围为0.179～0.189,其中具最低f-比值的图被选作为类群归类和讨论亲缘关系的基础。在支序图上龙胆属归为15个组;其中5个组又划分为系,共包括23个系,其余组为单型组,故共有33个属下类群。一个严格的一致性谱系分支图总结了所有的一致点,从而支持了支序分析的结果。     

金缕梅类科的系统发育分析

本文运用分支分类的方法对金缕梅类进行了系统发育的分析。金缕梅类作为单元发生群包括下列19科：昆栏树科、水青树科、连香树科、领春木科、杜仲科、金缕梅科、悬铃木科、交让木科、假槲树科、双颊果科、折扇叶科、黄杨科、西蒙得木科、木麻黄科、山毛榉科、桦木科、杨梅科、马尾树科和胡桃科。木兰科在分析中被选择作为外群类。在对大量性状进行评估之后,选择了32对性状作为建立数据矩阵的基本资料。性状极化主要以外类群比较、化石证据和通行的形态演化规律为依据。首次引入了不合谐数的概念来检测性状极化结果的正确程度,并对少数不合谐数较大的性状的极性进行了调整。采用最大同步法、最小平行进化法和综合分析法进行运算,按照最简约的原则,选出演化长度最短的谱系分支图,作为本文讨论的基础,并在此基础上,探讨了金缕梅类科的系统关系。     

马铃薯Y病毒多基因系统发育分析及其在株系鉴定中的应用

为实现马铃薯Y病毒(Potato virus Y, PVY)常见株系的快速鉴定,本文以PVY的P1、HC-pro、VPg和CP 4个基因为研究对象建立了快速准确的多基因联合体系。根据基因的不同组合建立5个不同数据集,分别进行系统发育分析,并通过贝叶斯标签关联显著性(Bayesian tip-association significance, BaTS)分析各数据集中代表分离物与株系的关联性,以确定实现PVY快速鉴定的最佳组合。不同数据集的系统发育及BaTS分析结果显示,除了联合P1、VPg和CP 3个基因数据集外,其他4个数据集均无法实现PVY常见株系的准确鉴定。采用不同建树方法对联合P1、VPg和CP 3个基因数据集比较分析显示,基于ML法和NJ法的系统发育树在拓扑结构上基本一致,均优于基于贝叶斯算法的最大分支置信(maximum clade credibility, MCC)树。同时,以HLJ26分离物为研究对象,对建立的多基因联合体系进行实际应用,结果显示该分离物与PVY^NTN-NW株系的3个分离物SYR-Ⅱ-2-8、SYR-Ⅱ-Be1和SYR-Ⅱ-DrH以高置信值聚为一亚簇,表明该分离物可能属于PVY^NTN-NW株系(SYR-Ⅱ型)。重组分析显示,HLJ26基因组存在4个潜在的重组信号,分别位于P1、HC-pro/P3、VPg和CP的5°-末端,与PVY^NTN-NW株系(SYR-Ⅱ型)的重组位点相一致,表明其属于PVY^NTN-NW株系(SYR-Ⅱ型)。同时,应用多重RT-PCR成功扩增出约为1000 bp和400 bp的2个特异性片段,与PVY^NTN-NW株系(SYR-Ⅱ型)的特异条带大小相一致。这些结果进一步支持了多基因联合体系的鉴定结果。联合P1、VPg和CP 3个基因数据集系统发育分析,可以实现PVY常见株系的准确鉴定。     

应用系统发育树分析DDBJ基因库中HBV基因序列的基因型

为了充分利用核酸库中的HBV序列信息,探讨DDBJ核酸库中HBV基因序列的基因分型,采用Clustal X（1.8）软件比较HBV基因序列前S区序列差异并产生系统发育树。通过对下载的1471条HBV基因序列进行系统分析。获得了228条前S/S区完整的HBV基因序列,其中有66条序列的基因型已被各种方法所证实。利用软件分析绘制了基于228条HBV前S区基因序列的系统发育树。66条已知基因型HBV基因序列在系统发育树上的分型与其原有基因型完全吻合。在228条HBV基因序列中,有207条序列分别属于A、B、C、D、E、F和G等7个基因型,但另外21条序列不能归属于上述7个基因型的任何一种,而且它们又分为彼此相互独立存在的两群,暂分别称之为未分型I和未分型Ⅱ,经比较未分型I、Ⅱ和其他7个基因型前S区核苷酸序列,发现未分型I、Ⅱ和D型前S区都有33个核苷酸缺失,但三者基因缺失片段的位置和形式各不相同,但其它六型前S区无大片段基因缺失。结果说明采用基于前S区的系统发育树基因分型分析方法正确可靠,除了现已证实的7个基因型外,尚可能存在另外两个新的HBV基因型。     

PHYLOGENETIC ANALYSES OF THE CORRELATED EVOLUTION OF CONTINUOUS CHARACTERS: A SIMULATION STUDY

We use computer simulation to compare the statistical properties of several methods that have been proposed for estimating the evolutionary correlation between two continuous traits, and define alternative evolutionary correlations that may be of interest. We focus on Felsenstein's (1985) method and some variations of it and on several “minimum evolution” methods (of which the procedure of Huey and Bennett [1987] is a special case), as compared with a nonphylogenetic correlation. The last, a simple correlation of trait values across the tips of a phylogeny, virtually always yields inflated Type I error rates, relatively low power, and relatively poor estimates of evolutionary correlations. We therefore cannot recommend its use. In contrast, Felsenstein's (1985) method yields acceptable significance tests, high power, and good estimates of what we term the input correlation and the standardized realized evolutionary correlation, given complete phylogenetic information and knowledge of the rate and mode of character change (e.g., gradual and proportional to time [“Brownian motion”] or punctuational, with change only at speciation events). Inaccurate branch length information may affect any method adversely, but only rarely does it cause Felsenstein's (1985) method to perform worse than do the others tested. Other proposed methods generally yield inflated Type I error rates and have lower power. However, certain minimum evolution methods (although not the specific procedure used by Huey and Bennett [1987]) often provide more accurate estimates of what we term the unstandardized realized evolutionary correlation, and their use is recommended when estimation of this correlation is desired. We also demonstrate how correct Type I error rates can be obtained for any method by reference to an empirical null distribution derived from computer simulations, and provide practical suggestions on choosing an analytical method, based both on the evolutionary correlation of interest and on the availability of branch lengths and knowledge of the model of evolutionary change appropriate for the characters being analyzed. Computer programs that implement the various methods and that will simulate (correlated) character evolution along a known phylogeny are available from the authors on request. These programs can be used to test the effectiveness of any new methods that might be proposed, and to check the generality of our conclusions with regard to other phylogenies.     

PHYLOGENETIC VARIATION IN THE TOLERANCE AND UPTAKE OF ORGANIC CONTAMINANTS

An investigation into the phylogenetic variation of plant tolerance and the root and shoot uptake of organic contaminants was undertaken. The aim was to determine if particular families or genera were tolerant of, or accumulated organic pollutants. Data were collected from sixty-nine studies. The variation between experiments was accounted for using a residual maximum likelihood analysis to approximate means for individual taxa. A nested ANOVA was subsequently used to determine differences at a number of differing phylogenetic levels. Significant differences were observed at a number of phylogenetic levels for the tolerance to TPH, the root concentration factor and the shoot concentration factor. There was no correlation between the uptake of organic pollutants and that of heavy metals. The data indicate that plant phylogeny is an important influence on both the plant tolerance and uptake of organic pollutants. If this study can be expanded, such information can be used when designing plantings for phytoremediation or risk reduction during the restoration of contaminated sites.     

福建省闽南地区稻水象甲疫情监测与分析

稻水象甲作为水稻生产上的一种毁灭性害虫．近年来已先后侵入许多国家和地区,特别是与福建省一水之隔的台湾等地已严重发生为害。为了摸清该虫是否在福建南部发生,我们自1993年起至1995年对闽南地区(包括厦门市、漳州市、泉州市）进行系统的监测与调查。结果表明：该虫尚未侵入福建的闽南地区。但通过对该虫生物生态学特性以及福建闽南地区的环境气候、生态条件综合分析,该虫随时都有可能入侵闽南地区．并在本地区大发生。     

PROBLEMS AND PROMISE IN CODING MORPHO-LOGICAL CHARACTERS FOR PHYLOGENETIC ANALYSIS: AN EXAMPLE FROM AULACOSEIRA (BACILLARIOPHYCEAE)

Edgar, S. M. & Theriot, E. C. Section of Integrative Biology, University of Texas at Austin, Austin TX 78713 USA Understanding the phylogenetic relationships among species of Aulacoseira Thwaites (formerly Melosira, in part) and their relationships to other genera is important for several reasons. Aulacoseira is globally distributed and is often a large component of planktonic communities in lakes, ponds and large rivers. Consequently, it plays a significant ecological role as a primary producer in grazer-based aquatic food webs. Although species of Aulacoseira (along with other diatom species) are used profitably as tools for reconstruction of paleo-environments, ecological monitoring, and other ecological studies which have generated a large amount of data, much of this data is not really informative for a systematic understanding of the group. There are currently around 60 extant and 20 extinct described species of Aulacoseira. However, there is no estimate of phylogeny within this genus that includes more than five species. Here we present the first comprehensive estimate of phylogeny for 30 species of Aulacoseira based on a cladistic analysis of morphological features gathered from the literature. Complications of gathering morphological data from the literature that was largely focused on refining species identifications for practical purposes of ecological identification will be addressed. Morphological characters chosen for the analysis and challenges associated with coding of characters will be discussed along with the resulting Aulacoseira phylogeny and our methods of its estimation.     

蛋白质编码区与非编码区的特征与识别

在核苷酸序列分析中,一个重要的问题是如何识别一段未知序列中的编码区和非编码区．近年来提出了一些方法,但效果都不够理想．本文在对编码区与非编码区特征进行大量统计分析的基础上,提出一种加权距离判别法,并对该方法的精度进行了评价．     

几种蚊虫线粒体DNA-16SrRNA序列及其相互关系的研究

测定我国尖音库蚊复合组4亚种（尖音库蚊、淡色库蚊、致倦库蚊和骚扰库蚊）、三带喙库蚊、白纹伊蚊和中华按蚊的线粒体DNA 16S rRNA基因（mtDNA-16S rRNA)序列,发现我国尖音库蚊复合组4亚种mtDNA-16S rRNA序列基本一致,长度为555bp(554bp),GC含量为25．41％。该序列与其他3种蚊虫在种间存在差异,与三带喙库蚊的种间差异为0．54％;与白纹伊蚊的种间差异为5．77％;与中华按蚊的种间差异为9．62％。分子系统关系分析表明该序列与传统分类系统的同属或同亚科种类近似性相一致。     

基于16S rRNA和Cyt b基因序列的鰶亚科系统发育研究

对鰶亚科4属5种鱼类的线粒体基因组16S rRNA和Cyt b基因片段序列进行序列比较和系统发育关系分析。结果显示:5种鰶亚科鱼类的16S rRNA和Cy tb基因片段同源序列长度分别为525 bp和402 bp,序列联合后的序列总长度为927 bp,其中多态位点178个,简约信息位点123个。选取太平洋鲱Clupea pallasii和大西洋鲱C.harengus为外类群,采用邻接法(NJ)、最大简约法(MP)、最大似然法(ML)和贝叶斯法(BI)分别对2个基因片段序列进行了聚类分析,并联合2个基因片段利用邻接法、最大简约法和贝叶斯法进行分析。系统发育分析显示:斑鰶Konosirus punctatus与花鰶Clupanodon thriss亲缘关系最近,分布于美洲大陆的真鰶属Dorosoma鱼类与印度洋、太平洋分布的斑鰶属、花鰶属和海鰶属Nematalosa鱼类亲缘关系较远。     

HYBRIDS AND PHYLOGENETIC SYSTEMATICS II. THE IMPACT OF HYBRIDS ON CLADISTIC ANALYSIS

I examined three aspects of the cladistic treatment of a set of 17 F₁ hybrids of known parental origin: (1) impact of hybrids on consistency index (CI) and number of most parsimonious trees (Trees), (2) placement of hybrids in cladograms, and (3) impact of hybrids on hypotheses of relationship among species. The hybrids were added singly and in randomly selected sets of two to five to a data set composed of Central American species of Aphelandra (including the parents of all hybrids). Compared to analyses with the same number of OTUs all of which were species, the analyses with hybrids yielded results with significantly higher CI. There was no difference in Trees between analyses with hybrids versus species. There was thus no evidence that hybrids would appear to be more problematic for cladistic methods than species. Accordingly, hybrids will not be readily identifiable as taxa that cause marked change in these indices. About % of the hybrids were placed as the cladistically basal members of the lineage that included the most apomorphic parent. Relatively apomorphic hybrids were placed proximate to the most derived parent (ca. 13% of hybrids). Other placements occurred more rarely. The most frequent placements of hybrids thus did not distinguish them from normal intermediate or apomorphic taxa. When analyses with hybrids yielded multiple most parsimonious trees, these were no more different from each other than were the equally parsimonious trees that resulted from analyses with species. Most analyses with one or two hybrids resulted in minor or no change in topology. When hybrids caused topological change, they frequently caused rearrangements of weakly supported portions of the cladogram that did not include their parents. When they disrupted the cladistic placement of their parents, they often caused their parents to change positions, with at least one topology bringing the parental lineages into closer proximity with the hybrid placed between them. Hybrids between parents from the two main lineages of the group caused total cladistic restructuring. In fact, the degree of relationship between a hybrid's parents (measured by both cladistic and patristic distance) was strongly correlated with CI (negatively) and with the degree of disturbance to cladistic relationships (positively). Thus, hybrids between distantly related parents resulted in cladograms with low CI and major topological changes. This study suggests that hybrids are unlikely to cause breakdown of cladistic structure unless they are between distantly related parents. However, these results also indicate that cladistics may not be specially useful in distinguishing hybrids from normal taxa. The applicability of these results to other kinds of hybrids is examined and the likely cladistic treatment of hybrids using other sources of data is discussed.