mtDNA基因树拓扑距离比较和基因分群

基因树间拓扑距离数据的比较进一步证明：与分割拓扑距离相比,能经拓扑距离是一种更为精确的测度,利用相对通经拓扑距离构建了8个基因的拓扑距离树。基因的拓扑距离树能直观地反映不同基因树的拓扑结构差异大小,可用来对基因进行分群。此外,发现不同DNA序列用于构建多基因树中其系统发生信息存在“累加”,“合取”,“含盖”,“相斥”等数学关系。这可解释在mtDNA基因组中一些基因比另一些基因更适合用来的构建树的结果。结果提示从GenBank中应选择具有累加基因的DNA序列或蛋白质氨基酸序列合并来构建物种。在讨论中还提出了一种获得真树的新建树策略。     

切叶蚁亚科七属十二种的分子系统学研究

测定了切叶蚁亚科7属12种的线粒体CO1、CO2的部分基因及完整的tRNA_Leu基因DNA序列,对DNA序列进行了分析,对tRNA_Leu 基因进行了二级结构分析;根据DNA序列数据和氨基酸序列数据,以臭蚁亚科的Forelius chalybaeus作为外群,采用最大似然法(ML)、最大简约法(MP)、邻接法(NJ)、未加权组对算术平均法(UPGMA)构建分子系统树,通过自举检验,得到自举置信水平,以此检验该分子系统树的可靠性。研究结果显示,基于以上基因的分子系统分析与传统分类分析的结果基本一致,且在属级的一致性高于种级的一致性。     

基于DNA分子标记数据构建系统进化树的新策略

结合DPS软件和MEGA软件优点,进行DNA分子标记数据处理和系统发育树构建的新策略：首先使用DPS软件进行0,1数据系统聚类方法获得遗传距离矩阵,然后将此矩阵输入MEGA3,利用NJ或者UPGMA进行系统进化树的构建和树的优化。该方法操作简单,得到的树形美观。     

芍药属牡丹组基于形态学证据的系统发育关系分析

对芍药属牡丹组Paeonia L.sect.Moutan DC.（全部野生种）40个居群进行了基于形态学证据的系统学分析,试图建立组内种间的系统发育关系。利用PAUP （4.0）计算机程序分别构建了建立在25个形态学性状基础上的所有研究类群的距离树（UPGMA、NJ）和最大简约树（MP）。所得树的拓扑结构基本一致,差异只发生在距离树和简约树之间,在由形态和细胞学关系都很近的5个种（牡丹P.suffruticosa、矮牡丹P.jishanensis、卵叶牡丹P.qiui、紫斑牡丹P.rockii和凤丹P.o     

UPGMA树的不惟一性问题及其解决方法

对于一组给定的DNA或蛋白质序列,UPGMA算法构建的二叉进化树可能是不惟一的,其具体拓扑结构与序列输入顺序相关,这一现象通常被称为"tied trees"。提出了UPGMA的一种改进算法——不加权算术平均组群方法(UMGMA),用以解决UPGMA树的不惟一问题。在UPGMA树惟一时,该方法产生的进化树与UPGMA树相同;而在UPGMA树不惟一时,该方法可以产生一棵惟一的、与序列输入顺序无关的多叉进化树,而且该算法还具有一个可调的容差参数,来控制生成进化树的主要分枝结构,这对于突出大规模进化树的总体脉络具有重要意义。     

利用肠道菌群的分布和16S DNA序列研究鲤科肠道菌系统演化关系

肠道微生物与寄主具有复杂的、多方面的相互依存效应,这种依存效应所产生的共生关系或协同进化关系既可反映寄主间的系统演化关系,也可显示肠道微生物间的系统演化关系,共生关系或协同进化关系是由于寄主与肠道微生物两者之间存在着相互自然选择作用所形成的,在长期的进化历程中逐步发生的共生关系信息很可能被记录在DNA序列中。本文通过检测鱼鲤鱼科8种鱼中9种肠道菌群的分布含量对这9种菌群进行分析,且利用从GenBank调取这9种肠道细菌菌属的43个种或亚种的16S DNA序列的构建NJ树和MP树,将这6个科9个属43个种或亚种分为革兰氏阴性和革兰氏阳性两大类群（一级分枝）。在这两类群中,又以科为单位分为6个亚类群（二级分枝）,而肠杆菌科中则以属为单位分为4个小类群（三级分枝）,此外球状菌与杆状菌也能截然分开。将16S DNA的NJ树隐去所有的种,以属为单位所得到的以分枝形式的无根树在拓扑结构上与菌群分布含量（寄主范围）所构建的无根树相近,但芽孢杆菌在两种无根树的位置中有较大的差异。如果提高检测水平,扩大所检测的寄主对象,这种差异有可能消除。     

用RAPD标记研究蚱属五个种间的亲缘关系

用RAPD技术对蚱属5种蚱基因组DNA的多态性进行研究。在事先优化的反应条件下用12个随机引物扩增, 共得到84条清晰稳定的多态性片段,片段长度为200～2 000 bp。统计这些片段,根据扩增片段的共享度计算出相对遗传距离指数,然后用UPGMA和NJ聚类方法对其进行分析,构建系统树,确定了它们相互间的亲缘关系。     

中国蔗蝗属三种之间亲缘关系的RAPD分析（直翅目：蝗总科：斑腿蝗科）

用RAPD技术对中国蔗蝗属3种蝗虫基因组DNA的多态性进行研究。在事先优化的反应条件下用12个随机引物扩增,共得到179条清晰稳定的多态性片段,片段长度为200—2000bp。统计这些片段,根据扩增片段的共享度计算出相对遗传距离指数,然后用NJ和UPGMA聚类方法对其进行分析,构建系统树,以确定这3种间的亲缘关系。结果表明：等歧蔗蝗与异歧蔗蝗二者的亲缘关系较近,而与斑角蔗蝗的关系较远。     

基于16S rDNA与Cytb序列的疏广蜡蝉属三个近似种的分子鉴定

本文通过PCR扩增首次获得了疏广蜡蝉属Euricania Melichar,1898 3个近似种:透明疏广蜡蝉E.clara Kato,1932、长刺疏广蜡蝉E.longa Xu,LiangJiang,2006和短刺疏广蜡蝉E.brevicula Xu,LiangJiang,2006的16S r DNA序列和Cytb序列;使用MEGA 6.0软件,分析了其序列组成及变异,计算了遗传距离,以宽广蜡蝉属Pochazia AmyotServille,1843的圆纹宽广蜡蝉P.guttifera Walker,1851和眼斑宽广蜡蝉P.discreta Melichar,1898为外群,利用邻接法(NJ)和最大简约法(MP)构建了系统发育树。结果显示:透明疏广蜡蝉、长刺疏广蜡蝉和短刺疏广蜡蝉的16S r DNA序列长度分别为414 bp,404 bp,435 bp,而Cytb基因序列长度分别为492 bp,468 bp,472 bp,三者的序列比对、碱基组成成分存在差异;2属5种广翅蜡蝉16S r DNA基因的种间遗传距离为0.008-0.098,属间遗传距离为0.122-0.197,而Cytb基因的种间遗传距离为0.038-0.055,属间遗传距离为0.181-0.188,表明16S r DNA和Cytb基因序列可作为DNA条形码候选基因片段,用于广翅蜡蝉近似属、种的分子鉴定。系统发育树的拓扑结构显示,3个近似种的亲缘关系基本一致,各自聚为一支,且置信值均达96%以上。本文亦结合了透明疏广蜡蝉、长刺疏广蜡蝉和短刺疏广蜡蝉形态学特征的差异对其进行了讨论和分析。     

基于12S rRNA基因序列探讨凹耳蛙(无尾目,蛙科)的分类地位

为探讨凹耳蛙Rana tormotus的分类地位,测定了凹耳蛙线粒体12S rRNA基因序列,并从GenBank中下载了蛙科33种蛙的同源序列进行分析,用BI法、NJ法和MP法构建分子系统树.结果表明:3种树拓扑结构基本一致,都显示凹耳蛙与长吻胡湍蛙Huia nasica亲缘关系最近,凹耳蛙与长吻胡湍蛙相聚后再与臭蛙Odorrana组成单系群,而与湍蛙Amolops亲缘关系较远.据此,支持将该蛙从湍蛙属划出,并建议归入臭蛙属.     

Relative efficiencies of the maximum-parsimony and distance-matrix methods of phylogeny construction for restriction data.

The relative efficiencies of the maximum-parsimony (MP), UPGMA, and neighbor-joining (NJ) methods in obtaining the correct tree (topology) for restriction-site and restriction-fragment data were studied by computer simulation. In this simulation, six DNA sequences of 16,000 nucleotides were assumed to evolve following a given model tree. The recognition sequences of 20 different six-base restriction enzymes were used to identify the restriction sites of the DNA sequences generated. The restriction-site data and restriction-fragment data thus obtained were used to reconstruct a phylogenetic tree, and the tree obtained was compared with the model tree. This process was repeated 300 times. The results obtained indicate that when the rate of nucleotide substitution is constant the probability of obtaining the correct tree (Pc) is generally higher in the NJ method than in the MP method. However, if we use the average topological deviation from the model tree (dT) as the criterion of comparison, the NJ and MP methods are nearly equally efficient. When the rate of nucleotide substitution varies with evolutionary lineage, the NJ method is better than the MP method, whether Pc or dT is used as the criterion of comparison. With 500 nucleotides and when the number of nucleotide substitutions per site was very small, restriction-site data were, contrary to our expectation, more useful than sequence data. Restriction-fragment data were less useful than restriction-site data, except when the sequence divergence was very small. UPGMA seems to be useful only when the rate of nucleotide substitution is constant and sequence divergence is high.     

九种绢丝昆虫线粒体12S rRNA基因的序列特征和系统发育分析

为探讨鳞翅目中绢丝昆虫之间的系统发育关系和分子进化特征,本研究测定了中国柞蚕Antheraea pernyi野生型和放养型的线粒体12S rRNA基因的部分序列,结合来自GenBank数据库的17条序列,对总共9种绢丝昆虫（2科3属）的12S rRNA基因序列进行了分析。利用软件MEGA 3.1进行碱基组成、变异位点的统计和分子进化分析,分别用类平均聚类法（UPGMA）、邻接法（NJ）、最小进化法（ME）、最大简约法（MP）重建系统发生树。测定的中国柞蚕野生型的12S rRNA基因序列（427 bp）与放养型“豫早1号”的序列完全一致。序列对齐后共鉴定80个变异位点,50个简约信息位点。碱基组成分析显示在科属间具有明显差异,AT含量蚕蛾科高于大蚕蛾科;在A和T碱基的使用上,大蚕蛾科偏好使用T,而蚕蛾科则偏好使用A。与动物中常见的以转换为主的碱基替换模式不同,所分析的9种昆虫中除桑蚕属内部为转换与颠换基本一致外,其余物种间均是颠换多于转换。进化分析支持柞蚕属、樗蚕属和桑蚕属的单系。基于UPGMA法的进化树支持琥珀蚕是柞蚕属的较原始类型,而NJ、ME和MP法则支持印度柞蚕是较原始的类型,因此,柞蚕属种间的进化关系尚需进一步研究。     

重建系统演化树的一种新方法--试错法

重建系统演化树是进化研究的一个极为重要的方面。系统树的构建依赖于一定的方法和数据。在分子系统演化研究中,所使用的数据大多是ＤＮＡ序列、氨基酸序列和分子标记。而就构树方法来说,ＮＪ法、ＭＬ法和ＭＰ法是三种最为普遍使用的方法。本文给出了一种新的建树方法,即试错法。该方法不但具有与ＮＪ法一样好的建树效果,而且不存在难以解释的负枝长问题。     

Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.     

Accuracy of estimated phylogenetic trees from molecular data

The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's f theta, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogenetic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.     

THE ACCURACY OF PHYLOGENETIC ESTIMATION USING THE NEIGHBOR-JOINING METHOD

We studied the factors affecting the accuracy of the neighbor-joining (NJ) method for estimating phylogenies by simulating character change under different evolutionary models applied to twenty different 8-OTU tree topologies that varied widely with respect to tree imbalance and stemminess. The models incorporated three evolutionary rates—constant, varying among lineages, varying among characters—and three evolutionary contexts concerning patterns of character change relative to speciation events—phyletic, speciational, and punctuational. All combinations of the rate and context models were studied. In addition, three different absolute rates of change were investigated. To measure the accuracy, the strict consensus index was computed between the estimated tree and the tree topology along which the data had been generated. The results were analyzed by analysis of variance and compared to a previous study that evaluated UPGMA clustering and maximum parsimony (MP) as phylogenetic estimation techniques. We found evolutionary context and tree imbalance to be the most important factors affecting the accuracy of the NJ method. NJ was more accurate than UPGMA or MP in terms of the average strict consensus index over all treatments. However, no one method was more accurate than the other two for all combinations of treatments. Higher absolute rate of change generally resulted in higher accuracy for all three methods.     

基于18S rRNA和线粒体16S rRNA基因序列的柳蚕进化分析

为探讨柳蚕Actias selene Hübner与鳞翅目昆虫的系统发育关系,本研究利用PCR扩增获得了柳蚕核糖体18S rRNA和线粒体16S rRNA基因的部分序列,长度分别为391bp和428bp。并采用邻近距离法(NJ)、最大简约法(MP)、类平均聚类法(UPGMA)构建系统进化树。结果表明,柳蚕线粒体16SrRNA基因序列与大蚕蛾科昆虫的16SrRNA基因序列均表现出偏好于碱基AT的倾向。柳蚕与所研究的其它蚕类的遗传距离介于0.016至0.140之间,其中与温带柞蚕Antheraea roylii的遗传距离最小,与野桑蚕Bombyx mandarina的遗传距离最大。而基于鳞翅目昆虫18S rRNA基因部分序列的进化分析显示,柳蚕与柞蚕Antheraea pernyi之间的遗传距离最小(0.010),与蓖麻蚕Samia ricini的遗传距离最大(0.017)。     

PHYLOGENETIC RELATIONSHIPS WITHIN THE COLONIAL VOLVOCALES (CHLOROPHYTA) INFERRED FROM rbcL GENE SEQUENCE DATA

The chloroplast-encoded large subunit of the ribulose-1, 5-bisphosphate carboxylase / oxygenase (rbcL) gene was sequenced from 20 species of the colonial Volvocales (the Volvacaceae, Goniaceae, and Tetrabaenaceae) in order to elucidate phylogenetic relationships within the colonial Volvocales. Eleven hundred twenty-eight base pairs in the coding regions of the (rbcL) gene were analyzed by the neighbor-joining (NJ) method using three kinds of distance estimations, as well as by the maximum parsimony (MP) method. A large group comprising all the anisogamous and oogamous volvocacean species was resolved in the MP tree as well as in the NJ trees based on overall and synonymous substitutions. In all the trees constructed, Basichlamys and Tetrabaena (Tetrabaenaceae) constituted a very robust phylogenetic group. Although not supported by high bootstrap values, the MP tree and the NJ tree based on nonsynonymous substitutions indicated that the Tetrabaenaceae is the sister group to the large group comprising the Volvocaceae and the Goniaceae. In addition, the present analysis strongly suggested that Pandorina and Astrephomene are monophyletic genera whereas Eudorina is nonmonophyletic. These results are essentially consistent with the results of the recent cladistic analyses of morphological data. However, the monophyly of the Volvocaceae previously supported by four morphological synapomorphies is found only in the NJ tree based on nonsynonymous substitutions (with very low bootstrap values). The genus Volvox was clearly resolved as a polyphyletic group with V. rousseletii Pocock separated from other species of Volvox in the rbcL gene comparisons, although this genus represents a monophyletic group in the previous morphological analyses. Furthermore, none of the rbcL gene trees supported the monophyly of the Goniaceae; Astrephomene was placed in various phylogenetic positions .