基于质体基因组学方法研究广义玄参科的系统发育

该研究利用GenBank数据库已公开发表的玄参科及相关类群的107属129个物种的质体基因组数据对广义玄参科的系统发育关系进行了分析。该文利用蛋白质编码基因构建了矩阵，并采用最大似然法及贝叶斯推断重建系统发育树。基于两种分析方法获得的系统发育树的拓扑结构完全一致且分辨率及支持率较高。在ML树中，总分支数为129个，其中支持率≥70%的分支数目为123个。结果表明：(1)广义玄参科不是一个单系类群，隶属于广义玄参科的51个物种(37属)分散于列当科、泡桐科、美丽桐科、通泉草科、母草科、狭义玄参科和车前科。(2)狭义玄参科为单系类群，除原隶属于广义玄参科的Bontia、Calamphoreus、Diocirea、Eremophila、Glycocystis、Leucophyllum、玄参属和毛蕊花属外，还包括了原隶属于马钱科的醉鱼草属和原隶属于苦槛蓝科的苦槛蓝属。(3)唇形目为一个单系，目下共形成了14个支持率高的单系分支，对应于14个科(其中美丽桐科和胡麻科仅包括一个物种，不包括在内),科间关系得到较好的解决，木犀科为最早分化出来的类群，其余的类群共同组成核心唇形目。在核心唇形目中，类群...     

最大似然法和贝叶斯推论与似然比检验探讨泽泻目系统发育关系

应用最大似然法(ML)、贝叶斯推论(BI)、邻接法(NJ)和似然比检验(hLRTs)进行泽泻目分子系统学研究。所用的rbcL基因序列代表了泽泻目14科46属以及作为外类群的6相关属。研究结果表明,*等级制似然比检验表明泽泻目rbcL序列最适合的DNA进化模型为GTR+I+G,最大似然法、贝叶斯法和邻接法构建的系统发育树拓扑结构相似,没有显著的差异,但贝叶斯树支持率较高;泽泻目为一单系类群,由两个主要谱系分支构成,深层分布格局由5个主要分支构成。基于分子系统发育树,文中对泽泻目科间、水鳖科+茨藻科、泽泻科+花蔺科+黄花蔺科、和"Cymodoeaceae complex"的系统发育关系进行了讨论。研究结果还表明,泽泻目系统发育关系可能还需要更多的证据进一步的澄清。     

菝葜科基于形态学证据的系统发育分析

对全世界范围分布的菝葜科Smilacaceae的79个代表种(包括了全部的属和组), 以分布于南美洲的Philesia Comm. ex Juss.和Lapageria Ruiz &; Pav.属为外类群, 选取包括花粉和染色体性状在内的47个广义的形态学性状进行了分支分类系统发育分析, 同时以表征分类的方法构建了距离树(NJ)辅助分析, 首次对世界分布的菝葜科各属间及属内的系统发育关系作了探讨。(1)Ripogonum与菝葜属Smilax +肖菝葜属Heterosmilax互为姐妹群, 但是距离较远, 支持将类菝葜属(新拟中文名)Ripogonum独立为科的观点; (2)肖菝葜属在菝葜科内处于较为进化的分支上, 并与菝葜属土茯苓组sect. Coilanthus的部分种组成一个具较高支持率(88%)的单系分支, 分析表明肖菝葜属并非是一个好属, 应归入菝葜属; (3)菝葜属6个组的划分大都没有得到支持, 只有东亚北美间断分布的草本菝葜组sect. Nemexia的单系得到很好的支持(93%); (4)分布于南美洲巴西的种类聚为一个单系类群, 表明它们可能有共同的起源, 但由于取样局限, 南美洲种类的系统地位有待进一步研究。     

贝叶斯推论及其在百合目分子系统学中的应用

贝叶斯推论作为进化生物学的最新进展,在适用复杂模型、大型数据集、计算速度和结果容易解释等方面明显优于其它算法。本文简要介绍了贝叶斯推论原理及其在分子进化和系统发育研究中的重要性,并使用该方法对百合目主要类群的系统发育关系进行了重建。结果显示,百合目rbcL基因最适合的DNA进化模型为GTR I G,贝叶斯法与距离法和最大简约法构建的系统发育树拓扑结构相似,没有显著差异,但是分辨率和支持率明显比后者高。贝叶斯分析结果显示,百合目内划分的7个科,除Smilacaceae科外,其余各科均为高后验概率(PP=1·0)支持的单系类群;文中作者还对各科间的系统关系进行了探讨。     

基于叶绿体基因组数据的芸香科属间系统发育初步分析

为探究花椒属种水平系统进化关系以及为新品种培育研究奠定理论基础，该研究以芸香科物种的叶片为材料，采用改良CTAB法提取叶绿体DNA,利用BGISEQ-500平台进行叶绿体基因组测序，并对叶绿体基因组进行组装、注释，联合NCBI数据库数据，共获得芸香科19属49个物种的全叶绿体基因组序列。构建了芸香科属间系统进化关系。结果表明，(1)基于叶绿体基因组序列矩阵(总长196 641 bp),ML和BI 2种方法得到的系统发育树的拓扑结够基本一致，系统发育树各分支具有较强的支持率，叶绿体基因组数据可以解决芸香科属间的系统发育关系。(2)芸香科为单系类群，并进一步形成两大分支，其中柑橘亚科为单系，与芸香亚科内的芸香属聚为分支I,分支Ⅱ由芸香亚科和飞龙掌血亚科组成，两亚科均不是单系，其中飞龙掌血亚科的香肉果属，茵芋属与芸香亚科的白鲜属，臭常山属是最早分化出来的类群，其次是蜜茱萸属和山油柑属；黄檗属和吴茱萸属与花椒属类群形成姊妹群，飞龙掌血属的物种飞龙掌血嵌套于花椒属分支中，支持飞龙掌血物种并入花椒属的处理。     

基于叶绿体DNA trnL内含子序列数据的檀香目科间系统发育关系的研究

应用叶绿体DNAtrnL内含子序列分析檀香目科间的系统发育关系。取样研究的檀香目个体的trnL内含子序列长度在科间呈现较大差异(从291bp到587bp)。最大简约性分析产生的严格一致树与以前已发表的基于其它基因的檀香目的分子系统学研究结果大体一致。香芙木属(铁青树科)是最早分支出的类群：桑寄生科、槲寄生科分别表现为单系类群,檀香科为并系;桑寄生科和槲寄生科并不具密切亲缘关系,槲寄生科从檀香科内衍生出来。本研究表明,具相对高的核苷酸替换率的叶绿体DNAtrnL内含子序列可为高等级类群系统发育关系的研究提供更多的信息位点。     

速足目主要类群系统发育的分子证据

文章基于速足目现生主要类群18S rDNA、28S rDNA和COI基因序列,采用贝叶斯法、邻接法和最大简约法,尝试构建速足目的分子系统树;结合形态特征和化石记录,主要对速足目各超科级分类阶元的系统发育关系进行探讨。结果表明,速足目现生超科Bairdiacea、Darwinulacea、Cypridacea和Cytheracea均为单系群,支持形态学上关于上述4个超科的的界定;3种基因均支持形态学上Darwinulacea和Cypridacea具有较近的亲缘关系的观点。18S rDNA序列分析在较显著水平上支持Darwinulacea和Bairdiacea为姐妹群,Darwinulacea可能从Bairdia-cea中的一支演化而来;Bairdiacea和Darwinulacea组成的分支是Cypridacea的姐妹群,支持将三者合并为Bairdio-copina亚目的观点;Cytheracea是Cypridacea(Darwinulacea Bairdiacea)的姐妹群,可提升为Cytheracopina亚目。     

介形纲丽足目和速足目及相关类群18S rDNA分子系统发育的研究

文中分析现生介形类 (Ostracoda) 4目 2 1科 2 9属的 18SrDNA部分序列 ,采用最大似然法 (ML)、邻接法 (NJ)和最大简约法 (MP) ,尝试构建介形类的分子系统树 ;结合介形类的形态特征和化石记录 ,主要对速足目(Podocopida)、丽足目 (Myodocopida)及其超科级分类阶元的系统发生关系进行探讨。 3种分析方法均支持形态学上Podocopida ,Myodocopida和海萤超科 (Cypridinacea)的界定 ;但对Podocopida目土菱介超科 (Bairdiacea)的系统地位提出质疑 ,该类群可能不是单系发生的自然类群。上述分析显示 ,Podocopida,Myodocopida,Platycopida和Halo cypridina组成一个单系群 ;介形类在目、超科、科和属的水平上可能发生过多次辐射分化     

基于线粒体ND2基因的直翅目部分种类分子系统发育分析

测定了39种直翅目昆虫线粒体ND2基因全长序列,联合GenBank中41种直翅目昆虫的ND2基因序列,探讨ND2基因在解决直翅目系统发育分析上的功效,为建立直翅目的主要类群之间稳定的系统发育关系提供更多的数据。研究结果表明,直翅目昆虫的ND2基因序列全长为996～1 029 bp,平均长度为1 020 bp,A+T含量平均为73%。用贝叶斯法(Bayesian,BI)、最简约法(maximum parsimony,MP)和最大似然法(maximum likelihood,ML)构建系统树,SH检验显示,RAxML法构建的ML树似然值最大,与PAUP*的ML法构建的ML树差异显著,而与贝叶斯树和简约树没有明显差异。所有系统树都显示直翅目为单系群;而蝗亚目的剑角蝗科、网翅蝗科、槌角蝗科和斑腿蝗科均不是单系群,锥头蝗科与瘤锥蝗科亲缘关系较近,这与Otte分类系统一致。螽亚目基本由两大分支构成,一支是蝼蛄总科和蟋蟀总科聚集而成,且具有很高的置信度;另一大分支由螽斯总科独自构成。     

质体系统发育基因组解析旋花科系统发育关系

旋花科是一个世界广布的类群,具有丰富的形态特征和重要的经济价值。然而,目前该科主要分支或族间的系统发育关系问题一直未解决。为解析旋花科内系统发育关系,该研究代表性选取旋花科内8个族40个物种,基于质体全基因组数据,使用最大似然法和贝叶斯推论进行系统发育分析。结果表明：(1)旋花科质体基因组均为四分体结构,质体基因组大小为113 273～164 112 bp,蛋白质编码基因数目为66～79个。(2)基于五种DNA矩阵(即WCG、CDS、LSC、IR、SSC)的系统发育分析结果显示,WCG矩阵和CDS矩阵的拓扑结构基本一致,仅少数分支的支持率略有差异;LSC矩阵和WCG矩阵的拓扑结构差异在于菟丝子族、马蹄金族和盐帚花族的系统位置;AU检验和SH检验结果显示,WCG矩阵和SSC矩阵与IR矩阵的拓扑结构有显著冲突。(3)所有系统发育分析结果均显示,菟丝子属和马蹄金族都包括在旋花亚科内,应处理为族等级。(4)基于WCG矩阵和CDS矩阵较好地解决了旋花科8个族之间的系统发育关系,即心被藤族和丁公藤族聚为一支,最先从旋花亚科分化出来,随后是菟丝子族,剩下的5个族分成2个分支。(5)系统发育基因组分析...     

SuperTRI: A new approach based on branch support analyses of multiple independent data sets for assessing reliability of phylogenetic inferences

Supermatrix and supertree are two methods for constructing a phylogenetic tree by using multiple data sets. However, these methods are not a panacea, as conflicting signals between data sets can lead to misinterpret the evolutionary history of taxa. In particular, the supermatrix approach is expected to be misleading if the species-tree signal is not dominant after the combination of the data sets. Moreover, most current supertree methods suffer from two limitations: (i) they ignore or misinterpret secondary (non-dominant) phylogenetic signals of the different data sets; and (ii) the logical basis of node robustness measures is unclear.To overcome these limitations, we propose a new approach, called SuperTRI, which is based on the branch support analyses of the independent data sets, and where the reliability of the nodes is assessed using three measures: the supertree Bootstrap percentage and two other values calculated from the separate analyses: the mean branch support (mean Bootstrap percentage or mean posterior probability) and the reproducibility index.The SuperTRI approach is tested on a data matrix including seven genes for 82 taxa of the family Bovidae (Mammalia, Ruminantia), and the results are compared to those found with the supermatrix approach. The phylogenetic analyses of the supermatrix and independent data sets were done using four methods of tree reconstruction: Bayesian inference, maximum likelihood, and unweighted and weighted maximum parsimony. The results indicate, firstly, that the SuperTRI approach shows less sensitivity to the four phylogenetic methods, secondly, that it is more accurate to interpret the relationships among taxa, and thirdly, that interesting conclusions on introgression and radiation can be drawn from the comparisons between SuperTRI and supermatrix analyses. To cite this article: A. Ropiquet et al., C. R. Biologies 332 (2009).     

中国绿水螅分子系统发生地位的初步探讨

目的:初步探讨中国绿水螅(Hydra sinensis)分子系统发生地位以及水螅属内部各类群系统发生关系。方法:采用酚-氯仿法提取中国绿水螅总DNA,扩增线粒体COI和16S r RNA基因片段并进行DNA序列测定,再利用Clustal及MEGA等生物信息学分析软件进行系统发生分析。结果:在本研究重建的所有系统发生树中,中国绿水螅始终与绿水螅Hydra viridissima的不同种群一起构成绿水螅单系群。同时,棕色水螅群的单系性被基于COI基因的NJ树以及基于16S r RNA基因的NJ树和ML树支持,唯独基于COI基因的ML树不支持棕色水螅群的单系发生。在基于COI基因的ML树中纤弱水螅族在系统树的基部独立为一支系,而绿水螅群和其他棕色水螅群水螅一起组成另一支系,提示纤弱水螅族水螅的系统发生地位值得进一步探讨。值得注意的是,根据本文的结果,棕色水螅群内3族的划分仍然有一定疑问。基于COI基因的NJ树和ML树支持普通水螅族、寡水螅族和纤弱水螅族各自族内的单系发生,但16S r RNA基因的NJ树和ML树中仅普通水螅族水螅聚为单系群,而寡水螅族和纤弱水螅族水螅各自并非单系发生。结论:把水螅属划分为绿水螅群及棕色水螅群有一定的合理性,但棕色水螅群内寡水螅族、普通水螅族和纤弱水螅族3族的划分还有待商榷。     

Phylogenetic analyses of a combined data set suggest that the Attheya lineage is the closest living relative of the pennate diatoms (Bacillariophyceae)

A Bayesian analysis of a seven gene data set was conducted to reconstruct phylogenetic relationships among a sample of centric and pennate diatoms and to test alternative hypotheses about the closest living relative of Bacillariophyceae. A lineage, composed of two Attheya species, was inferred to share the most recent common ancestor with Bacillariophyceae--a relationship that was also corroborated by the combined parsimony analysis. All competing hypotheses about the closest living relative of Bacillariophyceae were rejected because 100% of the trees in the post-burn-in sample in the Bayesian analysis supported the Attheya-Bacillariophyceae clade. According to a partitioned Bremer support analysis, the majority of the genes in the combined data matrix supported the Attheya--Bacillariophyceae relationship. The global topology of the phylogenetic tree indicated that a monophyletic group consisting of Thalassiosirales and Toxarium undulatum formed the deepest branch followed by a node uniting a clade composed of Bacillariophyceae/Attheya species and a lineage made up of Eucampia zoodiacus, Chaetocerotales, Lithodesmiales, Triceratiales, Biddulphiales and Cymatosirales. Except for the phylogenetic positions of Lithodesmiales, Thalassiosira sp and Skeletonema costatum, the optimal tree obtained from the combined parsimony analysis showed the same branching order of taxa as those seen in the consensus tree inferred from three independent Markov chain Monte Carlo analyses. Noteworthy findings are that Toxarium undulatum shares a strongly supported node with Thalassiosirales and that the genus Attheya is not a member of the Chaetocerotales lineage.     

Phylogeny of Polygonia, Nymphalis and related butterflies (Lepidoptera: Nymphalidae): a total-evidence analysis

We investigated the phylogeny of butterflies in the tribe Nymphalini sensu Harvey 1991, comprising the genera Vanessa, Cynthia, Bassaris, Aglais, Inachis, Nymphalis, Polygonia, Kaniska, Antanartia, Hypanartia, Symbrenthia, Mynes and Araschnia . Evidence from the mitochondrial gene ndl, the nuclear gene 'wingless' and from morphology/ ecology/behaviour were used separately and combined to analyse relationships. Phylogenies based on the different types of data agreed in many aspects of basic topology. We show that an analysis of only wing pattern characters (based on Nijhout's homology system) results in a topology broadly similar to the one resulting from analysis of the complete matrix. We found support for a monophyletic Nymphalini, where Hypanartia may be the sister clade to all other genera. Mynes, Symbrenthia and Araschnia together seem to form another basal clade. Evidence presented gives only moderate support for a monophyletic Vanessa in the wide sense, including also Cynthia and Bassaris , but strong support for the monophyly of the largely holarctic clade Aglais + Inachis + Nymphalis + Polygonia + Kaniska + Roddia . Within the latter group there is strong support for a clade consisting of Aglais + Inachis and for a second clade which includes Nymphalis, Polygonia (and its sister clade, the monotypic Kaniska) as well as Roddia l-album (= Nymphalis vaualbum ). As a consequence of this topology, Aglais is recognized as a taxon separate from Nymphalis . We present a hypothesis of species relationships within the focal group of genera. We also analyse and discuss the implications of excluding or including ecological data in phylogenetic tree construction, when the tree is to be used for studies in phylogenetic ecology.     

Molecular phylogeny of the Dictyotales and their position within the Phaeophyceae, based on nuclear, plastid and mitochondrial DNA sequence data

For the first time, on the basis of nuclear, plastid and mitochondrial sequence data, the most comprehensive molecular phylogeny of the Dictyotales to date is presented, in a broad context where all brown algal orders are included (except Discosporangiales, Ascoseirales and Nemodermatales). A veto supertree approach was used here to evaluate congruency and conflicts between genes: phylogenetic signal was congruent and mainly carried by chloroplastic information. Supermatrix analyses (BI, ML and MP) revealed that Dictyotales is sister to Onslowiales, this ensemble being sister of a clade also encompassing Sphacelariales and Syringodermatales. The family Scoresbyellaceae is merged into the family Dictyotaceae. Furthermore, the current subdivision of the Dictyotaceae into two tribes was not supported. The enigmatic genus Stoechospermum was shown to belong to the same clade as Dictyota, Rugulopteryx, Scoresbyella and Canistrocarpus. Homoeostrichus and Dictyopteris did not appear monophyletic. Zonaria stipitata clustered with the Spatoglossum species; since this is consistent with its morphological features, the new combination Spatoglossum stipitatum is proposed accordingly.     

Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia

Recent phylogenetic analyses of a large dataset for mammalian families (169 taxa, 26 loci) portray contrasting results. Supermatrix (concatenation) methods support a generally robust tree with only a few inconsistently resolved polytomies, whereas MP‐EST coalescence analysis of the same dataset yields a weakly supported tree that conflicts with many traditionally recognized clades. Here, we evaluate this discrepancy via improved coalescence analyses with reference to the rich history of phylogenetic studies on mammals. This integration clearly demonstrates that both supermatrix and coalescence analyses of just 26 loci yield a congruent, well‐supported phylogenetic hypothesis for Mammalia. Discrepancies between published studies are explained by implementation of overly simple DNA substitution models, inadequate tree‐search routines and limitations of the MP‐EST method. We develop a simple measure, partitioned coalescence support (PCS), which summarizes the distribution of support and conflict among gene trees for a given clade. Extremely high PCS scores for outlier gene trees at two nodes in the mammalian tree indicate a troubling bias in the MP‐EST method. We conclude that in this age of phylogenomics, a solid understanding of systematics fundamentals, choice of valid methodology and a broad knowledge of a clade's taxonomic history are still required to yield coherent phylogenetic inferences.     

Species divergence and relationships in Stephanomeria (Compositae): PgiC phylogeny compared to prior biosystematic studies

We present a maximum likelihood tree of 41 PgiC sequences for the monophyletic Stephanomeria, with 10 perennial and six annual species, widely distributed in western North America and exemplary of different speciation processes. The phylogenetic analysis represents the first use of PgiC sequences for Compositae. The annual species were originally delimited by biosystematic studies that provided evidence of their reproductive compatibility and chromosome structural homology. The perennial species are highly distinctive in morphology and have not been examined similarly. The PgiC tree provides more resolution than our previous ITS/ETS tree and reflects both past and ongoing hybridization and/or incomplete lineage sorting. Two major PgiC clades were resolved in Stephanomeria. One clade contains the genes from the annual species plus the perennial, insular endemic S. guadalupensis, which appears closely related to a monophyletic S. virgata. Stephanomeria exigua is not monophyletic. The second clade includes the genes from all other sampled perennial species and a monophyletic subclade of four genes from two annual species. The results are compared to previous studies, also using PgiC, of Clarkia (Onagraceae). Both molecular systematic and biosystematic approaches are essential to discern the very different courses of evolution in these two, well-studied genera of western North America.     

A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants

Flowering plants represent the most significant branch in the tree of land plants, with respect to the number of extant species, their impact on the shaping of modern ecosystems and their economic importance. However, unlike so many persistent phylogenetic problems that have yielded to insights from DNA sequence data, the mystery surrounding the origin of angiosperms has deepened with the advent and advance of molecular systematics. Strong statistical support for competing hypotheses and recent novel trees from molecular data suggest that the accuracy of current molecular trees requires further testing. Analyses of phytochrome amino acids using a duplicate gene-rooting approach yield trees that unite cycads and angiosperms in a clade that is sister to a clade in which Gingko and Cupressophyta are successive sister taxa to gnetophytes plus Pinaceae. Application of a cycads + angiosperms backbone constraint in analyses of a morphological dataset yields better resolved trees than do analyses in which extant gymnosperms are forced to be monophyletic. The results have implications both for our assessment of uncertainty in trees from sequence data and for our use of molecular constraints as a way to integrate insights from morphological and molecular evidence.     

PHYLOGENETIC POSITION OF CHAETOSPHAERIDIUM (CHLOROPHYTA), A BASAL LINEAGE IN THE CHAROPHYCEAE INFERRED FROM 18S rDNA SEQUENCES

We sequenced the nuclear-encoded small-subunit ribosomal RNA gene (18S rDNA) of Chaetosphaeridium globosum (Nordst.) Klebahn, a microscopic freshwater epiphytic chlorophyte, to assess its phylogenetic affinities in the Chlorophyta. A phylogenetic analysis of a broad sampling of green algal taxa and Chaetosphaeridium confirmed that this alga is a member of the Charophyceae (Streptophyta) as earlier microscopical studies had suggested. However, more detailed phylogenetic analyses of the streptophyte lineage showed that contrary to expectations based on the ultrastructure of the zoospores, the presence of a unique type of setae, the oogamous mode of reproduction, and the occurrence of oscillatory rotations of the cytoplasm, Chaetosphaeridium and Coleochaete are not closely related and do not form a monophyletic clade. Instead, Chaetosphaeridium represents an early branch in the streptophyte lineage that had a near-simultaneous origin as the Charalean clade and a clade formed by all remaining streptophytes examined ( Klebsormidium, Coleochaete, Chlorokybus, Zygnematales, and bryophytes). All phylogenetic inference methods used (neighbor-joining analysis of Kimura distances, maximum likelihood, and maximum parsimony) resulted in essentially the same tree topology. No Group I introns were found in the 18S rDNA coding region of Chaetosphaeridium. Our molecular phylogenetic analysis of Chaetosphaeridium supports a recent cladistic classification of the Streptobionta by Kenrick and Crane in which Chaetosphaeridium is placed in a monotypic division and class, Chaetosphaeridiophyta and Chaetosphaeridiophyceae, respectively.