马尾树科的系统位置：来自rbcL基因核苷序列的证据

本根据叶绿体基因ｒｂｃＬ的核苷酸序列证据讨论了单型科－－马尾树科的系统关系。数据矩陈中包括了马尾树科及其它“高等”金缕梅类各科，并分别利用Ｃｕｍｏｎｉａｃｅａｅ科的Ｂａｕｅｒａ属，“低等”金缕梅类植物连香树属和枫香权属作为外类群进行分支分析。两种分析的结果是一致的。在ｒｂｃＬ基因树上，马尾树属和被用于分析的胡桃科各属紧密地结合在一起，支持马虱对科和胡桃科有非常近的亲缘关系。     

据叶绿体trnL—F序列分析“高等”金缕梅类植物的系统发育关系

研究对“高等”金缕梅类的 8科 2 4属 2 5种植物和外类群Hamamelis两种植物的叶绿体DNAtrnL_F区进行了测序 ,并根据DNA序列对该类植物的系统发育关系进行了分析。结果表明 :所有“高等”金缕梅类植物的科结合成一支 ,bootstrap分析支持率为 10 0 % ,各科之间的关系得到很好分辨。Nothofagus是最基部的一支 ;山毛榉科 (Fa gaceae)作为姐妹群与“核心”金缕梅类的科 (桦木科Betulaceae ,胡桃科Juglandaceae ,木麻黄科Casuarinaceae ,杨梅科Myricaceae,Ticodendraceae和马尾树科Rhoipteleaceae)组成一支 ,并得到很强的支持。“核心”金缕梅类构成三支 ,关系如下 :(1)Casuarina (Ticodendron ,(Betulaceae) ) ,(2 )Juglandaceae_Rhoipteleaceae ,(3)Myricaceae。本研究显示叶绿体DNAtrnL_F区对分辨“高等”金缕梅类科间关系及部分科内的属间关系十分有效。     

据叶绿体trnL_F序列分析"高等"金缕梅类植物的系统发育关系

研究对"高等"金缕梅类的8科24属25种植物和外类群Hamamelis两种植物的叶绿体DNA trnL-F区进行了测序,并根据DNA序列对该类植物的系统发育关系进行了分析.结果表明: 所有"高等"金缕梅类植物的科结合成一支, bootstrap 分析支持率为100%,各科之间的关系得到很好分辨.Nothofagus是最基部的一支;山毛榉科(Fagaceae)作为姐妹群与"核心"金缕梅类的科(桦木科Betulaceae,胡桃科Juglandaceae, 木麻黄科Casuarinaceae, 杨梅科Myricaceae, Ticodendraceae 和马尾树科Rhoipteleaceae)组成一支,并得到很强的支持."核心"金缕梅类构成三支,关系如下:(1) Casuarina (Ticodendron, (Betulaceae)), (2) Juglandaceae-Rhoipteleaceae, (3) Myricaceae.本研究显示叶绿体DNA trnL-F区对分辨"高等"金缕梅类科间关系及部分科内的属间关系十分有效.     

胡桃目的分化、进化和系统关系

本文所讨论的胡桃目的概念包括胡桃科和马尾树科。作者详细地对该类群植物性的分化,果实传播方式及分化,生态及地理的分化等方面进行了较系统的分析,最后探讨了该目的系统位置,认为胡桃目与杨梅目和山毛榉目有密切的联系,是金缕梅类植物演化最高级的一个类群。     

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。     

“低等”金缕梅类植物的起源和散布

本文根据植物类群的系统发育和地理分布相统一的原理,讨论了“低等”金缕梅类植物的起 源和散布。 “低等”金缕梅类植物(Endress1989a的概念)包括下列7科：昆栏树科、水青树科、连香 树科、折扇叶科、领春木科、悬铃木科和金缕梅科。 该类群共有13种分布区类型,东亚区的南部和 印度支那区的北部是它的现代分布中心;根据化石证据及原始类群和外类群的分布分析,以上地区最 有可能是这类植物的起源地。 “低等”金缕梅类植物起源的时间至少可追溯到早白垩纪巴列姆期,较可 靠的化石证据说明悬铃木类植物在早白垩纪阿尔必晚期出现,而昆栏树科、水青树科、连香树科和金 缕梅科植物的出现均不晚于晚白垩纪。 最后,从环境变迁和生物演化两个方面探讨了“低等”金缕梅类植物现代分布格局的形成原因。     

L基因序列分析对连香树科和交让木科系统位置的重新评价——兼论低等金缕梅类的关系

测定了悬铃木科和金缕梅科5个亚科的6个代表种的rbcL基因序列, 对低等金缕梅类植物及新近提出的相关类群进行了分子系统发育分析, 获得4个最简约树。 简约树步长为893, 其CI值和RI值分别为0.558和0.591。 连香树科和交让木科与金缕梅科及虎耳草科关系较近。 尽管增加了金缕梅科的取样密度, 它们之间进一步的关系仍未得到分辨, 结合它们的形态特征, 连香树科和交让木科应置于金缕梅目内。 rbcL基因树上反映出传统的“低等”金缕梅类成员领春木科与毛茛类植物聚在一起; 悬铃木科与昆栏树科和水青树科关系较近, 而与金缕梅科关系较远; 杜仲科与低等金缕类的核心科——金缕梅科的关系似乎较除连香树科之外的其它低等金缕类成员近。 低等金缕类植物由一些古老、孤立的科组成, 且是多系的。     

马尾树科及其近缘科花粉形态研究

本文观察了马尾树科(Rhoipteleaceae)、胡桃科(Juglandaceae)以及桦木科(Be-tulaceae)、9属9种植物花粉形态。马尾树科与桦木科桦木属(Betula L.)花粉粒均为扁球形,极面观呈钝三角形,萌发孔类型均为多孔类型,孔之间均有弓形加厚,而且外表面均具细颗粒状雕纹。而胡桃科大多为多边形、散孔类型。根据花粉形态资料,探讨了马尾树科的系统位置。     

rbcL基因序列分析对连香树科和交让木科系统位置的重新评价——兼论低等金缕梅类的关系

测定了悬铃木科和金缕梅科５个亚科的６个代表种的ｒｂｃＬ基因序列,对低等金缕梅类植物及新近提出的相关类群进行了分子系统发育分析,获得４个最简约树。简约树步长为８９３,其ＣＩ值和ＲＩ值分别为０．５５８和０．５９１。连香树科和交让木科与金缕梅科及虎耳草科关系较近。尽管增加了金缕梅科的取样密度,它们之间进一步的关系仍未得到分辨,结合它们的形态特征,连香树科和交让木科应置于金缕梅目内。ｒｂｃＬ基因树上反映出传统的“低等”金缕梅类成员领春木科与毛茛类植物聚在一起;悬铃木科与昆栏树科和水青树科关系较近,而与金缕梅科关系较远;杜仲科与低等金缕类的核心科———金缕梅科的关系似乎较除连香树科之外的其它低等金缕类成员近。低等金缕类植物由一些古老、孤立的科组成,且是多系的。     

基于叶绿体基因rbcL和psbA-trnH间区探讨石杉科植物系统关系

关于石杉科Huperziaceae植物的分类,一直存在一些争议。在旧的分类体系中石杉科植物被包含在一个混合的石松科Lycopodiaceae和多谱系的石松属Lycopodium中。本文利用叶绿体rbcL基因和psbA-trnH基因间区序列探讨石杉科植物的系统位置及石杉科内部的分类关系,用最大简约法和邻接法对自测序列结合由GenBank下载的rbcL及psbA-trnH基因间区序列进行系统发育分析。结果显示,石杉科与Phylloglossum属关系较近,与石松科关系较疏远。在石杉科中热带石杉属Huperzia植物和马尾杉属Phlegmariurus植物的关系要比它们与其他石杉属植物更近。所以,我们的rbcL基因数据不支持秦仁昌关于石杉科分为石杉属和马尾杉属的分类处理。但是,因为我们的psbA-trnH序列没有包括热带种类,对石杉属植物和马尾杉属植物的关系无验证。因此需要更多的样品和序列数据进一步探讨石杉科的演化关系。     

中国角叉菜属(Chondrus)的分类研究：形态观察和rbcL序列分析

采用rbcL序列分析结合传统形态观察的方法 ,对我国福建省平潭县和漳浦县、山东省青岛市及辽宁省大连市采集的角叉菜属样品进行了研究。新鲜或硅胶干燥样品被用于总DNA提取并用于PCR反应 ,PCR扩增产物回收后直接用于测序反应 ,序列数据经ClustalX1 .8软件排序后 ,采用MEGA2 .1软件根据Kimura’s双因子法计算遗传距离 ,并应用邻接法 (neighbor - joint ing)和最大简约法 (MaximumParsimony)构建系统树 ,Bootstrap法 (5 0 0次重复 )评估分支可信度。研究表明 :确认中国存在Chondrusocellatus、Chondrusnipponicus和Chondrusarmatus三种角叉菜 ;原报道产于我国东南沿海的角叉菜Chondrusocellatus应为Grateloupiaimbricata ;原报道产于大连小平岛的角叉菜Chondrusyendoi应为Mazzaellajaponica。     

Phylogenetic relationships of the enigmatic angiosperm family Podostemaceae inferred from 18S rDNA and rbcL sequence data

The phylogenetic relationships of some angiosperm families have remained enigmatic despite broad phylogenetic analyses of rbcL sequences. One example is the aquatic family Podostemaceae, the relationships of which have long been controversial because of major morphological modifications associated with their aquatic habit. Podostemaceae have variously been associated with Piperaceae, Nepenthaceae, Polygonaceae, Caryophyllaceae, Scrophulariaceae, Rosaceae, Crassulaceae, and Saxifragaceae. Two recent analyses of rbcL sequences suggest a possible sister-group relationship of Podostemaceae to Crassulaceae (Saxifragales). However, the branch leading to Podostemaceae was long, and use of different outgroups resulted in alternative placements. We explored the phylogenetic relationships of Podostemaceae using 18S rDNA sequences and a combined rbcL + 18S rDNA matrix representing over 250 angiosperms. In analyses based on 18S rDNA data, Podostemaceae are not characterized by a long branch; the family consistently appears as part of a Malpighiales clade that also includes Malpighiaceae, Turneraceae, Passifloraceae, Salicaceae, Euphorbiaceae, Violaceae, Linaceae, Chrysobalanaceae, Trigoniaceae, Humiriaceae, and Ochnaceae. Phylogenetic analyses based on a combined 18S rDNA + rbcL data set (223 ingroup taxa) with basal angiosperms as the outgroup also suggest that Podostemaceae are part of a Malpighiales clade. These searches swapped to completion, and the shortest trees showed enhanced resolution and increased internal support compared to those based on 18S rDNA or rbcL alone. However, when Gnetales are used as the outgroup, Podostemaceae appear with members of the nitrogen fixing clade (e.g., Elaeagnaceae, Ulmaceae, Rhamnaceae, Cannabaceae, Moraceae, and Urticaceae). None of the relationships suggested here for Podostemaceae receives strong bootstrap support. Our analyses indicate that Podostemaceae are not closely allied with Crassulaceae or with other members of the Saxifragales clade; their closest relatives, although still uncertain, appear to lie elsewhere in the rosids.     

The evolution of the atpbeta-rbcL intergenic spacer in the epacrids (Ericales) and its systematic and evolutionary implications

Sequence data from the noncoding region separating the plastid genes atpbeta and rbcL were gathered for 27 epacrid taxa, representing all previously recognized infrafamilial groups, and four outgroup taxa (Ericaceae), to address several persistent phylogenetic questions in the group. Parsimony analyses were conducted on these data, as well as on a complementary rbcL sequence dataset assembled from the literature and the combined dataset. The atpbeta-rbcL spacer was notable for the high frequency of insertion-deletion mutations (indels); their distributions were coded as binary characters and included as a adjunct matrix in some of the analyses. The phylogenetic patterns derived from the spacer and rbcL data and the combined analyses, both including and excluding the indel data, concur in resolving seven major lineages corresponding to the tribes of Crayn et al. (1998, Aust. J. Bot. 46, 187-200), viz. Prionoteae, Archerieae, Oligarrheneae, Cosmelieae, Richeeae, Epacrideae, and Styphelieae. The relationships of the tribes and within Styphelieae, however, are not convincingly resolved. Minor conflicts in the positions of some taxa between the spacer and the rbcL trees are poorly supported. Among epacrids, the spacer region provided more cladistically informative characters than rbcL and resulted in trees with lower homoplasy. Further, the spacer data, when analyzed alone and when combined with rbcL, resolved several clades that could not be retrieved on rbcL data alone and provided increased support for many other relationships. The evolution of a putative three-base inversion associated with a hairpin secondary structure in the spacer region is discussed in the light of the inferred phylogeny.     

A MOLECULAR PHYLOGENY OF THE HETEROKONT ALGAE BASED ON ANALYSES OF CHLOROPLAST-ENCODED rbcL SEQUENCE DATA1

Nearly complete ribulose-1,5-bisphosphate carboxylase/ oxygenase (rbcL)sequences from 27 taxa of heterokont algae were determined and combined with rbcL sequences obtained from GenBank for four other heterokont algae and three red algae. The phylogeny of the morphologically diverse haterokont algae was inferred from an unambiguously aligned data matrix using the red algae as the root, Significantly higher levels of mutational saturation in third codon positions were found when plotting the pair-wise substitutions with and without corrections for multiple substitutions at the same site for first and second codon positions only and for third positions only. In light of this observation, third codon positions were excluded from phylogenetic analyses. Both weighted-parsimony and maximum-likelihood analyses supported with high bootstrap values the monophyly of the nine currently recognized classes of heterokont algae. The Eustigmatophyceae were the most basal group, and the Dictyochophyceae branched off as the second most basal group. The branching pattern for the other classes was well supported in terms of bootstrap values in the weightedparsimony analysis but was weakly supported in the maximum-likelihood analysis (<50%). In the parsimony analysis, the diatoms formed a sister group to the branch containing the Chrysophyceae and Synurophyceae. This clade, charactetized by siliceous structures (frustules, cysts, scales), was the sister group to the Pelagophyceae/Sarcinochrysidales and Phaeo-/Xantho-/ Raphidophyceae clades. In the latter clade, the raphido-phytes were sister to the Phaeophyceae and Xanthophyceae. A relative rate test revealed that the rbcL gene in the Chrysophyceae and Synurophyceae has experienced a significantly different rate of substitutions compared to other classes of heterokont algae. The branch lengths in the maximum-likelihood reconstruction suggest that these two classes have evolved at an accelerated rate. Six major carotenoids were analyzed cladistically to study the usefulness of carotenoid pigmentation as a class-level character in the heterokont algae. In addition, each carotenoid was mapped onto both the rbcL tree and a consensus tree derived from nuclear-encoded small-subunit ribosomal DNA (SSU rDNA) sequences. Carotenoid pigmentation does not provide unambiguous phylogenetic information, whether analyzed cladistically by itself or when mapped onto phylogenetic trees based upon molecular sequence data.     

Molecular phylogenetics of Meliaceae (Sapindales) based on nuclear and plastid DNA sequences

Phylogenetic analyses of Meliaceae, including representatives of all four currently recognized subfamilies and all but two tribes (32 genera and 35 species, respectively), were carried out using DNA sequence data from three regions: plastid genes rbcL, matK (partial), and nuclear 26S rDNA (partial). Individual and combined phylogenetic analyses were performed for the rbcL, matK, and 26S rDNA data sets. Although the percentage of informative characters is highest in the segment of matK sequenced, rbcL provides the greatest number of informative characters of the three regions, resulting in the best resolved trees. Results of parsimony analyses support the recognition of only two subfamilies (Melioideae and Swietenioideae), which are sister groups. Melieae are the only tribe recognized previously that are strongly supported as monophyletic. The members of the two small monogeneric subfamilies, Quivisianthe and Capuronianthus, fall within Melioideae and Swietenioideae, respectively, supporting their taxonomic inclusion in these groups. Furthermore, the data indicate a close relationship between Aglaieae and Guareeae and a possible monophyletic origin of Cedreleae of Swietenioideae. For Trichilieae (Melioideae) and Swietenieae (Swietenioideae) lack of monophyly is indicated.     

A MOLECULAR PHYLOGENY OF THE GELIDIALES (RHODOPHYTA) BASED ON ANALYSIS OF PLASTID rbcL NUCLEOTIDE SEQUENCES1

Parsimony analyses of rbcL nucleotide. sequences were used to develop hypotheses of relationships among taxa in the taxonomically difficult order Celidiales including species from seven currently recognized genera: Capreolia, Gelidiella, Gelidium, Onikusa, Pterocladia, Ptilophora, and Suhria. Nucleotide. sequences of rbcL from red algae are variable and provide a large number of informative characters for phylogenetic analysis, yet the absence of insertion/deletion mutations allows for the unambiguous alignment of sequences. Species were resolved into 10 well-.supported major clades representing genera and species complexes. The topological positions of these 10 clades within trees are also well supported and indicate that Gelidium and Pterocladia as currently circumscribed are not monophyletic. These results call for a revision of the classification of the Gelidiales .     

Testing for endemism, genotypic diversity and species concepts in Antarctic terrestrial microalgae of the Tribonemataceae (Stramenopiles, Xanthophyceae)

The genetic diversity of all available culture strains of the Tribonemataceae ( Stramenopiles , Xanthophyceae ) from Antarctica was assessed using the chloroplast-encoded psbA /rbcL spacer region sequences, a highly variable molecular marker, to test for endemism when compared with their closest temperate relatives. There was no species endemic for Antarctica, and no phylogenetic clade corresponded to a limited geographical region. However, species of the Tribonemataceae may have Antarctic populations that are distinct from those of other regions because the Antarctic strain spacer sequences were not identical to sequences from temperate regions. Spacer sequences from five new Antarctic isolates were identical to one or more previously available Antarctic strains, indicating that the Tribonemataceae diversity in Antarctic may be rather limited. Direct comparisons of the spacer sequences and phylogenetic analyses of the more conserved rbcL gene revealed that current morphospecies were inadequate to describe the actual biodiversity of the group. For example, the genus Xanthonema , as currently circumscribed, was paraphyletic. Fortunately, the presence of distinctive sequence regions within the psbA/rbcL spacer, together with differences in the rbcL phylogeny, provided significant autoapomorphic criteria to re-define the Tribonemataceae species.     

Phylogenetic relationships of Lecythidaceae: a cladistic analysis using rbcL sequence and morphological data

This study examined in detail the rbcL sequence and morphological support for subfamilial relationships and monophyly of Lecythidaceae. Initially we needed to establish relationships of Lecythidaceae among other dicot families. To complete this we examined 47 rbcL sequences of 25 families along with molecular observations from several large analyses of rbcL data. All analyses strongly support the monophyly of the asterid III grouping. This analysis revealed Lecythidaceae to be paraphyletic and indicated potential outgroup relationships with Sapotaceae. Once relationships had been evaluated using molecular data we then concentrated on analyzing separate and combined morphological and molecular databases. The topology of the morphological data set was similar to the rbcL sequence and combined data sets except for the positioning of Napoleonaeoideae, Grias, Gustavia, and Oubanguia. According to the combined results, Planchonioideae, Lecythidoideae. and Foetidioideae are monophyletic, whereas the subfamily Napoleonaeoideae are paraphyletic. Nested within Napolconaeoideae, we found Asteronthos forms a strongly supported clade with Oubanguia (Scytopetalaceae). Foetidia, the only genus of Foetidioideae, is sister to Planchonioideae, and this clade is sister to Lecythidoideae. The [(Planchonioideae, Foetidioideae) Lecythidoideae are sister to Asteranthos/Oubanguia. Napoleonaeoideae are sister to the rest of Lecythidaceae.     

Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase

A 492- to 495-bp fragment of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) (rbcL) was amplified by PCR from facultatively lithotrophic aerobic CO-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic DNA extracts from tephra and ash deposits from Kilauea volcano, for which atmospheric CO and hydrogen have been previously documented as important substrates. PCR products from the mats and volcanic sites were used to construct rbcL clone libraries. Phylogenetic analyses showed that the rbcL sequences from all isolates clustered with form IC rbcL sequences derived from facultative lithotrophs. In contrast, the microbial mat clone sequences clustered with sequences from obligate lithotrophs representative of form IA rbcL. Clone sequences from volcanic sites fell within the form IC clade, suggesting that these sites were dominated by facultative lithotrophs, an observation consistent with biogeochemical patterns at the sites. Based on phylogenetic and statistical analyses, clone libraries differed significantly among volcanic sites, indicating that they support distinct lithotrophic assemblages. Although some of the clone sequences were similar to known rbcL sequences, most were novel. Based on nucleotide diversity and average pairwise difference, a forested site and an 1894 lava flow were found to support the most diverse and least diverse lithotrophic populations, respectively. These indices of diversity were not correlated with rates of atmospheric CO and hydrogen uptake but were correlated with estimates of respiration and microbial biomass.