Genetic and Physiological Diversity in the Diatom Nitzschia inconspicua

Nitzschia inconspicua is an ecologically important diatom species, which is believed to have a widespread distribution and to be tolerant to salinity and to organic or nutrient pollution. However, its identification is not straightforward and there is no information on genetic and ecophysiological diversity within the species. We used morphological, molecular (rbcL and LSU D1–D3), ecophysiological and reproductive data to investigate whether N. inconspicua constitutes a single species with a broad ecological tolerance or two or more cryptic species with shared or different ecological preferences. Molecular genetic data for clones from upstream and deltaic sites in the Ebro River basin (Catalonia, Spain) revealed seven N. inconspicua rbcL + LSU genotypes grouped into three major clades. Two of the clades were related to other Nitzschia and Denticula species, making N. inconspicua paraphyletic and suggesting the need for taxonomic revision. Most clones were observed to be automictic, exhibiting paedogamy, and so the biological species concept cannot be used to establish species boundaries. Although there were morphological differences among clones, we found no consistent differences among genotypes belonging to different clades, which are definable only through sequence data. Nevertheless, separating the genotypes could be important for ecological purposes because two different ecophysiological responses were encountered among them.     

用叶绿体rbcL和rps4-trnS区序列确定亚洲特有单型属——篦齿蕨属的系统位置

篦齿蕨属Metapolypodium Ching是亚洲大陆特有植物, 仅含篦齿蕨Metapolypodium manmeiense (Christ) Ching 1种, 分布于中国西南及其邻近地区, 其系统位置一直是一个有待解决的问题。本文用叶绿体rbcL和rps4-trnS区序列探讨篦齿蕨属的系统位置。我们对篦齿蕨及其近缘类群的叶绿体rbcL和rps4-trnS区进行PCR扩增和序列测定。用最大简约法、邻接法和贝叶斯推断法对自测序列结合由GenBank下载的rbcL和rps4-trnS区序列进行独立和联合的系统发育分析, 所构建的系统发生树的拓扑结构基本一致。结果显示: 篦齿蕨属与多足蕨属Polypodium L. emend. Ching的关系较疏远, 而与水龙骨属Polypodiodes Ching和拟水龙骨属Polypodiastrum Ching的成员聚成一个支系, 与栗柄水龙骨Polypodiodes microrhizoma (C. B. Clarke ex Baker) Ching的关系最近。根据本文的研究结果, 我们赞成秦仁昌1978年的分类系统, 即分别承认多足蕨属、篦齿蕨属、水龙骨属、拟水龙骨属和棱脉蕨属Schellolepis J. Sm.为独立的类群。根据分子系统学证据, 宜将栗柄水龙骨转移到篦齿蕨属中。     

鳞毛蕨科植物的系统发育: 叶绿体rbcL序列的证据

运用MEGA2和MrBayes 3.0b4软件包对105种鳞毛蕨类及近缘植物(其中新测定36种)的叶绿体DNA rbcL基因序列进行系统发育分析, 探讨了其主要分类群(属级水平)的系统演化关系。用最大简约法、邻接法和贝叶斯分析方法构建的系统树基本一致, 结果显示: (1)秦仁昌系统所定义的鳞毛蕨科Dryopteridaceae, 除了拟贯众属Cyclopeltis外, 均包含在两个单系群之中, 支持鳞毛蕨族Dryopterideae和耳蕨族Polysticheae的成立; 但是鳞毛蕨族还包含秦仁昌系统所定义的球盖蕨科Peranemaceae和三叉蕨科Tectariaceae肋毛蕨属Ctenitis的部分种类; 耳蕨族还包含产于美洲的Phanerophlebia属和Polystichopsis属; 确认石盖蕨属Lithostegia属鳞毛蕨族的成员, 且与复叶耳蕨属Arachniodes具有较近的亲缘关系。(2)拟贯众属与所分析的其他任何鳞毛蕨类植物的关系都比较疏远, 单独为一支。(3)秦仁昌系统所定义的球盖蕨科与肉刺蕨属Nothoperanema聚成一个分支, 属于鳞毛蕨族的成员。(4)鳞毛蕨属Dryopteris为多系类群, 耳蕨属Polystichum和贯众属Cyrtomium均为并系类群。(5)黔蕨属Phanerophlebiopsis、毛枝蕨属Leptorumohra和石盖蕨属与复叶耳蕨属构成一支; 柳叶蕨属Cyrtogonellum与Polystichum属和Cyrtomium属的部分种类聚成一支; 肉刺蕨属与球盖蕨科及鳞毛蕨属的部分种类聚成一支。对鳞毛蕨科的系统关系、球盖蕨科与鳞毛蕨科的系统关系、肋毛蕨属与鳞毛蕨科的系统关系以及中国或亚洲特有属(拟贯众属、肉刺蕨属、黔蕨属、毛枝蕨属、石盖蕨属和柳叶蕨属)的系统位置进行了讨论。     

Sequence repeats enlarge the internal transcribed spacer 1 region of the brown alga Colpomenia sinuosa (Scytosiphonaceae, Phaeophyceae)

Colpomenia sinuosa is an annual brown algal species that occurs in temperate to tropical waters of the world. In order to examine the genetic diversity among populations of the species and to discuss its current distribution, we analyzed the nuclear ribosomal DNA internal transcribed spacer (ITS) region from 18 specimens of C. sinuosa , and, for comparison, plastid rbc L from the same specimens. The C. sinuosa ITS region (2141–2534 base pairs) is approximately 2.2 times the length of most other brown algae. We found a long repeated sequence of approximately 190 base pairs in the first half of the ITS1 region; five repeats in Northern Hemisphere collections and three in those from the Southern Hemisphere, which result in ITS length variation. The unequal occurrence of tandem repeats of C. sinuosa corresponds to the geographical distribution of the species. The rbc L sequences from all the specimens of C. sinuosa , except the Canary Island samples, were identical, indicating that they indeed belong to the same species.     

Phylogenetic relationships of Combretaceae inferred from nuclear and plastid DNA sequence data: implications for generic classification

The putative complexity of Combretaceae and lack of information on phylogenetic relationships within the family led us to explore relationships between genera of Combretaceae by means of combined analyses of plastid and nuclear sequences. We collected DNA sequence data from the nuclear ribosomal internal transcribed spacer region and plastid rbcL, psaA‐ycf3 spacer and psbA‐trnH spacer for 14 of the 17 genera of Combretaceae. The current classification of the family into two subfamilies, Strephonematoideae and Combretoideae, is corroborated. Within Combretoideae, division into two tribes, Laguncularieae and Combreteae, is strongly supported. Within Combreteae subtribe Terminaliinae, relationships between genera are largely unresolved. Terminalia is not supported as monophyletic and two groups were identified, one containing mainly African species and another of mostly Asian species. Pteleopsis, Buchenavia and Anogeissus are embedded within Terminalia, and we suggest that all genera of Terminaliinae, with the exception of Conocarpus, should be included in an expanded circumscrition of Terminalia. Within subtribe Combretinae, a clade formed by the two monotypic genera Guiera and Calycopteris is sister to the rest of the subtribe. Groupings in Combretinae are consistent with recent results based on morphological data. Combretum is currently divided into three subgenera: Apethalanthum, Cacoucia and Combretum. The last two were included in this study and supported as monophyletic if Quisqualis is included within subgenus Cacoucia. Meiostemon is sister to subgenus Combretum. We recommend that subgenus Combretum should be expanded to include Meiostemon and subgenus Cacoucia to include Quisqualis. The sectional classification within Combretum proposed in earlier morphological studies is confirmed except for the exclusion of C. imberbe from section Hypocrateropsis in a separate and monotypic section and the inclusion of C. zeyheri (section Spathulipetala) in section Macrostigmatea. In order to accommodate C. imberbe, a new section is suggested. The reinstatement of previously recognized sections Grandiflora and Trichopetala, both of which had been sunk into subgenus Cacoucia section Poivrea, is proposed. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 453–476.     

MOLECULAR PHYLOGENY AND REVISION OF THE GENUS NETRIUM (ZYGNEMATOPHYCEAE,STREPTOPHYTA): NUCLEOTAENIUM GEN. NOV.1

Nuclear‐encoded SSU rDNA, chloroplast LSU rDNA, and rbcL genes were sequenced from 53 strains of conjugating green algae (Zygnematophyceae, Streptophyta) and used to analyze phylogenetic relationships in the traditional order Zygnematales. Analyses of a concatenated data set (5,220 nt) established 12 well‐supported clades in the order; seven of these constituted a superclade, termed “Zygnemataceae.” Together with genera (Zygnema, Mougeotia) traditionally placed in the family Zygnemataceae, the “Zygnemataceae” also included representatives of the genera Cylindrocystis and Mesotaenium, traditionally placed in the family Mesotaeniaceae. A synapomorphic amino acid replacement (codon 192, cysteine replaced by valine) in the LSU of RUBISCO characterized this superclade. The traditional genera Netrium, Cylindrocystis, and Mesotaenium were shown to be para‐ or polyphyletic, highlighting the inadequacy of phenotypic traits used to define these genera. Species of the traditional genus Netrium were resolved as three well‐supported clades each distinct in the number of chloroplasts per cell, their surface morphology (structure and arrangement of lamellae) and the position of the nucleus or nuclear behavior during cell division. Based on molecular phylogenetic analyses and synapomorphic phenotypic traits, the genus Netrium has been revised, and a new genus, Nucleotaenium gen. nov., was established. The genus Planotaenium, also formerly a part of Netrium, was identified as the sister group of the derived Roya/Desmidiales clade and thus occupies a key position in the evolutionary radiation leading to the most species‐rich group of streptophyte green algae.     

Morphology and molecular relationships of Leptofauchea rhodymenioides (Rhodymeniales,Rhodophyta), a new record for Japan

Leptofauchea rhodymenioides Taylor (Faucheaceae, Rhodymeniales) is reported from Japan for the first time, based on detailed morphological studies and molecular phylogenetic analyses of nuclear‐encoded small subunit ribosomal RNA (SSU rRNA) and plastid‐encoded rbcL gene sequences. This is the first report of male gametophytes and detailed carposporophyte development in the genus Leptofauchea. This species is characterized as follows: (i) flat, membranous, and regularly and dichotomously branched thalli; (ii) the older blades are constricted below the apices; (iii) the cortex is composed of a continuous layer with an irregularly arranged outer layer, and the medulla of two to three incomplete layers; (iv) gametophytes are dioecious; (v) in males, the cortical cells cut off two to three spermatangial mother cells, which produce terminal spermatangia; (vi) in females, the procarp is composed of a three‐celled carpogonial branch and a two‐celled auxiliary cell branch; (vii) upon fertilization, the carpogonium directly contacts the auxiliary cell; (viii) the auxiliary mother cell fuses with vegetative cells, and forms a large trunk‐like fusion cell; (ix) gonimoblast filaments develop outwardly, and transform completely into carposporangia; (x) the carposporophyte is covered with a pericarp with a well‐defined tela arachnoidea; (xi) the mature cystocarp is spherical, has an ostiole, and protrudes from the blade margins; and (xii) the cruciately divided tetrasporangia are formed in nemathecia, produced laterally from paraphyses or terminally on short filaments. Molecular analyses suggest that Leptofauchea forms a strong sister alliance with the genus Webervanbossea. The families Faucheaceae and Lomentariaceae, and the genera Leptofauchea and Webervanbossea are monophyletic, but the latter two genera are not included in the Faucheaceae.     

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。