由部分核糖体RNA序列确定的绿僵菌属种系统发育关系

本研究应用特异寡聚核苷酸引物和双脱氧核苷酸终止法测定绿僵菌Metarhizium不同种的部分rRNA序列。这些序列分别选自小亚基(18S)和大亚基(25S)rRNA上的不同区域。校排的不同序列用于计算核苷酸的差异。绿僵菌的系统发育关系采用最大可能性(Maximum-Likelihood)方法分析。所有的分类单元聚类成二个分支。在产生圆柱状瓶形小梗的种中,M.anisopliae var.anisopliae,M.anisopliae var.majus,M.brunneum(NRRL1944),M.guizhouense,M.pingshaense和未知种M.sp.2组成一个密切相关的群组,而M.anisopliae(ACCC 30104)位于这群组之外。在产生棍棒状瓶形小梗的种中,M.album,M.cylindrosporae和M.flavoviride互相独立成支。实验结果不支持Metarhizium只能区分为M.anisopliae和M.flavoviride二个种的分类观点。文中还讨论了经典分类标准的系统发育价值。     

PHYLOGENY OF THE BATRACHOSPERMALES (RHODOPHYTA) INFERRED FROM rbcL AND 18S RIBOSOMAL DNA GENE SEQUENCES

The sequence data from the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase ( rbc L) gene and 18S ribosomal DNA (small subunit) of taxa in the freshwater rhodophyte order Batrachospermales were used to construct phylogenetic hypotheses. Taxa examined in this study represent four families, eight genera, and six sections of the genus Batrachospermum . In addition, Rhododraparnaldia oregonica Sheath, Whittick et Cole, was included in the analysis because it shares particular ultrastructural, reproductive, and morphological characteristics with members of the Batrachospermales and Acrochaetiales. The trees generated from each gene, as well as a combined data set, were largely congruent. Rhododraparnaldia consistently occurs on an early branch within the Acrochaetiales – Palmariales clade and does not appear to be a member of the Batrachospermales. In addition, Thorea violacea Bory de St. Vincent was not closely related to the other taxa of the Batrachospermales in all trees and hence the family Thoreaceae does not appear to be a natural grouping within this order. All other taxa analyzed, which are presently classified within this order, formed a monophyletic clade in most analyses. Psilosiphon scoparium Entwisle was not closely allied with the taxa of the Lemaneaceae, lending support to the newly proposed family Psilosiphonaceae. Sequence data from the remaining taxa of the Lemaneaceae support the concept of a derived monophyletic clade. The genus Batrachospermum appears to comprise many morphologically similar but distantly related taxa, which will need further investigation to resolve their taxonomic status. Tuomeya, Sirodotia and Nothocladus are retained at the generic level until further data are obtained.     

PHYLOGENY OF THE HYDRODICTYACEAE (CHLOROPHYCEAE): INFERENCES FROM rDNA DATA1

The hydrodictyacean green algal lineage has been the focus of much research due to the fossil record of at least some members, their ornamented cell walls, and their distinctive reproductive strategies. The phylogeny of the family was, until recently, exclusively morphology based. This investigation examines hydrodictyacean isolates from several culture collections, focusing on sequences from ribosomal data: 18S rDNA, 26S rDNA (partial), and internal transcribed spacer (ITS)‐2 data. Results from phylogenetic analyses of independent and combined data matrices support the Hydrodictyaceae as a monophyletic lineage that includes isolates of Chlorotetraedron, Hydrodictyon, Pediastrum, Sorastrum, and Tetraedron. Phylogenetic analyses of rDNA data indicate that the three‐dimensional coenobium of Hydrodictyon is evolutionarily distinct from the three‐dimensional coenobium of Sorastrum. The more robust aspects of the ITS‐2 data corroborate the 18S+26S rDNA topology and provide a structural autapomorphy for the Hydrodictyaceae and Neochloridaceae, that is, an abridgment of helix IV in the secondary structure. The rDNA data do not support monophyly of Pediastrum but rather suggest the existence of four additional hydrodictyacean genera: Monactinus, Parapediastrum, Pseudopediastrum, and Stauridium.     

PHYLOGENY OF THE EUGLENALES INFERRED FROM PLASTID LSU rDNA SEQUENCES1

To gain insights into the phylogeny of the Euglenales, we analyzed the plastid LSU rDNA sequences from 101 strains of the photosynthetic euglenoids belonging to nine ingroup genera (Euglena, Trachelomonas, Strombomonas, Monomorphina, Cryptoglena, Colacium, Discoplastis, Phacus, and Lepocinclis) and two outgroup genera (Eutreptia and Eutreptiella). Bayesian and maximum‐likelihood (ML) analyses resulted in trees of similar topologies and four major clades: a Phacus and Lepocinclis clade; a Colacium clade; a Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade; and a Euglena clade. The Phacus and Lepocinclis clade was the sister group of all other euglenalian genera, followed by Discoplastis spathirhyncha (Skuja) Triemer and the Colacium clade, respectively, which was inconsistent with their placement based on nuclear rDNA genes. The Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade was sister to the Euglena clade. The loricate genera, Trachelomonas and Strombomonas, were closely related to each other, while Monomorphina and Cryptoglena also grouped together. The Euglena clade formed a monophyletic lineage comprising most species from taxa formerly allocated to the subgenera Calliglena and Euglena. However, within this genus, none of the subgenera was monophyletic.     

NUCLEOTIDE SEQUENCES OF THE SMALL-SUBUNIT RIBOSOMAL RNA GENES FROM SELECTED LAMINARIALES (PHAEOPHYTA): IMPLICATIONS FOR KELP EVOLUTION1

The entire small-subunit (SSU) ribosomal ribonucleic acid sequence was inferred for kelp representing seven genera: Alaria marginata Postels and Ruprecht (1824 bp), Egregia menziesii (Turner) Areschoug (1825 bp), Lessoniopsis littoralis (Tilden) Reinke (1825 bp), Macrocystis integrifolia Bory (1825 bp), Nereocystis leutkeana (Mertens) Postels and Ruprecht (1824 bp), Postelsia palmaeformis Ruprecht (1826 bp), and Pterygophora californica Ruprecht (1825 bp). We obtained a partial sequence for Eisenia arborea Areschoug (1669 bp) from a single clone of polymerase chain reaction-amplified product. The SSU sequence was too conserved among these morphologically distinct taxa to permit phylogenetic analysis. The divergence between the most distant taxa was only 0.66%. This value was used in a SSU molecular clock to suggest that the most distantly related kelp investigated in this study diverged between 16 and 30 (more probably 16 and 20) million years ago.     

核苷酸序列比对在生物系统发育研究中的应用

作为确定分子数据初级同源性(primary homology)的过程,比对的重要性在于后续算法的选择.本文对其在生物系统发育研究中的作用及其基本步骤与算法做了简要说明;从理论与实践相结合的角度介绍了使用最为广泛的软件,讨论了其中的空位(gap)问题、参数问题和比对结果校正等问题;并且对此领域中前沿的基因组比对研究进展做了概述.     

PHYLOGENY OF THE SUBFAMILY SCOTIELLOCYSTOIDEAE (CHLOROPHYCEAE, CHLOROPHYTA) AND RELATED TAXA INFERRED FROM 18S RIBOSOMAL RNA GENE SEQUENCE DATA

Nuclear-encoded small subunit ribosomal RNA gene (18SrDNA) sequences were determined for Coelastrella multistriata (Trenkwalder) Kalina et Punčochářová, two species of Scotiellopsis ( S. oocystiformis (Lund) Kalina et Punčochářová and S. terrestris (Reisigl) Kalina et Punčochářová) and two species of Muriella ( M. aurantiaca Vischer and M. terrestris Boye- Petersen). Coelastrella and Scotiellopsis are members of the subfamily Scotiellocystoideae, and Muriella is a member of the subfamily Chlorelloideae in the family Chlorellaceae. Phylogenetic trees were constructed based on these sequence data and on previously known 18SrDNA sequences of 25 taxa. Coelastrella and Scotiellopsis were closely related to each other and formed a cluster with Scenedesmus vacuolatus (Shihira et Krauss) Kessler et al. This cluster shared a monophyletic ancestry with other Scenedesmus species. Muriella aurantiaca formed a sister relationship with the monophyletic lineage of Scenedesmus. However, another species, M. terrestris, was placed in the Trebouxiophyceae and was strongly related to Chlorella. The genus Mychonastes belonging to the Scotiellocystoideae was also not monophyletic. This study suggests that the subfamily Scotiellocystoideae should be removed from the Chlorellaceae.     

EVOLUTIONARY INFERENCES FROM THE ANALYSIS OF EXCHANGEABILITY

Evolutionary inferences are usually based on statistical models that compare mean genotypes or phenotypes (or their frequencies) among populations. An alternative is to use the full distribution of genotypes and phenotypes to infer the “exchangeability” of individuals among populations. We illustrate this approach by using discriminant functions on principal components to classify individuals among paired lake and stream populations of threespine stickleback in each of six independent watersheds. Classification based on neutral and nonneutral microsatellite markers was highest to the population of origin and next highest to populations in the same watershed. These patterns are consistent with the influence of historical contingency (separate colonization of each watershed) and subsequent gene flow (within but not between watersheds). In comparison to this low genetic exchangeability, ecological (diet) and morphological (trophic and armor traits) exchangeability was relatively high—particularly among populations from similar habitats. These patterns reflect the role of natural selection in driving parallel adaptive changes when independent populations colonize similar habitats. Importantly, however, substantial nonparallelism was also evident. Our results show that analyses based on exchangeability can confirm inferences based on statistical analyses of means or frequencies, while also refining insights into the drivers of—and constraints on—evolutionary diversification.     

苔藓动物18S rRNA基因的分子系统发生初探

本文对我国沿海较为常见的8种唇口目苔藓动物的18SrRNA基因进行了PCR扩增和序列测定。结合已知的其它苔藓动物（包括内肛动物和外肛动物）以及腕足动物和帚虫的相应序列,运用分子系统学方法,研究苔藓动物门的系统发生关系,结果表明,外肛动物和内肛动物构成苔藓动物分子系统树中的二大平行支;本文测定的大室膜孔苔虫与Giribet等测定的膜孔苔虫在系统树中的位置间隔较远。结果也支持外肛动物包含被唇纲和裸唇纲两大类群的形态划分,而关于裸唇纲特别是唇口目内部的系统发生关系。分子数据的分析结果和形态分类之间的分歧有待于进一步研究。     

中华鳖太湖养殖种群和日本引进种群线粒体DNA Cyt b基因片段序列分析及分子进化初探

对中华鳖太湖养殖种群和日本引进种群共38个个体的线粒体DNA细胞色素b基因中间部分序列进行测定,比较其同源性,计算碱基组成,并用乌龟为外群构建不同单倍型的UPGMA和NJ分子系统树.在获得的408bp的序列中,A T约占58.8%,其中15个核苷酸位点存在变异(约占3.7%).两种群共有6种单倍型(haplotype),其中太湖养殖种群有4种单倍型,日本引进种群有2种单倍型.由系统树显示,中华鳖太湖种群的4种单倍型聚合成一大支,日本引进种群的2种单倍型以很高的置信度(99%)聚成一支.两种群序列上的差异,可以成为种群鉴别的分子标记.     

PHYLOGENY OF THE ULVOPHYCEAE (CHLOROPHYTA): CLADISTIC ANALYSIS OF NUCLEAR-ENCODED rRNA SEQUENCE DATA1

Cladistic analysis of nuclear-encoded rRNA sequence data provided us with the basis for some new hypotheses of relationships within the green algal class Ulvophyceae. The orders Ulotrichales and Ulvales are separated from the clade formed by the remaining orders of siphonous and siphonocladous Ulvophyceae (Caulerpales, Siphonocladales /Cladophorales [S/C] complex, and the Dasycladales), by the Chlorophyceae and Pleurastrophyceae. Our results suggest that the Ulvophyceae is not a monophyletic group. Examination of inter- and intra-ordinal relationships within the siphonous and siphonocladous ulvophycean algae revealed that Cladophora, Chaetomorpha, Anadyomene, Microdictyon, Cladophoropsis and Dictyosphaeria form a clade. Thus the hypothesis, based on ultrastructural features, that the Siphonocladales and Cladophorales are closely related is supported. Also, the Caulerpales is a monophyletic group with two lineages; Caulerpa, Halimeda, and Udotea comprise one, and Bryopsis and Codium comprise the other. The Dasycladales (Cymopolia and Batophora) also forms a clade, but this clade is not inferred to be the sister group to the S/C complex as has been proposed. Instead, it is either the sister taxon to the Caulerpales or basal to the Caulerpales and S/C clade The Trentepohliales is also included at the base of the siphonous and siphonocladous ulvophycean clade. The Pleurastrophyceae, which, like the Ulvophyceae, posses a counter-clockwise arrangement of flagellar basal bodies, are more closely related to the Chlorophyceae than to the Ulvophyceae based on rRNA sequences. Thus, the arrangement of basal bodies does not diagnose a monophyletic group. Previously reported hypotheses of phylogenetic relationships of ulvophycean algae were tested. In each case, additional evolutionary steps were required to obtain the proposed relationships. Relationships of ulvophycean algae to other classes of green algae are discussed.     

粒毛盘菌属种间关系的分子系统学初探*

粒毛盘菌属包括晶杯菌科中子囊盘表面具有毛状物,毛状物全表面具有颗粒状纹饰以及外囊盘被结构为矩胞组织的部分种类,种间形态解剖结构多样,研究采用ITS15.8S rDNAITS2序列分析的方法探讨该属种间的系统发育关系。在供试的粒毛盘菌15个分类单元中,14个以89%的支持强度值相聚在一起,其中Lachnum clandestinum与 L. fuscescens关系最近,其支持强度值为100%;其次为L. controversum 与L. spartinae,其支持强度值为97%;而姊妹群L. euterpes,L. pteridophyllum,L. singerianum和L. lushanense彼此关系较远,其支持强度值均小于50%;L. sclerotii位于系统发育树的最外侧,为供试15个分类单元中距离最远的一个,结果表明粒毛盘菌属可能是多起源的。     

THE RIBOSOMAL RNA OF HAMSTER-MOUSE HYBRID CELLS

The ribosomal RNA (rRNA) of a series of hamster-mouse somatic cell hybrids was studied. Mouse 28S rRNA was separated from its hamster counterpart by a two-step procedure involving sucrose gradient centrifugation of ribosomes and polyacrylamide gel electrophoresis of rRNA. Both hamster and mouse types of rRNA were synthesized in the 11 hybrids tested, including hybrids containing only about one-half the haploid number of either mouse or hamster chromosomes. It appears that, for both hamster and mouse rRNA, when the chromosomes of one species constituted the majority of the chromosomes of a hybrid, a disproportionately higher percentage of rRNA of that species was present in the hybrid. Some hybrid clones, having a majority of mouse chromosomes, had a mouse rRNA cell concentration approximately four to five times higher than the concentration expected from linear extrapolation of the value found for the mouse parental cell line.     

THE PHYLOGENY OF CAULERPA BASED ON RDNA INTERNAL TRANSCRIBED SPACER SEQUENCES

Phylogenetic hypotheses for the pantropical marine green algal genus, Caulerpa , were inferred based on analyses of nuclear-encoded rDNA internal transcribed spacer (ITS) sequences. Results of these analyses were used to assess the correspondence between rDNA phylogeny and traditional sectional taxonomy, to identify synapomorphic morphological characters (including assimilator morphology and chloroplast ultrastructure), and to examine marine biogeographic hypotheses for the genus. Ribosomal DNA ITS sequences were aligned for thirty-three species and intraspecific taxa of Caulerpa. Results indicate limited correspondence between phylogeny and sectional taxonomy for the genus, (e.g., the sections Filicoideae and Sedoideae were not monophyletic). In contrast, chloroplast morphology could be mapped to the tree topology with limited homoplasy. Pantropical isolates of the filicoidean species, Caulerpa sertularioides and Caulerpa mexicana each formed monophyletic groups. Caulerpa reyesii was included as a derived taxon within the Caulerpa taxifolia clade, suggesting that these species were conspecific and affirmed the lack of correspondence between phylogeny and assimilator morphology. Isolates and various intraspecific taxa of Caulerpa racemosa did not form a monophyletic group. Instead, these taxa formed a heterogeneous assemblage with other sedoidean and filicoidean taxa. Within the C. sertularioides clade, Caribbean and Atlantic isolates formed a basal paraphyletic group, whereas eastern and western Pacific isolates formed a more derived monophyletic group. Therefore, these results are not consistent with an Indo-West Pacific origin of this species.     

PHYLOGENY OF AUREOCOCCUS ANOPHAGEFFERENS AND A MORPHOLOGICALLY SIMILAR BLOOM-FORMING ALGA FROM TEXAS AS DETERMINED BY 18S RIBOSOMAL RNA SEQUENCE ANALYSIS1

The 18S ribosomal RNA genes from isolates of the east coast “brown tide” alga Aureococcus anophagefferens (strain Pt-1) and the Texas “brown tide” alga (strain TBA-2) were sequenced and compared to the gene sequences of Pelagomonas calceolata, a member of the Pelagophyceae, and 10 other organisms. The genes of A. anophagefferens and strain TBA-2 consisted of 1814 and 2236 bases, respectively. The difference in length was largely due to a 423-base insert occurring in the gene of strain TBA-2. Excluding the insert, 93% of the bases of the aligned sequences were identical. Phylogenetic analyses were performed based on two different alignment refinement methods (eye refinement and Gatesy refinement). Trees inferred from the Jukes-Cantor distance matrices using the neighbor-joining method were similar for both alignment methods. In both trees, A. anophagefferens, strain TBA-2, and P. calceolata formed a monophyletic group with A. anophagefferens and P. calceolata being sister taxa and strain TBA-2 occurring on a deeper-rooted branch. Bootstrap data sets for both alignment methods gave strong support for the Pelagophyceae group and the branches within that group. Parsimony analyses using the two alignments gave one tree for the eye-refined alignment and two trees for the Gatesy method. All three trees had nearly the same topology as the trees inferred from the distance method. In addition, the Pelagophyceae group and the branches within that group were supported by bootstrap analyses and decay indices. Based on the available data, A. anophagefferens and strain TBA-2 should be placed in the Pelagophyceae but not in the same order and family as P. calceolata.     

乌鳢肝5S rRNA的核苷酸序列

应用Peattie,Maxum等化学裂解法,辅以酶解直读法等测定了乌醴(Ophiocephalus argus)肝5S rRNA的核苷酸序列;与已知的虹鳟鱼和纵带泥鳅5S rRNA序列比较,发现它们之间的核苷酸序列具有高度的保守性.利用其一级结构所给出的信息,初步提出二级结构模型.     

从幼苗形态学特征探讨红豆杉科各属间的系统演化

本文根据幼苗的形态学特征,尤其是子叶的结构、说明在红豆杉科中最原始的属是榧树属,其幼苗为留土萌发,植株粗壮;子叶肥厚,有吸收功能,叶肉不分化,其细胞中充满淀粉粒：维管束在子叶的上部或顶部为单束2条,下部合并成双束1条。其次是穗花杉属,幼苗为出土萌发,植株粗壮,下胚轴的下部肥厚;子叶稍肉质,叶肉不分化,质体淡绿,有一定的光合功能,但主要是积累淀粉,维管束双束1条,在子叶的顶端趋于分裂。最进化的是红豆杉属和白豆杉属,可能还有澳洲红豆杉属,其幼苗为出土萌发,植株纤细;子叶薄,叶状,叶肉分化成栅栏和海绵组织,维管束单束1条。本科中族的划分和属的系统排列,从原始到进化,应该是：族1．榧树族(1．榧树属);族2．穗花杉族(2．穗花杉属);族3．红豆杉族(3．澳洲红豆杉属,4．红豆杉属,5．白豆杉属)。