PHYLOGENETIC RELATIONSHIPS OF SELECTED EUGLENOID GENERA BASED ON MORPHOLOGICAL AND MOLECULAR DATA1

The small subunit rRNA (SSU rRNA) coding regions sequenced from the euglenoids Petalomonas cantuscygni, Peranema trichophorum, and Khawkinea quartana were used to assess the phylogenetic relationships of these genera within the Euglenozoa. Phylogenies derived from distance, parsimony, and maximum likelihood methods infer that the euglenoids and kinetoplastids form sister clades within a monophyletic assemblage. Distances representative of closely related lineages separate the genera within the Kinetoplastida, whereas larger distance values separate genera within the euglenoid assemblage. The results of the morphological and molecular studies suggest that phagotrophy arose early in the euglenozoan lineage with the subsequent acquisition of phototrophy, osmotrophy, and parasitism. Phagotrophic euglenoids with a pellicle composed of longitudinal strips appear to have diverged prior to genera with helically arranged strips. This study suggests that the hypothetical ancestor to the Euglenozoa was a phagotroph with two flagella, both containing paraxonemal rods. Furthermore, its basal bodies contained proximal cartwheels, were connected by a prominent fiber, and were anchored with three asymmetrically arranged flagellar roots.     

DIVERSITY AND PHYLOGENETIC PLACEMENT OF BRACTEACOCCUS TEREG (CHLOROPHYCEAE,CHLOROPHYTA) BASED ON 18S RIBOSOMAL RNA GENE SEQUENCE DATA1

Sequence data from the nuclear small-subunit ribosomal RNA gene was obtained for nine strains of Bracteacoccus Tereg, representing at least five morphological species and four distinct geographic locations. These, along with sequence data from two additional chlorophycean taxa, Spongiochloris spongiosa Starr and Ascochloris multinucleata Bold et MacEntee, and 48 published sequences from green algal taxa, were used to determine the phylogenetic placement of Bracteacoccus with respect to other chlorophycean green algae. Results support the monophyly of Bracteacoccus strains, contrasting with patterns observed so far for many other coccoid green algae. The range of variation among Bracteacoccus strains is similar to that of other congeners. Basal body orientation in Bracteacoccus has been interpreted as clockwise; however, the 18S data point to a relationship between Bracteacoccus and taxa with the directly opposed configuration of the flagellar apparatus. No close relationship was found to the multinucleated green coccoids with clockwise orientation of basal bodies, such as Spongiochloris, or to those with parallel basal bodies, such as Spermatozopsis. However, 18S data confirm that the motile and vegetative cells of Bracteacoccus are structurally distinct from the representatives of sphaeroplealean families currently studied. It is premature to reclassify Bracteacoccus until 18S comparisons can be made with additional sphaeroplealean taxa and with algae with similar flagellar structure such as Dictyochloris and Heterochlamydomonas.     

基于18S rRNA基因序列分析唇口目苔藓动物主要类群的系统发生关系

对隶属于3亚目、5次目、20科、23属共25个种类的唇口目(裸唇纲)苔藓虫18S rRNA基因部分序列进行了序列测定.结合从GenBank中获得的该类群其它7个种类的18S rRNA基因同源序列,以序列分析软件对其序列组成和变异进行了比较分析;同时,以羽苔虫(被唇纲)和管孔苔虫(窄唇纲)为外类群,以邻接法和最大简约法重建了它们的系统发生树,分析了该目主要类群系统发生关系.序列分析结果显示:经比对后序列长度为884 bp,其中保守位点241个,可变位点643个,简约信息位点357个;A,T,C和G 4碱基平均含量分别为23.8%、22.8%、24.4%和28.9%.分子系统树表明:本研究所有有囊类构成1个单系群,其中檐胞次目的几种苔虫位于皮壳次目内部;无囊类形成1个多系群,其中的亚目级(新唇口亚目)和次目级分类阶元(枝室次目、假软壁次目和隐壁次目)也都为多系发生,这些结果与前人的分子系统学研究结果大体一致,而与传统的形态分类体系间存在明显的冲突.     

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.     

基于16S rRNA基因序列探讨中国粉蛉科的系统发育关系

本研究测定了粉蛉科Coniopterygidae9属15种昆虫16SrRNA基因部分序列,对序列的碱基组成、转换/颠换比率、遗传距离、变异位点等进行分析。基于16SrRNA基因序列数据,分别采用邻接法（NJ）、最大简约法（MP）和最大相似法（ML）建立粉蛉科分子系统发育关系。研究结果表明：粉蛉亚科的粉蛉属Coniopteryx与重粉蛉属Semilalis是姊妹群,（虫齿）粉蛉属Conwentzia较前二者原始;囊粉蛉亚科的卷粉蛉属Helicoconis和隐粉蛉属Cryptoscenea的亲缘关系较近。曲粉蛉属Coniocompsa和异粉蛉属Heteroconis聚类在一起,但自展值较低。瑕粉蛉属Spiloconis和囊粉蛉属Aleuropteryx的位置在囊粉蛉亚科中不够稳定。     

凤蝶亚科(凤蝶科,鳞翅目)16S rRNA基因的分子系统发生分析

对15种凤蝶亚科蝶类线粒体16S rRNA基因部分序列进行了测定,并结合GenBank中其它相关类群的序列,采用邻接法(NJ)、最大简约法(MP)、最大似然法(ML)和贝叶斯法构建凤蝶亚科的分子系统树,探讨该亚科各类群间的系统发生关系.结果表明,燕凤蝶族构成凤蝶亚科蝶类系统树基部的一个独立分支;燕凤蝶族和裳凤蝶族为单系发生,且裳凤蝶族聚在凤蝶族内部;喙凤蝶族的单系性尚不能确定.综合分子系统学、形态学及寄主植物等相关证据,推测斑凤蝶类为凤蝶族中早期分化的一支;较之裳凤蝶类,斑凤蝶类可能更早从二者最近的共同祖先中分化出来.     

PHYLOGENETIC AFFINITIES OF CRYSONEPHELE PALUSTRIS (CHRYSOPHYCEAE) BASED ON INFERRED NUCLEAR SMALL-SUBUNIT RIBOSOMAL RNA SEQUENCE

The nuclear small-subunit ribosomal DNA sequence was determined from the colonial chromophytic alga Chrysonephele palustris Pipes, Tyler, et Leedale using polymerase chain reaction methods. The inferred ribosomal RNA sequence was included in a multiple alignment, containing heterokont chromophytes, and subjected to molecular systematic analyses in order to determine the phylogenetic relationships of this alga . Chrysonephele palustris grouped within the Chrysophyceae and not in an intermediate position between the Chrysophyceae and Eustigmatophyceae, suggesting that Chrysonephele is not a phylogenetic link between these algal classes .     

介形类系统分类与起源演化的形态、分子和化石证据

介形类(Ostracoda)因其丰富的化石记录和广布的海陆现生代表类群,而被认为是进化生物学中研究生物多样性产生机制和演变历程的颇具潜力的重要模式生物。介形类在甲壳亚门中的谱系发生位置、起源及其内部各类群间的系统关系还存在诸多争议。基于其体制构造的形态学特征,介形类被归入甲壳亚门下的颚足纲(Maxillopoda),但来自18S rDNA序列数据分析却显示Maxillopoda不是单系群。基于化石记录和壳体形态特征,高肌虫(Bradoriida)长期以来被认为是介形类的一个祖先类群,但保存有软躯体的早寒武世化石的研究表明,Bradoriida不是介形类甚至可能也不属于甲壳类。不同的研究者所强调的壳体和肢体形态特征各异,导致介形类最大的现生类群速足目(Podocopida)的四个超科之间的关系也存在诸多推测。壳体和肢体特征在系统演化意义上的不兼容,需要分子生物学等证据的介入。分子、形态和化石证据的积累及各种信息整合是系统演化研究的必然趋势。     

A PHYLOGENETIC ANALYSIS OF THE SYNUROPHYCEAE USING MOLECULAR DATA AND SCALE CASE MORPHOLOGY

The phylogeny of the Synurophyceae was investigated by parsimony analysis of scale case characters and small-sub unit (18S) ribosomal RNA (rRNA) sequence data. Analysis of 1 eustigmatophycean (outgroup), 3 chrysophycean, and 10 synurophycean 18S rRNA sequences corroborated the inference from ultrastructural information that the Synurophyceae is a monophyletic assemblage . Tessellaria vol-vocina, which had been tentatively proposed as a member of the Synurophyceae, was confirmed as the earliest lineage within the Synurophyceae by both the molecular analysis and an evaluation of published ultrastructural data. A second set of analyses investigated the relationships among Tessellaria volvocina, 6 Synura species, and 10 Mallomonas species/varieties, with particular reference to the validity of current classifications of the Synurophyceae and the characters upon which they are based. The molecular and scale case phylogenies were not totally resolved but were largely congruent. The data sets were combined to produce another phylogeny, which showed greater resolution. The combined phylogeny weakly supported our representatives of Synura and Mallomonas as monophyletic groupings and also upheld several of the sections within these genera that are recognized by current classifications. However, some changes to the classification and delineation of these genera are recommended and predicted. Both our 18S rRNA sequence and scale case data sets were more appropriate for examining the branching order among the more closely related text rather than resolving the deeper branching points of the synurophycean phylogeny .     

BIOGEOGRAPHYOF BATRACHOSPERMUM GELATINOSUM (BATRACHOSPERMALES,RHODOPHYTA) IN NORTH AMERICA BASED ON MOLECULAR AND MORPHOLOGICAL DATA1

Fifteen populations of the widespread fieshwater red alga Batrachospermum gelatinosum (L.) De Candolle were sampled throughout the geographic range in North America from central Alabama, U.S.A. (33° N), to Ellesmere Island, Northwest Territories (NWT), Canada (80° N). Analysis of ribosomal DNA internal transcribed spacer (ITS) 1 and 2 sequences yielded a parsimony tree with a large polytomy consisting of most populations plus a branch with one Nova Scotia and two NWT populations. The nucleotide variation, both within the polytomy and within the branch, was small (< 1%). The sequence divergence between the branch and polytomy was 3%. The lengths of the ITS 1 and 2 sequences of B. gelatinosum, 216–229 and 448–458 base pairs, respectively, fall within the very broad ranges reported for other red algae. The cluster analysis of 11 morphometric characteristics revealed three groupings of populations, partly based on geographic distribution. All tundra, eastern boreal forest, and mid-western hemlock-hardwood populations were in one grouping, whereas the deciduous forest, coastal plain, and eastern hemlock-hardwood populations were in a second. How ever, one deciduous forest population from Rhode Island, U.S.A. was unassociated. There was considerable overlap in morphometric characteristics among the three groupings. Based on this fact and the relatively small nucleotade variation in ITS sequences, we conclude that B. gelatinosum is a morphologically variable and geographically widespread species that is a valid taxonomic entity.     

PHYLOGENETIC ANALYSIS OF YAMAGISHLELLA AND PLATYDORINA (VOLVOCACEAE,CHLOROPHYTA) BASED ON rbcL GENE SEQUENCES1

Yamagishiella, based on Pandorina unicocca Rayburn et Starr, is distinguished from Eudorina by its isogamous sexual reproduction, whereas Platydorina exhibits anisogamous sexual reproduction. In the present study, we sequenced the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) genes from five Japanese and North American strains of Y. unicocca (Rayburn et Starr) Nozaki, two Platydorina caudata Kofoid strains, and two strains of Eudorina unicocca G. M. Smith, as well as eight related colonial and unicellular species. Phylogenetic trees were constructed based on these sequence data and on previously published rbcL gene sequences from 23 volvocalean species in order to deduce phylogenetic relationships within the colonial Volvocales, with particular regard to the phylogenetic positions and status of the genera Yamagishiella and Platydorina. Two robust monophyletic groups of the anisogamous/oogamous volvocacean species were resolved in the maximum-parsimony tree as well as in the neighbor-joining distance tree. One of the two groups comprises three species of Volvox section Volvox, whereas the other is composed of other sections of Volvox as well as of all the species of Eudorina and Pleodorina. Platydorina, however, was positioned outside these two monopliyletic groups. Therefore, derivation of the Platydorina lineage may be earlier than that of such anisogamous/oogamous groups, or orgin of “anisogamy with sperm packets” in Platydorina may be independent of sperm packet evolution in Eudorina, Pleodorina, and Volvox. It was also resolved with high bootstrap values that all of the Y. unicocca strains form a monophyletic group positioned outside the large monophyletic group including Eudorina and Pleodorina. These reject the possibility of the reverse evolution of isogamy from anisogamy to give rise to Yamagishiella within the lineage of Eudorina.     

A PHYLOGENETIC STUDY OF THE CORALLINALES (RHODOPHYTA) BASED ON NUCLEAR SMALL-SUBUNIT rRNA GENE SEQUENCES

Conflicting classifications for the Corallinales were tested by analyzing partial sequences for the nuclear small-subunit ribosomal RNA (SSU) gene of 35 species of coralline algae. Parsimony and likelihood analyses of these data yielded congruent hypotheses that are inconsistent with classifications for the group that include as many as eight subfamilies. Four major clades are resolved within the order, including the early-diverging Sporolithaceae as well as the Melobesioideae and Corallinoideae. The fourth clade, which is supported robustly, includes both nongeniculate and geniculate species classified in the subfamilies Mastophoroideae, Metagoniolithoideae, Lithophylloideae, and Amphiroideae. Molecular and morphological data support the proposal that the latter two subfamilies are sister taxa. Although relationships among some genera are not resolved clearly, the order of branching of taxa among and within the four principal lineages is concordant with paleontological evidence for the group. Relationships inferred among genera within each of the clades is discussed. Seven morphological characters delimiting higher taxonomic groups within the order were combined with the sequence data, analyzed, and optimized onto the resulting tree(s). Except for the presence or absence of genicula, all other characters were found to be phylogenetically informative. Genicula are nonhomologous structures that evolved independently in the Amphiroideae, Corallinoideae, and Metagoniolithoideae. The phenetic practice of separating coralline algae into two categories solely on the basis of the presence or absence of genicula does not accurately reflect the evolutionary history of the group.     

CHARACTERIZATION AND MOLECULAR PHYLOGENYOF A PROTEIN KINASE cDNA FROM THE DINOFLAGELLATE GONYAULAX (DINOPHYCEAE)1

Degenerate primers corresponding to conserved protein kinase motifs were used to amplify potential kinase DNA fragments from a Gonyaulax polyedra Stein cDNA library using PCR. One PCR fragment, potentially encoding a CAMP-dependent protein kinase, was used as a probe to isolate a near full-length cDNA from the library. The nucleic acid sequence of the entire cDNA clone had a high homology to the catalytic subunit of cAMP-dependent protein kinase (cAPK subfamily and affiliated members. Northern blot analysis showed that the corresponding mRNA had a size (about 1.4 kb) and a relative high abundance consistent with a cAPK homologue. Southern blot analysis showed that while there are roughly 30 copies of the kinase gene per genome, the pattern of restriction fragments is inconsistent with the hypothesis of a large gene family. Phylogenetic analyses comparing the deduced amino acid sequence from the Gonyaulax cDNA with other cAPK sequences place Gonyaulax close to the slime mold Dictyostelium discoideum. This is the first phylogenetic analysis of dinoflagellates based on protein sequence, and the results are in agreement with similar analyses based on rRNA sequences.     

PHYLOGENETIC RELATIONSHIPS OF THE FRESHWATER ALGA BOLDIA ERYTHROSIPHON (COMPSOPOGONALES, RHODOPHYTA) BASED ON 18S rRNA GENE SEQUENCES

The nuclear small-subunit ribosomal DNA sequence from the freshwater red alga Boldia erythrosiphon Herndon emend Howard et Parker was determined. Phylogenetic analysis confirms the positioning of this species within the bangiophycidean order of the Compsopogonales. The results strongly suggest that occupation of freshwater habitats by marine red algae has happened at least twice during red algal evolution.     

PHYLOGENETIC POSITION OF BOTRYOCOCCUS BRAUNII (CHLOROPHYCEAE) BASED ON SMALL SUBUNIT RIBOSOMAL RNA SEQUENCE DATA1

A small subunit ribosomal RNA (16S-like rRNA) in the hydrocarbon-rich microalga Botryococcus braunii Kützing (Chlorophyceae) was amplified using RNA polymerase chain reaction, and its sequence was determined. The sequence data of B. braunii were analyzed with those of several other algae in order to determine phylogenetic relationships among these algae. Phylogenetic analysis indicated B. braunii to be a member of the Chlorophyta and possibly related to Characium vacuolatum and Dunaliella parva.     

PHYLOGENYOF THE VLE-14 CHLAMYOMONAS (CHLOROPHYCEAE) GROUP: A STUDY OF 18S rRNA GENE SEQUENCES1

Comparative specificity of sporangial wall autolysins (i.e. vegetative lytic enzymes [VLE]) derived from sporulating cultures has been used to group Chlamydomonas taxa into 15 different VLE types. The VLE-14 group, including isolates of C. geitleri, C. noctigama, C. monoica, C. pinicola, C. terricoia, and C. hindakii, is one of the largest of these VLE groups. Genetic studies have shown that a number of the VLE-14 taxa are interfertile, albeit with little or reduced viability of progeny. A reevaluation of the VLE-14 group suggested that all members should be regarded as distinct isolates of C. noctigama. The present investigation tests the phylogenetic implications of the VLE evidence and examines the validity of the taxonomic reevaluation in a phylogenetic context by analysis of 18S rRNA gene sequence data. Results from analyses of the sequence data are consistent with an interpretation of the VLE evidence as indicative of monophyletic taxa. Phylogenetic analyses of the sequence data are also consistent with the taxonomic reevaluation and reidentification of the group. However, at least some of the VLE-14 isolates studied in this investigation fit criteria for distinct biologic or phylogenetic species. It is concluded that the VLE-14 taxa represent a very closely allied group that includes some isolates that are in the early stages of speciation ly reproductive isolation.     

PHYLOGENETIC POSITION OF THE OOCYSTACEAE (CHLOROPHYTA)

The complete 18S rRNA gene sequences of three Oocystis A. Braun species (Oocystaceae) and three other chlorococcal algae, Tetrachlorella alternans (G. M. Smith) Korš. (Scenedesmaceae), Makinoella tosaensis Okada (Scenedesmaceae), and Amphikrikos cf. nanus (Fott & Heynig) Hind. (Chlorellaceae) were determined and subjected to four different phylogenetic analysis algorithms. Independent of the reconstruction method, these taxa clustered together as a monophyletic group (Oocystaceae) within the Trebouxiophyceae. This result was supported by high bootstrap values. A comparison of morphological data with the phylogenetic reconstructions indicated that the evolution of Oocystaceae was accompanied by a reduction in the number of plastids. This study fully supports the taxonomic assignment of the Oocystaceae as a distinct family. The diacritic criterion that the cell walls are composed of several cellulose layers with perpendicular fibril orientations is in accordance with the molecular data.     

几种蚊虫线粒体DNA-16SrRNA序列及其相互关系的研究

测定我国尖音库蚊复合组4亚种（尖音库蚊、淡色库蚊、致倦库蚊和骚扰库蚊）、三带喙库蚊、白纹伊蚊和中华按蚊的线粒体DNA 16S rRNA基因（mtDNA-16S rRNA)序列,发现我国尖音库蚊复合组4亚种mtDNA-16S rRNA序列基本一致,长度为555bp(554bp),GC含量为25．41％。该序列与其他3种蚊虫在种间存在差异,与三带喙库蚊的种间差异为0．54％;与白纹伊蚊的种间差异为5．77％;与中华按蚊的种间差异为9．62％。分子系统关系分析表明该序列与传统分类系统的同属或同亚科种类近似性相一致。     

ANALYSIS OF CLONAL CULTURES OF THE BROWN TIDE ALGAE AUREOCOCCUS AND AUREOUMBRA (PELAGOPHYCEAE) USING 18S rRNA, rbcL, AND RUBISCO SPACER SEQUENCES

Variability among clonal cultures of the brown tide algae Aureococcus anophagefferens Hargraves et Sieburth and Aureoumbra lagunensis Stockwell, DeYoe, Hargraves et Johnson was examined by DNA sequence comparisons. Nuclear-encoded 18S rRNA and plastid-encoded rbc L gene sequences were determined for six Aureococcus strains. RUBISCO spacer sequences were determined for 14 strains of Aureococcus. No differences among Aureococcus strains were found in the DNA regions examined. The rbc L and RUBISCO spacer sequences for three Aureoumbra strains were identical but differed from those of Aureococcus. These data indicate that blooms of these species are comprised of cells that are very similar and also imply that Aureococcus and Aureoumbra do not contain varieties or cryptic species. Separate and combined phylogenetic analyses of the 18S rRNA and rbc L gene sequences were performed. Results confirm that the brown-tide-causing algae of Long Island Sound, New York ( Aureococcus ), and Laguna Madre, Texas ( Aureoumbra ), are best classified in separate genera within the Pelagophyceae. Phylogenetic trees place Aureococcus and Aureoumbra within the Pelagomonadales and Sarcinochrysidales, respectively.