Molecular Phylogeny of Conjugating Green Algae (Zygnemophyceae, Streptophyta) Inferred from SSU rDNA Sequence Comparisons

Abstract Nuclear-encoded SSU rDNA sequences have been obtained from 64 strains of conjugating green algae (Zygnemophyceae, Streptophyta, Viridiplantae). Molecular phylogenetic analyses of 90 SSU rDNA sequences of Viridiplantae (inciuding 78 from the Zygnemophyceae) were performed using complex evolutionary models and maximum likelihood, distance, and maximum parsimony methods. The significance of the results was tested by bootstrap analyses, deletion of long-branch taxa, relative rate tests, and Kishino–Hasegawa tests with user-defined trees. All results support the monophyly of the class Zygnemophyceae and of the order Desmidiales. The second order, Zygnematales, forms a series of early-branching clades in paraphyletic succession, with the two traditional families Mesotaeniaceae and Zygnemataceae not recovered as lineages. Instead, a long-branch Spirogyra/Sirogonium clade and the later-diverging Netrium and Roya clades represent independent clades. Within the order Desmidiales, the families Gonatozygaceae and Closteriaceae are monophyletic, whereas the Peniaceae (represented only by Penium margaritaceum) and the Desmidiaceae represent a single weakly supported lineage. Within the Desmidiaceae short internal branches and varying rates of sequence evolution among taxa reduce the phylogenetic resolution significantly. The SSU rDNA-based phylogeny is largely congruent with a published analysis of the rbcL phylogeny of the Zygnemophyceae (McCourt et al. 2000) and is also in general agreement with classification schemes based on cell wall ultrastructure. The extended taxon sampling at the subgenus level provides solid evidence that many genera in the Zygnemophyceae are not monophyletic and that the genus concept in the group needs to be revised.     

Phylogenetic Relationships of Scenedesmus and Scenedesmus-like Coccoid Green Algae as Inferred from ITS-2 rDNA Sequence Comparisons

Abstract: Analyses of ITS-2 ribosomal DNA from Scenedesmus and Scenedesmus-like strains showed that this molecule is well suited for resolving evolutionary relationships at various taxo-nomic levels. The analyses clearly suggested the separation of the investigated strains into two groups which corresponded to the "subgenera" Desmodesmus and Scenedesmus/Acutodesmus . No clear distinction between Acutodesmus and Scenedesmus was seen. It is proposed to regard both groups as distinct genera, Desmodesmus gen. nov. and Scenedesmus sensu strictu , and to merge Acutodesmus into Scenedesmus . Monophyly of both genera, Scenedesmus and Desmodesmus , is further supported by certain secondary structure features of ITS-2. The relationships resolved by the ITS-2 analyses are congruent with findings from cell wall ultrastructure, but not with those from other morphological features such as cell wall surface structures or cell shape. Didymocystis inermis and Dicloster acuatus , though somewhat similar in vegetative cell morphology to species of Scenedesmus and Desmodesmus , were seen as members of independent genera because of substantial differences in primary structure and length variations in ITS-2 when compared with each other and the latter two genera.     

Nitrogen Limitation and Slow Drying Induce Desiccation Tolerance in Conjugating Green Algae (Zygnematophyceae,Streptophyta) from Polar Habitats

Background

Filamentous Zygnematophyceae are typical components of algal mats in the polar hydro-terrestrial environment. Under field conditions, they form senescent vegetative cells, designated as pre-akinetes, which are tolerant to desiccation and osmotic stress.

Key Findings

Pre-akinete formation and desiccation tolerance was investigated experimentally under monitored laboratory conditions in four strains of Arctic and Antarctic isolates with vegetative Zygnema sp. morphology. Phylogenetic analyses of rbcL sequences revealed one Arctic strain as genus Zygnemopsis, phylogenetically distant from the closely related Zygnema strains. Algae were cultivated in liquid or on solidified medium (9 weeks), supplemented with or lacking nitrogen. Nitrogen-free cultures (liquid as well as solidified) consisted of well-developed pre-akinetes after this period. Desiccation experiments were performed at three different drying rates (rapid: 10% relative humidity, slow: 86% rh and very slow); viability, effective quantum yield of PS II, visual and ultrastructural changes were monitored. Recovery and viability of pre-akinetes were clearly dependent on the drying rate: slower desiccation led to higher levels of survival. Pre-akinetes survived rapid drying after acclimation by very slow desiccation.

Conclusions

The formation of pre-akinetes in polar Zygnema spp. and Zygnemopsis sp. is induced by nitrogen limitation. Pre-akinetes, modified vegetative cells, rather than specialized stages of the life cycle, can be hardened by mild desiccation stress to survive rapid drying. Naturally hardened pre-akinetes play a key role in stress tolerance and dispersal under the extreme conditions of polar regions, where sexual reproduction and production of dormant stages is largely suppressed.     

The Phylogeny of the Families Lecanoraceae and Bacidiaceae (Lichenized Ascomycota) Inferred from Nuclear SSU rDNA Sequences

Abstract: The phylogeny of the families Lecanoraceae and Bacidiaceae (Lecanorales, Ascomycota) was investigated using 29 nuclear small subunit ribosomal DNA sequences, 9 of which were newly determined. The data set contained 368 variable characters, 234 of which were parsimony-informative. Phylogenetic estimations were performed with maximum parsimony and maximum likelihood optimality criteria. In the most parsimonious and most likely reconstructions, the Bacidiaceae sensu Hafellner 1988 forms a monophyletic group and the Lecanoraceae sensu Hafellner a paraphyletic group. The genera Tephromela and Scoliciosporum appear to belong outside these families. However, the hypothesis that the Lecanoraceae sensu Hafellner is monophyletic cannot be rejected, as indicated by a Kishino-Hasegawa test. Three hypotheses were rejected by Kishino-Hasegawa tests, viz. (1) that the Lecanoraceae and Bacidiaceae together form a monophyletic group; (2) that both the Lecanoraceae (incl. Scoliciosporum ) and Bacidiaceae (incl. Tephromela ) are monophyletic; and (3) that the ascus apex anatomy reflects phylogeny. The suborder Lecanorineae is paraphyletic unless the Stereocaulaceae and Cladoniaceae are included. One or both of the Bacidia and Lecanora types of ascus have probably evolved at least twice.     

Molecular Phylogeny of the Family Ophryscolecidae (Ciliophora,Litostomatea) Inferred from 18S rDNA Sequences

The 18S rDNA was used to infer oral ciliature patterns of evolution within the family Ophryoscolecidae, with the addition of five new sequences of ciliates from the genus Ostracodinium. Our data confirmed the monophyly of the subfamilies Entodiniinae and Ophryoscolecinae, but more analysis would be required for the definition of the status of the subfamily Diplodiniinae. The oral infraciliature patterns reflect evolutionary divergence in the family Ophryscolecidae, observing monophyly on Entodinium‐type, Diplodinium‐type, Ostracodinium‐type, Epidinium‐type, and Ophryoscolex‐type. The ancestral infraciliature of Entodinium‐type cannot be proven, however, the position of Entodinium‐type showed closer of Diplodinium‐type than Ophryoscolex‐type, corroborating previous studies using morphological characters. The observed inconsistencies reflect the need to increase the number of 18S rDNA sequences to family Ophryoscolecidae and investigate the evolution of this group using other molecular markers.     

基于SSU序列的串珠藻目植物系统发育分析

通过18S rDNA基因(SSU)序列,构建了串珠藻目植物的系统发育关系.结果显示:SSU基因序列片段长度为1 871 bp,核苷酸变异位点有709个,占序列长度的38％;其中简约信息位点有169个,占序列长度的9％.用最大似然法、邻接法和贝叶斯法构建的系统树拓扑结构基本一致,都显示红索藻目的2个属独立于串珠藻目成单独分支,支持红索藻目的建立;胶串珠藻独立于其他串珠藻组植物,支持将其单独分组;数据同时支持将扭曲组和杂生组合并,建立Kumanoa属;但多芒组、绿色组、沼生组等因分子序列数据涉及的种类较少,其系统关系的确定还需要更多的证据.     

基于线粒体16S rDNA基因的天牛科部分种类分子系统学研究(鞘翅目:天牛科)

研究测定了天牛科3亚科9种昆虫线粒体16S rDNA基因约500bp的序列,对序列的碱基组成和遗传距离进行分析。并基于16S rDNA基因序列数据,采用邻接法(NJ)和最大简约法(MP)分析天牛科3亚科分子系统发育关系。研究结果表明,2种方法得到的分子系统树其分支结果一致,可将内群分为2个分支,第1个分支包括沟胫天牛亚科和天牛亚科;第2个分支包括花天牛亚科。16SrDNA基因对天牛科亚科间系统发育的研究是有价值的。     

Phylogeny of the Prolecithophora (Platyhelminthes) Inferred from 18S rDNA Sequences

Complete nuclear 18S rDNA sequences from 14 species of the Prolecithophora were obtained and used, in combination with literature data, to generate the first parsimony-based hypothesis of the phylogeny of the order Prolecithophora (Platyhelminthes). Bootstrap, parsimony jack-knife, and Bremer support values were computed and compared. The monophyly of the Prolecithophora sensu stricto and the family Plagiostomidae is strongly supported. The taxa Separata, Combinata, and Plagiostomum are shown to be nonmonophyletic. Cylindrostomidae and Ulianinidae are transferred to Pseudostomidae. The Urastomidae is not part of the Prolecithophora.     

Molecular Phylogeny of the Suborder Leucodontineae (Musci; Leucodontales) Inferred from rbcL Sequence Data

rbcL sequence data (1324 bp on average). Our analyses indicate (1) that Antitrichia is distantly related to the other members of Leucodontaceae and should be excluded from the family, (2) that Cryphaeaceae form a monophyletic clade, not with Anomodontaceae and Leptodontaceae, but with Leucodontaceae, refuting the placement of Leucodontaceae and Cryphaeaceae in different superfamilies, (3) that Forsstroemia, variously classified in Leucodontaceae, Cryphaeaceae or Leptodontaceae, forms a monophyletic clade with Neckera (Neckeraceae), and (4) that the presumed monophyly of Anomodon and that of Anomodontaceae are not supported. Received 18 September 1999/ Accepted in revised form 27 December 1999     

Phylogeny and Molecular Evolution of the Green Algae

The green lineage (Viridiplantae) comprises the green algae and their descendants the land plants, and is one of the major groups of oxygenic photosynthetic eukaryotes. Current hypotheses posit the early divergence of two discrete clades from an ancestral green flagellate. One clade, the Chlorophyta, comprises the early diverging prasinophytes, which gave rise to the core chlorophytes. The other clade, the Streptophyta, includes the charophyte green algae from which the land plants evolved. Multi-marker and genome scale phylogenetic studies have greatly improved our understanding of broad-scale relationships of the green lineage, yet many questions persist, including the branching orders of the prasinophyte lineages, the relationships among core chlorophyte clades (Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae), and the relationships among the streptophytes. Current phylogenetic hypotheses provide an evolutionary framework for molecular evolutionary studies and comparative genomics. This review summarizes our current understanding of organelle genome evolution in the green algae, genomic insights into the ecology of oceanic picoplanktonic prasinophytes, molecular mechanisms underlying the evolution of complexity in volvocine green algae, and the evolution of genetic codes and the translational apparatus in green seaweeds. Finally, we discuss molecular evolution in the streptophyte lineage, emphasizing the genetic facilitation of land plant origins.     

Phylogeny of the Centrohelida Inferred from SSU rRNA, Tubulins, and Actin Genes

Amoeboid protists are major targets of recent molecular phylogeny in connection with reconstruction of global phylogeny of eukaryotes as well as the search for the root of eukaryotes. The Centrohelida are one of the major groups of Heliozoa, classified in the Actinopodida, whose evolutionary position is not well understood. To clarify the relationships between the Centrohelida and other eukaryotes, we sequenced SSU rRNA, α-tubulin, and β-tubulin genes from a centroheliozoan protist, Raphidiophrys contractilis. The SSU rRNA phylogeny showed that the Centrohelida are not closely related to other heliozoan groups, Actinophryida, Desmothoracida, or Taxopodida. Maximum likelihood analyses of the combined phylogeny using a concatenate model for an α- + β-tubulin + actin data set, and a separate model for SSU rRNA, α- and β-tubulin, and actin gene data sets revealed the best tree, in which the Centrohelida have a closer relationship to Rhodophyta than to other major eukaryotic groups. However, both weighted Shimodaira–Hasegawa and approximately unbiased tests for the concatenate protein phylogeny did not reject alternative trees in which Centrohelida were constrained to be sisters to the Amoebozoa. Moreover, alternative trees in which Centrohelida were placed at the node branching before and after Amoebozoa or Viridiplantae were not rejected by the WSH tests. These results narrowed the possibilities for the position of Centrohelida to a sister to the Rhodophyta, to the Amoebozoa, or to an independent branch between the branchings of Amoebozoa and Rhodophyta (or possibly Plantae) at the basal position within the bikonts clade in the eukaryotic tree. [Reviewing Editor: Dr. Martin Kreitman]     

基于COI基因序列的九种真蝽属昆虫的分子系统学研究(半翅目:蝽科)

通过对真蝽属Pentatoma 9种昆虫线粒体COI基因约798bp的序列进行分子进化分析,并以同蝽科宽铗同蝽Acanthosoma labiduroides为外群,采用最大简约法、最大似然法和邻接法构建了分子系统树,来探讨真蝽属的系统发育关系.研究结果支持褐真蝽群P. semiannulata-group的划分,绿角真蝽Pentatoma viridicornuta应划归到褐真蝽群P. Semiannulata-group;红足真蝽群中的角肩真蝽P. angulata与红足真蝽P. rufipes遗传距离较小,它们是否为1个物种值得关注;真蝽属各群之间的系统发育关系以及是否可分为3个属值得进一步研究.     

Phylogeny of Saururaceae Inferred from matR Sequence Data

基于线粒体matR 基因序列初步探讨三白草科的系统发育 孟少武¹ 陈之端²李德铢¹梁汉兴¹      

Contributions to the Phylogeny of the Cyclophyllidea (Cestoda) Inferred from Mitochondrial 12S rDNA

A 314-bp fragment of the mitochondrial 12S rRNA gene from 21 cestodes species of eight families was synthesized by PCR with specially designed primers. These allowed amplification of parasite DNA without concomitant synthesis of host DNA. Phylogenetic trees were inferred from the sequence data using three methods (maximum parsimony, maximum likelihood, and Fitch–Margoliash). At the major nodes all three trees were similar. For the first time the genus Mesocestoides could be arranged into the Cyclophyllidea and a narrow relationship between the Mesocestoididae, Taeniidae, Hymenolepididae, Anoplocephalidae, and Dipylidiidae was shown. Members of the families Catenotaeniidae and a cluster of two families (Hymenolepididae and Dilepididae) form two monophyletic groups which derive prior to the remaining families of this phylogenetic study. A third and a fourth clear monophyletic group were formed by the Taeniidae and by the Mesocestoididae. A high degree of variation within the examined 304-bp fragment was observed between two isolates of Taenia taeniaeformis, supporting often discussed genetic heterogeneity within this species. In contrast, only one nucleotide exchange was found in 23 isolates of Echinococcus multilocularis of various geographic origin, indicating that this species is genetically homogenous. Received: 1 October 1997 / Accepted: 4 December 1997     

Molecular Phylogeny of Nycticebus Inferred from Mitochondrial Genes

Researchers are still discussing the classification of Nycticebus. We established a molecular phylogeny covering all recognized taxa in Nycticebus to provide information for further evaluation. We sequenced partial D-loop (ca. 390 bp) and cytochrome b genes (425 bp) from 22 specimens. We separated most of the major groups except for some mixing of Nycticebus. coucang coucang and N. bengalensis. Nycticebus pygmaeus diverged earlier from the ancestral stock than the other taxa. Nycticebus coucang menagensis was well discriminated from N. c. coucang. It may be possible to explain the mixing of Nycticebus coucang coucang and N. bengalensis by the hybridization between the 2 groups in the field. Although our data did not provide direct evidence for or against the new proposal that Nycticebus coucang javanicus be raised to the rank of a distinct species (N. javanicus), we have good evidence for regarding N. c. menagensis as a species.Jing-Hua Chen and Deng Pan made equal contributions to the work.     

Phylogenetic Position of Psalteriomonas lanterna Deduced from the SSU rDNA Sequence

ABSTRACT. The small subunit ribosomal DNA sequence (SSU rDNA) of the microaerophilic free-living amoeboflagellate Psalteriomonas lanterna has been sequenced and analyzed. The gene is 1,945 bp long and has a G + C content of 33.4%. Based upon ultrastructural studies, P. lanterna has been placed in the class Lyromonadea within the phylum Percolozoa Cavalier-Smith, 1991. However, based upon cytological characteristics, this microaerophilic free-living amoeboflagellate appears to be very primitive. It shares certain characteristics in common with some archezoans, i.e. it lacks mitochondria and dictyosomes but contains hydrogenosomes. Despite sharing these characteristics with the amitochondriate taxa, P. lanterna is not related to any of these taxa but instead to the Vahlkampfiidae. Therefore, we used primary sequence data and the secondary structure of the SSU rDNA gene to determine the placement P. lanterna in the phylogenetic tree. Our analyses showed that P. lanterna groups as a sister taxon to the Vahlkampfiidae but probably diverged from them quite early.