A MOLECULAR ANALYSIS OF THE EUGLENOPHYTES USING SSU RDNA

Almost since the creation of the genus Euglena (Ehrenberg), the taxa assigned to it have been separated, split apart, and reorganized into new genera based on morphological relationships, resulting in the creation of the genera Phacus (Dujardin) , Lepocinclis (Perty) , Astasia (Pringsheim), and Khawkinea ( Jahn and McKibben) based on intuitive methods. In an effort to assess the validity of these genera, we have used small subunit (SSU) rDNA data to generate a phylogenetic framework for these genera, with particular attention to the genus Euglena . Using the conserved sequence areas, we performed a phylogenetic analysis using parsimony, maximum likelihood, and distance methods. These different criteria have resulted in trees of the same topology. The euglenoid clade was composed of phagotrophic euglenoids at the base, which gave rise to phototrophs that in turn gave rise to osmotrophs. Among the photosynthetic taxa, the biflagellate form diverged prior to the uniflagellate form. Additionally, the need for a revision in the taxonomy of some of these genera was demonstrated. Currently, taxa from the photosynthetic genera Euglena, Phacus, and Lepocinclis do not form monophyletic clades, but are intermixed with each other as well as with the osmotrophic taxa, Astasia and Khawkinea.     

Phylogenetic analyses of various euglenoid taxa (euglenozoa) based on 18s rdna sequence data

18S rRNA genes (SSU rDNA) of five newly sequenced species were used as molecular markers to infer phylogenetic relationships within the euglenoids. Two members of the order Euglenales ( Lepocinclis ovata Playfair , Phacus similis Christen), two of the order Eutreptiales ( Distigma proteus Ehrenberg, , D. curvata Pringsheim) and Gyropaigne lefévrei Bourelly et Georges of the order Rhabdomonadales were used in parsimony, maximum likelihood, and distance analyses. All trees derived from SSU rRNA data strongly supported the monophyletic origin of the Euglenozoa, with kinetoplastids as sister clade to the euglenoids and Petalomonas cantuscygni Cann et Pennick diverging at the base of the monophyletic euglenoid lineage. The data also supported the theory that phagotrophic euglenoids arose prior to osmotrophs and phototrophs. A lineage of Peranema trichophorum Ehrenberg and all sequenced Euglenales formed a sister clade to the osmotrophs. This suggests that the evolution of phototrophy within the euglenoids radiated from a single event.     

PHYLOGENY OF THE EUGLENOPHYTES: ANALYSIS USING SSU RDNA AND ULTRASTRUCTURAL CHARACTERS

The use of both molecular and morphological data to determine relationships among the euglenoids is vital for a complete understanding of their phylogeny, and the development of an accurate taxonomy. Analyses of the SSU (18S) rDNA from 12 euglenoid genera have resulted in tree topologies that are in agreement with many defining morphological characters. The euglenoid lineage is formed by phagotrophic euglenoids at its base, followed by the divergence of phototrophs that in-turn gave rise to osmotrophs. The photosynthetic lineage is anchored by euglenoids with two emergent flagella, Eutreptia and Eutreptiella , while the remainder of the lineage is composed of euglenoids with a single emergent flagellum. Among the photosynthetic euglenoids with a single emergent flagellum those that secrete mucilaginous stalks, Colacium , or form a lorica, Trachelomonas and Strombomonas , are closely associated. The remaining photosynthetic genera Euglena , Phacus , and Lepocinclis are intermixed with each other and the osmotrophic genera Astasia , and Khawkinea. Hence, they are not monophyletic, sensu Hennig. To reinforce molecular phylogenies, a robust morphological character database is necessary. For taxa with complex internal structures complete serial reconstruction is required. Serial reconstruction of the flagellar and feeding apparatuses in Ploeotia costata illustrate this necessity. Originally described as having both an MTR (Type I) and a Type II feeding apparatus, reconstruction has shown P. costata to have a single, Type II, feeding apparatus. Moreover, the Type II now appears to be an autapomorphy for Ploeotia species, while euglenoid feeding apparatuses, in toto, appear to form a continuum of structural types.     

PHYLOGENY OF PHAGOTROPHIC EUGLENIDS (EUGLENOZOA): A MOLECULAR APPROACH BASED ON CULTURE MATERIAL AND ENVIRONMENTAL SAMPLES1

Molecular studies based on small subunit (SSU) rDNA sequences addressing euglenid phylogeny hitherto suffered from the lack of available data about phagotrophic species. To extend the taxon sampling, SSU rRNA genes from species of seven genera of phagotrophic euglenids were investigated. Sequence analyses revealed an increasing genetic diversity among euglenid SSU rDNA sequences compared with other well‐known eukaryotic groups, reflecting an equally broad diversity of morphological characters among euglenid phagotrophs. Phylogenetic inference using standard parsimony and likelihood approaches as well as Bayesian inference and spectral analyses revealed no clear support for euglenid monophyly. Among phagotrophs, monophyly of Petalomonas cantuscygni and Notosolenus ostium, both comprising simple ingestion apparatuses, is strongly supported. A moderately supported clade comprises phototrophic euglenids and primary osmotrophic euglenids together with phagotrophs, exhibiting a primarily flexible pellicle composed of numerous helically arranged strips and a complex ingestion apparatus with two supporting rods and four curved vanes. Comparison of molecular and morphological data is used to demonstrate the difficulties to formulate a hypothesis about how the ingestion apparatus evolved in this group.     

Phylogeny and taxonomic revision of plastid-containing euglenophytes based on SSU rDNA sequence comparisons and synapomorphic signatures in the SSU rRNA secondary structure

Sequence comparisons and a revised classification of the Euglenophyceae were based on 92 new SSU rDNA sequences obtained from strains of Euglena, Astasia, Phacus, Trachelomonas, Colacium, Cryptoglena, Lepocinclis, Eutreptia, Eutreptiella and Tetreutreptia. Sequence data also provided molecular signatures for taxa from genus to class level in the SSU rRNA secondary structure, revealed by a novel approach (search for non-homoplasious synapomorphies) and used for taxonomic diagnoses. Photosynthetic euglenoids and secondary heterotrophs formed a clade, designated as Euglenophyceae (emend.) with two orders: Euglenales and Eutreptiales. The mostly marine Eutreptiales (Eutreptia, Eutreptiella; not Distigma) comprised taxa with two or four emergent flagella (the quadriflagellate Tetreutreptia was integrated within Eutreptiella). The Euglenales (freshwater genera with < or = one emergent flagellum) formed nine clades and two individual branches (single strains); however, only two clades were congruent with traditional genera: Trachelomonas (incl. Strombomonas) and Colacium. Euglena was polyphyletic and diverged into four independent clades (intermixed with Astasia, Khawkinea and Lepocinclis) and two individual branches (e.g. E. polymorpha). Phacus was also subdivided into Phacus s. str. and two combined lineages (mixed with Lepocinclis spp. or Cryptoglena). In consequence, Euglena (s. str.), Phacus and other genera were emended and one lineage (mixed Phacus/Lepocinclis-clade) was recognized as the previously neglected genus Monomorphina Mereschkowsky (1877). The sister clade of Phacus s. str. (mixed Euglena/Lepocinclis-clade) was identified as Lepocinclis Perty (emended).     

151 Phylogenetic Analysis of The Subgenus Euglena with Particualr Reference to the Type Species Euglena Viridis (Euglenophyceae)

Euglena viridis was first described by Antony van Leeuwenhoek in 1674. This taxon later became the type for the genus Euglena erected by Ehrenberg in 1838. The primary characters that distinguish this taxon are the single stellate chloroplast and spherical mucocysts. A number of related Euglena species are similar in size, bear one or two stellate plastids and possess spherical or spindle-shaped mucocysts. We conducted morphological and molecular studies on taxa in the subgenus Euglena (all of which bear stellate chloroplasts) and compared this to genera in the subgenus Calliglena (non-stellate chloroplasts). Morphologically the strains in subgenus Euglena were very similar, except for chloroplast number and mucocyst shape. The E. stellata group has one chloroplast and a distinctive spindle-shaped mucocyst; the E. geniculata group has two chloroplasts and spherical mucocysts; the E. viridis group has one chloroplast and spherical mucocysts. Molecular analyses using SSU and LSU rDNA demonstrated that the subgenus Euglena is not monophyletic. The combined SSU/LSU trees provide strong support for a stellate clade (subgenus Euglena ), but one strain of E. viridis diverges at the base of the Euglena/Calliglena lineage. Multiple subclades are found within the main stellate clade. E. tristellata forms a separate divergence and four E. stellata strains form a single, well-supported subclade. Two E. viridis strains are among the E. geniculata group clade, while six others form two separate, but well-supported clades. This study demonstrates that the type species, E. viridis , is paraphyletic and will need to be redefined.     

MULTIGENE ANALYSES OF PHOTOSYNTHETIC EUGLENOIDS AND NEW FAMILY,PHACACEAE (EUGLENALES)1

Bayesian and maximum‐likelihood (ML) analyses of the combined multigene data (nuclear SSU rDNA, and plastid SSU and LSU rDNA) were conducted to evaluate the phylogeny of photosynthetic euglenoids. The combined data set consisted of 108 strains of photosynthetic euglenoids including a colorless sister taxon. Bayesian and ML analyses recovered trees of almost identical topology. The results indicated that photosynthetic euglenoids were divided into two major clades, the Euglenaceae clade (Euglena, Euglenaria, Trachelomonas, Strombomonas, Monomorphina, Cryptoglena, Colacium) and the Phacaceae clade (Phacus, Lepocinclis, Discoplastis). The Euglenaceae clade was monophyletic with high support and subdivided into four main clades: the Colacium, the Strombomonas and Trachelomonas, the Cryptoglena and Monomorphina, and the Euglena and Euglenaria clades. The genus Colacium was positioned at the base of the Euglenaceae and was well supported as a monophyletic lineage. The loricate genera (Strombomonas and Trachelomonas) were located at the middle of the Euglenaceae clade and formed a robust monophyletic lineage. The genera Cryptoglena and Monomorphina also formed a well‐supported monophyletic clade. Euglena and the recently erected genus Euglenaria emerged as sister groups. However, Euglena proxima branched off at the base of the Euglenaceae. The Phacaceae clade was also a monophyletic group with high support values and subdivided into three clades, the Discoplastis, Phacus, and Lepocinclis clades. The genus Discoplastis branched first, and then Phacus and Lepocinclis emerged as sister groups. These genera shared a common characteristic, numerous small discoid chloroplasts without pyrenoids. These results clearly separated the Phacaceae clade from the Euglenaceae clade. Therefore, we propose to limit the family Euglenaceae to the members of the Euglena clade and erect a new family, the Phacaceae, to house the genera Phacus, Lepocinclis, and Discoplastis.     

PHYLOGENETIC ANALYSIS OF THE GENUS EUGLENA (EUGLENOPHYCEAE) WITH PARTICULAR REFERENCE TO THE TYPE SPECIES EUGLENA VIRIDIS1

Euglena viridis (subgenus Euglena) serves as the type species for the genus Euglena. In this study, molecular phylogenetic analyses using a small subunit (SSU) and a combined SSU–partial large subunit rDNA data set for members of the genus Euglena showed that strains identified as E. viridis on the basis of morphology are distributed between two separate nonsister clades. Although all the E. viridis strains examined were morphologically indistinguishable and possessed spherical mucocysts and stellate chloroplasts with one paramylon center, there was a high degree of sequence divergence between the E. viridis strains in different clades, making this a cryptic species. Like E. viridis, all taxa from the subgenus Euglena are characterized by having one or more stellate chloroplasts with paramylon grains clustered around the center of the chloroplast. These additional taxa were divided into four clades in all the molecular analyses. Strains of Euglena stellata formed two nonsister clades whose members had a single aggregate chloroplast with paramylon center and spindle‐shaped mucocysts. A geniculata clade included species with one or two stellate chloroplasts with paramylon centers and spherical mucocysts, and the cantabrica clade had members with one stellate chloroplast with paramylon center and spherical mucocysts often arranged in spiral rows. Interspersed among these were three additional clades bearing taxa from the subgenus Calliglena that contains members with discoid plastids and pyrenoids that may or may not be capped with paramylon. These taxa formed a laciniata clade, mutabilis clade, and gracilis clade. This study demonstrates that E. viridis and E. stellata are cryptic species that can only be distinguished at the molecular level. Because E. viridis is the designated type species for the genus Euglena, we designated an epitype for E. viridis.     

EVOLUTION OF PHACUS (EUGLENOPHYCEAE) AS INFERRED FROM PELLICLE MORPHOLOGY AND SSU rDNA

This research integrates a large morphological data set into a molecular context. Nineteen pellicle characters and 62 states from 13 euglenid taxa were analyzed cladistically. The pellicle morphology of Euglena tripteris (Klebs), Lepocinclis ovata (Conrad), Phacus brachykentron (Pochmann), P. oscillans (Klebs), P. pyrum (Stein), and P. triqueter (Dujardin) is described comprehensively. These data are compared with new information on the pellicle morphology of Euglena acus (Ehrenberg), E. stellata (Mainx), and Peranema trichophorum (Stein) in addition to published data on Entosiphon sulcatum (Dujardin), Euglena gracilis (Klebs), Distigma proteus (Pringsheim), and Petalomonas cantuscygni (Cann and Pennick). Nuclear small subunit (SSU) rDNA sequences provided an independent test for establishing a robust organismal pedigree of the same taxa. A synthetic tree derived from the combined phylogenetic analyses of pellicle morphology and SSU rDNA enabled us to parsimoniously map morphological character states. This approach demonstrated the utility of pellicle morphology for inferring phylogenetic relationships of euglenids and establishing apomorphy-based clade definitions. Three robust clades with unambiguous pellicle-based apomorphies can be recognized within taxa traditionally classified as Phacus : (1) L. ovata and P. pyrum , (2) E. tripteris and P. triqueter , and (3) P. brachykentron and P. oscillans. Taxonomic concerns that emerged from these results are discussed.     

A PHYSICAL MAP OF THE CHLAMYDOMONAS REINHARDTII NUCLEAR GENOME

Shin, W., Zimmermann, S. & Triemer, R. E. Department of Life Science, Rutgers University, Piscataway, NJ 08854, USA In 1985, Willey and Wibel described the existence of a cytoplasmic pocket formed from the reservoir membrane in Colacium. A band of microtubules derived from the ventral flagellar root (MTR) lined the pocket and a dense fibrillar mesh was associated with the membrane. A comparison of bodonid cytostomes, colorless euglenoid cytostomes, and the reservoir pocket found in Colacium suggested that the three structures were homologous and that photosynthetic euglenoids arose from phagotrophic ancestors. MTR/pockets have since been reported in other photosynthetic euglenoids including Euglena, Eutreptia, Eutreptiella, Cryptoglena, and Tetreutreptia. We now report on MTR/pockets in Lepocinclis, Trachelomonas, Strombomonas and Phacus thereby demonstrating the presence of this complex in representatives of all of the major photosynthetic genera. A comparison of the MTR/complex across genera indicates a reduction in structural complexity that is consistent with recent phylogenetic schemes based on molecular characters.     

PHYLOGENY OF THE EUGLENOID LORICATE GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) INFERRED FROM NUCLEAR SSU AND LSU rDNA1

Previous studies using the nuclear SSU rDNA and partial LSU rDNA have demonstrated that the euglenoid loricate taxa form a monophyletic clade within the photosynthetic euglenoid lineage. It was unclear, however, whether the loricate genera Trachelomonas and Strombomonas were monophyletic. In order to determine the relationships among the loricate taxa, SSU and LSU nuclear rDNA sequences were obtained for eight Strombomonas and 25 Trachelomonas strains and combined in a multigene phylogenetic analysis. Conserved regions of the aligned data set were used to generate maximum‐likelihood (ML) and Bayesian phylogenies. Both methods recovered a strongly supported monophyletic loricate clade with Strombomonas and Trachelomonas species separated into two sister clades. Taxa in the genus Strombomonas sorted into three subclades. Within the genus Trachelomonas, five strongly supported subclades were recovered in all analyses. Key morphological features could be attributed to each of the subclades, with the major separation being that all of the spine‐bearing taxa were located in two sister subclades, while the more rounded, spineless taxa formed the remaining three subclades. The separation of genera and subclades was supported by 42 distinct molecular signatures (33 in Trachelomonas and nine in Strombomonas). The morphological and molecular data supported the retention of Trachelomonas and Strombomonas as separate loricate genera.     

裸藻类植物的分支系统学研究

本文选取了裸藻类的33个属级分类单位,以及它们的35个性状,利用分支系统学的原理和方法,对性状的演化极性进行了分析,同时对性状间的极性关系进行了和谐性分析,使性状间极性关系处在较为合理的状态,然后建立了分支分析的数据矩阵。应用徐克学建立的“演化极端结合法”进行微机运算．得简约系数远小于1(o．2159)的分支谱系图。根据分支诺系图对裸藻类的系统发育关系进行了探讨,井与已有的关于裸藻类分类系统和演化假设进行了比较。在此基础上按照裸藻类的亲缘关系及单系原则,对裸藻类的分类等级进行了划分,初步提出了建立1门1纲5目的分类系统。按照在分支谱系中的演化地位,认为裸藻属的5个亚属,明显地都应是独立的属。同时对裸藻类的共生起源与演化的关系也进行了讨论。     

ARE CYTOPLASMIC POCKETS (MTR/POCKET) PRESENT IN ALL PHOTOSYNTHETIC EUGLENOID GENERA?1

In 1985, the existence of a cytoplasmic pocket formed from the reservoir membrane in the photosynthetic euglenoid Colacium was described. A band of reinforcing microtubules (MTR) derived from the ventral flagellar root lined the pocket, and a dense fibrillar mesh was associated with the membrane. A comparison of bodonid cytostomes, colorless euglenoid cytostomes, and the reservoir pocket found in Colacium suggested that the three structures were homologous and that photosynthetic euglenoids arose from phagotrophic ancestors. MTR/pockets have since been reported in other photosynthetic euglenoids, including Euglena, Eutreptia, Eutreptiella, Cryptoglena, Tetreutreptia, and Phacus. We found MTR/pockets in three additional taxa, Lepocinclis, Trachelomonas, and Strombomonas, thereby demonstrating the presence of this complex in representatives of all the major photosynthetic genera. A comparison of the MTR/pocket complex across genera indicated a reduction in structural complexity that was consistent with recent phylogenetic schemes based on molecular characters. Three alternative hypotheses of the origin of MTR/pockets in phototrophic euglenoids are presented and discussed.     

PHYLOGENY OF THE DUMONTIACEAE (GIGARTINALES, RHODOPHYTA) AND ASSOCIATED FAMILIES BASED ON SSU rDNA AND INTERNAL TRANSCRIBED SPACER SEQUENCE DATA

Small subunit (SSU) rDNA was sequenced for 25 species in 19 genera of the Gigartinales (Rhodophyta). As well, the internal transcribed spacer (ITS) region was sequenced, and a data matrix of 36 morphological characters was constructed for 16 species of Dumontiaceae. Phylogenetic trees were calculated from a multiple alignment of the SSU sequence data to infer relationships between species of Dumontiaceae and other gigartinalean taxa. The SSU analysis produced a polyphyletic Dumontiaceae. Notably, Acrosymphyton failed to associate with the included Gigartinales, let alone the Dumontiaceae, supporting an earlier proposal to remove it to a new family. The analyses were equivocal about the phylogenetic affinities of Dudresnaya , which clustered with the Kallymeniaceae, and the affinities of the Indo-West Pacific Gibsmithia , Kraftia , and Dasyphloea , the last-mentioned clustering with the Antarctic Gainiaceae, and these four taxa with Portieria (Rhizophyllidaceae). Further investigations are necessary to resolve relationships among these taxa. Rhodopeltis , a genus recently moved to the Dumontiaceae from the Polyideaceae, showed a weak association with the remaining northern Dumontiaceae. The final group consisted of cold-temperate Northern Hemisphere species. Phylogenetic analyses using a combination of SSU, ITS, and morphological data within this clade produced two strongly supported clades, a Dilsea / Neodilsea clade and a Cryptosiphonia / Dumontia clade. Dilsea is derived from a paraphyletic Neodilsea and may itself be polyphyletic. Atlantic and Pacific isolates of Dumontia contorta clearly showed sufficient divergence to warrant recognition as distinct species, and Dumontia alaskana , sp. nov. is proposed for the Pacific species.     

Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea)

Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level.     

Amphitremida (Poche, 1913) Is a New Major,Ubiquitous Labyrinthulomycete Clade

Micro-eukaryotic diversity is poorly documented at all taxonomic levels and the phylogenetic affiliation of many taxa – including many well-known and common organisms - remains unknown. Among these incertae sedis taxa are Archerella flavum (Loeblich and Tappan, 1961) and Amphitrema wrightianum (Archer, 1869) (Amphitremidae), two filose testate amoebae commonly found in Sphagnum peatlands. To clarify their phylogenetic position, we amplified and sequenced the SSU rRNA gene obtained from four independent DNA extractions of A. flavum and three independent DNA extractions of A. wrightianum. Our molecular data demonstrate that genera Archerella and Amphitrema form a fully supported deep-branching clade within the Labyrinthulomycetes (Stramenopiles), together with Diplophrys sp. (ATCC50360) and several environmental clones obtained from a wide range of environments. This newly described clade we named Amphitremida is diverse genetically, ecologically and physiologically. Our phylogenetic analysis suggests that osmotrophic species evolved most likely from phagotrophic ancestors and that the bothrosome, an organelle that produces cytoplasmic networks used for attachment to the substratum and to absorb nutrients from the environments, appeared lately in labyrithulomycete evolution.     

Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.     

Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes

Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.