Sphaeriid and corbiculid clams represent separate heterodont bivalve radiations into freshwater environments

Nine families of bivalve molluscs have undergone successful radiations in freshwater habitats, including three heterodont taxa: the Sphaeriidae, Corbiculidae, and Dreissenidae. Although the phylogenetic relationships of these freshwater heterodont families are controversial, most workers place the first two in the superfamily Corbiculoidea and assume that they represent a monophyletic grouping. We have tested competing phylogenetic hypotheses for the Corbiculoidea by constructing a representative molecular phylogeny, based on domains D1-D3 of the nuclear large subunit 28S rDNA, for 18 heterodont bivalves and for two oyster outgroup taxa. Our results do not support the monophyly of the Corbiculoidea and are consistent with the hypothesis that all three families of freshwater heterodonts represent independent colonization events by marine ancestors. Similarities in developmental mode specializations exhibited by some sphaeriids and corbiculids, such as sequential direct-developing broods, represent convergent adaptations to the freshwater environment. The corbiculid taxa form a clade with venerid and mactrid outgroups but we were not able to identify a putative marine outgroup for the sphaeriids.     

Molecular phylogeny of land and freshwater planarians (Tricladida, Platyhelminthes): from freshwater to land and back

The suborder Tricladida (phylum Platyhelminthes) comprises the well-known free-living flatworms, taxonomically grouped into three infraorders according to their ecology: Maricola (marine planarians), Paludicola (freshwater planarians), and Terricola (land planarians). Molecular analyses have demonstrated that the Paludicola are paraphyletic, the Terricola being the sister group of one of the three paludicolan families, the Dugesiidae. However, neither 18S rDNA nor COI based trees have been able to resolve the relationships among species of Terricola and Dugesiidae, particularly the monophyly of Terricola. Here, we present new molecular data including sequences of nuclear genes (18S rDNA, 28S rDNA) and a mitochondrial gene (COI) of a wider sample of dugesiid and terricolan species. The new sequences have been analyzed, together with those previously obtained, in independent and concatenated analyses using maximum likelihood and bayesian methods. The results show that, although some parts of the trees remain poorly resolved, they support a monophyletic origin for Terricola followed by a likely return of some species to freshwater habitats. Relationships within the monophyletic group of Dugesiidae are clearly resolved, and relationships among some terricolan subfamilies are also clearly established and point to the need for a thorough revision of Terricola taxonomy.     

Phylogeny of the gastropod superfamily Cerithioidea using morphology and molecules

The Cerithioidea is an ecologically important superfamily of basal Caenogastropoda with speciose marine, brackish water, and freshwater lineages primarily in tropical, subtropical, and warm temperate regions of the world. They often represent significant components of the communities where they occur and have given rise to several spectacular endemic radiations in rivers and ancient lakes. Earlier attempts to resolve the phylogenetic history of the group have been based on smaller taxon and character subsets with incongruent results. Here the monophyly and phylogeny of the group is evaluated with expanded morphological and molecular (16S, 28S rRNA) data sets. For morphological analyses, 151 characters (shell, operculum, radula, alimentary tract, kidney, nervous system, reproductive anatomy, and sperm ultrastructure) were scored for 47 cerithioideans (representing 17 families) and nine outgroup taxa. To test monophyly of the Cerithioidea, extended molecular data sets of 16S and 28S sequences for 57 and 44 taxa, respectively, were compiled using new and previously published sources. For combined analyses, a pruned molecular data set was combined with the morphological partition. The morphological data were analysed alone using only parsimony; molecular and simultaneous analyses were performed using both parsimony and Bayesian inference. The effect of excluding unconserved regions of the alignments was also explored. All analyses, with the exception of the individual 16S and 28S data sets, support monophyly of the Cerithioidea as currently formulated. Of the 12 families represented by more than one terminal, only two (Planaxidae, Potamididae) are always supported as monophyletic; Batillariidae, Cerithiidae, Pachychilidae, Pleuroceridae, Semisulcospiridae, Thiaridae, and Turritellidae are monophyletic in most but not all topologies. The combination of diverse data sources (morphology, 16S and 28S sequences) and inclusion of unconserved regions of the alignments improved the recovery of monophyletic families. At deeper levels, a consensus is beginning to emerge in the recognition of three main assemblages, but whether these represent clades or grades is still unclear; the resolution of these assemblages and the branching order within them are sensitive to exclusion of unconserved regions and choice of optimality criterion. No clear conclusion is reached with respect to the number of freshwater invasions, with two invasions supported on some topologies and three supported on others. Progress toward a robust and stable resolution of cerithioidean relationships will require (1) strategically coordinated sampling for additional morphological and molecular data; (2) comprehensive anatomical treatments for several poorly documented limnic lineages (e.g. Melanopsidae, Thiaridae) and comparative data for poorly understood organ systems (e.g. renal system); (3) the addition of poorly known, minute, and/or rare marine taxa, to provide novel character combinations, insight into putative homologies, and to help anchor basal nodes and break up long branches. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 43–89.     

Molecular phylogeny of a circum-global, diverse gastropod superfamily (Cerithioidea: Mollusca: Caenogastropoda): pushing the deepest phylogenetic limits of mitochondrial LSU rDNA sequences

The Cerithioidea is a very diverse group of gastropods with ca. 14 extant families and more than 200 genera occupying, and often dominating, marine, estuarine, and freshwater habitats. While the composition of Cerithioidea is now better understood due to recent anatomical and ultrastructural studies, the phylogenetic relationships among families remain chaotic. Morphology-based studies have provided conflicting views of relationships among families. We generated a phylogeny of cerithioideans based on mitochondrial large subunit rRNA and flanking tRNA gene sequences (total aligned data set 1873 bp). Nucleotide evidence and the presence of a unique pair of tRNA genes (i.e., threonine + glycine) between valine-mtLSU and the mtSSU rRNA gene support conclusions based on ultrastructural data that Vermetidae and Campanilidae are not Cerithioidea, certain anatomical similarities being due to convergent evolution. The molecular phylogeny shows support for the monophyly of the marine families Cerithiidae [corrected], Turritellidae, Batillariidae, Potamididae, and Scaliolidae as currently recognized. The phylogenetic data reveal that freshwater taxa evolved on three separate occasions; however, all three recognized freshwater families (Pleuroceridae, Melanopsidae, and Thiaridae) are polyphyletic. Mitochondrial rDNA sequences provide valuable data for testing the monophyly of cerithioidean [corrected] families and relationships within families, but fail to provide strong evidence for resolving relationships among families. It appears that the deepest phylogenetic limits for resolving caenogastropod relationships is less than about 245--241 mya, based on estimates of divergence derived from the fossil record.     

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.     

Concatenated data and dense taxon sampling clarify phylogeny and ecological transitions within Hypotricha

Ciliates are single‐cell eukaryotes playing important roles in various ecosystems. Phylogenetic relationships within Hypotricha, one of the most polymorphic and highly derived ciliate groups, remain uncertain. Previous studies suggested that low genetic divergence might be the reason for poorly supported SSU rDNA tree topologies, despite the high morphological diversity of this group. In this study, we substantially increase the number of available hypotrich LSU rDNA gene sequences by the addition of 857 environmental sequences, and we investigate whether a more divergent gene and dense taxon sampling could better resolve the phylogeny of Hypotricha and shed light on the patterns of ecological transitions in the evolutionary history of the group. Pairwise distances of LSU rDNA sequences are generally higher than those for SSU rDNA within each order of Hypotricha, and both concatenated rDNA and LSU rDNA trees provide more resolution for hypotrich phylogenetics. Three traditional (morphology based) hypotrich orders, Stichotrichida, Sporadotrichida and Urostylida, are polyphyletic, but a monophyletic core Urostylida are found in our trees. A brackish/marine environment is inferred as ancestral within Hypotricha, with subsequent ecological diversification into freshwater, soil environments before the origin of major clades and some transitions back to the marine. However, inferred ecological transitions in Hypotricha are influenced by genes, methods and taxa.     

Family‐level relationships of the spittlebugs and froghoppers (Hemiptera: Cicadomorpha: Cercopoidea)

The spittlebug superfamily Cercopoidea (Hemiptera: Cicadomorpha) comprises approximately 3000 phytophagous species (including some economically important pests of grass crops) classified among the families Cercopidae, Aphrophoridae, Epipygidae, Clastopteridae and Machaerotidae. However, the monophyly of these taxa has never been tested and the evolutionary relationships among these major lineages are unknown. Presented here are the results of the first ever phylogenetic investigation of the higher‐level relationships within Cercopoidea, based on DNA nucleotide sequence data from six loci (18S rDNA, 28S rDNA, histone 3, wingless, cytochrome oxidase I and cytochrome oxidase II) generated from exemplars of 109 spittlebug species representing all five described families, seven of eight subfamilies and 61 genera (eight additional exemplars, representing a selection of other Auchenorrhyncha taxa, were included as outgroups). The resulting topologies are used to evaluate the monophyly of each cercopoid family, and further to calculate divergence date estimates to examine the chronological origins and historical diversification of Cercopoidea. The results of this investigation suggest that: (i) four of the five described families are monophyletic; Epipygidae was recovered consistently as originating within Aphrophoridae; (ii) the exclusively Old World Machaerotidae is the most anciently diversified family of extant spittlebugs; (iii) New World Cercopidae (i.e. Ischnorhininae) constitute a derived monophyletic lineage; (iv) the genus Microsargane Fowler, classified currently within Aphrophoridae, actually belongs within Cercopidae; and (v) the origins of the major spittlebug lineages probably coincided with the breakup of Pangaea and, subsequently, Gondwana, as well as major floristic diversification such as the rise of angiosperms.     

Phylogeny of Tubificidae (Annelida, Clitellata) based on mitochondrial and nuclear sequence data

The tubificid clitellates are a common component in the freshwater bottom fauna and are also the most abundant oligochaete group in marine habitats. There are over 800 described species classified in six subfamilies; Tubificinae, Limnodriloidinae, Rhyacodrilinae, Telmatodrilinae, Phallodrilinae, and Naidinae. In this study we examine the phylogenetic relationships in Tubificidae using a combination of mitochondrial 16S rDNA and nuclear 18S rDNA sequence data. Sequences were obtained from five outgroup and 56 ingroup taxa, including five of the six subfamilies of Tubificidae. The data were analysed by maximum parsimony and Bayesian inference. The resulting tree topologies are virtually without conflict. Several associations traditionally recognized within the family Tubificidae are supported, in the Bayesian analysis including a sister group relationship between Tubificinae and Limnodriloidinae. The results also indicate that Rhyacodrilinae is polyphyletic--some of its members (Heterodrilus spp.) fall into a clade with Phallodrilinae, all other groups with Naidinae. Naidinae is also polyphyletic with two rhyacodriline genera, Monopylephorus and Ainudrilus, nested within. Most of the tubificid genera included in the study are supported as monophyletic; however, Tubifex and Limnodriloides are refuted, and Tubificoides is unresolved from other tubificine taxa.     

Additional gene data and increased sampling give new insights into the phylogenetic relationships of Neogastropoda, within the caenogastropod phylogenetic framework

Neogastropoda, a highly diversified group of predatory marine snails, has often been contradicted in molecular phylogenetic studies. This is partly the consequence of limited neogastropod taxa or outgroups analyzed or insufficient gene sequences employed. This paper reports the most extensive molecular study of the group published to date with increased neogastropod taxa, multiple representatives of caenogastropod outgroups, and additional gene sequences. Data were collected from the entire 18S rRNA, histone H3, and three partial mitochondrial genes. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted. In the caenogastropod phylogenetic framework, Hypsogastropoda was contradicted owing to the inclusion of Cerithioidea. Contrary to previous molecular studies, all the results recovered Neogastropoda as a monophyletic group, which confirms the monophyly of Neogastropoda and the validity of morphological synapomorphies that usually define Neogastropoda as monophyletic. Tonnoidea was shown to be paraphyletic with respect to Ficidae, and together this group formed a monophyletic clade as the sister group to Neogastropoda, which supported the “high mesogastropod” hypothesis of the origin of Neogastropoda. All neogastropod families were strongly supported except Buccinidae, Turridae and Cancellariidae. Our results shed light on the status of Neogastropoda, a controversial group, within Caenogastropoda.     

Molecular phylogeny of parasitic zygomycota (Dimargaritales, zoopagales) based on nuclear small subunit ribosomal DNA sequences

We analyzed sequence data of the 18S rDNA gene from representatives of nine mycoparasitic or zooparasitic genera to infer the phylogenetic relationships of these fungi within the Zygomycota. Phylogenetic analyses identified a novel monophyletic clade consisting of the Zoopagales, Kickxellales, Spiromyces, and Harpellales. Analyses also identified a monophyletic mycoparasitic-zooparasitic Zoopagales clade in which Syncephalis, Thamnocephalis, and Rhopalomyces form a sister group to a Piptocephalis-Kuzuhaea clade. Although monophyly of the mycoparasitic Dimargaritales received strong bootstrap and decay index support, phylogenetic relationships of this order could not be resolved because of the unusually high rate of base substitutions within the 18S rDNA gene. Overall, the 18S gene tree topology is weak, as reflected by low bootstrap and decay index support for virtually all internal nodes uniting ordinal and superordinal taxa. Nevertheless, the 18S rDNA phylogeny is mostly consistent with traditional phenotypic-based classification schemes of the Fungi.     

Phylogeny of Chaetonotidae and other Paucitubulatina (Gastrotricha: Chaetonotida) and the colonization of aquatic ecosystems

Kånneby, T., Todaro, M. A., Jondelius, U. (2012). Phylogeny of Chaetonotidae and other Paucitubulatina (Gastrotricha: Chaetonotida) and the colonization of aquatic ecosystems. —Zoologica Scripta, 42, 88–105. Chaetonotidae is the largest family within Gastrotricha with almost 400 nominal species represented in both freshwater and marine habitats. The group is probably non‐monophyletic and suffers from a troubled taxonomy. Current classification is to a great extent based on shape and distribution of cuticular structures, characters that are highly variable. We present the most densely sampled molecular study so far where 17 of the 31 genera belonging to Chaetonotida are represented. Bayesian and maximum likelihood approaches based on 18S rDNA, 28S rDNA and COI mtDNA are used to reconstruct relationships within Chaetonotidae. The use of cuticular structures for supra‐specific classification within the group is evaluated and the question of dispersal between marine and freshwater habitats is addressed. Moreover, the subgeneric classification of Chaetonotus is tested in a phylogenetic context. Our results show high support for a clade containing Dasydytidae nested within Chaetonotidae. Within this clade, only three genera are monophyletic following current classification. Genera containing both marine and freshwater species never form monophyletic clades and group with other species according to habitat. Marine members of Aspidiophorus appear to be the sister group of all other Chaetonotidae and Dasydytidae, indicating a marine origin of the clade. Halichaetonotus and marine Heterolepidoderma form a monophyletic group in a sister group relationship to freshwater species, pointing towards a secondary invasion of marine environments of these taxa. Our study highlights the problems of current classification based on cuticular structures, characters that show homoplasy for deeper relationships.     

Searching factors causing implausible non-monophyly: ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats

This contribution addresses two questions: which alignment patterns are causing non-monophyly of the Asellota and what is the phylogenetic history of this group? The Asellota are small benthic crustaceans occurring in most aquatic habitats. In view of the complex morphological apomorphies known for this group, monophyly of the Asellota has never been questioned. Using ssu rDNA sequences of outgroups and of 16 asellote species from fresh water, littoral marine habitats and from deep-sea localities, the early divergence between the lineages in fresh water and in the ocean, and the monophyly of the deep-sea taxon Munnopsidae are confirmed. Relative substitution rates of freshwater species are much lower than in other isopod species, rates being highest in some littoral marine genera (Carpias and Jaera). Furthermore, more sequence sites are variable in marine than in freshwater species, the latter conserve outgroup character states. Monophyly is recovered with parsimony methods, but not with distance and maximum likelihood analyses, which tear apart the marine from the freshwater species. The information content of alignments was studied with spectra of supporting positions. The scarcity of signal (=apomorphic nucleotides) supporting monophyly of the Asellota is attributed to a short stem-line of this group or to erosion of signal in fast evolving marine species. Parametric boostrapping in combination with spectra indicates that a tree model cannot explain the data and that monophyly of the Asellota should not be rejected even though many topologies do not recover this taxon.     

Filling a gap in the phylogeny of flatworms: relationships within the Rhabdocoela (Platyhelminthes), inferred from 18S ribosomal DNA sequences

The phylogeny of the Rhabdocoela, a species-rich taxon of free-living flatworms, is reconstructed based on complete 18S rDNA sequences. The analysis includes 62 rhabdocoels and 102 representatives of all major flatworm taxa. In total, 46 new sequences are used, 41 of them from rhabdocoel species, five from proseriates. Phylogenetic analysis was performed using maximum parsimony and Bayesian inference. Clade support was evaluated with parsimony jackknifing, Bremer support indices and Bayesian posterior probabilities. The resulting cladogram corroborates that the Rhabdocoela is monophyletic, but its sister group remains uncertain. The 'Dalyellioida' and the 'Typhloplanoida', both former rhabdocoel subtaxa, are polyphyletic. Within the Rhabdocoela the monophyletic Kalyptorhynchia, characterized by a muscular proboscis, forms the sister group of all other rhabdocoels. The Schizorhynchia is a monophyletic subtaxon of the Kalyptorhynchia, with the split proboscis as a synapomorphy. Except for the Dalyelliidae and the Typhloplanidae, both freshwater taxa, none of the 'families' previously included in the 'Typhloplanoida' and the 'Dalyellioida' appears to be monophyletic. As a result of this analysis, three existing and four new taxon names are formally defined following the rules of the Phylocode.     

Extensive dinoflagellate phylogenies indicate infrequent marine-freshwater transitions

We have constructed extensive 18S-28S rDNA dinoflagellate phylogenies (>200 sequences for each marker) using Maximum Likelihood and Bayesian Inference to study the evolutionary relationships among marine and freshwater species (43 new sequences). Our results indicated that (a) marine and freshwater species are usually not closely related, (b) several freshwater species cluster into monophyletic groups, (c) most marine-freshwater transitions do not seem to have occurred recently and, (d) only a small fraction of the marine lineages seem to have colonized fresh waters. Thus, it becomes apparent that the marine-freshwater boundary has acted as a barrier during the evolutionary diversification of dinoflagellates. Our results also shed light on the phylogenetic positions of several freshwater dinoflagellates which, to date, were uncertain.     

DNA barcoding identifies Eimeria species and contributes to the phylogenetics of coccidian parasites (Eimeriorina, Apicomplexa, Alveolata)

Partial (～ 780 bp) mitochondrial cytochrome c oxidase subunit I (COI) and near complete nuclear 18S rDNA (～ 1,780 bp) sequences were directly compared to assess their relative usefulness as markers for species identification and phylogenetic analysis of coccidian parasites (phylum Apicomplexa). Fifteen new COI partial sequences were obtained using two pairs of new primers from rigorously characterised (sensu Reid and Long, 1979) laboratory strains of seven Eimeria spp. infecting chickens as well as three additional sequences from cloned laboratory strains of Toxoplasma gondii (ME49 and GT1) and Neospora caninum (NC1) that were used as outgroup taxa for phylogenetic analyses. Phylogenetic analyses based on COI sequences yielded robust support for the monophyly of individual Eimeria spp. infecting poultry except for the Eimeria mitis/mivati clade; however, the lack of a phenotypically characterised strain of E. mivati precludes drawing any firm conclusions regarding this observation. Unlike in the 18S rDNA-based phylogenetic reconstructions, Eimerianecatrix and Eimeria tenella formed monophyletic clades based on partial COI sequences. A species delimitation test was performed to determine the probability of making a correct identification of an unknown specimen (sequence) based on either complete 18S rDNA or partial COI sequences; in almost all cases, the partial COI sequences were more reliable as species-specific markers than complete 18S rDNA sequences. These observations demonstrate that partial COI sequences provide more synapomorphic characters at the species level than complete 18S rDNA sequences from the same taxa. We conclude that COI performs well as a marker for the identification of coccidian taxa (Eimeriorina) and will make an excellent DNA 'barcode' target for coccidia. The COI locus, in combination with an 18S rDNA sequence as an 'anchor', has sufficient phylogenetic signal to assist in the resolution of apparent paraphylies within the coccidia and likely more broadly within the Apicomplexa.     

Interrelationships of the Gastrotricha and their place among the Metazoa inferred from 18S rRNA genes

The phylum Gastrotricha includes about 700 species. They are small worm‐like organisms abundant among marine and freshwater meiobenthos. In spite of their ubiquity, diversity and relative abundance, phylogenetic relationships of these animals remain enigmatic due to the conflicting results of morphological and molecular cladistic analyses. Also unclear are the alliances within the phylum. In order to best estimate the position of Gastrotricha among the Metazoa and to shed some light on the ingroup phylogenetic relationships, small subunit (SSU) ribosomal DNA (rDNA) from 15 species of Chaetonotida (eight genera) and 28 species of Macrodasyida (26 genera) were included in an alignment of 50 metazoan taxa representing 26 phyla. Of the gastrotrich SSU rDNA sequences, eight are new and, along with published sequences represent eight families, including the five marine most speciose. Gastrotricha were resolved within a monophyletic Lophotrochozoa as part of a clade including Micrognathozoa, Rotifera and Cycliophora. The Gnathostomulida were sister to this clade. Nodal support was low for all of these relationships except the grouping of the Micrognathozoa, Rotifera and Cycliophora. Bayesian inference resolved the Gastrotricha as monophyletic with weak nodal support; the Macrodasyida were resolved as paraphyletic with many basal nodes poorly supported. Within the Chaetonotida, the monotypic Multitubulatina Neodasys was found in alliance with the macrodasyidan Urodasys while all the Paucitubulatina were found to form a single, well‐supported clade, with Musellifer as the most basal member. Among the more densely sampled Macrodasyida the Lepidodasyidae and Macrodasyidae were each found to be polyphyletic while monophyly was well supported for the Turbanellidae and Thaumastodermatidae. The congruence of our results with those of the cladistic analysis based on morphological traits provides confidence about the value of each dataset, and calls for widening of the research to include additional taxa of particular phylogenetic significance such as the Dactylopodolidae, Diuronotus, Heteroxenotrichula and Draculiciteria. The study highlights the problems in working with small species, the need for voucher specimens and the confused taxonomic status and membership of various gastrotrich families.     

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

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 position of endosymbiotic green algae in Paramecium bursaria Ehrenberg from Japan

Endosymbiotic green algae of Japanese Paramecium bursaria were phylogenetically analyzed based on DNA sequences from the ribosomal DNA operon (18S rDNA, ITS1, 5.8S rDNA, and ITS2). Phylogenetic trees constructed using 18S rDNA sequences showed that the symbionts belong to the Chlorella sensu stricto (Trebouxiophyceae) group. They are genetically closer to the C. vulgaris Beijerinck group than to C. kessleri Fott et Nováková as proposed previously. Branching order in C. vulgaris group was unresolved in 18S rDNA trees. Compared heterogeneities of 18S rDNA, ITS1, 5.8S r, and ITS2 among symbionts and two Chlorella species, indicated that the ITS2 region (and probably also ITS1) is better able to resolve phylogenetic problems in such closely related taxa. All six symbiotic sequences obtained here (approximately 4000-bp sequences of 18S rDNA, ITS1, 5.8S rDNA, and ITS2) were completely identical in each, strongly suggesting a common origin.     

Initial results on the molecular phylogeny of the Nudibranchia (Gastropoda, Opisthobranchia) based on 18S rDNA data

This study investigated nudibranch phylogeny on the basis of 18S rDNA sequence data. 18S rDNA sequence data of 19 taxa representing the major living orders and families of the Nudibranchia were analyzed. Representatives of the Cephalaspidea, Anaspidea, Gymnomorpha, Prosobranchia, and Pulmonata were also sequenced and used as outgroups. An additional 28 gastropod sequences taken from GenBank were also included in our analyses. Phylogenetic analyses of these more than 50 gastropod taxa provide strong evidence for support of the monophyly of the Nudibranchia. The monophyly of the Doridoidea, Cladobranchia, and Aeolidoidea within the Nudibranchia are also strongly supported. Phylogenetic utility and information content of the 18S rDNA sequences for Nudibranchia, and Opisthobranchia in general, are examined using the program SplitsTree as well as phylogenetic reconstructions using distance and parsimony approaches. 0Results based on these molecular data are compared with hypotheses about nudibranch phylogeny inferred from morphological data.     

A phylogeny of the damselfly genus calopteryx (Odonata) using mitochondrial 16S rDNA markers

We seek to reconstruct the phylogenetic relationships of the damselfly genus Calopteryx, for which extensive behavioral and morphological knowledge already exists. To date, analyses of the evolutionary pathways of different life history traits have been hampered by the absence of a robust phylogeny based on morphological data. In this study, we concentrate on establishing phylogenetic information from parts of the 16S rDNA gene, which we sequenced for nine Calopteryx species and five outgroup species. The mt 16S rDNA data set did not show signs of saturated variation for ingroup taxa, and phylogenetic reconstructions were insensitive to variation of outgroup taxa. Parsimony, neighbor-joining, and maximum-likelihood reconstructions agreed on parts of the tree. A consensus tree summarizes the significant results and indicates problematic nodes. The 16S rDNA sequences support monophyly of the genera Mnais, Matrona, and Calopteryx. However, the genus Calopteryx may not be monophyletic, since Matrona basilaris and Calopteryx atrata are sister taxa under every parameter setting. The North American and European taxa each appear as monophyletic clades, while the Asian Calopteryx atrata and Calopteryx cornelia are not monophyletic. Our data implies a different paleobiogeographic history of the Eurasian and North American species, with extant Eurasian species complexes shaped by glacial periods, in contrast to extant North American species groups.