Scale Biogenesis in Synurophycean Protists: Phylogenetic Implications

The Synurophyceae is a class of golden-brown, freshwater, photosynthetic flagellates with a world-wide distribution. A well-developed taxonomy exists where genera and species are distinguished by colony or cell morphology or by the siliceous scales that cover the cells. However, phylogenetic relationships within the class are poorly understood, and incongruous taxonomic concepts occur. This study reviews scale morphology from field-collected samples and controlled culturing experiments as well as from studies of scale biogenesis. The information is used to identify homologous silicification surfaces among taxa and to document the diversity of the resulting scale structures. Thirty-two character states are coded into 11 characters in a cladistic analysis of 13 pivotal taxa. Colonial species are emphasized. One most-parsimonious phylogenetic tree is found (HI = 0, CI = 1). Synura lapponica is shown to be most closely related to Tessellaria volvocina. S. sphagnicola emerges at the base of the tree. Mallomonas caudata and the S. petersenii clade emerge from within Sectio Synura. Chrysodidymus synuroideus appears as an ancestral taxon in the Synura spinosa-like clade (i.e., Series Spinosae). The poorly understood developmental bases for some characters, especially secondary scale structures, are identified and may help focus future research.     

Sicilica-scaled chrysophytes from Korea, a preliminary study

Phytoplankton samples obtained from 10 localities in Korea (Democratic People's Republic of Korea, DPRK) have been examined by means of electron microscopy. 27 species of silica-scaled chrysophytes (Chrysophyceae and Synurophyceae) have been identified, belonging to the genera Chrysosphaerella, Spiniferomonas, Paraphysomo-nas, Mallomonas , and Synura. Almost all of these species are new to Korea, only two of them have with certainty been found there before.     

Synurophyceae from the Southern Atlantic Coastal Plain of North America: A preliminary survey in Louisiana, USA

Forty-three taxa of Synurophyceae were identified by means of transmission electron microscopy of samples from ten different localities in southeastern Louisiana, USA, on the southern portion of the Atlantic Coastal Plain Province of North America. Samples were collected during a one month period when water temperatures ranged from 15.5–24.5"C. Sample pH values ranged from 4.4–7.2. Notable scale morphology variation was described for some taxa. The flora included three warm water taxa but was dominated by temperate and cosmopolitan taxa. Mallomonas prora and Synura australiensis are reported for the first time from North America. Comparisons with related studies from New World subtropical regions in Florida, USA, and Argentina were made, and significant North American range expansions were noted. The large number of aquatic habitats, 7–8 consecutive months at temperatures (6–20°C) best suited for development of synurophycean populations, and proximity to major bird migrations routes are postulated as explanations for the large number of reported species.     

Evolution of Filamentous Ascomycetes Inferred from LSU rDNA Sequence Data

Abstract: The nuclear LSU rRNA gene was examined in order to evaluate the current phylogeny of ascomycetes, which is mainly based on nuclear SSU rRNA data. Partial LSU rRNA gene sequences of 19 ascomycetes were determined and aligned with the corresponding sequences of 13 other ascomycetes retrieved from Genbank, including all classes traditionally distinguished and most of the recently accepted classes. The classification based on SSU rDNA data and morphological characters is supported, while the traditional classification and classifications based on the ascus type are rejected. Ascomycetes with perithecia and cleistothecia form monophyletic groups, while the discomycetes are a paraphyletic assemblage. The Pezizales are basal to all other filamentous ascomycetes. The monophyly of Loculoascomycetes is uncertain. The results of the LSU rDNA analysis agree with those of the SSU rDNA and RPB2 gene analyses, suggesting that most classes circumscribed in the filamentous ascomycetes are monophyletic. The branching order and relationships among these classes, however, cannot be elucidated with any of these data sets.     

A "Total Evidence" Analysis of the Phylogenetic Relationships among the Photosynthetic Stramenopiles

Phylogenetic relationships among the nine major autotrophic stramenopile taxa were inferred in a combined analysis of the rbcL, SSU rDNA, partial LSU rRNA, carotenoid, and ultrastructural data sets. The structure of the shortest combined tree is: (Outgroup, ((((Bacillariophyceae, (Pelagophyceae, Dictyochophyceae)),((Phaeophyceae, Xanthophyceae), Raphidophyceae)), Eustigmatophyceae),(Chrysophyceae, Synurophyceae))). The Synurophyceae/Chrysophyceae is the best supported group followed by the Phaeophyceae/Xanthophyceae and the Pelagophyceae/Dictyochophyceae clades. The monophyletic groups composed of Bacillariophyceae/Pelagophyceae/Dictyochophyceae and Phaeophyceae/Xanthophyceae/Raphidophyceae received the lowest Bremer support values. The optimal combined tree suggests that the diatom frustule is derived from the siliceous "skeleton" in Dictyochophyceae, that the reduced flagellar apparatus arose once in the Bacillariophyceae/Dictyochophyceae/Pelagophyceae clade, and that the specific photoreceptor-eyespot apparatus in Chrysophyceae and the Phaeophyceae/Xantophyceae clade originated independently within the autotrophic stramenopiles. Despite conflicts in tree structure between the most-parsimonious combined phylogeny and the optimal tree(s) of each data partition, it cannot be concluded that extensive incongruence exists between the data sets.     

Towards the phylogeny of the Curculionoidea (Coleoptera): Reconstructions from mitochondrial and nuclear ribosomal DNA sequences

With about 60,000 described species, Curculionoidea represent the most species-rich superfamily in the animal kingdom. The immense diversity apparently creates difficulties in the reconstruction of the phylogenetic relationships. Independent morphological studies have led to very different classifications. This study is based on molecular data from two independent molecular sources, the 16S and 18S rDNA. Sensitivity analyses were conducted for the sequence alignment (gap costs were varied) as well as the phylogenetic reconstruction algorithms and some of their parameters. The higher-level relationships reconstructed within Curculionoidea are sensitive to alignment and reconstruction method. Nemonychidae or Oxycorynidae+Belidae were found to be sister to all remaining Curculionoidea in many analyses. The 16S rDNA sequence data (obtained from 157 species) corroborate many tribes and genera as monophyletic. It is observed that the phylogenetic reconstruction of genera with specific genetic features such as polyploidy and parthenogenetic reproduction is difficult in weevils. The curculionid subfamily Lixinae appears monophyletic. A new monophylum consisting of Entiminae, Hyperinae, Cyclominae, Myllorhinus plus possibly the Cossoninae is distinguished and we call it Entiminae s.l. For most other subfamilies and families homoplasy concealed the phylogenetic signal (due to saturation of the 16S sequences), or the species sampling was insufficient, although our sampling scheme was rather broad. We observed that although data from one source can easily be misleading (16S) or hardly informative (18S), the combination of the two independent data sets can result in useful information for such a speciose group of organisms. Our study represents the most thorough analysis of molecular sequence data of the Curculionoidea to date and although the phylogenetic results appear less stable than expected, they reflect the information content of these sequence data realistically and thus contribute to the total knowledge about the phylogeny of the Curculionoidea.     

A modern approach to rotiferan phylogeny: combining morphological and molecular data

The phylogeny of selected members of the phylum Rotifera is examined based on analyses under parsimony direct optimization and Bayesian inference of phylogeny. Species of the higher metazoan lineages Acanthocephala, Micrognathozoa, Cycliophora, and potential outgroups are included to test rotiferan monophyly. The data include 74 morphological characters combined with DNA sequence data from four molecular loci, including the nuclear 18S rRNA, 28S rRNA, histone H3, and the mitochondrial cytochrome c oxidase subunit I. The combined molecular and total evidence analyses support the inclusion of Acanthocephala as a rotiferan ingroup, but do not support the inclusion of Micrognathozoa and Cycliophora. Within Rotifera, the monophyletic Monogononta is sister group to a clade consisting of Acanthocephala, Seisonidea, and Bdelloidea-for which we propose the name Hemirotifera. We also formally propose the inclusion of Acanthocephala within Rotifera, but maintaining the name Rotifera for the new expanded phylum. Within Monogononta, Gnesiotrocha and Ploima are also supported by the data. The relationships within Ploima remain unstable to parameter variation or to the method of phylogeny reconstruction and poorly supported, and the analyses showed that monophyly was questionable for the families Dicranophoridae, Notommatidae, and Brachionidae, and for the genus Proales. Otherwise, monophyly was generally supported for the represented ploimid families and genera.     

Silica‐scaled chrysophytes from Abisko (Swedish Lapland)

The silica‐scaled chrysophyte flora of Swedish Lapland (near Abisko) was examined. Chrysophyte scales were found in 18 of the 32 investigated water bodies (lakes and pools). Altogether, 28 taxa from the classes Chrysophyceae and Synurophyceae were found. The most abundant species was Synura echinulata. Three species were observed for the first time in Sweden: Mallomonas maculata, M. rasilis and Spiniferomonas serrata.     

Performance of 18S rRNA in Littorinid Phylogeny (Gastropoda: Caenogastropoda)

In the past, 18S rRNA sequences have proved to be very useful for tracing ancient divergences but were rarely used for resolving more recent ones. Moreover, it was suggested that the molecule does not contain useful information to resolve divergences which took place during less than 40 Myr. The present paper takes littorinid phylogeny as a case study to reevaluate the utility of the molecule for resolving recent divergences. Two data sets for nine species of the snail family Littorinidae were analyzed, both separately and combined. One data set comprised 7 new complete 18S rRNA sequences aligned with 2 published littorinid sequences; the other comprised 12 morphological, 1 biochemical, and 2 18S rRNA secondary structure characters. On the basis of its ability to confirm generally accepted relationships and the congruence of results derived from the different data sets, it is concluded that 18S rRNA sequences do contain information to resolve ``rapid' cladogenetic events, provided that they occurred in the not too distant past. 18S rRNA sequences yielded support for (1) the branching order (L. littorea, (L. obtusata, (L. saxatilis, L. compressa))) and (2) the basal position of L. striata in the Littorina clade. Received: 6 February 1998 / Accepted: 20 March 1998     

An integrative approach to the evolution of shrimps of the genus Palaemon (Decapoda,Palaemonidae)

Shrimps of the genus Palaemon Weber, 1795 comprise of 86 species with a wide morphological and ecological variability along the tropical and temperate regions. Studies based on molecular data have indicated that despite a recent taxonomic rearrangement, it may remain not monophyletic. On the other hand, cladistic, morphological analyses have suggested the presence of synapomorphies, implying a natural status for the genus. In this work, a broad taxonomic and molecular sampling is applied to verify whether Palaemon is a monophyletic taxon and, based on the recovered phylogeny, identify geographical and morphological patterns related to the lineages. Partial sequences of 16S rRNA, histone H3 and 18S rRNA from 60 species of Palaemon and 15 species from other genera of Palaemonidae were analysed. In addition, previously used characters as well as novel diagnostic characters were scrutinized. The present phylogeny indicates that the species of Palaemon fall into three distinct lineages and that the colonization of America and Europe likely occurred multiple times. Morphological characters allow for the identification of at least four monophyletic groups in Palaemon; two of which are monospecific at the moment. Based on the present results, it may become necessary to establish two new genera (to accommodate Palaemon concinnus and Palaemon mercedae, respectively), as well as re‐erect the genus Alaocaris Holthuis, 1949 for Palaemon antrorum, potentially including a further six American species.     

Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: an example with the North American genera

The phylogenetic relationships among the numerous genera of diaptomid copepods remain elusive due to difficulties in obtaining sufficient numbers of phylogenetically informative morphological characters for cladistic analysis. Molecular phylogenetic techniques offer high potential to resolve phylogenetic relationships in the absence of sufficient morphological characters because of the ease in which many characters can be unambiguously coded. I present the first molecular phylogeny for diaptomid copepod genera using 18S rDNA. Specifically, I test Light’s (1939) hypothesis regarding the interrelationships among the North American diaptomid genera. The 18S phylogeny is remarkably consistent with Light’s hypothesis. The endemic North American genera represent a monophyletic group exclusive of the non-endemic genera. Moreover, his hypothesized basal genus for the North America genera, Hesperodiaptomus, is the basal genus in this analysis. However, his Leptodiaptomus group is not reciprocally monophyletic with his Hesperodiaptomus group, but is rather a derived member of the latter group. Finally, the genus Mastigodiaptomus is found to be more closely allied with the non-endemic genera, as Light suggested. This phylogeny contributes heavily to the understanding of phylogenetic relationships among North American diaptomids and has large implications for the systematics of diaptomids in general. The use of 18S rDNA sequences in phylogenetic analyses of diaptomid copepods can be used to confirm the monophyly of recognized genera, the interrelationships among genera, and subsequent biogeographic interpretation of the family’s diversification. The use of molecular data, such as 18S rDNA sequences, to test phylogenetic hypotheses based on a very limited number of morphological characters will be a particularly useful approach to phylogenetic analysis in this system.     

Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?

The Parabasala are a primitive group of protists divided into two classes: the trichomonads and the hypermastigids. Until recently, phylogeny and taxonomy of parabasalids were mainly based on the comparative analysis of morphological characters primarily linked to the development of their cytoskeleton. Recent use of molecular markers, such as small subunit (SSU) rRNA has led to now insights into the systematics of the Parabasala and other groups of prolists. An updated phylogeny based on SSU rRNA is provided and compared to that inferred from ultrastructural data. The SSU rRNA phylogeny contradicts the dogma equating simple characters with pumitive characters. Hypermastigids, possessing a hyperdeveloped cytoskeleton, exhibit the most basal emergence in the parabasalid lineage. Other observations emerge from the SSU rRNA analysis, such as the secondary loss of some cytoskeleton structures in all representatives of the Monocercomonadidae, the existence of secondarily free living taxa (reversibility of parasitism) and the evidence against the co-evolution of the endobiotic parabasalids and their animal hosts. According to phylogenies based on SSU rRNA, all the trichomonad families are not monophyletic groups, putting into question the validity of current taxonomic assignments. The precise branching order of some taxa remains unclear, but this issue can possibly be addressed by the molecular analysis of additional parabasalids. The goal of such additional analyses would be to propose, in a near future, a revision of the taxonomy of this group of protists that takes into account both molecular and morphological data.     

A new model Gondwanan taxon: systematics and biogeography of the harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi), with a taxonomic revision of genera from Australia and New Zealand

The phylogeny of the temperate Gondwanan harvestman family Pettalidae is investigated by means of a new morphological matrix of 45 characters, and DNA sequence data from five markers, including two nuclear ribosomal genes (18S rRNA and 28S rRNA), one nuclear protein coding gene (histone H3), and two mitochondrial genes–one protein coding (cytochrome c oxidase subunit I) and one ribosomal (16S rRNA). Phylogenetic analyses using an array of homology schemes (dynamic and static), criteria (parsimony and maximum likelihood), and sampling strategies (optimal trees versus Bayesian phylogenetics) all agree on the monophyly of Pettalidae as well as several of its subclades, each of which is restricted to a modern landmass. While most genera as traditionally defined are monophyletic, Rakaia and Neopurcellia, distributed across Queensland (Australia) and New Zealand, are not. Instead, the species from Queensland, previously described under three genera, constitute a well‐supported clade, suggesting that in this case biogeography prevails over traditional taxonomy. A taxonomic emendation of the genera from Queensland and New Zealand is presented, and the new genus Aoraki is erected to include the species of the New Zealand denticulata group. A biogeographical hypothesis of the relationships of the former temperate Gondwana landmasses (with the exception of Madagascar) is presented, although ambiguity in the deep nodes of the pettalid tree renders such inference provisional. The data suggest that neither the South African fauna, the New Zealand fauna nor the Australian fauna is monophyletic but instead monophyly is found at smaller geographic scales (e.g., Western Australia, Queensland, NE South Africa). © The Willi Hennig Society 2007.     

Evolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): insight from an expanded sampling of molecular data

Relative to its diversity (34 genera, 700 species), Scolopendromorpha has been undersampled in molecular phylogenetic analyses compared with the other chilopod orders. Previous analyses based on morphology have not resolved several key controversies in systematics and evolutionary morphology unambiguously. Here we apply new molecular and morphological data to scolopendromorph phylogenetics, with a focus on the evolution of blindness. The taxonomic sample includes 19 genera, many lacking previous molecular data, and diverse, cosmopolitan genera of Scolopendridae are sampled by multiple species. Phylogenetic analysis with Direct Optimization used 94 morphological characters and ca. 4.5 kb of sequence data from two nuclear (18S and 28S rRNA) and two mitochondrial (16S rRNA and COI) loci. A single most‐parsimonious cladogram selected after sensitivity analyses resolves Scolopendromorpha as monophyletic, and divides it into a blind clade of three families (Plutoniumidae, Cryptopidae, Scolopocryptopidae) and its ocellate sister group, Scolopendridae. Some species‐rich, cosmopolitan genera (Cormocephalus, Otostigmus, Scolopendra) in Scolopendridae are non‐monophyletic, and in several instances (e.g. New and Old World Scolopendra) relationships are more congruent with geographical distributions than with traditional classifications. The tribe Asanadini is particularly subject to parameter‐sensitivity, nesting in the combined analysis within Scolopendrini but as sister to all other Scolopendrinae for molecular data alone. The total‐evidence tree unambiguously optimizes trunk segmentation: a 23‐segmented trunk has a single origin in the blind clade. © The Willi Hennig Society 2011.     

Analysis of the systematic relationships among ticks of the genera Rhipicephalus and Boophilus (Acari: Ixodidae) based on mitochondrial 12S ribosomal DNA gene sequences and morphological characters

A portion of mitochondrial 12S rDNA sequences (337-355 base pairs) and 63 morphological characters of 36 hard-tick species belonging to 7 genera were analyzed to determine the phylogenetic relationships among groups and species of Rhipicephalus and between the genera Rhipicephalus and Boophilus. Molecular and morphological data sets were first examined separately. The molecular data were analyzed by maximum parsimony (MP), maximum likelihood, and neighbor-joining distance methods; the morphological data were analyzed by MP After their level of congruence was evaluated by a partition homogeneity test, all characters were combined and analyzed by MP. The branches of the tree obtained by combining the data sets were better resolved than those of the trees inferred from the separate analyses. Boophilus is monophyletic and arose within Rhipicephalus. Boophilus species clustered with species of the Rhipicephalus evertsi group. Most of the clustering within Rhipicephalus was, however, consistent with previous classifications based on morphological data. Morphological characters were traced on the molecular reconstruction in order to identify characters diagnostic for monophyletic clades. Within the Rhipicephalus sanguineus complex, the sequences of specimens morphologically identified as Rhipicephalus turanicus were characterized by a high level of variability, indicating that R. turanicus-like morphology may cover a spectrum of distinct species.     

Phylogeny of the cricket subfamily Eneopterinae (Orthoptera, Grylloidea, Eneopteridae) based on four molecular loci and morphology

The phylogenetic relationships of 39 species of Eneopterinae crickets are reconstructed using four molecular markers (16S rRNA, 12S rRNA, cytochrome b, 18S rRNA) and a large morphological data set. Phylogenetic analysis via direct optimisation of DNA sequence data using parsimony as optimality criterion is done for six combinations of weighting parameter sets in a sensitivity analysis. The results are discussed in a twofold purpose: first, in term of significance of the molecular markers for phylogeny reconstruction in Ensifera, as our study represents the first molecular phylogeny performed for this insect suborder at this level of diversity; second, in term of corroboration of a previous phylogeny of Eneopterinae, built on morphological data alone. The four molecular markers all convey phylogenetic signal, although variously distributed on the tree. The monophyly of the subfamily, that of three over five tribes, and of 10 over 13 genera, are recovered. Finally, previous hypotheses on the evolution of acoustic devices and signals in the Eneopterinae clade are briefly tested, and supported, by our new data set.