Phylogeny of Tunicata inferred from molecular and morphological characters

The phylogeny of the Tunicata was reconstructed using molecular and morphological characters. Mitochondrial cytochrome oxidase I (cox1) and 18S rDNA sequences were obtained for 14 and 4 tunicate species, respectively. 18S rDNA sequences were aligned with gene sequences obtained from GenBank of 57 tunicates, a cephalochordate, and a selachian craniate. Cox1 sequences were aligned with the sequence of two ascidians and a cephalochordate obtained from GenBank. Traditional, morphological, life history, and biochemical characters of larval and adult stages were compiled from the literature and analyzed cladistically. Separate and simultaneous parsimony analyses of molecular and morphological data were carried out. Aplousobranch ascidians from three different families were included in a molecular phylogenetic analysis for the first time. Analysis of the morphological, life history, and biochemical characters results in a highly unresolved tree. Aplousobranchiata form a strongly supported monophylum in the analysis of the 18S rDNA data, the morphological data, and the combined data set. Cionidae is not included in the Aplousobranchiata but nests within the Phlebobranchiata. Appendicularia (=Larvacea) nest within the 'Ascidiacea' as the sister taxon of Aplousobranchiata in the parsimony analysis of the 18S rDNA data and the combined analysis. A potential morphological synapomorphy of Aplousobranchiata plus Appendicularia is the horizontal orientation of the larval tail. In the 18S rDNA and the combined analysis, Thaliacea is included in the 'Ascidiacea' as the sister group to Phlebobranchiata. Pyrosomatida is found to be the sister taxon to the Salpidae in analyses of 18S rDNA and combined data, whereas the analysis of the morphological data recovers a sister group relationship between Doliolidae and Salpidae. Results of cox1 analyses are incongruent with both the 18S rDNA and the morphological phylogenies. Cox1 sequences may evolve too rapidly to resolve relationships of higher tunicate taxa. However, the cox1 data may be useful at lower taxonomic levels.     

New molecular data for tardigrade phylogeny, with the erection of Paramacrobiotus gen. nov.

Up to few years ago, the phylogenies of tardigrade taxa have been investigated using morphological data, but relationships within and between many taxa are still unresolved. Our aim has been to verify those relationships adding molecular analysis to morphological analysis, using nearly complete 18S ribosomal DNA gene sequences (five new) of 19 species, as well as cytochrome oxidase subunit 1 (COI) mitochondrial DNA gene sequences (15 new) from 20 species, from a total of seven families. The 18S rDNA tree was calculated by minimum evolution, maximum parsimony (MP) and maximum likelihood (ML) analyses. DNA sequences coding for COI were translated to amino acid sequences and a tree was also calculated by neighbour-joining, MP and ML analyses. For both trees (18S rDNA and COI) posterior probabilities were calculated by MrBayes. Prominent findings are as follows: the molecular data on Echiniscidae (Heterotardigrada) are in line with the phylogenetic relationships identifiable by morphological analysis. Among Eutardigrada, orders Apochela and Parachela are confirmed as sister groups. Ramazzottius (Hypsibiidae) results more related to Macrobiotidae than to the genera here considered of Hypsibiidae. Macrobiotidae and Macrobiotus result not monophyletic and confirm morphological data on the presence of at least two large groups within Macrobiotus. Using 18S rDNA and COI mtDNA genes, a new phylogenetic line has been identified within Macrobiotus , corresponding to the ' richtersi-areolatus group'. Moreover, cryptic species have been identified within the Macrobiotus ' richtersi group' and within Richtersius . Some evolutionary lines of tardigrades are confirmed, but others suggest taxonomic revision. In particular, the new genus Paramacrobiotus gen. n. has been identified, corresponding to the phylogenetic line represented by the ' richtersi-areolatus group'.     

Phylogeny of the Platyhelminthes and the evolution of parasitism

Robust phylogenies provide the basis for interpreting biological variation in the light of evolution. Homologous features provide phylogenetically informative characters whereas homoplasious characters provide phylogenetic noise. Both provide evolutionary signal. We have constructed molecular and morphologically based phylogenies of the phylum Platyhelminthes using a recently revised morphological character matrix and complete 18S and two partial 28S rRNA gene sequences in order to evaluate the emergence and subsequent divergence of parasitic forms. In total we examine 65 morphological characters, 97 18S rDNA, 41 Dl domain 28S rDNA, and 49 D3-D6 domain 28S rDNA sequences. For the molecular data there were 748, 132 and 249 phylogenetically informative sites for the 18S, Dl and D3-D6 28S rDNA data sets respectively. Morphological and molecular phylogenetic solutions are incongruent but not incompatible, and using the principles of conditional combination (18S rDNA + morphology passing Templeton's test) they demonstrate: a single and relatively early origin for the parasitic Neodermata (including the cestodes, trematodes and monogeneans); sister-group status between the cestodes and monogeneans, and between these taxa and the trematodes (digeneans and aspidogastreans). The sister-group to the Neodermata is likely to be a large clade of neoophoran turbellarians, based on combined evidence, or a clade consisting of the Fecampiid + Urastomid turbellarians, based on morphological evidence alone. The combined evidence solution for the phylogeny of fiatworms based on 18S rDNA and morphology is used to interpret morphological and life-history data and to support a model for the evolution and radiation of neodermatan parasites in the group.     

PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology,biogeography and evolution

Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR², the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six‐rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR² website, available at http://pfr2.sb-roscoff.fr , allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent.     

DISCRIMINATIVE POWER OF NUCLEAR rDNA SEQUENCES FOR THE DNA TAXONOMY OF THE DINOFLAGELLATE GENUS PERIDINIUM (DINOPHYCEAE)1

The genus Peridinium Ehrenb. comprises a group of highly diversified dinoflagellates. Their morphological taxonomy has been established over the last century. Here, we examined relationships within the genus Peridinium, including Peridinium bipes F. Stein sensu lato, based on a molecular phylogeny derived from nuclear rDNA sequences. Extensive rDNA analyses of nine selected Peridinium species showed that intraspecies genetic variation was considerably low, but interspecies genetic divergence was high (>1.5% dissimilarity in the nearly complete 18S sequence; >4.4% in the 28S rDNA D1/D2). The 18S and 28S rDNA Bayesian tree topologies showed that Peridinium species grouped according to their taxonomic positions and certain morphological characters (e.g., epithecal plate formula). Of these groups, the quinquecorne group (plate formula of 3′, 2a, 7″) diverged first, followed by the umbonatum group (4′, 2a, 7″) and polonicum group (4′, 1a, 7″). Peridinium species with a plate formula of 4′, 3a, 7″ diverged last. Thus, 18S and 28S rDNA D1/D2 sequences are informative about relationships among Peridinium species. Statistical analyses revealed that the 28S rDNA D1/D2 region had a significantly higher genetic divergence than the 18S rDNA region, suggesting that the former as DNA markers may be more suitable for sequence‐based delimitation of Peridinium. The rDNA sequences had sufficient discriminative power to separate P. bipes f. occultaum (Er. Lindem.) M. Lefèvre and P. bipes f. globosum Er. Lindem. into two distinct species, even though these taxa are morphologically only marginally discriminated by spines on antapical plates and the shape of red bodies during the generation of cysts. Our results suggest that 28S rDNA can be used for all Peridinium species to make species‐level taxonomic distinctions, allowing improved taxonomic classification of Peridinium.     

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.     

The phylogenetic position of the Prolecithophora (Rhabditophora, 'Platyhelminthes')

Complete 18S ribosomal DNA (rDNA) sequences and partial 28S rDNA sequences from a selection of rhabditophoran taxa were obtained and used in combination with literature data to determine the phylogenetic position of the Prolecithophora and of two families sometimes included in the Prolecithophora, the Urastomidae and the Genostomatidae. The results are largely compatible with earlier molecular studies when supported clades are considered, and adjusting for the denser taxonomic sampling of this study. The position of the Proseriata is not compatible with the taxon Seriata, which is rejected. The Rhabdocoela excluding the Fecampiida and the Neodermata is monophyletic. The phylogenetic position of the Neodermata cannot be determined, but its placement is not compatible with the proposed taxa Revertospermata and Mediofusata Kornakova & Joffe, 1999, which are rejected. The Urastomidae and the Genostomatidae in all analyses group with the Fecampiida, and it is our recommendation that these taxa be included in the Fecampiida. The amended Fecampiida always group separately from the Prolecithophora sensu stricto , the Rhabdocoela, and the Neodermata. Our analyses reveal the existence of a strongly supported clade consisting of Prolecithophora + Tricladida + the amended Fecampiida, and we propose the name Adiaphanida for this clade. Tentatively the sister group of the Prolecithophora is a clade consisting of the Tricladida + amended Fecampiida.     

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.     

Phylogenetic inference regarding Parergodrilidae and Hrabeiella periglandulata ('Polychaeta', Annelida) based on 18S rDNA, 28S rDNA and COI sequences

Parergodrilidae and Hrabeiella periglandulata are Annelida showing different combinations of clitellate-like and aclitellate characters. Similarities between both of these taxa and Clitellata have widely been regarded as the result of convergent evolution due to similar selection pressures. The position of the three taxa in the phylogenetic system of Annelida is still in debate. However, in analyses based on 18S rDNA sequences a close relationship of Parergodrilidae with Orbiniidae and Questidae was suggested. To infer their phylogeny the sequences of the 28S rDNA and of the cytochrome oxidase I (COI) gene of Stygocapitella subterranea , Parergodrilus heideri and H. periglandulata were determined. The data were extended by sequences of various species including species from Clitellata and Orbiniidae. Prior to tree reconstruction the dataset was analysed in detail for phylogenetic content by applying a sliding window analysis, a likelihood mapping and Modeltest V.3.04. Subsequently, generalized parsimony and maximum likelihood methods were employed. Clade robustness was estimated by bootstrapping. In addition, combined analyses of the sequences of 18S rDNA and 28S rDNA as well as of 18S rDNA, 28S rDNA and COI were performed. The combination of the data of the two structure genes and a mitochondrial gene improved the resolution obtained with the single datasets slightly. These analyses support a close relationship of Parergodrilidae and Orbiniidae but cannot resolve the position of H. periglandulata . In every analysis Clitellata cluster within 'Polychaeta', confirming previous investigations.     

New insights into polychaete phylogeny (Annelida) inferred from 18S rDNA sequences

Annelid systematics and the ingroup relationships of polychaete annelids are matter of ongoing debates in recent analyses. For the investigation of sedentary polychaete relationships a molecular phylogenetic analysis was conducted based on 94 sequences of 18S rDNA, including unpublished sequences of 13 polychaete species. The data set was analyzed with maximum parsimony and maximum likelihood methods, as wells as Bayesian inference. As in previous molecular analyses the monophyly of many traditional polychaete families is confirmed. No evidence has been found for a possible monophyly of Canalipalpata or Scolecida. In all analyses a placement of the Echiura as a derived polychaete ingroup with a close relationship to the Capitellidae is confirmed. The orbiniids appear paraphyletic with regard to Questa. Travisia is transferred from Opheliidae to Scalibregmatidae. The remaining opheliids include a yet undescribed ctenodrilid species from Elba, whereas the other investigated ctenodrilid Ctenodrilus serratus groups with the Cirratulidae and shows a close affinity to the cirratulid genus Dodecaceria. A common ancestry of Branchiomaldane and Arenicola, which has been predicted on morphological data, is confirmed by the analysis and a sistergroup relationship between Arenicolidae and Maldanidae is also recovered. These results support our assumption that on the basis of a broader taxon sampling the phylogenetic position of controversially discussed taxa can be inferred by using 18S rDNA sequence data.     

On the position of Archigetes and its bearing on the early evolution of the tapeworms

The tapeworm Archigetes sieboldi Leuckart, 1878 (Platyhelminthes: Cestoda: Caryophyllidea) has been cited as a likely representative of the "protocestode" condition, owing to its lack of segmentation and ability to attain sexual maturity in the invertebrate host (aquatic oligochaetes). The idea has been variously amplified or rejected in the literature, although the actual phylogenetic position of the species has not been investigated until now. New collections of Archigetes sp. from both its vertebrate and invertebrate hosts provided the opportunity to estimate its phylogenetic position with the use of molecular systematics, while prompting new analyses aimed at assessing the early diversification of the Cestoda. Additional collections representing the Amphilinidea, Caryophyllidea, and Gyrocotylidea were combined with published gene sequences to construct data sets of complete 18S (110 taxa) and partial (D1-D3) 28S (107 taxa) rDNA sequences, including 8 neodermatan outgroup taxa. Estimates resulting from Bayesian inference, maximum likelihood, and maximum parsimony analyses of the separate and combined data sets supported a derived position of the genus within the Caryophyllidea, and thus reject the idea that Archigetes sp. may exemplify a "primitive" condition. Topological constraint analyses rejected the hypothesis that Archigetes represents the most basal lineage of the Eucestoda, but did not rule out that it could represent the earliest branching taxon of the Caryophyllidea. In all analyses, the Eucestoda were monophyletic and supported basal positions of the nonsegmented Caryophyllidea and Spathebothriidea relative to other major lineages of the Eucestoda, implying that segmentation is a derived feature of the common ancestor of the di- and tetrafossate eucestodes. However, constraint analyses could not provide unequivocal evidence as to the precise branching patterns of the cestodarian, spathebothriidean, and caryophyllidean lineages. Phylogenetic analyses favor the interpretation that sexual maturity of Archigetes sp. in the invertebrate host, and similar examples in members of the Spathebothriidea, are the result of progenesis and have little if any bearing on understanding the protocestode condition.     

Progenesis in Eunicida ("Polychaeta," Annelida)--separate evolutionary events? Evidence from molecular data

The Eunicida are a well-defined annelid taxon currently comprising Dorvilleidae, Lumbrineridae, Eunicidae, Onuphidae, and Hartmanniellidae. Especially the Dorvilleidae include several species of small body size and apparently simple organisation, resembling larvae and juveniles of larger species. One hypothesis to explain the evolution of such species is progenesis. By this criterion the Dinophilidae were included in this group as well. Although their overall similarity suggests monophyly, parallel evolution of such progenetic taxa cannot be excluded. To infer the phylogeny of Eunicida and their presumed relationship to Dinophilidae and progenetic dorvilleids, 18S rDNA sequences from various Dinophilidae, Dorvilleidae, and members of other Eunicida were determined. The data matrix were extended by adding sequences from several annelid and molluscan species and analysed with maximum-parsimony, distance, and maximum-likelihood algorithms. Highly significant bootstrap-values support monophyly of the Dinophilidae, of a clade enclosing the Eunicidae and the Onuphidae, and of a dorvilleid group comprising six species including the presumed progenetic Parapodrilus psammophilus. The position of the Dinophilidae remains unresolved, so that their inclusion within the Eunicida can neither be corroborated nor rejected. However, a constraint monophyly of Dinophilidae and P. psammophilus is rejected by several tests, substantiating the hypothesis of separate progenetic evolutionary events. Furthermore, the molecular data indicate polyphyly of the Dorvilleidae.     

Morphology and molecular phylogeny of Pauciconfibuloides amazonica gen. n. sp. n. (Platyhelminthes,Monogenoidea) parasitizing the Amazonian croaker Plagioscion squamosissimus

An integrative study was performed to understand the phylogenetic relationships of an undescribed, freshwater species of microcotylid parasitizing Plagioscion squamosissimus from the Amazon River Basin. Based on morphological and molecular analysis (18S rDNA and partial 28S rDNA genes), a new genus is proposed to accommodate this new species, Pauciconfibuloides amazonica gen. n. sp. n. The new genus is closely related to Protastomicrocotylinae and Pauciconfibula by sharing the vagina, male copulatory organ, and genital atrium all unarmed. However, Pauciconfibuloides gen. n. can be distinguished from those taxa by the prostatic system and position of the vaginal pore. Molecular phylogenetic inference suggests a sister relationship with species of Polylabris (Prostatomicrocotylinae), but to date, there are no available 18S or 28S rDNA sequences of Pauciconfibula to be compared. This is the first report of a microcotylid parasitizing a freshwater sciaenid from South America.     

Phylogenetic Relationships Among Selected Heteroderoidea Based on 18S and ITS Ribosomal DNA

In a study of relationships among selected cyst-forming and noncyst-forming species of Heteroderoidea, combined sequences comprised of DNA from part of the conserved 18S ribosomal RNA gene (rDNA) plus the complete ITS rDNA segment were more similar to analyses based on the ITS data alone than to analyses based on the 18S data alone. One of the two noncyst-forming species, Ekphymatodera thomasoni, grouped with cyst-forming species of Heteroderoidea. Bilobodera flexa, also a noncyst-forming species, was separated from all the other taxa by a long branch. Afenestrata koreana, with a weakly sclerotized cyst, grouped closely with H. bifenestra. These observations suggest that phylogenetic analyses using molecular data may aid in our understanding of the evolution of cyst formation in nematodes, including the possibility of secondary loss. The usefulness of molecular phylogenetic analyses in nematodes may depend more on the particular selection of taxa than on mere addition of data from additional genes.     

The interrelationships of proseriata (Platyhelminthes: seriata) tested with molecules and morphology

Proseriate flatworms are common members of the interstitial benthic fauna worldwide, predominantly occupying marine environments. As minute animals, having relatively few characters useful for cladistic analysis, they have been difficult to present in a phylogenetic framework using morphology alone. Here we present a new morphological matrix consisting of 16 putatively homologous characters and two molecular data sets to investigate further this major group of free-living members of the Platyhelminthes. Complete 18S rDNA (representing 277 parsimony-informative characters) from 17 ingroup taxa and partial 28S rDNA spanning variable expansion regions D1 to D3 and D1 to D6 (representing 219 and 361 parsimony-informative characters, respectively) from 27 and 14 ingroup taxa, respectively, were determined and aligned as complementary data sets. Morphological and molecular data sets were analyzed separately and together to determine underlying phylogenetic patterns and to resolve conflict between published scenarios based on morphology alone. The monophyly of the Proseriata cannot be confirmed categorically with any of these data sets. However, the constituent taxa are confirmed as basal members of the Neoophora, and a sister group relationship with Tricladida is rejected. Similarly, the monophyly of one of the two subtaxa of the Proseriata, the Lithophora, could not be confirmed with molecules. Concerning intragroup relationships, we could reject one of the two phylogenetic trees formerly proposed, as well as the clade Otoplanidae + Coelogynoporidae. However, a clade Otoplanidae + Archimonocelididae + Monocelididae (to which the Monotoplanidae belong) was supported, and the position of the genus Calviria shifted from the Archimonocelididae to the Coelogynoporidae.     

The sister group relationship of Aeolosomatidae and Potamodrilidae (Annelida: “Polychaeta”) — a molecular phylogenetic approach based on 18S rDNA and cytochrome oxidase I

Aeolosomatidae and Potamodrilidae are small meiofauna annelids of apparently simple organization and uncertain phylogenetic position. Potamodrilidae was regarded either as a subtaxon of Aeolosomatidae, united with them as Aphanoneura, or entirely unrelated to Aeolosomatidae. Moreover, the groups have been placed in various positions within Annelida: as sister group of Clitellata, as a highly derived clitellate taxon, or excluded from Clitellata and not closely related to them due to great morphological differences. Although molecular studies give strong support for the exclusion of these two taxa from Clitellata their questionable sister group relationship to each other has not been addressed specifically. In the present study sequences of the nuclear 18S rDNA and the mitochondrial Cytochrome Oxidase I gene were used for addressing this question. In addition to the available nuclear 18S rDNA sequences, partial sequences of Cytochrome Oxidase I of Rheomorpha neiswestnovae (Lastochkin, 1935) and Potamodrilus fluviatilis Lastochkin, 1935 along with other polychaete taxa were determined. Combined analyses of these two genes were conducted using Maximum Parsimony and Bayesian analysis. A sister group relationship of Aeolosomatidae and Potamodrilidae is significantly supported in all. As in previous studies a relationship to Clitellata is not supported but the phylogenetic position of both Aeolosomatidae and Clitellata within the polychaetes remains enigmatic.     

Molecular phylogenetic analysis of ant subfamily relationship inferred from rDNA sequences

The relationships among ant subfamilies were studied by phylogenetic analysis of rDNA sequences of 15 species from seven subfamilies. PCR primers were designed on the basis of the rDNA sequence of the Australian bulldog ant, Myrmecia croslandi, previously determined. Phylogenetic trees were constructed using sequences of a fragment of 18S rDNA (1.8 kb), a fragment of 28S rDNA (0.7 kb excluding variable regions) and a combination of the 18S and 28S rDNAs, by neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML). rDNA sequences corresponding to the same fragments from three non-ant hymenopteran species (a sawfly, a bee and a wasp) were employed as outgroups. These trees indicated that the ant subfamilies were clustered singly, and, among the seven subfamilies examined, Ponerinae and six other subfamilies are in a sister-groups relationship. The relationship among the six subfamilies, however, was not clarified. The phylogenetic trees constructed in the present study are not in contradiction to the tree from cladistic analysis of morphological data by Baroni Urbani et al. (1992) and the tree from morphological and molecular data (Ward and Brady, 2003), but are inconsistent with the traditional phylogeny. The present results thus raise a question as to the status of some traditionally employed "key" morphological characters. The present results also call for a reexamination of Amblyopone traditionally treated as a member of Ponerinae as belonging to a new subfamily.     

A molecular and karyological approach to the taxonomy of Nautilus

Nautiloids, the externally shelled cephalopods of Cambrian origin, are the most ancient lineage among extant cephalopods. Their ancestral characters are explored based on morphological and molecular data (18S rDNA sequence) to investigate the evolution of present cephalopod lineages. Among molluscs, nautilus 18S rDNA gene is the longest reported so far, due to large nucleotidic insertions. By comparison with other 18S sequences, the complete gene of N. macromphalus helps to clarify the taxonomic status of the three universally recognised Nautilus species. The range of interspecific molecular differences supports separation of the present species into two surviving ectocochleate genera, Nautilus and Allonautilus. Nautiloid 18S is considered as corresponding to the ancestral form of 18S as is the number of chromosomes in Nautilus (52), the lowest among cephalopods. Comparison of karyological characteristics amongst cephalopods in a phylogenetic context suggests a possible correlation between duplication events and lineage divergence.     

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.