16S rDNA Data Research Articles

Bias and conflict in phylogenetic inference of myco-heterotrophic plants: a case study in Thismiaceae.

Due to morphological reduction and absence of amplifiable plastid genes, the identification of photosynthetic relatives of heterotrophic plants is problematic. Although nuclear and mitochondrial gene sequences may offer a welcome alternative source of phylogenetic markers, the presence of rate heterogeneity in these genes may introduce bias/systematic error in phylogenetic analyses. We examine the phylogenetic position of Thismiaceae based on nuclear 18S rDNA and mitochondrial atpA DNA sequence data, as well as using parsimony, likelihood and Bayesian inference methods. Significant differences in evolutionary rates of these genes between closely related taxa lead to conflicting results: while parsimony analyses of 18S rDNA and combined data strongly support the monophyly of Thismiaceae, Bayesian inference, with and without a relaxed molecular clock, as well as the Swofford-Olsen-Waddell-Hillis (SOWH) test confidently reject this hypothesis. We show that rate heterogeneity in our data leads to long-branch attraction artifacts in parsimony analysis. However, using model-based inference methods the question of whether Thismiaceae are monophyletic remains elusive. On the one hand maximum likelihood nonparametric bootstrapping and parametric hypothesis tests fail to support a paraphyletic Thismiaceae, on the other hand Bayesian inference methods (both without and with a relaxed clock) significantly reject a monophyletic Thismiaceae. These results show that an adequate sampling, the use of rate homogeneous data, and the application of different inference methods are important factors for developing phylogenetic hypotheses of myco-heterotrophic plants. © The Willi Hennig Society 2009.

The Chloroplast Genomes of the Green Algae Pyramimonas, Monomastix, and Pycnococcus Shed New light on the Evolutionary History of Prasinophytes and the Origin of the Secondary Chloroplasts of Euglenids

Because they represent the earliest divergences of the Chlorophyta and include the smallest known eukaryotes (e.g., the coccoid Ostreococcus), the morphologically diverse unicellular green algae making up the Prasinophyceae are central to our understanding of the evolutionary patterns that accompanied the radiation of chlorophytes and the reduction of cell size in some lineages. Seven prasinophyte lineages, four of which exhibit a coccoid cell organization (no flagella nor scales), were uncovered from analysis of nuclear-encoded 18S rDNA data; however, their order of divergence remains unknown. In this study, the chloroplast genome sequences of the scaly quadriflagellate Pyramimonas parkeae (clade I), the coccoid Pycnococcus provasolii (clade V), and the scaly uniflagellate Monomastix (unknown affiliation) were determined, annotated, and compared with those previously reported for green algae/land plants, including two prasinophytes (Nephroselmis olivacea, clade III and Ostreococcus tauri, clade II). The chlorarachniophyte Bigelowiella natans and the euglenid Euglena gracilis, whose chloroplasts originate presumably from distinct green algal endosymbionts, were also included in our comparisons. The three newly sequenced prasinophyte genomes differ considerably from one another and from their homologs in overall structure, gene content, and gene order, with the 80,211-bp Pycnococcus and 114,528-bp Monomastix genomes (98 and 94 conserved genes, respectively) resembling the 71,666-bp Ostreococcus genome (88 genes) in featuring a significantly reduced gene content. The 101,605-bp Pyramimonas genome (110 genes) features two conserved genes (rpl22 and ycf65) and ancestral gene linkages previously unrecognized in chlorophytes as well as a DNA primase gene putatively acquired from a virus. The Pyramimonas and Euglena cpDNAs revealed uniquely shared derived gene clusters. Besides providing unequivocal evidence that the green algal ancestor of the euglenid chloroplasts belonged to the Pyramimonadales, phylogenetic analyses of concatenated chloroplast genes and proteins elucidated the position of Monomastix and showed that the Mamiellales, a clade comprising Ostreococcus and Monomastix, are sister to the Pyramimonadales + Euglena clade. Our results also revealed that major reduction in gene content and restructuring of the chloroplast genome occurred in conjunction with important changes in cell organization in at least two independent prasinophyte lineages, the Mamiellales and the Pycnococcaceae.

Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson

Phylogenetic relationships and species boundaries of Australian burrowing freshwater crayfish belonging to the genera Engaeus, Engaewa, Geocharax, Gramastacus and Tenuibranchiurus are investigated using combined mitochondrial and nuclear DNA sequence data and Bayesian and Maximum Parsimony methods. Phylogenies are statistically compared to previously published hypotheses. Engaeus, Engaewa, Geocharax, Gramastacus and Tenuibranchiurus form a strongly supported monophyletic clade. This grouping is independently supported by morphology but unites geographically highly disjunct lineages. Our data show two cryptic species in Geocharax, one cryptic species in Gramastacus and two cryptic species within the highly divergent Engaeus lyelli lineage. Using a Bayesian relaxed molecular clock method, the 16S rDNA data show generic-level diversification coinciding with the transition from a wet to arid palaeoclimate near the mid Miocene.

Phylogeny of Catenulida and support for Platyhelminthes

Molecular studies have shown that Platyhelminthes is polyphyletic, placing Rhabditophora within Lophotrochozoa, whereas Acoela and Nemertodermatida are separate early bilaterian branches. However, there has been little evidence to support the position of Catenulida, a group that was traditionally classified within Platyhelminthes. In Ehlers’ pioneering cladistic system of the Platyhelminthes they were placed as the earliest clade. Other morphologists have considered the Catenulida as an early bilaterian clade separate from Rhabditophora, a position that was supported in an early molecular study. Subsequent molecular phylogenetic studies, which placed Catenulida as the sister group of Rhabditophora with no or low branch support, included 18S rDNA data from only one or two catenulid species. The aims of the present study were (1) to test the putative sister-group relationship of Catenulida and Rhabditophora by improving the taxon sampling of molecular data spanning a larger part of catenulid taxonomic diversity and (2) to provide a phylogenetic framework for the systematization of Catenulida. Twelve catenulid species were sampled around Sweden. Both the 18S rDNA gene and the 28S rDNA gene were sequenced and analysed in a Metazoa-wide data set within parsimony and Bayesian frameworks. The results unambiguously support Catenulida as the sister group of Rhabditophora within Lophotrochozoa. Parsimony-based inferences about the common ancestor of Catenulida and Rhabditophora are presented. A definition of the name Platyhelminthes is suggested.

Molecular systematics of the Capoeta (Cypriniformes: Cyprinidae) species complex inferred from mitochondrial 16S rDNA sequence data

Capoeta species from Anatolia, Turkey were studied using mitochondrial 16S rDNA gene sequencing to determine whether traditionally defined species and subspecies correspond to taxonomic entities. The systematic topology and genetic divergence for C. antalyensis, C. pestai, C. tinca, C. trutta, C. damascina and C. barroisi was enough to classify them as different species. The 16S rDNA data does not corroborate the use of the classic subspecies nomenclature for C. c. angorae, C. c. capoeta and C. c. sieboldi, but supports the use of species nomenclature for C. angorae, C. capoeta and C. sieboldi. On the other hand the genetic evidence does not support the classic subspecies designation for C.c. umbla and C.c. koswigi because no fixed differences were observed between them. The systematic topology and haplotype differences between these lineages may suggest that these two subspecies are genetically contiguous, and are a member of the species C. trutta. Based on combined molecular and morphologic data, the present study suggests that two undescribed Capoeta species may exist in Anatolia; one species in the Goksu River, and the second species in the Dalaman stream. The 16S mtDNA gene is a useful genetic marker for species and subspecies identification of the genus Capoeta because of its interspecific heterogeneity producing a species specific pattern.

DEEP DIVISION IN THE CHLOROPHYCEAE (CHLOROPHYTA) REVEALED BY CHLOROPLAST PHYLOGENOMIC ANALYSES(1).

The Chlorophyceae (sensu Mattox and Stewart) is a morphologically diverse class of the Chlorophyta displaying biflagellate and quadriflagellate motile cells with varying configurations of the flagellar apparatus. Phylogenetic analyses of 18S rDNA data and combined 18S and 26S rDNA data from a broad range of chlorophycean taxa uncovered five major monophyletic groups (Chlamydomonadales, Sphaeropleales, Oedogoniales, Chaetophorales, and Chaetopeltidales) but could not resolve their branching order. To gain insight into the interrelationships of these groups, we analyzed multiple genes encoded by the chloroplast genomes of Chlamydomonas reinhardtii P. A. Dang. and Chlamydomonas moewusii Gerloff (Chlamydomonadales), Scenedesmus obliquus (Turpin) Kütz. (Sphaeropleales), Oedogonium cardiacum Wittr. (Oedogoniales), Stigeoclonium helveticum Vischer (Chaetophorales), and Floydiella terrestris (Groover et Hofstetter) Friedl et O'Kelly (Chaetopeltidales). The C. moewusii, Oedogonium, and Floydiella chloroplast DNAs were partly sequenced using a random strategy. Trees were reconstructed from nucleotide and amino acid data sets derived from 44 protein-coding genes of 11 chlorophytes and nine streptophytes as well as from 57 protein-coding genes of the six chlorophycean taxa. All best trees identified two robustly supported major lineages within the Chlorophyceae: a clade uniting the Chlamydomonadales and Sphaeropleales, and a clade uniting the Oedogoniales, Chaetophorales, and Chaetopeltidales (OCC clade). This dichotomy is independently supported by molecular signatures in chloroplast genes, such as insertions/deletions and the distribution of trans-spliced group II introns. Within the OCC clade, the sister relationship observed for the Chaetophorales and Chaetopeltidales is also strengthened by independent data. Character state reconstruction of basal body orientation allowed us to refine hypotheses regarding the evolution of the flagellar apparatus.

Extended hydroxyarchaeol, a novel lipid biomarker for anaerobic methanotrophy in cold seepage habitats

A new archaeal lipid biomarker, C 20,25 sn-2, C-7 hydroxy isoprenoid glycerol diether, has been identified in methane-related carbonates from six methane seep locations. The molecular structure resembles that of sn-2 hydroxyarchaeol but the hydroxy group-bearing moiety at the sn-2 position comprises a regular C 25 instead of a C 20 isoprenoid chain. Compound specific stable carbon isotope measurements revealed δ 13C values ranging from −96‰ to −129‰, which are similar to δ 13C values of sn-2 hydroxyarchaeol. This supports the origin of the novel compound from archaea involved in the anaerobic oxidation of methane. It also suggests a common source, i.e. archaea within the ANME-2 group, which is consistent with the previously reported 16S rDNA data for the same samples. The frequent appearance of the novel sn-2 isoprenoidal hydroxy glycerol diether in cold seepage sediments with high salinity environments, and its distinct structural similarities with membrane lipids of halophilic and methanogenic microbes, suggests that ANME-2 methanotrophic archaea thriving at elevated salinity are the possible biological source for this specific lipid.

Towards a DNA taxonomy of Caribbean demosponges: a gene tree reconstructed from partial mitochondrial CO1 gene sequences supports previous rDNA phylogenies and provides a new perspective on the systematics of Demospongiae

We present the most comprehensive cytochrome oxidase subunit 1 gene tree published to date for demosponges based on new sequences. The CO1 barcoding fragment is sequenced for 65 species from the Caribbean Sea, and its gene tree reconstructed. Although its deeper nodes are not particularly well-supported, the gene tree provides a variety of information for new phylogenetic patterns, as well as support for previously published 28S rDNA gene trees. In our analysis Halichondriidae cluster with Suberitidae, supporting previous 28S rDNA data. Chelae-bearing Poecilosclerida are monophyletic but most taxa lacking chelae in this dataset cluster more distantly. Haplosclerida are not resolved monophyletically under this fragment. While some species exhibit distinct barcodes, some genera contain species that share CO1 haplotypes.

COMPARATIVE MOLECULAR EVOLUTION OF NEWLY DISCOVERED PICOCYANOBACTERIAL STRAINS REVEALS A PHYLOGENETICALLY INFORMATIVE VARIABLE REGION OF β‐PHYCOERYTHRIN1

The genetic diversity and phylogenetic position of 10 strains of picocyanobacteria from the Arabian Sea were examined using partial sequences from three loci: 16S rDNA, RNA polymerase rpoC1, and two elements of the phycoerythrin (PE) locus, cpeA and cpeB which encode for the α and β subunit of PE. Nine of the strains showed nearly identical spectral phenotypes based on the in vivo excitation spectrum for PE fluorescence emission and appear to be strains synthesizing a phycourobilin (PUB)–lacking PE. These strains include one, Synechococcus sp. G2.1, already known to be closely related to filamentous cyanobacteria and not to the commonly studied 5.1 subcluster of marine Synechococcus. The 10th strain was a PE‐lacking strain that was of interest because it was isolated from open‐ocean conditions where picocyanobacteria with this phenotype are relatively uncommon. Phylogenetic analysis of the concatenated 16S rDNA and rpoC1 data sets showed that none of the previously described strains were members of the 5.1 subcluster of marine Synechococcus, nor were they closely related to strain G2.1. Instead, they form a well‐supported and previously undescribed clade of cyanobacteria that is sister to Cyanobium. Thus, these strains represent the first PE‐containing Cyanobium from oceanic waters, and the lineage they define includes a strain with a PE‐lacking phenotype from the same environment. Analysis of the PE sequence data showed the PE apoprotein has evolved independently in the G2.1 lineage and the Cyanobium‐like lineage represented by the study strains. It also revealed a hypervariable region of the β‐subunit not described previously; variation in this region shows a pattern among a wide range of PE‐containing organisms congruent with the phylogenetic relationships inferred from other genes. This suggests that the PUB‐lacking spectral phenotype is more likely to have evolved in distantly related phylogenetic lineages by either divergent or convergent evolution than by lateral gene transfer. Both the conserved PE gene sequences and the inferred amino acid sequences for the hypervariable region show considerable divergence among Prochlorococcus PEs, red algal PEs, PUB‐containing PEs from the marine Synechococcus 5.1 subcluster, PEs from the Cyanobium‐like strains, and PEs from other cyanobacteria (including strain G2.1). Thus, it appears that the hypervariable region of the PE gene can be used as a taxon‐specific marker.

Phylogeny and evolution of Burmanniaceae (Dioscoreales) based on nuclear and mitochondrial data

The mycoheterotrophic Burmanniaceae are one of the three families currently recognized in the order Dioscoreales. Phylogenetic inference using nucleotide sequences of the nuclear 18S rDNA region and the mitochondrial nad1 b-c intron revealed two well-supported, major lineages within the family, corresponding to the two tribes recognized in the family: Burmannieae and Thismieae. All data supported a strong relationship between Thismieae and Tacca (Dioscoreaceae) making both Burmanniaceae and Dioscoreaceae polyphyletic. The three largest Burmanniaceae genera, Burmannia, Gymnosiphon, and Thismia, are paraphyletic. The splitting of Burmanniaceae into Burmannieae and Thismieae indicates two independent origins of mycoheterotrophy and correlated loss of chlorophyll in Dioscoreales. In the genus Burmannia, in which many species still contain chlorophyll, the achlorophyllous species are nested in between the autotrophic species, suggesting many independent changes from autotrophy to heterotrophy or vice versa. A Bayesian relative rates test on the 18S rDNA data showed considerable variation in substitution rates among Burmanniaceae. The substitution rates in all Thismieae and many Burmannieae are significantly faster than in Dioscoreaceae, but there seems to be no correlation between rate increases and the loss of photosynthesis.

Identification of Enterobacter sakazakii from closely related species: The use of Artificial Neural Networks in the analysis of biochemical and 16S rDNA data

BackgroundEnterobacter sakazakii is an emergent pathogen associated with ingestion of infant formula and accurate identification is important in both industrial and clinical settings. Bacterial species can be difficult to accurately characterise from complex biochemical datasets and computer algorithms can potentially simplify the process.ResultsArtificial Neural Networks were applied to biochemical and 16S rDNA data derived from 282 strains of Enterobacteriaceae, including 189 E. sakazakii isolates, in order to identify key characteristics which could improve the identification of E. sakazakii. The models developed resulted in a predictive performance for blind (validation) data of 99.3 % correct discrimination between E. sakazakii and closely related species for both phenotypic and genotypic data. Three main regions of the partial rDNA sequence were found to be key in discriminating the species. Comparison between E. sakazakii and other strains also constitutively positive for expression of the enzyme α-glucosidase resulted in a predictive performance of 98.7 % for 16S rDNA sequence data and 100% for phenotypic data.ConclusionThe computationally based methods developed here show a remarkable ability in reducing data dimensionality and complexity, in order to eliminate noise from the system in order to facilitate the speed and reliability of a potential strain identification system. Furthermore, the approaches described are also able to provide valuable information regarding the population structure and distribution of individual species thus providing the foundations for novel assays and diagnostic tests for rapid identification of pathogens.

Phylogenetic analysis of the insect order Odonata using 28S and 16S rDNA sequences: a comparison between data sets with different evolutionary rates

AbstractMolecular phylogenetic analyses were conducted for the insect order Odonata with a focus on testing the effectiveness of a slowly evolving gene to resolve deep branching and also to examine: (i) the monophyly of damselflies (the suborder Zygoptera); and (ii) the phylogenetic position of the relict dragonfly Epiophlebia superstes. Two independent molecular sources were used to reconstruct phylogeny: the 16S rRNA gene on the mitochondrial genome and the 28S rRNA gene on the nuclear genome. A comparison of the sequences showed that the obtained 28S rDNA sequences have evolved at a much slower rate than the 16S rDNA, and that the former is better than the latter for resolving deep branching in the Odonata. Both molecular sources indicated that the Zygoptera are paraphyletic, and when a reasonable weighting for among‐site rate variation was enforced for the 16S rDNA data set, E. superstes was placed between the two remaining major suborders, namely, Zygoptera and Anisoptera (dragonflies). Character reconstruction analysis suggests that multiple hits at the rapidly evolving sites in the 16S rDNA degenerated the phylogenetic signals of the data set.

PROPOSAL OF THE EUPTILOTEAE HOMMERSAND ET FREDERICQ, TRIB. NOV. AND TRANSFER OF SOME SOUTHERN HEMISPHERE PTILOTEAE TO THE CALLITHAMNIEAE (CERAMIACEAE, RHODOPHYTA)1

Morphological and molecular studies demonstrate that the tribe Ptiloteae (Ceramiaceae, Ceramiales) is polyphyletic. The Ptiloteae, sensu stricto, occur only in the Northern Hemisphere and all Southern Hemisphere representatives belong in other tribes. Three genera (Euptilota, Seirospora, and Sciurothamnion) are transferred to the Euptiloteae Hommersand et Fredericq, trib. nov., and the Callithamnieae is revised to include three Ptilota‐like genera, Georgiella, Falklandiella, and Diapse, and two new genera. Heteroptilon Hommersand, gen. nov. is erected to receive Euptilota pappeana Kützing 1849 and Aglaothamnion rigidulum De Clerck, Bolton, Anderson et Coppejans 2004 from South Africa, and Aristoptilon Hommersand et W. A. Nelson, gen. nov. is established to receive Euptilota mooreana Lindauer 1949 from New Zealand. The principal difference between the Euptiloteae and the Callithamnieae is seen in the earliest stages after fertilization. The fertilized carpogonium enlarges and forms a pair of tube‐like protuberances directed toward the auxiliary cells that are cut off as connecting cells in the Euptiloteae, whereas in the Callithamnieae the carpogonium usually divides into two cells, each of which cuts off a small connecting cell that fuses with an adjacent enlarging auxiliary cell. Nuclei are terminal in spermatangia of the Euptiloteae, subtended by mucilaginous vesicles, and are medial in the Callithamnieae situated between apical and basal vesicles. The Euptiloteae and Callithamnieae (including the Ptilota‐like members) are each strongly supported in maximum‐likelihood tree topologies resulting from analyses of combined 18S rDNA, 28S rDNA, 16S rDNA, and rbcL data sets. Their sister relationship is also well supported.

Unearthing the Molecular Phylodiversity of Desert Soil Green Algae (Chlorophyta)

Deserts are not usually considered biodiversity hotspots, but desert microbiotic crust communities exhibit a rich diversity of both eukaryotic and prokaryotic life forms. Like many communities dominated by microscopic organisms, they defy characterization by traditional species-counting approaches to assessing biodiversity. Here we use exclusive molecular phylodiversity (E) to quantify the amount of evolutionary divergence unique to desert-dwelling green algae (Chlorophyta) in microbiotic crust communities. Given a phylogenetic tree with branch lengths expressed in units of expected substitutions per site, E is the total length of all tree segments representing exclusively desert lineages. Using MCMC to integrate over tree topologies and branch lengths provides 95% Bayesian credible intervals for phylodiversity measures. We found substantial exclusive molecular phylodiversity based on 18S rDNA data, showing that desert lineages are distantly related to their nearest aquatic relatives. Our results challenge conventional wisdom, which holds that there was a single origin of terrestrial green plants and that green algae are merely incidental visitors rather than indigenous components of desert communities. We identify examples of lineage diversification within deserts and at least 12 separate transitions from aquatic to terrestrial life apart from the most celebrated transition leading to the embryophyte land plants. [Bayesian phylogenetics; biodiversity; exclusive molecular phylodiversity; microbiotic crusts.].

The complete mitochondrial genome of Anisakis simplex (Ascaridida: Nematoda) and phylogenetic implications

We determined the nucleotide sequence of the complete mitochondrial genome of the nematode species Anisakis simplex. The genome is circular, 13,916 bp in size and conforms to the general characteristics of nematode mitochondrial DNAs. The gene arrangement of A. simplex is the same as that of Ascaris suum and almost identical to those of rhabditid species with a minor exception concerning the relative position of the AT-rich and non-coding regions and radically different from those of spirurid species. Along with comparisons of gene arrangement, phylogenetic analyses (maximum parsimony, neighbour joining and maximum likelihood methods) based on concatenated amino acid sequences of 12 protein-coding genes from 13 nematode species provided strong support for the sister-group relationship between Ascaridida and Rhabditida. The Shimodaira–Hasegawa and Templeton's tests both rejected the alternative hypothesis of a closer relationship between Ascaridida and Spirurida. These results contradicted the traditional view of nematode classification and a recent molecular phylogenetic study of 18S rDNA data that assigned Ascaridida and Spirurida as being a sister-group. Mapping of gene arrangement across the phylogenetic tree lead to the assumption that the conserved gene arrangement found in Ascaridida–Rhabditida members might have been acquired after the most recent common ancestor of ascaridid/rhabditid members branched off from the basal stock of the rhabditid lineage.

Caespitotheca gen. nov., an ancestral genus in the Erysiphales

The phylogenetic position of Uncinula forestalis within the Erysiphales has been inferred from 5.8S, 18S, and 28S rDNA sequences. Although the appendages of the ascomata are Uncinula-like, i.e. unbranched with curved-coiled apices, U. forestalis is situated at the very base of the large Erysiphales cluster, far from the 'Pseudoidium' clade (Erysiphe, including Microsphaera and Uncinula) and separate from the recently introduced basal genus Parauncinula. U. forestalis differs morphologically from the species of Erysiphe sect. Uncinula in having terminal, fasciculate (as in Podosphaera tridactyla), septate ascoma appendages and a Euoidium-like anamorph (conidia catenate). In Parauncinula, the appendages are also terminal but not fasciculate, the ascospores are curved, and the anamorph is lacking. Uncinula forestalis is a basal, tree-inhabiting powdery mildew with some additional ancestral characteristics, including Uncinula-like appendages and 6-8-spored asci. The new genus Caespitotheca gen. nov. is described with C. forestalis comb. nov. (syn. Uncinula forestalis) as the type species. We calculated the timing of the divergence of U. forestalis and P. septata using a molecular clock of the Erysiphales (6.5 x 10-10 changes per site per year in domains D1 and D2 of 28S rDNA) and a 28S rDNA data set. The results suggest that the divergence of U. forestalis and P. septata from other Ervsiphales occurred between 90 and 80 Myr ago; i.e. the divergence of the two ancestral species may have occurred in the late Cretaceous.

Phylogenetic relationships within the class holothuroidea, inferred from 18S rRNA gene data

This molecular phylogenetic analysis of 18S ribosomal RNA (18SrDNA) gene sequences from 16 species of holothuroid, suggests strong support for an alternative taxonomic scheme to replace the existing classification. When trees drawn from the 18S rDNA data were constrained to show expected relationships between the holothourid orders, they were significantly worse than the best tree under SH tests. These analyses indicated strongly that the subclass Aspidochirotacea is paraphyletic. Sequences from the order Dendrochirotida grouped with aspidochiroitid sequences, with high bootstrap support, to the exclusion of the elasipod sequence. In line with recent morphological studies the order Apodida were a basal sister group to the other three holothuroid orders examined and the Dendrochirotida was a derived holothuroid order.

Implications from a 28S rRNA gene fragment for the phylogenetic relationships of halichondrid sponges (Porifera: Demospongiae)

Halichondrida is a pivotal demosponge order of which the classification underwent major changes in the recent history. The monophyly of this order and its intra-ordinal phylogeny cannot be reliably determined on the basis of morphology. Here we present a 28Sr RNA gene tree of selected halichondrids, which supports the hypothesis of halichondrid non-monophyly and elucidates further inter-ordinal relationships. We enlarged the analysis by previously published sequences, discuss how previous analyses suffer from taxon bias and analyse the resulting phylogenetic implications. Most halichondrid families (in particular Axinellidae und Dictyonellidae) cluster polyphyletic and the molecular classification of several genera does not agree with the current (morphological) system. Zusammenfassung Die Systematik der Ordnung Halichondrida ist von Bedeutung fur die Phylogenie aller Demospongien und hat in den letzten Jahren grose Veranderungen vollzogen. Dennoch konnte die Monophylie dieser Ordnung und ihrer Familien noch nicht mit morphologischen Merkmalen deutlich gemacht werden. Hier prasentieren und diskutieren wir eine 28SrDNA-Phylogenie reprasentativer Halichondrien. Teils wurde diese Stammbaumrekonstruktion durch Sequenzen aus anderen Arbeiten erweitert und der Einfluss des Taxonsets auf das Resultat analysiert. Die Monophylie der Ordnung wird durch diese Fragmentanalyse nicht gestutzt, und mehrere Familien (insbesondere Axinellidae und Dictyonellidae) gruppieren polyphyletisch. Die Position mehrerer Gattungen, insbesondere Axinyssa und Stylissa, ist nicht im Einklang mit dem aktuellen (morphologischen) System.

Phylogeny of Nerillidae (Polychaeta, Annelida) as inferred from combined 18S rDNA and morphological data.

A phylogeny of the meiofaunal polychaete family Nerillidae based on morphological, molecular and combined data is presented here. The data sets comprise nearly complete sequences of 18S rDNA and 40 morphological characters of 17 taxa. Sequences were analyzed simultaneously with the morphological data by direct optimization in the program POY, with a variety of parameter sets (costs of gaps: transversions: transitions). Three outgroups were selected from the major polychaete group Aciculata and one from Scolecida. The 13 nerillid species from 11 genera were monophyletic in all analyses with very high support, and three new apomorphies for Nerillidae are identified. The topology of the ingroup varied according to the various parameter settings. Reducing the number of outgroups to one decreased the variance among the phylogenetic hypotheses. The congruence among these was tested and a parameter set, with equal weights (222) and extension gap weighted 1, yielded minimum incongruence (ILD). Several terminal clades of the combined analysis were highly supported, as well as the position of Leptonerilla prospera as sister terminal to the other nerillids. The evolution of morphological characters such as segment numbers, chaetae, appendages and ciliation are traced and discussed. A regressive pathway within Nerillidae is indicated for several characters, however, generally implying several convergent losses. Numerous genera are shown to require revision.

Candida khmerensis sp. nov., a novel cation-tolerant yeast isolated from dry salted shrimp and sewage in Cambodia

Two cation-tolerant yeasts with powdered colonies, K28-3-2T and K26-1-4, were isolated from dry salted shrimp and sewage, respectively, in Siem Reap province, Cambodia. The D1/D2 sequences of the 26S rDNA data showed that the two isolates were conspecific and related to the Pichia burtonii and Candida fennica. Two isolates were examined by a polyphasic taxonomic approach, including molecular phylogenetic analysis, morphological, physiological and biochemical tests, DNA hybridization and MSP-PCR fingerprinting, in comparison with P. burtonii and C. fennica. The two isolates were found to grow by multilateral budding with true and pseudo-mycelium, to not produce ascospores, and to contain ubiquinone Q-8 similar to that of P. burtonii and C. fennica. The two isolates were not differentiated from the two closest species, P. burtonii and C. fennica, by the phenotypic character examined, except for the cation (Li+)-tolerance. From DNA-DNA reassociation studies, however, the two isolates showed low similarities to the closest two species. Based on D1/D2 sequences of 26S rDNA and DNA-DNA reassociation data, they were shown to be a new distinct species from P. burtonii and C. fennica. Therefore, a novel species is proposed, Candida khmerensis sp. nov., represented by strain K28-3-2T (=JCM 13262(T)=CBS 9784T). The novel species, Candida khmerensis sp. nov. can be clearly distinguished from P. burtonii and C. fennica by either the 26S rDNA D1/D2 or ITS region with 5.8S rDNA sequencing, or by the MSP-PCR fingerprinting pattern.