Major discrepancy between phylogenetic hypotheses based on molecular and morphological criteria within the Order Haplosclerida (Phylum Porifera: Class Demospongiae)

Taxonomy within the sponge Order Haplosclerida remains somewhat contentious. Both morphology and biochemistry have been employed to help unravel the relationships of the Order with limited results perhaps because of the small number of reliable characters. We employed phylogenetic analysis of 750 base pairs of the 5′ end of the 28S rRNA gene to study relationships between 20 taxa within the Order. While preliminary (low number of taxa, one gene region) results suggested strong discrepancy to former phylogenies, there was no support for the monophyly of the Order and almost all morphologically defined genera appeared to be polyphyletic.     

Congruence between nuclear and mitochondrial genes in Demospongiae: a new hypothesis for relationships within the G4 clade (Porifera: Demospongiae)

The current morphological classification of the Demospongiae G4 clade was tested using large subunit ribosomal RNA (LSU rRNA) sequences from 119 taxa. Fifty-three mitochondrial cytochrome oxidase 1 (CO1) barcoding sequences were also analysed to test whether the 28S phylogeny could be recovered using an independent gene. This is the largest and most comprehensive study of the Demospongiae G4 clade. The 28S and CO1 genetrees result in congruent clades but conflict with the current morphological classification. The results confirm the polyphyly of Halichondrida, Hadromerida, Dictyonellidae, Axinellidae and Poecilosclerida and show that several of the characters used in morphological classifications are homoplasious. Robust clades are clearly shown and a new hypothesis for relationships of taxa allocated to G4 is proposed.     

Two new species in the family Axinellidae (Porifera,Demospongiae) from British Columbia and adjacent waters

Two new species of Demospongiae are described for British Columbia and adjacent waters in the family Axinellidae, Auletta krautteri sp. n. and Dragmacidon kishinensis sp. n. They represent range extensions for both of these genera. Both are fairly commonly encountered, Auletta krautteri below diving depths (87 to at least 300 m) and Dragmacidon kishinensis in shallow water (intertidal to 30 m). We propose an amended genus diagnosis for Auletta to account for the variability among species in principal spicules that form the ascending tracts to be either oxeas, styles or strongyles rather than just oxeas.     

Zoobenthos-inhabiting Sarcotragus muscarum (Porifera: Demospongiae) from the Aegean Sea

The cavities and outer surfaces of 20 individuals of the sponge Sarcotragus muscarum collected from the Turkish Aegean coast during July–September 1993 contained a total of 148 zoobenthic species with 5299 individuals belonging to seven taxonomic groups. Among these, Polychaeta accounted for 60% of the total number of species, while Crustacea comprised 71% of the total number of individuals and 40% of the wet weight of biomass. The amphipod and decapod crustaceans Tritaeta gibbosa and Synalpheus gambarelloides, and the bivalve Hiatella arctica, were the most abundant species on the sponge samples both in terms of number of individuals and biomass values. The community structure inside the sponges was greatly influenced by the nature of the substratum around the sponge, and by the overwhelming population of the Lessepsian echinoderm Ophiactis savignyi. Number of species, biomass and diversity index values were found to be positively related to the sponge volume. Mean density and biomass of the associated taxa are 0.22 ind cm^–3 and 11.63 mg cm^–3, respectively.     

Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies

The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in diverse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of divergent paralogs within individual genomes that can be phylogenetically misleading. For the first time we survey diverse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without (1) screening for IGPs in specimens from every population sampled; (2) including all divergent paralogs in phylogenetic analyses; (3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).     

A survey for biochemical synapomorphies to reveal phylogenetic relationships of halichondrid demosponges (Metazoa: Porifera)

Biochemical compounds are a suggested alternative for morphological characters in sponge systematics. The monophyly of the crucial demosponge order Halichondrida is still largely unresolved. Here, we performed a search for synapomorphies, which might aid to define the order and its five families Axinellidae, Bubaridae, Dictyonellidae, Desmoxyidae and Halichondriidae. We also investigated possible links of the order Halichondrida with other demosponge taxa such as suberitids (Hadromerida). Our survey of published compounds revealed hydroxy-nor-sterols as a potential synapomorphy for axinellid taxa, 2,3,6 sulfated sterol nuclei as possible connection between Agelasida and Halichondrida, besides the known pyrrol-2-carboxylic acids and galactosylceramides, furthermore carbonimidic dichlorides, pupukeananes, diterpene isocyanides for the order Halichondrida and linear and cyclic diterpenes for the family Desmoxyidae. The suitability of biochemical characters in systematics is discussed.     

Epibiontic and endobiontic polychaetes of Geodia cydonium (Porifera,Demospongiae) from the Mediterranean Sea

Polychaete assemblages associated to the sponge Geodia cydonium were investigated at two sampling sites in the Mediterranean Sea: Porto Cesareo Basin (Apulia) and Marsala Lagoon (Sicily), both characterized by sheltered hydrodynamic conditions. Samples were seasonally performed during 1997, in order to compare the assemblages coming from the two localities studied, considering separately the internal and external tissues of the sponge, and with the aim of evaluating the influence of sponge size on polychaete colonization. The examined sponge is characterized by a peculiar stratification of its tissues: an external thick and hard layer, the cortex, and an internal softer one, the choanosome. Statistical analysis showed that this was the main factor controlling polychaete assemblage, with the internal tissue, less rich and diversified, appearing impoverished with respect to the external layer. A similarity in species composition was observed between sites, even though some differences were evidenced in the abundance of some species, mainly reflecting differences in local environmental conditions. Species richness and density increased with the increasing sponge size. Such a situation is particularly evident at Porto Cesareo, where sponges are covered by an algal layer which is particularly rich on the largest specimens, thus suggesting that most of the species of polychaetes were linked more to the neighbouring environment than to the sponge itself.     

ITS-2 and 18S rRNA Gene Phylogeny of Aplysinidae (Verongida, Demospongiae)

18S ribosomal DNA and internal transcribed spacer 2 (ITS-2) full-length sequences, each of which was sequenced three times, were used to construct phylogenetic trees with alignments based on secondary structures, in order to elucidate genealogical relationships within the Aplysinidae (Verongida). The first poriferan ITS-2 secondary structures are reported. Altogether 11 Aplysina sponges and 3 additional sponges (Verongula gigantea, Aiolochroia crassa, Smenospongia aurea) from tropical and subtropical oceans were analyzed. Based on these molecular studies, S. aurea, which is currently affiliated with the Dictyoceratida, should be reclassified to the Verongida. Aplysina appears as monophyletic. A soft form of Aplysina lacunosa was separated from other Aplysina and stands at a basal position in both 18S and ITS-2 trees. Based on ITS-2 sequence information, the Aplysina sponges could be distinguished into a single Caribbean–Eastern Pacific cluster and a Mediterranean cluster. The species concept for Aplysina sponges as well as a phylogenetic history with a possibly Tethyan origin is discussed.Reviewing Editor: Dr. Martin Kreitman     

The extent of asexual reproduction in sponges of the genus Chondrilla (Demospongiae: Chondrosida) from the Caribbean and the Brazilian coasts

In this study, we estimated the extent of asexual reproduction and genotypic diversity at the intra- and interspecific levels in sponges of the genus Chondrilla in the Caribbean and along the coast of Brazil. Allozymes were used to identify the genotypes of specimens of Chondrilla in each location. The four species studied displayed a large variation in the extent of clonal reproduction and genotypic diversity, with the two species from the Bahamas having a greater proportion of asexually produced individuals than those along the coast of Brazil. Conspecific Brazilian populations of Chondrilla sp. had large differences in clonality: the population from a heterogeneous environment and under the influence of a strong upwelling had little clonality (7%), whereas the population located 350 km south along the coast, in a more homogeneous and temporally stable environment, had a five-fold larger (39%) proportion of asexually derived individuals. Finally, we were able to confirm that, besides fission, the genus Chondrilla displays a second mode of asexual reproduction, by fragmentation of teardrop shaped individuals.     

Phylogeny of Molting Protostomes (Ecdysozoa) as Inferred from 18S and 28S rRNA Gene Sequences

Phylogenetic relationships within the group of molting protostomes were reconstructed by comparing the sets of 18S and 28S rRNA gene sequences considered either separately or in combination. The reliability of reconstructions was estimated from the bootstrap indices for major phylogenetic tree nodes and from the degree of congruence of phylogenetic trees obtained by different methods. By either criterion, the phylogenetic trees reconstructed on the basis of both 18 and 28S rRNA gene sequences were better than those based on the 18S or 28S sequences alone. The results of reconstruction are consistent with the phylogenetic hypothesis classifying protostomes into two major clades: molting Ecdysozoa (Priapulida + Kinorhyncha, Nematoda + Nematomorpha, Onychophora + Tardigrada, Myriapoda + Chelicerata, and Crustacea + Hexapoda) and nonmolting Lophotrochozoa (Plathelminthes, Nemertini, Annelida, Mollusca, Echiura, and Sipuncula). Nematomorphs (Nematomorpha) do not belong to the clade Cephalorhyncha (Priapulida + Kinorhyncha). It is concluded that combined data on the 18S and 28S rRNA gene sequences provide a more reliable basis for phylogenetic inferences.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 4, 2005, pp. 590–601.Original Russian Text Copyright © 2005 by Petrov, Vladychenskaya.     

Taxonomic redescriptions of two ciliates, Protogastrostyla pulchra n. g., n. comb. and Hemigastrostyla enigmatica (ciliophora: spirotrichea, stichotrichia), with phylogenetic analyses based on 18S and 28S rRNA gene sequences

The morphology and infraciliature of two stichotrichid ciliates, Gastrostyla pulchra(Perejaslawzewa 1886) Kahl, 1932 and Hemigastrostyla enigmatica(Dragesco and Dragesco-Kernéis 1986) Song & Wilbert, 1997, collected from marine and brackish sediments, were investigated by using living observations and protargol impregnations. Both 18S and 28S rRNA genes of these two species were sequenced. The 18S rDNA show high similarities (98.4%-99.7%) among populations of each species. There is about 94% similarity in 18S rDNA genes between G. pulchra and Gastrostyla steinii, the type species of the genus, which has been confirmed to be an oxytrichid by previous studies. In the phylogenetic trees of 18S, 28S, and combined 18S and 28S rDNA, both G. pulchra and H. enigmatica are consistently placed outside the well-established oxytrichid clade. Based on our analyses and previous ontogenetic data, we conclude that these two species may represent some lower groups in the subclass Stichotrichia, and that G. pulchra should represent a new genus, Protogastrostyla n. g. This new genus, which is morphologically similar to Gastrostyla, differs in its morphogenesis: the apical part of the old AZM is retained combining with the newly built membranelles that develop from the proter's oral primordium; the primary primordia of the dorsal kinety; and marginal primordia commence de novo without a definite contribution from the old structure.     

Investigation of the budding process in Tethya citrina and Tethya aurantium (Porifera, Demospongiae)

The budding process has been studied in two congeneric Mediterranean species belonging to Tethya from different sampling sites: Marsala and Venice Lagoons (Tethya citrina); Marsala Lagoon and Porto Cesareo Basin (Tethya aurantium). Buds, connected to the adult by a spiculated stalk, differ between the two species in morphology and size, since those of T. citrina are small with elongated bodies, showing only a few spicules protruding from the apical region, whereas those of T. aurantium are round, larger, and show spicules radiating from the peripheral border. In T. citrina, cells with inclusions, varying in electron density and size, represent the main cell types of the buds. In T. aurantium, the cell component shows a major diversification, resulting from spherulous cells, grey cells, vacuolar cells and peculiar micro-vesicle cells. Neither canals nor choanocyte chambers were observed in the buds of the two species. In T. citrina, bud production is similar in both sampling sites. In T. aurantium, budding occurs more rarely in Porto Cesareo Basin, probably in relation with environmental factors, such as the covering of the cortex by sediment and micro-algae. Finally, in the buds of both species, the spicule size does not differ from that of the cortex of the adult sponges, further supporting the main involvement of the cortex in organizing the skeletal architecture of the buds.     

The diversity of relationships between Antarctic sponges and diatoms: the case of Mycale acerata Kirkpatrick, 1907 (Porifera,Demospongiae)

The diatom assemblage associated with the Antarctic sponge Mycale acerata was studied through an analysis of the diatom frustule and pigment concentrations in both the sponge ectosome and choanosome. Sponges were sampled weekly from November 2001 to February 2002 at Terra Nova Bay, Antarctica, at a depth of 25–35 m. The most abundant diatoms were Porannulus contentus, Fragilariopsis curta, Thalassiosira cf. gracilis, T. perpusilla and Plagiotropis sp. High abundances of P. contentus were found on the sponge ectosome up to the beginning of November, before the ice melted, while later frustules were incorporated inside, indicating that P. contentus lives epibiontically on M. acerata and represents a potential food source for the sponge. The presence of other diatom species was mainly related to the summer phytoplankton bloom. The sponge incorporates diatoms from the water column and utilises them as a food source, accumulating frustules inside the choanosome. The lack of planktonic diatom frustules at the beginning of the summer indicates that they are expelled or dissolved during the cold season.     

The secondary structure of human 28S rRNA: The structure and evolution of a mosaic rRNA gene

Summary We have determined the secondary structure of the human 28S rRNA molecule based on comparative analysis of available eukaryotic cytoplasmic and prokaryotic large-rRNA gene sequences. Examination of large-rRNA sequences of both distantly and closely related species has enabled us to derive a structure that accounts both for highly conserved sequence tracts and for previously unanalyzed variable-sequence tracts that account for the evolutionary differences in size among the large rRNAs.Human 28S rRNA is composed of two different types of sequence tracts: conserved and variable. They differ in composition, degree of conservation, and evolution. The conserved regions demonstrate a striking constancy of size and sequence. We have confirmed that the conserved regions of large-rRNA molecules are capable of forming structures that are superimposable on one another. The variable regions contain the sequences responsible for the 83% increase in size of the human large-rRNA molecule over that ofEscherichia coli. Their locations in the gene are maintained during evolution. They are G+C rich and largely nonhomologous, contain simple repetitive sequences, appear to evolve by frequent recombinational events, and are capable of forming large, stable hairpins.The secondary-structure model presented here is in close agreement with existing prokaryotic 23S rRNA secondary-structure models. The introduction of this model helps resolve differences between previously proposed prokaryotic and eukaryotic large-rRNA secondary-structure models.     

Phylogenetic relationships of the marine Haplosclerida (Phylum Porifera) employing ribosomal (28S rRNA) and mitochondrial (cox1, nad1) gene sequence data

The systematics of the poriferan Order Haplosclerida (Class Demospongiae) has been under scrutiny for a number of years without resolution. Molecular data suggests that the order needs revision at all taxonomic levels. Here, we provide a comprehensive view of the phylogenetic relationships of the marine Haplosclerida using many species from across the order, and three gene regions. Gene trees generated using 28S rRNA, nad1 and cox1 gene data, under maximum likelihood and Bayesian approaches, are highly congruent and suggest the presence of four clades. Clade A is comprised primarily of species of Haliclona and Callyspongia, and clade B is comprised of H. simulans and H. vansoesti (Family Chalinidae), Amphimedon queenslandica (Family Niphatidae) and Tabulocalyx (Family Phloeodictyidae), Clade C is comprised primarily of members of the Families Petrosiidae and Niphatidae, while Clade D is comprised of Aka species. The polyphletic nature of the suborders, families and genera described in other studies is also found here.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

The colubrid radiation in Africa (Serpentes: Golubridae): phylogenetic relationships and evolutionary patterns based on immunological data

Phylogenetic relationships among genera of African colubrids were evaluated using estimates of divergence among serum albumins compared by microcomplement fixation. Representatives of about half of the extant genera of African colubrids, as well as the Elapidae, Atractaspis and the Madagascan colubrid Leioheterodon, were analysed. The tree of best fit to the data has an unresolved basal polychotomy comprising at least five lineages of colubrids, as well as Elapidae and Atractaspis; thus, colubrids were not demonstrably monophyletic with these data. Two cosmopolitan clades, colubrines and natricines, are represented in Africa by series of closely related genera, but divergence among other genera is relatively great. Rate tests show that this is apparently not due to higher rates of albumin evolution in these, relative to other colubrids. Among the other associations supported by the immunological data are: (1) Psammophis-(Rhamphiophis-Dipsina)-Malpolon-Psammophylax; (2) Amblyodipsas-Macrelaps; (3) (Lycodonomorphus-Lamprophis)-Mehelya; and (4) Colubrinae-Natricinae. Grayia is questionably associated with the colubrine-natricine lineage. Prosymna and Lycodon are clearly members of the colubrine clade, and Amplorhinus possibly associates with Leioheterodon. Gonionotophis, Duherria, Lycophidion and Pseudaspis show no strong association with any other genera, and represent other basal or near-basal clades within the colubrid/elapid radiation. The immunological data do not support a clade comprising the Elapidae, Atractaspis and some ‘aparallactines’ relative to Viperidae and other colubrids. The basal colubrid-elapid-Atractaspis divergence occurred more than 30 Myr ago, and the fossil record of colubrids in Africa greatly underestimates both the age and clade diversity of this group. In contrast to the pattern of radiation in the neotropics, where most colubrids belong to one of three major clades, in Africa only the colubrine lineage comprises a substantial portion of the extant generic diversity; most other genera stem from relatively ancient cladogenetic events and have few living representatives.     

First evidences of surfactant biodegradation by marine sponges (Porifera): an experimental study with a linear alkylbenzenesulfonate

The main objective of this work was to better appreciate the role of benthic macro-organisms in the biodegradation of detergents in the marine environment. Sponges, which could be highly resistant to pollution and which are highly active filter-feeders, appear as interesting organisms in this topic. An experimental study conducted in aquarium with seawater enriched in a pure linear alkylbenzenesulfonate (LAS), namely 1-(p-Sulfophenyl)nonane, has shown that the primary degradation was 10 times more rapid in the presence of the sponge Spongia officinalis than in the presence of only marine bacteria. The main degradation metabolites, 3-(p-sulfophenyl)propionic acid and p-sulfobenzoic acid were produced in greater amounts in the presence of sponge. The very rapid degradation kinetics observed in this study may be due to the symbiotic microbial community present in S. officinalis. The sponge may also have promoted the activity of marine bacteria by transforming the original molecule in a more available secondary product. This study demonstrates for the first time that benthic macro-organisms can play an important role in the transformation of biodegradable contaminants, such as LAS.