Phylogenomics reveals deep molluscan relationships.

Evolutionary relationships among the eight major lineages of Mollusca have remained unresolved despite their diversity and importance. Previous investigations of molluscan phylogeny, based primarily on nuclear ribosomal gene sequences or morphological data, have been unsuccessful at elucidating these relationships. Recently, phylogenomic studies using dozens to hundreds of genes have greatly improved our understanding of deep animal relationships. However, limited genomic resources spanning molluscan diversity has prevented use of a phylogenomic approach. Here we use transcriptome and genome data from all major lineages (except Monoplacophora) and recover a well-supported topology for Mollusca. Our results strongly support the Aculifera hypothesis placing Polyplacophora (chitons) in a clade with a monophyletic Aplacophora (worm-like molluscs). Additionally, within Conchifera, a sister-taxon relationship between Gastropoda and Bivalvia is supported. This grouping has received little consideration and contains most (>95%) molluscan species. Thus we propose the node-based name Pleistomollusca. In light of these results, we examined the evolution of morphological characters and found support for advanced cephalization and shells as possibly having multiple origins within Mollusca.

Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida).

Deep-sea tubeworms in the annelid family Siboglinidae have drawn considerable interest regarding their ecology and evolutionary biology. As adults, they lack a digestive tract and rely on endosymbionts for nutrition. Moreover, they are important members of chemosynthetic environments including hydrothermal vents, cold seeps, muddy sediments, and whale bones. Evolution and diversification of siboglinids has been associated with host-symbiont relationships and reducing habitats. Despite their importance, the taxonomy and phylogenetics of this clade are debated due to conflicting results. In this study, 10 complete and 2 partial mitochondrial genomes and one transcriptome were sequenced and analyzed to address siboglinid evolution. Notably, repeated nucleotide motifs were found in control regions of these mt genomes, which may explain previous challenges of sequencing siboglinid mt genomes. Phylogenetic analyses of amino acid and nucleotide datasets were conducted in order to infer evolutionary history. Both analyses generally had strong nodal support and suggest Osedax is most closely related to the Vestimentifera+Sclerolinum clade, rather than Frenulata, as recently reported. These results imply Osedax, the only siboglinid lineage with heterotrophic endosymbionts, evolved from a lineage utilizing chemoautotrophic symbionts.

A soft-bodied mollusc with radula from the Middle Cambrian Burgess Shale.

Odontogriphus omalus was originally described as a problematic non-biomineralized lophophorate organism. Here we re-interpret Odontogriphus based on 189 new specimens including numerous exceptionally well preserved individuals from the Burgess Shale collections of the Royal Ontario Museum. This additional material provides compelling evidence that the feeding apparatus in Odontogriphus is a radula of molluscan architecture comprising two primary bipartite tooth rows attached to a radular membrane and showing replacement by posterior addition. Further characters supporting molluscan affinity include a broad foot bordered by numerous ctenidia located in a mantle groove and a stiffened cuticular dorsum. Odontogriphus has a radula similar to Wiwaxia corrugata but lacks a scleritome. We interpret these animals to be members of an early stem-group mollusc lineage that probably originated in the Neoproterozoic Ediacaran Period, providing support for the retention of a biomat-based grazing community from the late Precambrian Period until at least the Middle Cambrian.

Hard and soft anatomy in two genera of Dondersiidae (Mollusca, Aplacophora, Solenogastres).

Phylogenetic relationships and identifications in the aplacophoran taxon Solenogastres (Neomeniomorpha) are in flux largely because descriptions of hard parts--sclerites, radulae, copulatory spicules--and body shape have often not been adequately illustrated or utilized. With easily recognizable and accessible hard parts, descriptions of Solenogastres are of greater use, not just to solenogaster taxonomists, but also to ecologists, paleontologists, and evolutionary biologists. Phylogenetic studies of Aplacophora, Mollusca, and the Lophotrochozoa as a whole, whether morphological or molecular, would be enhanced. As an example, morphologic characters, both isolated hard parts and internal anatomy, are provided for two genera in the Dondersiidae. Five species are described or redescribed and earlier descriptions corrected and enhanced. Three belong to Dondersia: D. festiva Hubrecht, D. incali (Scheltema), and D. namibiensis n. sp., the latter differentiated unambiguously from D. incali only by sclerites and copulatory spicules. Two species belong to Lyratoherpia: L. carinata Salvini-Plawen and L. californica (Heath). Notes are given for other species in Dondersiidae: L. bracteata Salvini-Plawen, Ichthyomenia ichthyodes (Pruvot), and Heathia porosa (Heath). D. indica Stork is synonymized with D. annulata. A cladistic morphological analysis was conducted to examine the utility of hard parts for reconstructing solenogaster phylogeny. Results indicate monophyly of Dondersia and Lyratoherpia as described here.

Ecology of twelve species of Thyasiridae (Mollusca: Bivalvia).

Benthic samples from coastal locations off Southwestern Norway were examined and the specimens of Thyasiridae were identified to species. A multivariate analysis based on 13 parameters was carried out and the environmental preferences of all thyasirid species present were determined. The potential of the Thyasiridae as indicators of organic enrichment was investigated by using direct canonical correspondence analyses to identify correlations between selected environmental parameters and the collected biological data. The presence of Thyasira sarsi together with a low biodiversity is a good indicator of organic enrichment. High thyasirid species diversity seems to indicate good environmental conditions, and single thyasirid species that lack symbiotic bacteria might also be useful as indicators of good environmental conditions.

Molecular phylogeny of the Astrophorida (Porifera, Demospongiae(p)) reveals an unexpected high level of spicule homoplasy.

BACKGROUND: The Astrophorida (Porifera, Demospongiae(p)) is geographically and bathymetrically widely distributed. Systema Porifera currently includes five families in this order: Ancorinidae, Calthropellidae, Geodiidae, Pachastrellidae and Thrombidae. To date, molecular phylogenetic studies including Astrophorida species are scarce and offer limited sampling. Phylogenetic relationships within this order are therefore for the most part unknown and hypotheses based on morphology largely untested. Astrophorida taxa have very diverse spicule sets that make them a model of choice to investigate spicule evolution. METHODOLOGY/PRINCIPAL FINDINGS: With a sampling of 153 specimens (9 families, 29 genera, 89 species) covering the deep- and shallow-waters worldwide, this work presents the first comprehensive molecular phylogeny of the Astrophorida, using a cytochrome c oxidase subunit I (COI) gene partial sequence and the 5' end terminal part of the 28S rDNA gene (C1-D2 domains). The resulting tree suggested that i) the Astrophorida included some lithistid families and some Alectonidae species, ii) the sub-orders Euastrophorida and Streptosclerophorida were both polyphyletic, iii) the Geodiidae, the Ancorinidae and the Pachastrellidae were not monophyletic, iv) the Calthropellidae was part of the Geodiidae clade (Calthropella at least), and finally that v) many genera were polyphyletic (Ecionemia, Erylus, Poecillastra, Penares, Rhabdastrella, Stelletta and Vulcanella). CONCLUSION: The Astrophorida is a larger order than previously considered, comprising ca. 820 species. Based on these results, we propose new classifications for the Astrophorida using both the classical rank-based nomenclature (i.e., Linnaean classification) and the phylogenetic nomenclature following the PhyloCode, independent of taxonomic rank. A key to the Astrophorida families, sub-families and genera incertae sedis is also included. Incongruences between our molecular tree and the current classification can be explained by the banality of convergent evolution and secondary loss in spicule evolution. These processes have taken place many times, in all the major clades, for megascleres and microscleres.

Some Haliotrema (Monogenea: Dactylogyridae) from cultured grouper (Epinephelus Spp.) with emphasis on the phylogenetic position of Haliotrema cromileptis.

Three Haliotrema spp. are reported from the Vietnamese grouper. Morphological and morphometric characters show minor deviations from original descriptions of H. cromileptis Young, 1968 and H. epinepheli Young, 1968 . The third encountered species ( Haliotrema sp.) appears to be new to science. Genetically, H. cromileptis clusters with Bravohollisia , Pseudohaliotrema , and Haliotrema . The group is well supported by partial large subunit rDNA (LSU), complete small subunit rDNA (SSU), and partial SSU + ITS1 rDNA analyses. Ingroup phylogenetic relationships are not well resolved. Haliotrema cromileptis , H. fleti Young, 1968 , and Pseudohaliotrema sphincteroporus Yamaguti, 1953 are closely related to a monophyletic group of 5 Haliotrema spp. characterized by bell- or horn-shaped bases of the male copulatory organ (MCO), which contains an accessory piece. Based on SSU rDNA, H. cromileptis is a sister species to P. sphincteroporus and, together, they form a clade to 3 other Haliotrema spp. characterized by a bell-shape based MCO with an accessory piece. Data analysis conducted on partial SSU + ITS1 rDNA confirms the close phylogenetic relationship of H. cromileptis , H. fleti , H. chenhsintaoi Zhang, 2001 (possessing a horn-shaped base of the MCO), and Bravohollisia rosetta Lin, 1995. However, because major differences in diagnostic characters exist, this genetic relationship needs further elucidation.

Feeding ecology of Coryphaenoides rupestris from the mid-Atlantic Ridge.

The Macrourid fish roundnose grenadier, Coryphaenoides rupestris, is one of the most common benthopelagic fishes on the northern mid-Atlantic Ridge. The ecology of the species is comparatively well studied in continental slope waters of the North Atlantic, but not on the mid-Atlantic Ridge, which is a central mid-ocean area of its distribution. In total, 166 specimens from the RV G.O. Sars cruise in July 2004 were examined. The diet mainly comprised cephalopods, pelagic shrimps and fish. Pelagic and benthopelagic copepods were the most numerous prey, but did not contribute much on a weight basis. Cephalopods were by far the most important prey of the small grenadiers, while shrimps and fish became increasingly significant with increasing size. Previous studies from other areas have also found pelagic prey to be important, but in contrast to this study, cephalopods were generally of less importance. The study was an element of more wide-ranging food-web studies of the mid-Atlantic Ridge macro- and megafauna communities within the international MAR-ECO project.

Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences.

The Mollusca represent one of the most morphologically diverse animal phyla, prompting a variety of hypotheses on relationships between the major lineages within the phylum based upon morphological, developmental, and paleontological data. Analyses of small-ribosomal RNA (SSU rRNA) gene sequence have provided limited resolution of higher-level relationships within the Mollusca. Recent analyses suggest large-subunit (LSU) rRNA gene sequences are useful in resolving deep-level metazoan relationships, particularly when combined with SSU sequence. To this end, LSU (approximately 3.5 kb in length) and SSU (approximately 2 kb) sequences were collected for 33 taxa representing the major lineages within the Mollusca to improve resolution of intraphyletic relationships. Although the LSU and combined LSU+SSU datasets appear to hold potential for resolving branching order within the recognized molluscan classes, low bootstrap support was found for relationships between the major lineages within the Mollusca. LSU+SSU sequences also showed significant levels of rate heterogeneity between molluscan lineages. The Polyplacophora, Gastropoda, and Cephalopoda were each recovered as monophyletic clades with the LSU+SSU dataset. While the Bivalvia were not recovered as monophyletic clade in analyses of the SSU, LSU, or LSU+SSU, the Shimodaira-Hasegawa test showed that likelihood scores for these results did not differ significantly from topologies where the Bivalvia were monophyletic. Analyses of LSU sequences strongly contradict the widely accepted Diasoma hypotheses that bivalves and scaphopods are closely related to one another. The data are consistent with recent morphological and SSU analyses suggesting scaphopods are more closely related to gastropods and cephalopods than to bivalves. The dataset also presents the first published DNA sequences from a neomeniomorph aplacophoran, a group considered critical to our understanding of the origin and early radiation of the Mollusca.