A family-level Tree of Life for bivalves based on a Sanger-sequencing approach.

The systematics of the molluscan class Bivalvia are explored using a 5-gene Sanger-based approach including the largest taxon sampling to date, encompassing 219 ingroup species spanning 93 (or 82%) of the 113 currently accepted bivalve families. This study was designed to populate the bivalve Tree of Life at the family level and to place many genera into a clear phylogenetic context, but also pointing to several major clades where taxonomic work is sorely needed. Despite not recovering monophyly of Bivalvia or Protobranchia-as in most previous Sanger-based approaches to bivalve phylogeny-our study provides increased resolution in many higher-level clades, and supports the monophyly of Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Heterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata, Imparidentia, and Neoheterodontei, in addition to many other lower clades. However, deep nodes within some of these clades, especially Pteriomorphia and Imparidentia, could not be resolved with confidence. In addition, many families are not supported, and several are supported as non-monophyletic, including Malletiidae, Nuculanidae, Yoldiidae, Malleidae, Pteriidae, Arcidae, Propeamussiidae, Iridinidae, Carditidae, Myochamidae, Lyonsiidae, Pandoridae, Montacutidae, Galeommatidae, Tellinidae, Semelidae, Psammobiidae, Donacidae, Mactridae, and Cyrenidae; Veneridae is paraphyletic with respect to Chamidae, although this result appears to be an artifact. The denser sampling however allowed testing specific placement of species, showing, for example, that the unusual Australian Plebidonax deltoides is not a member of Donacidae and instead nests within Psammobiidae, suggesting that major revision of Tellinoidea may be required. We also showed that Cleidothaerus is sister group to the cementing member of Myochamidae, suggesting that Cleidothaeridae may not be a valid family and that cementation in Cleidothaerus and Myochama may have had a single origin. These results highlight the need for an integrative approach including as many genera as possible, and that the monophyly and relationships of many families require detailed reassessment. NGS approaches may be able to resolve the most recalcitrant nodes in the near future.

A phylogenetic backbone for Bivalvia: an RNA-seq approach.

Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000-20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals.

Molecular phylogenetics and historical biogeography amid shifting continents in the cockles and giant clams (Bivalvia: Cardiidae).

Reconstructing historical biogeography of the marine realm is complicated by indistinct barriers and, over deeper time scales, a dynamic landscape shaped by plate tectonics. Here we present the most extensive examination of model-based historical biogeography among marine invertebrates to date. We conducted the largest phylogenetic and molecular clock analyses to date for the bivalve family Cardiidae (cockles and giant clams) with three unlinked loci for 110 species representing 37 of the 50 genera. Ancestral ranges were reconstructed using the dispersal-extinction-cladogenesis (DEC) method with a time-stratified paleogeographic model wherein dispersal rates varied with shifting tectonics. Results were compared to previous classifications and the extensive paleontological record. Six of the eight prior subfamily groupings were found to be para- or polyphyletic. Cardiidae originated and subsequently diversified in the tropical Indo-Pacific starting in the Late Triassic. Eastern Atlantic species were mainly derived from the tropical Indo-Mediterranean region via the Tethys Sea. In contrast, the western Atlantic fauna was derived from Indo-Pacific clades. Our phylogenetic results demonstrated greater concordance with geography than did previous phylogenies based on morphology. Time-stratifying the DEC reconstruction improved the fit and was highly consistent with paleo-ocean currents and paleogeography. Lastly, combining molecular phylogenetics with a rich and well-documented fossil record allowed us to test the accuracy and precision of biogeographic range reconstructions.

Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca).

Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting morphological and molecular hypotheses. Marked incongruity of phylogenetic signal in datasets heavily represented by nuclear ribosomal genes versus mitochondrial genes has also impeded consensus on the type of molecular data best suited for investigating bivalve relationships. To arbitrate conflicting phylogenetic hypotheses, we evaluated the utility of four nuclear protein-encoding genes-ATP synthase ß, elongation factor-1α, myosin heavy chain type II, and RNA polymerase II-for resolving the basal relationships of Bivalvia. We sampled all five major lineages of bivalves (Archiheterodonta, Euheterodonta [including Anomalodesmata], Palaeoheterodonta, Protobranchia, and Pteriomorphia) and inferred relationships using maximum likelihood and Bayesian approaches. To investigate the robustness of the phylogenetic signal embedded in the data, we implemented additional datasets wherein length variability and/or third codon positions were eliminated. Results obtained include (a) the clade (Nuculanida+Opponobranchia), i.e., the traditionally defined Protobranchia; (b) the monophyly of Pteriomorphia; (c) the clade (Archiheterodonta+Palaeoheterodonta); (d) the monophyly of the traditionally defined Euheterodonta (including Anomalodesmata); and (e) the monophyly of Heteroconchia, i.e., (Palaeoheterodonta+Archiheterodonta+Euheterodonta). The stability of the basal tree topology to dataset manipulation is indicative of signal robustness in these four genes. The inferred tree topology corresponds closely to those obtained by datasets dominated by nuclear ribosomal genes (18S rRNA and 28S rRNA), controverting recent taxonomic actions based solely upon mitochondrial gene phylogenies.

Shelled opisthobranchs.

In his contributions to the monographic series "Manual of Conchology", Henry Pilsbry reviewed the subgroup Tectibranchiata, comprising those opisthobranch snails that (at least primitively) still possess a shell (Pilsbry, 1894-1896). Exemplified by the Cephalaspidea (bubble shells), others included in this group at Pilsbry's time and since were Anaspidea (sea hares) and the shelled members of Notaspidea (side-gilled slugs) and Sacoglossa (leaf slugs). Pilsbry (and others since his time) considered tectibranchs to be the "root stock" from which more advanced gastropods such as Nudibranchia and Pulmonata were derived. Tectibranch systematics is firmly based on conchology and most species were originally described from empty shells. However, soft-anatomical characters were acknowledged quite early on as equally important in tectibranchs, due to the reduction of their shells and their evolutionary proximity to unshelled gastropods. Today, Tectibranchiata is not recognized as a natural taxon although the word "tectibranch" (like "prosobranch" and "mesogastropod") continues in vernacular use. Shelled opisthobranchs have been redistributed among various taxa, including several new ones--the unresolved basal opisthobranchs (Architectibranchia) and the "lower Heterobranchia", an enigmatic and currently much-studied group of families considered basal to all of Euthyneura (Opisthobranchia and landsnails (Pulmonata)). Despite their polyphyletic status, shelled opisthobranchs remain important subjects in evolutionary studies of gastropods--as the most basal members of nearly every opisthobranch clade and as organisms with mosaic combinations of primitive and derived features within evolutionary "trends" (e.g., loss of the shell, detorsion, concentration of the nervous system, ecological specialization, etc.). Although they play a pivotal role, the shelled opisthobranchs have received minimal attention in more comprehensive gastropod studies, often relegated to token representatives at the derived end of prosobranchs or at the basal end of nudibranchs. The choice of this representative in a larger study is critical if its morphology and/or molecules are to adequately exemplify a larger group. This review explores the shelled opisthobranchs, including their history, current status and presumed synapomorphies, and emphasizes the importance of anatomical data to our current understanding of these "transitional" forms. A synthetic phylogenetic analysis, based on a combination of characters used in four published phylogenies involving tectibranchs, shows the current state of our knowledge and emphasizes areas for future study. The results indicate that Opisthobranchia, Cephalaspidea and Sacoglossa are monophyletic taxa, and that Acteon, the traditional basal opisthobranch, is convincingly a lower heterobranch. In most of the resulting cladograms, Anaspidea formed a monophyletic group with Cephalaspidea, as did pleurobranchoidean Notaspidea with Nudibranchia (the latter recently named as Nudipleura Wägele and Willan, 2000).

Ultrastructure of sperm development and mature sperm morphology in three species of commensal bivalves (Mollusca: Galeommatoidea).

Ultrastructural features of the ovotestes, spermatogenesis, and the mature sperm are described for three galeommatid bivalves, Divariscintilla yoyo, Divariscintilla troglodytes, and Scintilla sp., from stomatopod burrows in eastern Florida. All three species yielded similar results except with respect to mature sperm dimensions. The ovotestis contains three types of somatic cells within the testicular portion: flattened myoepithelial cells defining the outer acinal wall; underlying pleomorphic follicle cells containing abundant glycogen deposits; and scattered, amoeboid cells containing lysosomal-like inclusions which are closely associated with developing sperm. Early spermatogenesis is typical of that reported from other bivalves. In contrast, the late stages of spermiogenesis involve the migration and gradual rotation of the acrosomal vesicle, resulting in a mature acrosome tilted about 70° from the long axis of the cell. The mature sperm possesses an elongated, slightly curved nucleus; a subterminal, concave acrosome with a nipple-like central projection; five spherical mitochondria and two centnoles in the middlepiece; and a long flagellum. The rotational asymmetry and the presence of perimitochondrial glycogen deposits in these sperm are unusual in the Bivalvia and may be associated with fertilization specializations and larval brooding common among galeommatoideans.