Abstract. To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach 'types'. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia,

A new molecular phylogeny is presented for the highly diverse, bivalve molluscan subclass Heterodonta. The study, the most comprehensive for heterodonts to date, used new sequences of 18S and 28S rRNA genes for 103 species from 49 family groups with species of Palaeoheterodonta (Trigoniidae, Margaritiferidae and Unionidae) as outgroups. Results confirm previous analyses that the Carditidae/Astartidae/Crassatellidae clade is basal to all other heterodonts including Anomalodesmata (often classified as a separate subclass or order). Thyasiroidea occupy a near basal position between the Crassatelloidea and Anomalodesmata. Lucinidae form a well‐supported monophyletic group distinct from Thyasiridae and Ungulinidae. The Solenoidea and Hiatelloidea link as sister groups distant from the Tellinoidea and Myoidea, respectively, where they had been previously associated. The position of the Gastrochaenidae is unstable but does not group with myoidean taxa. Species of four families of Galeommatoidea form a clade that also includes Sportellidae of the Cyamioidea. The Cardioidea and Tellinoidea form highly supported, long branched, individual clades but group as sister taxa. A major clade including Veneroidea, Mactroidea, Myoidea and other families is given the unranked name Neoheterodontei. There is no support for a separate order Myoida (Myoidea and Pholadoidea). Dreissenidae group within the clade including Myidae, Corbulidae, Pholadidae and Teredinidae. The Corbiculoidea is confirmed as polyphyletic with the Sphaeriidae and Corbiculidae forming separate clades within the Neoheterodontei; Corbiculidae grouping with the Glauconomidae. Hemidonacidae are unrelated to the Cardiidae, as previously proposed, but nest within the Neoheterodontei. The Gaimardiidae group near to the Ungulinidae and not with Cyamioidea where most recently classified. The family Ungulinidae, previously classified in the Lucinoidea, forms a well‐supported clade within the Neoheterodontei and is elevated to superfamily rank — Ungulinoidea. The monophyletic status of Glossoidea, Arcticoidea and Veneroidea is unconfirmed. A brief review of the fossil record of the heterodonts indicates that the basal clades of Crassatelloidea, Anomalodesmata and Lucinoidea diverged very early in the Lower Palaeozoic. Other groups such as the Hiatelloidea, Solenoidea, Gastrochaenidae probably were of late Palaeozoic origins. The Cardioidea and Tellinoidea originated in the Triassic while major groups of Neoheterodontei radiated in the Late Mesozoic. The phylogenetic position of the Thyasiroidea and Galeommatoidea suggests a longer fossil history than has so far been recognized.

Recent molecular analyses have demonstrated that the traditional Lucinoidea, comprising the extant families Lucinidae, Thyasiridae, Ungulinidae, Fimbriidae, and Cyrenoididae, is not monophyletic. Thyasiridae and Ungulinidae are unrelated to Lucinidae, a result corroborated by clear morphological differences between the groups. Chemosymbiosis in Thyasiridae and Lucinidae has been independently derived. Within the family Lucinidae, previous ideas of relationship and subfamilial divisions based on shell characters have little support from molecular results. Anatomical characters of the ctenidia, mantle gills, and posterior apertures have potential in phylogenetic analysis but rigorous analysis of shell characters is also needed. Although there is a good fossil record of Lucinidae throughout the Cenozoic and Mesozoic, in the Palaeozoic fossils are less frequent and most need reappraisal. The Silurian Ilionia prisca is probably the earliest fossil with convincing lucinid features, followed in the Devonian by Phenacocyclas and some Paracyclas species.

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All Lucinidae species studied so far possess sulphide-oxidizing, chemosymbiotic bacteria housed in bacteriocytes of gill filaments. The ecology, functional anatomy and evolution of the Lucinidae must be considered in relation to this symbiosis. The ctenidia have been extensively studied but other anatomical structures peculiar to lucinids have received much less attention. Reviewed are the morphological diversity of living lucinids, highlighting features of their anatomy including ctenidia, pallial apertures, anterior adductor mucsle, pallial blood vessel and mantle gills. The latter are much more complex than previously understood and are here redescribed. They comprise folded structures located near the anterior adductor muscle in Codakia, Phacoides and Lucina, and on the septum of Anodontia. These are interpreted as secondary respiratory surfaces, their location enabling the separation of the anterior inflow of oxygenated water from sulphide-containing water. The latter is released from the sediment by the probing activities of the highly extensible foot and is pumped over the gill through the pedal gape and perhaps also via the exhalant tube. The shell features of Ilionia from the Silurian Period suggests that the lucinid chemosymbiosis is an ancient association.

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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.