A Phylogenomic Backbone for Gastropod Molluscs.

Gastropods have survived several mass extinctions during their evolutionary history resulting in extraordinary diversity in morphology, ecology, and developmental modes, which complicate the reconstruction of a robust phylogeny. Currently, gastropods are divided into six subclasses: Caenogastropoda, Heterobranchia, Neomphaliones, Neritimorpha, Patellogastropoda, and Vetigastropoda. Phylogenetic relationships among these taxa historically lack consensus, despite numerous efforts using morphological and molecular information. We generated sequence data for transcriptomes derived from 12 taxa belonging to clades with little or no prior representation in previous studies in order to infer the deeper cladogenetic events within Gastropoda and, for the first time, infer the position of the deep-sea Neomphaliones using a phylogenomic approach. We explored the impact of missing data, homoplasy, and compositional heterogeneity on the inferred phylogenetic hypotheses. We recovered a highly supported backbone for gastropod relationships that is congruent with morphological and mitogenomic evidence, in which Patellogastropoda, true limpets, are the sister lineage to all other gastropods (Orthogastropoda) which are divided into two main clades 1) Vetigastropoda $s.l.$ (including Pleurotomariida $+$ Neomphaliones) and 2) Neritimorpha $+$ (Caenogastropoda $+$ Heterobranchia). As such, our results support the recognition of five subclasses (or infraclasses) in Gastropoda: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia. [Compositional heterogeneity; fast-evolving; long-branch attraction; missing data; Mollusca; phylogenetics; systematic error.].

Phylogenetic relationships and evolution of pulmonate gastropods (Mollusca): new insights from increased taxon sampling.

Phylogenetic relationships among higher clades of pulmonate gastropods are reconstructed based on a data set including one nuclear marker (complete ribosomal 18S) and two mitochondrial markers (partial ribosomal 16S and Cytochrome oxidase I) for a total of 96 species. Sequences for 66 of these species are new to science, with a special emphasis on sampling the Ellobiidae, Onchidiidae, and Veronicellidae. Important results include the monophyly of Systellommatophora (Onchidiidae and Veronicellidae) as well as the monophyly of Ellobiidae (including Trimusculus, Otina, and Smeagol). Relationships within Ellobiidae, Onchidiidae, and Veronicellidae are evaluated here for the first time using molecular data. Present results are compared with those from the recent literature, and the current knowledge of phylogenetic relationships among pulmonate gastropods is reviewed: despite many efforts, deep nodes are still uncertain. Identification uncertainties about early fossils of pulmonates are reviewed. Impacts of those phylogenetic and fossil record uncertainties on our understanding of the macro-evolutionary history of pulmonates, especially transitions between aquatic and terrestrial habitats, are discussed.

The complete mitochondrial genome of Cerion uva uva (Gastropoda: Panpulmonata: Stylommatophora: Cerionidae).

We report the complete mitochondrial genome sequence of Cerion uva uva (Linnaeus 1758), the type species of the type genus of the family Cerionidae. The mitogenome is 15,043 bp in length, has a base composition of A (28.3%), T (34.4%), C (17.3%) and G (20.0%), and contains 13 protein-coding genes, 2 ribosomal RNA genes, as well as 22 transfer RNA genes. Gene order is the same as in Cerion incanum (Leidy 1851), but differs from those of all other Panpulmonata. This is the second mitochondrial genome sequenced within the family Cerionidae and will contribute to the assessment of the phylogeography of this family throughout the islands of the tropical western Atlantic.

The Genus Cerion (Gastropoda: Cerionidae) in the Florida Keys.

The systematic relationships and phylogeography of Cerion incanum, the only species of Cerion native to the Florida Keys, are reviewed based on partial sequences of the mitochondrial COI and 16S genes derived from 18 populations spanning the range of this species and including the type localities of all four described subspecies. Our samples included specimens of Cerion casablancae, a species introduced to Indian Key in 1912, and a population of C. incanum x C. casablancae hybrids descended from a population of C. casablancae introduced onto Bahia Honda Key in the same year. Molecular data did not support the partition of C. incanum into subspecies, nor could populations be apportioned reliably into subspecies based on morphological features used to define the subspecies. Phylogenetic analyses affirmed the derived relationship of C. incanum relative to other cerionids, and indicated a Bahamian origin for the Cerion fauna of southern Florida. Relationships among the populations throughout the Keys indicate that the northernmost populations, closest to the Tomeu paleoislands that had been inhabited by Cerion petuchi during the Calabrian Pleistocene, are the oldest. The range of Cerion incanum expanded as the archipelago that is the Florida Keys was formed since the lower Tarantian Pleistocene by extension from the northeast to the southwest, with new islands populated as they were formed. The faunas of the High Coral Keys in the northeast and the Oölite Keys in the southwest, both with large islands that host multiple discontinuous populations of Cerion, are each composed of well supported clades that are characterized by distinctive haplotypes. In contrast, the fauna of the intervening Low Coral Keys consist of a heterogeneous series of populations, some with haplotypes derived from the High Coral Keys, others from the Oölite Keys. Individuals from the C. incanum x C. casablancae hybrid population inhabiting the southeastern coast of Bahia Honda Key were readily segregated based on their mitogenome lineage, grouping either with C. incanum or with C. casablancae from Indian Key. Hybrids with C. casablancae mitogenomes had haplotypes that were more divergent from their parent mitogenome than were hybrids with C. incanum mitogenomes.

Pleurotomarioidean gastropods.

Pleurotomarioidean gastropods are continuously present in the fossil record since the Upper Cambrian and survive into the Recent fauna, thus providing rare insights into the evolutionary history of the class Gastropoda. Pleurotomarioidea achieved greatest numerical and morphological diversity during the Paleozoic, and dominated global shallow water marine gastropod faunas during the Paleozoic and Mesozoic. Only a single family, the Pleurotomariidae, survived the end-Cretaceous Extinction, but was restricted to deep water through most of the Cenozoic. The first living pleurotomariid was discovered during the mid-nineteenth century, along the bathyal zone of the western Atlantic. Subsequently collected specimens of these "living fossils" revealed that these animals comprise a mosaic of primitive and highly derived characters that originally inspired a new model of gastropod evolution, but more recently defy the orderly inclusion of this group within a cladistic framework of gastropod phylogeny. Molecular studies have likewise shown that the 18S rDNA gene of pleurotomariids contains novel insertions, and evolves more rapidly than in related taxa. A number of studies confirm that the Pleurotomarioidea may be included in the clade Vetigastropoda together with the Trochoidea, Fissurelloidea, Haliotoidea, and Scissurelloidea. However, neither the position of the superfamily within Vetigastropoda, nor the position of Vetigastropoda within Gastropoda is yet robustly resolved. The anatomical and molecular data are reviewed; the latter used to produce a well-resolved phylogeny of the genera within the family, and to justify the naming of the long-used informal grouping "Perotrochus Group B" as the genus Bayerotrochus. A review of the geographic and bathymetric distributions of pleurotomariids reveals that the higher taxa segregate bathymetrically, while the species within each genus generally segregate geographically, so that most species exist in allopartry. The diet of pleurotomariids is reviewed, based on direct observations as well as analyses of gut contents, and is shown to consist primarily of sponges, but may include stalked crinoids, octocorals and, under aquarium conditions, fish and clam tissue. Despite their thin and relatively fragile shells, Pleurotomariidae survive an extraordinary number of attacks by predators, primarily crustaceans and fish. Their hypobranchial glands are capable of rapidly secreting a white fluid that probably serves as a chemical defense to repel predators. Circumstantial evidence suggests that this defensive mechanism may have originated during the Paleozoic. Despite the great antiquity of this lineage, pleurotomariids possess a substantial number of morphological, molecular and ecological novelties.

A molecular phylogeny of the bivalve mollusks.

A phylogenetic reconstruction based on 506 nucleotides near the 5' end of the 18S subunit of ribosomal DNA (rDNA) in 2 gastropod, 3 chiton and 28 bivalve mollusks supported the monophyly and sister group relationship of the subclasses Heterodonta and Palaeoheterodonta but could not confidently establish either the monophyly or the phylogenetic relationships of the morphologically well defined subclasses Pteriomorphia, Protobranchia, and Anomalodesmata. When both gastropods and chitons were included in the analysis, one or the other invariably emerged within Bivalvia. Some evidence indicates that this apparent polyphyly may be the consequence of unequal rates of evolution and of rapid changes in the protobranch and anomalodesmatan lineages. The taxa usually included in Pteriomorpha emerge as a grade rather than a clade, although in a sequence that differs from morphologically based phylogenies.

Phylogeny and relationships of pleurotomariid gastropods (Mollusca: Gastropoda): an assessment based on partial 18S rDNA and cytochrome c oxidase I sequences.

The phylogenetic position of the ancient family Pleurotomariidae within the Molluscan class Gastropoda, as well as the relationships of its Recent genera and species, were assessed using an iterative, two-gene (18S rDNA and cytochrome c oxidase I) approach to phylogeny reconstruction. In order to orient the Pleurotomariidae within Gastropoda, partial 18S rDNA sequences were determined for 7 pleurotomariid and 22 other gastropods that span the major groups within the class as well as for one cephalopod and two polyplacophorans, which serve as outgroups. Cladistic analyses of a sequence of approximately 450 base pairs (bp) near the 5' end of the 18S rDNA support the monophyly of the following higher gastropod taxa: Patellogastropoda, Vetigastropoda, Neritopsina, Apogastropoda, and its subclades Caenogastropoda and Heterobranchia. The 18S rDNA sequences and 579 bp of cytochrome c oxidase I (COI) analyzed separately and together, indicate that Pleurotomariidae are included within Vetigastropoda but comprise a clade that is the sister group to the other families referred to this order. Monophyly of the Pleurotomariidae is also supported by the unique presence of seven separate inserts (ranging in length from 1 to 68 bp) within the V2 variable region of the 18S RNA. Relationships of the genera and species within Pleurotomariidae are fully resolved using "total molecular evidence" consisting of partial sequences of 18S rDNA and COI and including data on length variation within the inserts.