The nucleotide sequences of the complete or nearly complete mitochondrial (mt) genomes of seven vetigastropods were determined:Angaria neglecta(Angarioidea),Phasianella solida(Phasianelloidea),Granata lyrata(Seguenzioidea),Tegula lividomaculataandBolma rugosa(Trochoidea),Diodora graeca(Fissurelloidea) andLepetodrilus schrolli(Lepetodriloidea). While the mt genomes of the superfamilies Angarioidea, Phasianelloidea, Seguenzioidea and Trochoidea conform generally to the ancestral gene order of Vetigastropoda and Gastropoda, those of the superfamilies Fissurelloidea and Lepetodriloidea have suffered important rearrangements. The gene order of the mtDNAofChrysomallon squamiferum, a representative of Neomphalina, was also analysed since it has been proposed to be closely related to Vetigastropoda, and showed a distinct arrangement. The reconstructed phylogenies recovered Neomphalina as a distinct gastropod lineage that is the sister group (only with moderate bootstrap support) of a clade including Vetigastropoda and Neritimorpha + Caeno‐gastropoda while the relative position of Heterobranchia and Patellogastropoda in the gastropod tree could not be determined definitively due to their long branches. Within the monophyletic Vetigastropoda, the superfamily Fissurelloidea was recovered as the sister group of two lineages, one including Lepetodriloidea as the sister group of Seguenzioidea + Halitoidea, the other including Phasianelloidea, Angarioidea and Trochoidea without resolved relationships. The long branches of Fissurelloidea were found to introduce significant tree instability in phylogenetic reconstruction. The new phylogeny supports that the loss of the right pallial gill occurred multiple times in vetigastropod evolution as previously suggested and that Phasianelloidea, Angarioidea and Trochoidea radiated from a common asymmetric (single‐gilled) ancestor that lived in the middle Palaeozoic.

Living species of Cephalopoda are classified into two main lineages, Nautiloidea and Coleoidea. Within the latter, two main groups are distinguished, Octopodiformes and Decapodiformes. Phylogenetic relationships within Coleoidea have been the subject of numerous studies and the relative phylogenetic position of several enigmatic groups, such as Vampyromorpha, Idiosepioidea and Spirulida, among others, has been contentious. Here, we reconstruct the phylogeny of Cephalopoda using all (39) currently reported complete mitochondrial (mt) genomes; in addition, we concatenated available partial mt genes from five important lineages (represented by genera Opisthoteuthis, Argonauta, Japetella, Thaumeledone and Spirula) that lack complete mt genomes, in order to include them in the phylogenetic analyses. The reconstructed trees recovered the monophyly of Octopodiformes (Octopoda + Vampyromorpha), of Octopoda and of Decapodiformes. Within Octopoda, the first split was between Cirrata and Incirrata and, within the latter, between Argonautoidea and Octopodoidea. Within Octopodoidea, the family Octopodidae, as traditionally defined, was nonmonophyletic. Within Decapodiformes, Sepiida were recovered sister to a clade including Idiosepiida as the first-diverging lineage. Among the remaining lineages of this clade, Myopsina were recovered sister to a ‘pelagic’ clade including Bathyteuthoidea, Spirulida and Oegopsida, to the exclusion of Sepiolida. Based on this fully resolved phylogeny, we inferred the evolution of gene rearrangements among the studied mitochondrial genomes, following a tandem duplication and random loss model. Finally, a chronogram was estimated under an uncorrelated relaxed molecular clock, which gave estimates of dates of major cladogenetic events within Cephalopoda that were considerably younger than those in previous studies.

Despite the extraordinary morphological and ecological diversity of Neritimorpha, few studies have focused on the phylogenetic relationships of this lineage of gastropods, which includes four extant superfamilies: Neritopsoidea, Hydrocenoidea, Helicinoidea, and Neritoidea. Here, the nucleotide sequences of the complete mitochondrial genomes of Georissa bangueyensis (Hydrocenoidea), Neritina usnea (Neritoidea), and Pleuropoma jana (Helicinoidea) and the nearly complete mt genomes of Titiscania sp. (Neritopsoidea) and Theodoxus fluviatilis (Neritoidea) were determined. Phylogenetic reconstructions using probabilistic methods were based on mitochondrial (13 protein coding genes and two ribosomal rRNA genes), nuclear (partial 28S rRNA, 18S rRNA, actin, and histone H3 genes) and combined sequence data sets. All phylogenetic analyses except one converged on a single, highly supported tree in which Neritopsoidea was recovered as the sister group of a clade including Helicinoidea as the sister group of Hydrocenoidea and Neritoidea. This topology agrees with the fossil record and supports at least three independent invasions of land by neritimorph snails. The mitochondrial genomes of Titiscania sp., G. bangueyensis, N. usnea, and T. fluviatilis share the same gene organization previously described for Nerita mt genomes whereas that of P. jana has undergone major rearrangements. We sequenced about half of the mitochondrial genome of another species of Helicinoidea, Viana regina, and confirmed that this species shares the highly derived gene order of P. jana.

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 twelve 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 (i) Vetigastropoda s.l. (including Pleurotomariida + Neomphaliones) and (ii) Neritimorpha + (Caenogastropoda + Heterobranchia). As such, our results support the recognition of five subclasses (or infraclasses) in Gastropoda: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia.