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Phylogenetic analyses may suffer from multiple sources of error leading to conflict between genes and methods of inference. The evolutionary history of the mollusc clade Vetigastropoda makes them susceptible to these conflicts, their higher level phylogeny remaining largely unresolved. Originating over 350 Ma, vetigastropods were the dominant marine snails in the Paleozoic. Multiple extinction events and new radiations have resulted in both very long and very short branches and a large extant diversity of over 4000 species. This is the perfect setting of a hard phylogenetic question in which sources of conflict can be explored. We present 41 new transcriptomes across the diversity of vetigastropods (62 terminals total), and provide the first genomic-scale phylogeny for the group. We find that deep divergences differ from previous studies in which long branch attraction was likely pervasive. Robust results leading to changes in taxonomy include the paraphyly of the order Lepetellida and the family Tegulidae. Tectinae subfam. nov. is designated for the clade comprising Tectus, Cittarium, and Rochia. For two early divergences, topologies disagreed between concatenated analyses using site heterogeneous models versus concatenated partitioned analyses and summary coalescent methods. We investigated rate and composition heterogeneity among genes, as well as missing data by locus and by taxon, none of which had an impact on the inferred topologies. We also found no evidence for ancient introgression throughout the phylogeny. We further tested whether uninformative genes and over-partitioning were responsible for this discordance by evaluating the phylogenetic signal of individual genes using likelihood mapping, and by analyzing the most informative genes with a full multispecies coalescent (MSC) model. We find that most genes are not informative at the two conflicting nodes, but neither this nor gene-wise partitioning are the cause of discordant results. New method implementations that simultaneously integrate amino acid profile mixture models and the MSC might be necessary to resolve these and other recalcitrant nodes in the Tree of Life. [Fissurellidae; Haliotidae; likelihood mapping; multispecies coalescent; phylogenetic signal; phylogenomic conflict; site heterogeneity; Trochoidea.]

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. While conflicting hypotheses prevail in morphological and molecular datasets alike, the monophyly of Arachnida is nearly universally accepted. Though a small number of phylotranscriptomic analyses have recovered arachnid monophyly, these did not sample all living chelicerate orders. We generated a dataset of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternatives algorithmic approaches to species tree inference. Investigation of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the effect of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.

The phylogenetic relationships within the molluscan class Polyplacophora (chitons) have been studied using morphology, traditional Sanger markers and mitogenomics, but, to date, no analysis has been carried out using transcriptomic and genome-wide data. Here, we leverage the power of transcriptomes to investigate the chiton phylogeny to test current classification schemes and the position of Callochitonidae, a family whose phylogenetic position and taxonomic assignation are uncertain because of conflicting results from past studies. Using multiple data matrices with different taxon occupancy thresholds and inference methods, including both concatenated and coalescence-based approaches, we find a consistent resolution of the chiton phylogeny. Our results support a system with the orders Lepidopleurida, Chitonida and Callochitonida, with the latter two as sister groups. This resolution is compatible with recent mitogenomic results and rejects the position of Callochiton as a member of Chitonina.

Gastropod molluscs are among the most diverse and abundant animals in the oceans, and are successful colonizers of terrestrial and freshwater environments. Past phylogenetic efforts to resolve gastropod relationships resulted in a range of conflicting hypotheses. Here, we use phylogenomics to address deep relationships between the five major gastropod lineages—Caenogastropoda, Heterobranchia, Neritimorpha, Patellogastropoda and Vetigastropoda—and provide one congruent and well-supported topology. We substantially expand taxon sampling for outgroups and for previously underrepresented gastropod lineages, presenting new transcriptomes for neritimorphs and patellogastropods. We conduct analyses under maximum-likelihood, Bayesian inference and a coalescent-based approach, accounting for the most pervasive sources of systematic errors in large datasets: compositional heterogeneity, site heterogeneity, heterotachy, variation in evolutionary rates among genes, matrix completeness, outgroup choice and gene tree conflict. We find that vetigastropods and patellogastropods are sister taxa, and that neritimorphs are the sister group to caenogastropods and heterobranchs. We name these two major unranked clades Psilogastropoda and Angiogastropoda, respectively. We additionally provide the first genomic-scale data for internal relationships of neritimorphs and patellogastropods. Our results highlight the need for reinterpreting the evolution of morphological and developmental characters in gastropods, especially for inferring their ancestral states.

Gastropod mollusks are arguably the most diverse and abundant animals in the oceans, and are successful colonizers of terrestrial and freshwater environments. Here we resolve deep relationships between the five major gastropod lineages - Caenogastropoda, Heterobranchia, Neritimorpha, Patellogastropoda and Vetigastropoda - with highly congruent and supported phylogenomic analyses. We expand taxon sampling for underrepresented lineages with new transcriptomes, and conduct analyses accounting for the most pervasive sources of systematic errors in large datasets, namely compositional heterogeneity, site heterogeneity, heterotachy, variation in evolutionary rates among genes, matrix completeness and gene tree conflict. We find that vetigastropods and patellogastropods are sister taxa, and that neritimorphs are the sister group to caenogastropods and heterobranchs. With this topology, we reject the traditional Archaeogastropoda, which united neritimorphs, vetigastropods and patellogastropods, and is still used in the organization of collections of many natural history museums. Several traits related to development and life history support our molecular results. Importantly, the time of differentiation of the embryonic 4d cell (mesentoblast, responsible for mesoderm formation), differs between the two major clades, highlighting the degree of conservation and significance of development in the evolution of gastropods, as it is also known for spiralian animals more broadly.

Fissurellidae are marine gastropods with a worldwide distribution and a rich fossil record. We integrate molecular, geographical and fossil data to reconstruct the fissurellid phylogeny, estimate divergence times and investigate historical routes of oceanic dispersal. With five molecular markers for 143 terminals representing 27 genera, we resolve deep nodes and find that many genera (e.g., Emarginula, Diodora, Fissurella) are not monophyletic and need systematic revision. Several genera classified as Emarginulinae are recovered in Zeidorinae. Future work should prioritize emarginuline genera to improve understanding of ancestral traits and the early evolution of fissurellids. Tree calibration with the fossilized birth-death model indicates that crown fissurellids originated around 175 Ma, and generally resulted in younger ages for the earliest nodes than the node dating approach. Model-based biogeographic reconstruction, supported by fossils, infers an Indo-West Pacific origin, with a westward colonization of new oceans via the Tethys Seaway upon the breakup of Pangea. Western Atlantic clades then served as source for dispersal towards other parts of the globe. As the sister group to all other fissurellids, Rimula is ranked in its own subfamily, Rimulinae stat. nov. New synonyms: Hemitominae syn. nov. of Zeidorinae stat. nov.; Cranopsissyn. nov. of Puncturella; Variegemarginulasyn. nov. of Montfortula.

The taxonomic richness and distributional patterns of the macrofauna associated with the algae genus Dictyota from the Abrolhos Bank (Eastern Brazilian coast) are analyzed. Macrofauna comprised a total of 9586 specimens; a complete faunal list of the most abundant taxa (Crustacea, Polychaeta and Mollusca, accounting for 95.6%) resulted in 64 families and 120 species. Forty six species are registered for the first time for the Abrolhos Bank, of which 3 are also new for the Brazilian coast. The most abundant families were Ampithoidae amphipods (with Ampithoe ramondi as the main faunal component), Janiridae isopods, Rissoellidae gastropods and Syllidae polychaetes. Comparisons were made between summer and winter periods and among sites from Sebastiao Gomes Reef, near the coast, and from Siriba Island, in the Abrolhos Archipelago, away from the mainland. Algae size was lower in the summer, when faunal density was higher, suggesting a possible effect of grazing. Macrofaunal communities were significantly different among sites and periods. Coastal and external communities were markedly different and winter had the greatest effects on the fauna. Environmental conditions related to sediment type and origin and turbidity appear to be a good scenario for our macrofauna distribution results.