Phylogeny of Cladobranchia (Gastropoda: Nudibranchia): a total evidence analysis using DNA sequence data from public databases

Cladobranchia is a clade of charismatic and exclusively marine slugs (Gastropoda: Nudibranchia). Though Cladobranchia and its sister taxon, Anthobranchia, have been supported by molecular data, little resolution among the higher-level groups within these two clades has emerged from previous analyses. Cladobranchia is traditionally divided into three taxa (Dendronotida, Euarminida, and Aeolidida), none of which have been supported by molecular phylogenetic studies. Reconstructions of the evolutionary relationships within Cladobranchia have resulted in poorly supported phylogenies, rife with polytomies and non-monophyletic groups contradicting previous taxonomic hypotheses. In this study, we present a working hypothesis for the evolutionary history of Cladobranchia, utilizing publicly available data that have been generated since the last attempt at a detailed phylogeny for this group (we include approximately 200 more taxa and a total of five genes). Our results resolve Cladobranchia as monophyletic and provide support for a small proportion of genera and families, but it is clear that the presently available data are insufficient to provide a robust and well-resolved phylogeny of these taxa as a whole

Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)

The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversity. In this context, shifts between major prey types could constitute important factors explaining the biodiversity of marine taxa, particularly in groups with highly specialized diets. However, the scarcity of marine specialized consumers for which reliable phylogenies exist hampers attempts to test the role of trophic specialization in evolution. In this study, RNA-Seq data is used to produce a phylogeny of Cladobranchia, a group of marine invertebrates that feed on a diverse array of prey taxa but mostly specialize on cnidarians. The broad range of prey type preferences allegedly present in two major groups within Cladobranchia suggest that prey type shifts are relatively common over evolutionary timescales. In the present study, we generated a well-supported phylogeny of the major lineages within Cladobranchia using RNA-Seq data, and used ancestral state reconstruction analyses to better understand the evolution of prey preference. These analyses answered several fundamental questions regarding the evolutionary relationships within Cladobranchia, including support for a clade of species from Arminidae as sister to Tritoniidae (which both preferentially prey on Octocorallia). Ancestral state reconstruction analyses supported a cladobranchian ancestor with a preference for Hydrozoa and show that the few transitions identified only occur from lineages that prey on Hydrozoa to those that feed on other types of prey. There is strong phylogenetic correlation with prey preference within Cladobranchia, suggesting that prey type specialization within this group has inertia. Shifts between different types of prey have occurred rarely throughout the evolution of Cladobranchia, indicating that this may not have been an important driver of the diversity within this group.https://doi.org/10.1186/s12862-017-1066-

The role of taxonomic expertise in interpretation of metabarcoding studies

Abstract The performance of DNA metabarcoding approaches for characterizing biodiversity can be influenced by multiple factors. Here, we used morphological assessment of taxa in zooplankton samples to develop a large barcode database and to assess the congruence of taxonomic identification with metabarcoding under different conditions. We analysed taxonomic assignment of metabarcoded samples using two genetic markers (COI, 18S V1–2), two types of clustering into molecular operational taxonomic units (OTUs, ZOTUs), and three methods for taxonomic assignment (RDP Classifier, BLASTn to GenBank, BLASTn to a local barcode database). The local database includes 1042 COI and 1108 18S (SSU) barcode sequences, and we added new high-quality sequences to GenBank for both markers, including 109 contributions at the species level. The number of phyla detected and the number of taxa identified to phylum varied between a genetic marker and among the three methods used for taxonomic assignments. Blasting the metabarcodes to the local database generated multiple unique contributions to identify OTUs and ZOTUs. We argue that a multi-marker approach combined with taxonomic expertise to develop a curated, vouchered, local barcode database increases taxon detection with metabarcoding, and its potential as a tool for zooplankton biodiversity surveys

Identification guide to the heterobranch sea slugs (Mollusca: Gastropoda) from Bocas del Toro, Panama

The Bocas del Toro Archipelago is located off the Caribbean coast of Panama. Until now, only 19 species of heterobranch sea slugs have been formally reported from this area; this number constitutes a fraction of total diversity in the Caribbean region. The Bocas del Toro Archipelago is located off the Caribbean coast of Panama. Until now, only 19 species of heterobranch sea slugs have been formally reported from this area; this number constitutes a fraction of total diversity in the Caribbean region. This increase in known diversity strongly suggests that the distribution of species within the Caribbean is still poorly known and species ranges may need to be modified as more surveys are conducted.https://doi.org/10.1186/s41200-016-0048-

Dryad Repository

Data files found at https://doi.org/10.5061/dryad.7kh2

Cladobranchia phylogenomics - Pilot study

Compilation of methods, data, and paper for the publication, "Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation" Citation: Goodheart, Jessica A., Bazinet, Adam L., Collins, Allen G., Cummings, Michael P. 2015. Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: An initial investigation. Royal Society Open Science 2: 150196. doi: 10.1098/rsos.150196