BackgroundAlthough diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. We tested these hypotheses under a comparative phylogenetic framework using ecological data from past studies in conjunction with venom duct transcriptomes sequenced from 12 phylogenetically disparate cone snail species, including 10 vermivores (worm-eating), one molluscivore, and one generalist.ResultsWe discovered 2223 unique conotoxin precursor peptides that encoded 1864 unique mature toxins across all species, >90 % of which are new to this study. In addition, we identified two novel gene superfamilies and 16 novel cysteine frameworks. Each species exhibited unique venom profiles, with venom composition and expression patterns among species dominated by a restricted set of gene superfamilies and mature toxins. In contrast with the dominant paradigm for interpreting Conidae venom evolution, prey taxonomic class did not predict venom composition patterns among species. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity.ConclusionsThe poor performance of prey taxonomic class in predicting venom components suggests that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type (i.e., worms, mollusc, or fish) and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also show that species with more generalized diets tend to have more complex venoms and utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2755-6) contains supplementary material, which is available to authorized users.

Transcriptome-based exon capture methods provide an approach to recover several hundred markers from genomic DNA, allowing for robust phylogenetic estimation at deep timescales. We applied this method to a highly diverse group of venomous marine snails, Conoidea, for which published phylogenetic trees remain mostly unresolved for the deeper nodes. We targeted 850 protein coding genes (678,322 bp) in ca. 120 samples, spanning all (except one) known families of Conoidea and a broad selection of non-Conoidea neogastropods. The capture was successful for most samples, although capture efficiency decreased when DNA libraries were of insufficient quality and/or quantity (dried samples or low starting DNA concentration) and when targeting the most divergent lineages. An average of 75.4% of proteins was recovered, and the resulting tree, reconstructed using both supermatrix (IQ-tree) and supertree (Astral-II, combined with the Weighted Statistical Binning method) approaches, are almost fully supported. A reconstructed fossil-calibrated tree dates the origin of Conoidea to the Lower Cretaceous. We provide descriptions for two new families. The phylogeny revealed in this study provides a robust framework to reinterpret changes in Conoidea anatomy through time. Finally, we used the phylogeny to test the impact of the venom gland and radular type on diversification rates. Our analyses revealed that repeated losses of the venom gland had no effect on diversification rates, while families with a breadth of radula types showed increases in diversification rates, thus suggesting that trophic ecology may have an impact on the evolution of Conoidea.

To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and nontoxin loci from the genomes of 32 cone snail species (family, Conidae), a diverse group of marine gastropods that capture their prey using a cocktail of neurotoxic peptides (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species with high confidence (> 100Â coverage) and used these data to provide new insights into conotoxin evolution. First, we found that conotoxin gene superfamilies are composed of one to six exons and are typically short in length (mean ¼ $85 bp). Second, we expanded our understanding of the following genetic features of conotoxin evolution: 1) positive selection, where exons coding the mature toxin region were often three times more divergent than their adjacent noncoding regions, 2) expression regulation, with comparisons to transcriptome data showing that cone snails only express a fraction of the genes available in their genome (24-63%), and 3) extensive gene turnover, where Conidae species varied from 120 to 859 conotoxin gene copies. Finally, using comparative phylogenetic methods, we found that while diet specificity did not predict patterns of conotoxin evolution, dietary breadth was positively correlated with total conotoxin gene diversity. Overall, the targeted sequencing technique demonstrated here has the potential to radically increase the pace at which venom gene families are sequenced and studied, reshaping our ability to understand the impact of genetic changes on ecologically relevant phenotypes and subsequent diversification.

1Although venomous taxa provide an attractive system to study the genetic basis of adaptation and 2 speciation, the slow pace of toxin gene discovery through traditional laboratory techniques (e.g., cDNA 3 cloning) have limited their utility in the study of ecology and evolution. Here, we applied targeted 4 sequencing techniques to selectively recover venom gene superfamilies and non-toxin loci from the 5 genomes of 32 species of cone snails (family, Conidae), a hyper diverse group of carnivorous marine 6 gastropods that capture their prey using a cocktail of neurotoxic proteins (conotoxins). We were able to 7 successfully recover conotoxin gene superfamilies across all species sequenced in this study with high 8 confidence (> 100X coverage). We found that conotoxin gene superfamilies are composed of 1-6 exons 9and adjacent noncoding regions are not enriched for simple repetitive elements. Additionally, we 10 provided further evidence for several genetic factors shaping venom composition in cone snails, including 11 positive selection, extensive gene turnover, expression regulation, and potentially, presence-absence 12 variation. Using comparative phylogenetic methods, we found that while diet specificity did not predict 13 patterns of conotoxin gene superfamily size evolution, dietary breadth was positively correlated with total 14 conotoxin gene diversity. These results continue to emphasize the importance of dietary breadth in 15 shaping venom evolution, an underappreciated ecological correlate in venom biology. Finally, the 16 targeted sequencing technique demonstrated here has the potential to radically increase the pace at which 17 venom gene families are sequenced and studied, reshaping our ability to understand the impact of genetic 18 changes on ecologically relevant phenotypes and subsequent diversification.

We apply an integrative taxonomy approach to delimit species of ground squirrels in the genus Otospermophilus because the diverse evolutionary histories of organisms shape the existence of taxonomic characters. Previous studies of mitochondrial DNA from this group recovered three divergent lineages within Otospermophilus beecheyi separated into northern, central, and southern geographical populations, with Otospermophilus atricapillus nested within the southern lineage of O. beecheyi. To further evaluate species boundaries within this complex, we collected additional genetic data (one mitochondrial locus, 11 microsatellite markers, and 11 nuclear loci), environmental data (eight bioclimatic variables), and morphological data (23 skull measurements). We used the maximum number of possible taxa (O. atricapillus, Northern O. beecheyi, Central O. beecheyi, and Southern O. beecheyi) as our operational taxonomic units (OTUs) and examined patterns of divergence between these OTUs. Phenotypic measures (both environmental and morphological) showed little differentiation among OTUs. By contrast, all genetic datasets supported the evolutionary independence of Northern O. beecheyi, although they were less consistent in their support for other OTUs as distinct species. Based on these data, we support the conclusions from a previous study that synonymized O. atricapillus with O. beecheyi, and we elevate the northern lineage of O. beecheyi to a separate species.