Thomas F. Duda

Did tectonic activity stimulate Oligo-Miocene speciation in the Indo-West Pacific?

Abstract Analyses of molecular phylogenies of three unrelated tropical marine gastropod genera, Turbo, Echinolittorina, and Conus, reveal an increase in the rate of cladogenesis of some Indo-West Pacific (IWP) clades beginning in the Late Oligocene or Early Miocene between 23.7 and 21.0 million years ago. In all three genera, clades with an increased rate of diversification reach a maximum of diversity, in terms of species richness, in the central IWP. Congruence in both the geographical location and the narrow interval of timing suggests a common cause. The collision of the Australia and New Guinea plate with the southeast extremity of the Eurasian plate approximately 25 Mya resulted in geological changes to the central IWP, including an increase in shallow-water areas and length of coastline, and the creation of a mosaic of distinct habitats. This was followed by a period of rapid diversification of zooxanthellate corals between 20 and 25 Mya. The findings reported here provide the first molecular evidence from multiple groups that part of the present-day diversity of shallow-water gastropods in the IWP arose from a rapid pulse of speciation when new habitats became available in the Late Oligocene to Early Miocene. After the new habitats were filled, the rate of speciation likely decreased and this combined with high levels of extinction (in some groups), resulted in a slow down in the rate of diversification in the genera examined.

Extensive And Continuous Duplication Facilitates Rapid Evolution And Diversification Of Gene Families

The origin of novel gene functions through gene duplication, mutation, and natural selection represents one of the mechanisms by which organisms diversify and one of the possible paths leading to adaptation. Nonetheless, the extent, role, and consequences of duplications in the origins of ecological adaptations, especially in the context of species interactions, remain unclear. To explore the evolution of a gene family that is likely linked to species associations, we investigated the evolutionary history of the A-superfamily of conotoxin genes of predatory marine cone snails (Conus species). Members of this gene family are expressed in the venoms of Conus species and are presumably involved in predator-prey associations because of their utility in prey capture. We recovered sequences of this gene family from genomic DNA of four closely related species of Conus and reconstructed the evolutionary history of these genes. Our study is the first to directly recover conotoxin genes from Conus genomes to investigate the evolution of conotoxin gene families. Our results revealed a phenomenon of rapid and continuous gene turnover that is coupled with heightened rates of evolution. This continuous duplication pattern has not been observed previously, and the rate of gene turnover is at least two times higher than estimates from other multigene families. Conotoxin genes are among the most rapidly evolving protein-coding genes in metazoans, a phenomenon that may be facilitated by extensive gene duplications and have driven changes in conotoxin functions through neofunctionalization. Together these mechanisms led to dramatically divergent arrangements of A-superfamily conotoxin genes among closely related species of Conus. Our findings suggest that extensive and continuous gene duplication facilitates rapid evolution and drastic divergence in venom compositions among species, processes that may be associated with evolutionary responses to predator-prey interactions.

Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea)

We present a large-scale molecular phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published molecular phylogeny of the entire group nearly a decade ago. Most of the numerous molecular phylogenies published during the last 15years are limited to rather small fractions of its species diversity. Bayesian and maximum likelihood analyses are mostly congruent and confirm the presence of three previously reported highly divergent lineages among cone snails, and one identified here using molecular data. About 85% of the species cluster in the single Large Major Clade; the others are divided between the Small Major Clade (∼12%), the Conus californicus lineage (one species), and a newly defined clade (∼3%). We also define several subclades within the Large and Small major clades, but most of their relationships remain poorly supported. To illustrate the usefulness of molecular phylogenies in addressing specific evolutionary questions, we analyse the evolution of the diet, the biogeography and the toxins of cone snails. All cone snails whose feeding biology is known inject venom into large prey animals and swallow them whole. Predation on polychaete worms is inferred as the ancestral state, and diet shifts to molluscs and fishes occurred rarely. The ancestor of cone snails probably originated from the Indo-Pacific; rather few colonisations of other biogeographic provinces have probably occurred. A new classification of the Conidae, based on the molecular phylogeny, is published in an accompanying paper.

Geographic Variation in Venom Allelic Composition and Diets of the Widespread Predatory Marine Gastropod Conus ebraeus

Background Members of the predatory gastropod genus Conus use a venom comprised of a cocktail of peptide neurotoxins, termed conotoxins or conopeptides, to paralyze prey and conotoxin gene family members diversify via strong positive selection. Because Conus venoms are used primarily to subdue prey, the evolution of venoms is likely affected by predator-prey interactions. Methodology/Principal Findings To identify the selective forces that drive the differentiation of venoms within species of Conus, we examined the distribution of alleles of a polymorphic O-superfamily conotoxin locus of Conus ebraeus at Okinawa, Guam and Hawaii. Previous analyses of mitochondrial cytochrome oxidase I gene sequences suggest that populations of C. ebraeus, a worm-eating Conus, are not structured genetically in the western and central Pacific. Nonetheless, because the sample size from Guam was relatively low, we obtained additional data from this location and reexamined patterns of genetic variation at the mitochondrial gene at Okinawa, Guam and Hawaii. We also utilized a DNA-based approach to identify prey items of individuals of C. ebraeus from Guam and compared this information to published data on diets at Okinawa and Hawaii. Our results show that conotoxin allelic frequencies differ significantly among all three locations, with strongest differentiation at Hawaii. We also confirm previous inferences that C. ebraeus exhibits no genetic differentiation between Okinawa, Guam and Hawaii at the mitochondrial locus. Finally, DNA-based analyses show that eunicid polychaetes comprise the majority of the prey items of C. ebraeus at Guam; while this results compares well with observed diet of this species at Okinawa, C. ebraeus preys predominantly on nereid polychaetes at Hawaii. Conclusions/Significance These results imply that strong selection pressures affect conotoxin allelic frequencies. Based on the dietary information, the selection may derive from geographic variation in dietary specialization and local coevolutionary arms races between Conus and their prey.

Variation and evolution of toxin gene expression patterns of six closely related venomous marine snails

Venoms of predatory marine gastropods of the genus Conus show amazing levels of interspecific diversity and are comprised of a cocktail of peptide neurotoxins, termed conotoxins, that are encoded by large gene families. Conotoxin gene family evolution is characterized by gene duplications and high rates of nonsynonymous substitution among paralogues; yet, what controls the differentiation of venoms among species is not clear. We compared four‐loop conotoxin transcripts of six closely related Conus species to examine conotoxin expression patterns among species. The species examined appear to express different numbers of four‐loop conotoxin loci and similarity in expression patterns does not seem to correspond with phylogenetic affinity. Moreover, several loci appear to have been independently silenced while others appear to have been revived from previously silenced states. Some loci also appear to exhibit coordinated expression patterns. These results suggest that the evolution of conotoxin expression patterns is incredibly dynamic and the differentiation of venoms of Conus is controlled in part by the evolution of unique conotoxin expression patterns.

Hidden diversity in a hyperdiverse gastropod genus: Discovery of previously unidentified members of a Conus species complex

Molecular sequence data are a powerful tool for delimiting species, particularly in cases where morphological differences are obscure. Distinguishing species in the Conus sponsalis complex of tropical marine gastropods has long been difficult, because descriptions and identification has relied exclusively on shell characters, primarily color patterns, and these often appear to intergrade among putative species. Here we use molecular sequence data from two mitochondrial gene regions (16S rRNA and cytochrome oxidase subunit I) and one nuclear locus (a four-loop conotoxin gene) to characterize the genetic discontinuity of the nominal species of this group currently accepted as valid: the Indo-West Pacific C. sponsalis, C. nanus, C. ceylanensis, C. musicus and C. parvatus, and the eastern Pacific C. nux. In these analyses C. nanus and C. sponsalis resolve quite well and appear to represent distinct evolutionary units that are mostly congruent with morphology-based distinctions. We also identified several cryptic entities whose genetic uniqueness suggests species-level distinctions. Two of these fit the original description of C. sponsalis; three forms appear to represent C. nanus but differ in adult shell size or possess a unique shell color pattern.

Evolution of ecological specialization and venom of a predatory marine gastropod

Understanding the evolution of ecological specialization is important for making inferences about the origins of biodiversity. Members of the predatory, marine gastropod genus Conus exhibit a variety of diets and the ability to capture prey is linked to a venom comprised of peptide neurotoxins, termed conotoxins. We identified conotoxin transcripts from Conus leopardus, a species of Conus that uniquely preys exclusively on hemichordates, and compared its venom duct transcriptome to that of four other Conus species to determine whether a shift to a specialized diet is associated with changes in the venom composition of this species. We also examined the secondary structure of predicted amino acid sequences of conotoxin transcripts of C. leopardus to identify substitutions that may be linked to specialization on hemichordates. We identified seven distinct conotoxin sequences from C. leopardus that appear to represent transcripts of seven distinct loci. Expression levels and the diversity of conotoxins expressed by C. leopardus are considerably less than those of other Conus. Moreover, gene products of two transcripts exhibited unique secondary structures that have not been previously observed from other Conus. These results suggest that transition to a specialist diet is associated with reduction in the number of components expressed in venoms of Conus and that diverse venoms of Conus are maintained in species with a broad dietary width.

Ecological Release and Venom Evolution of a Predatory Marine Snail at Easter Island

Background Ecological release is coupled with adaptive radiation and ecological diversification yet little is known about the molecular basis of phenotypic changes associated with this phenomenon. The venomous, predatory marine gastropod Conus miliaris has undergone ecological release and exhibits increased dietary breadth at Easter Island. Methodology/Principal Findings We examined the extent of genetic differentiation of two genes expressed in the venom of C. miliaris among samples from Easter Island, American Samoa and Guam. The population from Easter Island exhibits unique frequencies of alleles that encode distinct peptides at both loci. Levels of divergence at these loci exceed observed levels of divergence observed at a mitochondrial gene region at Easter Island. Conclusions/Significance Patterns of genetic variation at two genes expressed in the venom of this C. miliaris suggest that selection has operated at these genes and contributed to the divergence of venom composition at Easter Island. These results show that ecological release is associated with strong selection pressures that promote the evolution of new phenotypes.

Connectivity of populations within and between major biogeographic regions of the tropical Pacific in Conus ebraeus, a widespread marine gastropod

Information on genetic connectivity and structure of populations in the tropical Pacific is critical for making inferences about the origins and maintenance of diversity in this region. Sequences of the mitochondrial COI gene from 92 individuals of the trans-Pacific gastropod Conus ebraeus from eight localities spanning the tropical Pacific were analyzed to determine whether populations in the western, central, and eastern Pacific exhibit genetic structure, to examine the demographic histories of populations, and to infer patterns of gene flow. A total of 43 unique haplotypes were recovered, including a common haplotype that occurred in six of the eight populations examined. AMOVA and pairwise F-statistics showed that populations in the western and central Pacific were significantly differentiated from populations in the eastern Pacific, but no other evidence of structure. Bayesian isolation–migration (IM) analysis suggested that populations in the western and central Pacific separated from those in eastern Pacific during the Pleistocene. Examination of mismatch distributions and results from IM revealed that populations in the western and central Pacific expanded during the Pleistocene. Gene flow across the East Pacific Barrier appears to occur predominantly westward.

Differentiation of Venoms of Predatory Marine Gastropods: Divergence of Orthologous Toxin Genes of Closely Related Conus Species with Different Dietary Specializations

Venoms of Conus are remarkably diverse among species and the genes that encode conotoxins show high rates of evolution. Yet no prior studies have specifically explored how conotoxin gene evolution contributes to the differentiation of venoms of closely related Conus species. Previous investigations of four-loop conotoxin expression patterns of six closely related Conus species identified 12 sets of putative orthologous loci from these species, including eight pairs of loci that are coexpressed by two of these six species, C. abbreviatus and C. miliaris. Here I analyze the molecular evolution of orthologous conotoxin loci of these species and specifically examine the divergence of the eight orthologous counterparts of C. abbreviatus and C. miliaris. Tree and maximum likelihood-based analyses of these sequences reveal that positive selection promotes the divergence of orthologous genes among species and that the evolution of orthologues of C. abbreviatus and C. miliaris is asymmetric among species. The asymmetric evolution of conotoxin loci among species may result from lineage-specific dietary shifts or interspecific differences in the impact of selection from predator-prey interactions on conotoxin loci.