Dr. Viktoria Esther Bogantes Aguilar

A complete picture of diet composition is an essential element to understanding the ecological role of organisms. Moreover, diet studies can serve as an important tool for monitoring species and changes to the food web. One method to provide resolution when studying the diet of avian species is DNA metabarcoding of fecal samples. As such, we used DNA analysis to determine the diet of the Least Tern Sternula antillarum and compare results with diet analysis based on composition of fish dropped within breeding colonies. Comparisons between adult and chick fecal samples were also made across three years and within three zones of sample collection. Results show differences in diet composition between the two methods as well as across zones and years. Significant differences between prey items of adults and chicks were also identified. Metabarcoding data indicate that Least Terns are consuming Lionfish Pterois spp. (most likely in larval stages), a prey item that had not been previously recorded for Least Terns, and that data obtained from dropped fish might not be representative of chick diet. Differences across years and zones are likely due to shifts in the abundance and availability of prey items.

Most efforts at improving accuracy in phylogenomic reconstructions have focused on improving tree-building methods or orthology determination. Even though the use of whole genome sequence or transcriptome data is increasing, the degree to which accurate genome assembly and annotation influence phylogenetic inference has not been well explored. Here, we use low-coverage whole genome sequencing of spionid annelids to explore the impact of different assemblers and annotation strategies on tree reconstruction. We also produce a phylogenetic hypothesis that spans the breadth of Spionidae, examining the current systematics of the group, which is based on morphological parsimony analyses and classical taxonomy. Our results show that both assembly and annotation can have important consequences for the pool of loci that may be available for tree reconstruction. When an identical phylogenomic pipeline is used, differences in assembly and annotation can account for variation in reconstructed topologies. Interestingly, the completeness and depth of the data used for training annotation software (i.e. data from model systems) appear to be more important, by some measures, than the degree of phylogenetic relatedness of the organism from which training data are drawn. Despite variation in recovered topologies, the recognised subfamily Spioninae is nested within Nerininae, suggesting that diagnostic characters of Nerininae (e.g. thick egg membrane, short-headed sperm) are symplesiomorphies of Spionidae rather than apomorphies of a particular subclade. With the increased use of genomic data, our results advocate for a broader consideration of how assembly and annotation may impact data matrices used in phylogenomic analyses.

Non-native organisms cause biodiversity loss to the ecosystems they enter. In marine habitats, foreign invertebrates can be introduced through ballast water or biofouling. When this occurs, native organisms must compete with the new species in addition to fighting predation. These new species can more easily thrive without natural predators. Thus, studying the presence of these introduced species is an important focus of conservation research.

Echinoderms, a group of marine invertebrates consisting of starfish, sea urchins, sea cucumbers, sand dollars, and brittle stars, can be morphologically analyzed and sorted into general taxonomic groups. Echinoderm identification is reliant upon morphological characteristics, but this approach can be challenging due to their complex features, which can be cryptic. DNA barcoding is a tool used in taxonomic assessment, allowing scientists to explore biodiversity with greater accuracy than relying on morphological characteristics alone.

In this study, we describe the complete mitochondrial genome of Diopatra cuprea (Bosc, 1802). The mitogenome was found to contain 14,990 base pairs (67.53% A + T content), with a total of 37 genes (13 protein coding, 22 transfer RNAs, and 2 ribosomal RNAs). This study also examined mitogenome phylogenetics relationships of closely related species and recovered that D. cuprea is closely related to eunicids. This work has added to the genetic resources for furthering evolutionary studies of Annelida.

The marine feather duster, Bispira melanostigma (Schmarda, 1861), is a tube-dwelling annelid that contributes to ecological and biogeochemical processes in benthic communities. Due to the lack of scientific data, B. melanostigma is often difficult to distinguish from other species of marine worms through morphological characteristics alone. In this study, we report the complete mitochondrial genome of Bispira melanostigma. The complete mitogenome contained 20,624 bp length with a total of 13 protein-encoding genes, 21 tRNA, and 2 rRNA genes. Phylogenetic analysis of the complete mitochondrial DNA of B.melanostigma can aid in the understanding of evolutionary relationships within Sabellidae.