Crustacean Genomics

Crustaceans are a group of arthropods that includes familiar animals like crabs, shrimp, and lobsters, as well as thousands of other species with extremely varied ways of life including ferocious mantis shrimp, lanky 12-foot wide Japanese spider crabs, miniscule sea monkeys (brine shrimp), shell-incased barnacles, giant deep-sea isopods, and many others. For centuries scientists have debated how these various animals evolved, and this largely remains a mystery today. By using large genomic and transcriptomic datasets and expanded taxon sampling I hope to better understand their evolution and resolve this large and important branch of the tree of life.

Copepod Diversity

Copepods are a group of small aquatic crustaceans containing >14,000 species that are likely the most abundant animals in the ocean. Most copepods are about the size and shape of a sesame seed or grain of rice, but their small size belies their essential role in ecosystems. They are ubiquitous in aquatic environments from mountain streams to all depths of the ocean and are even abundant in canopy mosses and wet soils. Most ocean animals are directly or indirectly dependent on copepods as a food source. In addition, about half of all copepods (>6,000 species) are parasites of other animals – my research largely focuses on parasitic copepods.

microCT of three spined stickleback with 2 Lernaea copepods (red) embedded

I combine field expeditions, traditional morphological identification, cutting-edge imaging technologies, and genomic analses to better understand copepod diversity. I use light microscopy, microCT, SEM, and histology to identify copepods, describe new species, and document their morphology. I use next-generation sequencing (NGS) to understand how copepods are related to each other and how they have diversified. Much of the copepod tree of life remains largely unresolved, with only >4% of copepod species included in phylogenetic analyses. Despite this lack of resultion, current data suggest copepods evolved to be parasitic at least 14 times which has resulted in spectacular morphological diversity and extreme host range (14 phyla). Taken together, this makes the Copepoda an ideal system to test hypothesis regarding the evolution of parastism, morphological evolution, and the evolutionary dynamics of host associations. My 3 year NSF postdoc research fellowship focuses on building the copepod tree of life by developing an AHE probe set for copepod phylogenomics.

A diversity of parasitic copepod body plans. Image Credit

Tapeworm Taxonomy and Systematics

Tapeworms are parasites that live in the intestines of vertebrates. They lack all elements of a digestive tract, instead they rely on their host for nutrients, which tapeworms absorb through the surfaces of their body. I have described 5 species of tapeworms from sharks and documented a novel attachment mechanism in a genus of shark tapeworms. While most tapeworms attach with their head, a specialized attachment organ called a scolex, species of Calliobothrium use, to a much greater extent, spikey structures along the length of their body to attach to the villi on the gut of their hosts.

Computational Biology

I apply computational biology methods to answer biological questions. Often, these questions are related to the topics above, but I have also collaborated in a variety of other areas including human gene expression in cancer, mouse models of human disease, microbiome characterization, and hookworm developmental gene expression. My computational biology work has involved phylogenetics, ortholog identification, transcriptomics, differential gene expression analysis, microbiome analysis, and genome annotation.