Copepods are an important group of aquatic crustaceans and are the most numerous animals in the ocean. They dominate marine zooplankton communities and support the majority of fisheries around the world. Over 5,000 species are parasitic, including many economically significant pathogens in wild fisheries and aquaculture. Parasitic copepods are estimated to cost the aquaculture industry approximately $1 billion annually. Despite their abundance and economic importance, copepod evolutionary relationships are poorly known and genomic resources for copepods are lacking. This has not only impacted our ability to diagnose, treat, and control parasitic copepod infections, it has also hampered the use of copepods as a model system for studying parasite evolution. This fellowship aimed to establish a robust phylogenomic framework for developing copepods as an emerging model system to study the evolution of parasitism and to expand taxonomic expertise in copepod research. Towards this end, the fellow visited three of the most significant copepod collections in the world: the Smithsonian’s National Museum of Natural History, the Natural History Museum in London, and the German Center for Marine Biodiversity Research at Senckenberg Am Meer and received taxonomic and methodological training with experts at each institution. 

This work produced the largest phylogenomic analysis of copepods to date and resolved several long-standing questions about copepod evolutionary relationships, including the first phylogenomic evidence supporting a major revision of the copepod order Harpacticoida. Our results show that Harpacticoida should be split into two separate orders: Harpacticoida and Canuelloida, with Harpacticoida being more closely related to Cyclopoida than Canuelloida. Additional evolutionary analyses revealed copepods have evolved to be parasitic at least 14 times, substantially altering our understanding of the evolution of parasitism in the group given that prior studies estimated only 6 transitions to parasitism. Copepods thus have the fourth greatest number of transitions to parasitism among all animal groups, surpassed only by insects, ticks and mites, and nematodes, which shows that copepods are among the best systems for studying the independent origins of parasitism.

To leverage existing copepod collections preserved in ethanol, we developed the first set of RNA probes for targeted capture sequencing of copepods. We manufactured the probes and validated them with bioinformatic simulations and DNA extracted from 64 copepod species spanning 60 genera, 40 families, and 6 orders, which represent a broad phylogenetic sample of all major groups of copepods. The probes effectively captured sequence data from over 1,000 gene regions (exons) across all major groups of copepods. Downstream filtering yielded a matrix of over 600 orthologs corresponding to over 200,000 base pairs of sequence data per specimen, validating that these probes are a cost-effective method for generating phylogenomic data from existing copepod collections. Given the scalability, affordability, and flexibility of the targeted capture approach developed here, this is likely to become a new standard for copepod phylogenomics. The target loci were selected for broad evolutionary utility, enabling studies from population-level divergences to deep-time relationships spanning the more than 400 million year evolutionary history of copepods.

To examine how copepods have adapted morphologically to parasitic lifestyles, this project involved training and applying advanced imaging techniques including confocal laser scanning microscopy (CLSM), z-stacked macrophotography, and microCT scanning. We collectively imaged more than 100 copepod species from over 60 genera and 18 families using these techniques, with the images being linked to species records in the World Register of Marine Species (WoRMS) after publication. This work includes the first high-resolution CLSM images for 72 species, macrophotography for 24 additional species, and microCT scans for 9 species. In addition to revealing copepod morphology in new detail, our results showed that microCT and CLSM can reveal internal muscle structure and body segmentation in highly modified copepods, even when their body shapes are so altered that segmentation is no longer visible externally. This demonstrates that these are powerful new tools for uncovering the evolutionary history of body plans in some of the most extremely modified parasitic copepod groups.

This project also featured extensive science communication and outreach. The fellow presented findings from this research in 18 talks at national and international conferences, including 13 invited presentations. The work led to 9 peer-reviewed publications, with several more accepted or under review. Several new identification keys have been published, and online interactive keys are in active development on WoRMS. The fellow served as an instructor for copepod identification as part the 2023 Dauphin Island Sea Lab Meiofauna Diversity and Taxonomy Workshop. The fellow cowrote 3 popular science pieces and was featured in 7 articles in major outlets such as National Geographic, Slate, and The Atlantic. Over a 3 year period, the fellow met with 12 separate K-12 classes across several states to discuss marine biology, parasitology, and science careers. 

Last Modified: 05/01/2025
Modified by: James Bernot