Collaborative Research: Comparing the roles of conserved and novel molecular building blocks underlying kleptocnidy in nudibranch gastropods.

Understanding how new biological traits arise is a fundamental question in evolutionary biology, with broad implications for explaining the origins of biodiversity, predicting how organisms respond to environmental change, and advancing biotechnology innovation. Most research into evolutionary novelty has focused on traits that arise through the gain of new genes or pathways; far less is known about how the loss or modification of existing pathways can generate novelty. This project investigates the process of kleptocnidy, which is the theft and storage of microscopic stinging structures (nematocysts) from cnidarian prey, a striking natural example of biological innovation that has evolved independently multiple times. The research will determine whether this unique process evolved in nudibranch sea slugs through specialization of phagocytosis, an ancient cellular process used across animals for immune defense and intracellular digestion. By generating high-quality genomic, transcriptomic, and single-cell data resources for marine invertebrates, the project produces strategic biological data assets useful to the broader scientific community for biotechnology applications and the development of fundamental knowledge across evolutionary biology, comparative immunology, and cell biology. This project will also support the training of graduate and undergraduate students and postdoctoral researchers in genomics and computational analysis through research experiences and will broaden participation in science through public engagement activities. Overall, these efforts will contribute substantially to the training of a competitive STEM workforce in molecular tools and biotechnology. This collaborative project tests whether kleptocnidy evolved primarily through specialization (loss of function) of conserved phagocytosis pathways or through the origin of new molecular machinery. Three objectives integrate complementary approaches across two laboratory-tractable nudibranch species, Berghia stephanieae and Hermissenda opalescens. Objective 1 characterizes the molecular processes underlying kleptocnidy in adult Hermissenda using RNA-sequencing of cerata tissues under cnidarian and non-cnidarian feeding regimes, paired with pharmacological inhibition assays targeting candidate phagocytosis pathways. Objective 2 reconstructs the regulatory networks involved in the development of the cnidophage, which is the specialized cell type that captures and stores nematocysts, using single-cell RNA-sequencing across early juvenile Berghia development, with in situ hybridization chain reaction validation, to test whether cnidophages develop through pathways conserved with generalist phagocytic cells. Objective 3 evaluates the role of lineage-specific (“novel”) genes through comparative differential expression and orthology analyses across approximately 20 cladobranch nudibranch species, including independent origins of nematocyst sequestration, collected from California and French Polynesia. Outputs will include a new reference genome, single-cell atlases, gene co-expression and regulatory networks, and a phylogenetically informed catalog of conserved versus lineage-specific genes underlying a charismatic case of evolutionary innovation, while providing foundational genomic resources for an emerging marine invertebrate model system. The results of this work will improve our understanding of the evolution of novelty. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria. NSF Award ID: 2611236 | Program: 01002627DB NSF RESEARCH & RELATED ACTIVIT | Principal Investigator: Jessica Goodheart | Institution: American Museum Natural History, NEW YORK, NY | Award Amount: $751,513 View on NSF Award Search: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2611236 View on Research.gov: https://www.research.gov/awardapi-service/v1/awards/2611236.html