EPSCoR Research Fellows: NSF: Using Ancient DNA From Ocean Sediments to Forecast Ecosystem Shifts

This Research Infrastructure Improvement (RII) EPSCoR Research Fellows project provides a fellowship to an Assistant Professor and training for a postdoctoral fellow at the University of Hawai‘i at Mānoa. This work is conducted in collaboration with Dr. Brice Semmens at the Scripps Institution of Oceanography. Through the fellowship, the PI will investigate how marine life reacted to past environmental changes to better predict how oceans will respond to future environmental conditions. Integrating computer science, statistics, and marine biology, the project will extract historical DNA preserved in deep-sea sediment cores and develop new software to identify highly degraded genetic fragments. These historical records will inform predictive models to forecast future shifts in ocean ecosystems. The award will benefit society by bringing advanced oceanographic forecasting capabilities to Hawai‘i and expanding the STEM workforce through hands-on training for students and researchers in data science and computational biology. This project will establish a novel computational method to reconstruct historical marine biodiversity and forecast ecosystem responses to environmental shifts. The primary intellectual contribution is a damage-aware phylogenetic placement algorithm that computationally rescues highly degraded sedimentary ancient DNA (sedaDNA) without relying on complete reference genomes. Methodologically, the PI will extract sedaDNA from refrigerated Pacific basin sediment cores using optimized target-capture protocols. To address chemical degradation, the PI will embed position-dependent substitution matrices into conditional likelihood calculations to accurately identify and place sequence reads. These historical baselines will then parameterize phylogenetically informed Bayesian Joint Species Distribution Models to forecast community-level shifts under future projected environmental scenarios. The project will substantially improve research infrastructure at the home institution by establishing a new, localized marine paleogenomics capability and advancing the PI’s professional trajectory. These activities are fully integrated with workforce expansion, providing specialized cross-disciplinary training for a postdoctoral researcher and local students, and incorporating the generated open-source software into graduate computer science curricula. This project is supported by the EPSCoR Research Infrastructure Improvement Program: EPSCoR Research Fellows (ERF). The ERF program supports early- and mid-career investigators in eligible jurisdictions to develop collaborations at the nation’s private, government or academic research institutions. 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.