Environmental Genomics and Bioinformatics

Research in our lab is centered on molecular tools, especially environmental DNA (eDNA), to study the relationships between humans, biological communities, and our ecosystem. A core focus of our lab is translational: partnering with resource managers and conservation practitioners to apply these methods where they matter, such as monitoring fish responses to dam removals or monitoring biodiversity in managed forests (see below for more!). On the analytical side, we are increasingly interested in the application and interpretation joint species distribution models (JSDMs), hierarchical modeling frameworks like HMSC, as well as the growing role of machine learning and AI in making sense of complex biodiversity data.

Current Projects:

Newly funded: Spider webs as eDNA samplers for forest wildlife, pests, and pathogens

Starting September 2026, a new three-year project funded by the New Hampshire Agricultural Experiment Station (Hatch program) will use spider webs as passive eDNA samplers to monitor forest biodiversity. Spider webs continuously trap airborne genetic material shed by insects, mammals, birds, and fungal pathogens, offering a low-cost, non-invasive complement to camera traps and acoustic recorders. The project builds on pilot sampling at UNH’s College Woods and during Deerfield, NH’s BioBlitz, which was featured by the Southeast Land Trust of NH as the cover story of The Understory.

Working with The Nature Conservancy, the Southeast Land Trust of NH, the Squam Lakes Natural Science Center, and NH Fish & Game, the project has three goals: 1) determine how biomass and distance from a source animal affect detection of NH wildlife species, using controlled wildlife enclosures at Squam Lakes; 2) test how forest management treatments (patch cuts, thinning, and unmanaged reserves) affect detection of wildlife and forest pathogens at TNC’s Green Hills and Surry Mountain Preserves; and 3) integrate spider-web eDNA with camera-trap and passive-acoustic data, in collaboration with Remington Moll and Laura Kloepper, to build multi-method species distribution models across New Hampshire’s Wildlife Management Units.

Newly funded: Monitoring fish and general biodiversity in response to dam removal

In collaboration with NH Fish & Game and with funding from NH Sea Grant, we are collecting daily water samples from the Oyster River at the Mill Pond Dam to monitor river herring using eDNA. A longer-term goal is to develop an easy-to-use platform that managers can use to regularly monitor herring runs. Alongside this, we are establishing a baseline of fish (12s metabarcoding) and general biodiversity (18s metabarcoding) for the Oyster River to compare against samples collected as the river recovers after dam removal. We are also sampling at the Pickpocket Dam on the Squamscott/Exeter River, which is currently under consideration for removal.

Other interests, projects, and collaborations:

• Monitoring very different, dynamic estuaries across the the NERRs system with PI Alison Watts
• Tracking the movement and diet of cod with PI Nathan Furey, and PhD students Aliya Caldwell and Sidney Axtell
• eDNA-based methods for assessing river health from algae with Ben Block and Ben Jessup at Tetra Tech
• In collaboration with Amanda McQuaid and the Lay Lakes Monitoring Program, Peter Countway and Robin Seith at Bigelow Marine Lab, and the town of Wolfeboro, NH, we will target picocyanobacteria from New Hampshire lakes for whole-genome sequencing to 1) assemble more genomes (and toxin producing genes) for pico-sized cyanobacteria, 2) measure the prevalence of toxins of pico-populations from different lakes in New Hampshire.
• eDNA for inferring population genetic parameters (structure and gene flow)
• Machine learning, statistical analysis/interpretation, and AI