UC Davis

Contemporary biodiversity loss is unprecedented and linked to decreased ecosystem function. Aquatic and wetland ecosystems are considered biodiversity hotspots and disproportionately at risk. In California, massive land-use changes continue to threaten freshwater, estuarine, and wetland ecosystems and species, but target species and species interactions are often difficult to study. Non-invasive genetic approaches are a suite of rapidly evolving technologies used to sample and study organisms non-invasively. These approaches facilitate better understanding of species, communities, and trophic interactions that are hard to glean using traditional methods. The research herein uses single- and multi-taxon methods in three local ecosystems. The theme that connects this work is the need to interpret a relatively new type of data in a manner that can be more easily operationalized for conservation and management. Chapter 1 examines and evaluates the use of single-taxon environmental DNA (eDNA) analysis for indirect detection of critically endangered delta smelt (Hypomesus transpacificus) from water samples in the San Francisco Estuary. Results indicate that turbidity and rarity of this small fish present challenges for eDNA detection. However, reliable and repeatable eDNA detection of rare species in turbid conditions is attainable with appropriate sampling and statistical methods. Chapter 2 applies multi-taxon eDNA metabarcoding to better understand fish community ecology in Putah Creek, a model system for stream restoration. Results show community differences across time and space, indicating that reordering is an important community dynamic. eDNA sampling was more sensitive for detection of rare species than conventional methods, facilitating a whole-ecosystem perspective. These findings complement long-term electrofishing survey data indicating that native fishes benefit from water management practices that replicate the natural flow regime. Finally, Chapter 3 applies non-invasive genetic sampling to study the diet of a widespread insectivorous predator in the Central Valley, a highly productive agricultural region. Results of guano analysis from the largest colony of Mexican free-tailed bats (Tadarida brasiliensis) in California show a diverse suite of prey characteristic of a generalist predator. Moths (Lepidoptera) and mosquitos (Diptera) comprised the highest relative abundance, including prey that are agricultural pests and disease vectors. Documenting this economically valuable ecosystem service may help increase support for bat conservation. Consumption of emergent taxa represents an aquatic-terrestrial food web linkage that has not been well-studied. Collectively, these studies demonstrate the value of emerging genetic technologies for conservation and provide new perspectives on ecologically relevant questions in imperiled, biodiverse ecosystems. Effective operationalization of non-invasive genetic approaches is part of the toolbox for conserving biodiversity and limiting the resulting socioeconomic and cultural losses.