Rockin’ in the eDNA world: Testing and applying environmental DNA (eDNA) for applied ecology and conservation

Environmental DNA (eDNA) is a rapidly emerging methodology with important applications to natural resource management and biodiversity conservation. Since the initial eDNA study in 2008, eDNA has been used to detect a variety of taxa across ecosystems (e.g., freshwater, marine, terrestrial). However, many areas of eDNA are understudied, which limits the full potential of this methodology for species detection and conservation. In this dissertation, I used eDNA as a tool for applied conservation, from single species detection at small scales to detection of entire fish communities across a large watershed. In the first half of this dissertation (Chapter 2, Chapter 3, Appendix D), I examined how important yet understudied methodological decisions influence eDNA concentrations and species detection. In Chapter 2, I found invasive red swamp crayfish (Procambarus clarkii) carcasses did not produce detectable eDNA. Thus, for rare or low abundance species, detection of DNA may indicate the presence of a living organism rather than false positives caused by carcasses. In Chapter 3, I showed that stream flow can dilute eDNA concentrations and result in false negatives (non-detections) of a common invasive clam (Corbicula fluminea). I also found a strong seasonal response in eDNA concentrations, in that C. fluminea eDNA was easier to detect in summer when water temperature was warm and stream flow was low than in autumn when water temperature was cooler and stream flow was higher. Therefore, sampling during baseflows and consideration of the life history (reproductive season) of the target species prior to sampling is recommended. In the last two chapters, I used eDNA as a conservation tool across the Tennessee River Basin in northern Alabama, a freshwater biodiversity hotspot. In Chapter 4, I used five years of eDNA sampling to show that eastern hellbender salamanders (Cryptobranchus alleganiensis) are still present in northern Alabama, despite previous unsuccessful conventional sampling attempts by other researchers. Additionally, I found a lack of clear evidence that these remaining populations in Alabama represent an unpaid extinction debt as a result of recent increased urbanization. Chapter 5 provided a proof-of-concept for an eDNA metabarcoding index of biotic integrity (IBI). The eDNA-IBI produced similar results to a traditional IBI but detected fewer species and lacked a metric to assess fish health. Refinement of an eDNA-IBI is needed and I propose future recommendations for others seeking to use eDNA in bioassessments. Ultimately, this dissertation examined understudied but crucial methodological considerations in eDNA research and provided novel ways in which eDNA can be used in applied conservation. The results from this dissertation may help researchers and managers to plan eDNA sampling to increase species detection. My research also highlights how others might seek to use eDNA for freshwater conservation in the future, by coupling eDNA results with GIS-derived estimates of land use to assess extinction debt in an imperiled salamander and application of eDNA metabarcoding for bioassessments.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Ecol, Evol, Conservation Biol

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Curtis, Amanda N.

Contributors dc:contributor

• Larson, Eric R
• Davis, Mark A
• Schooley, Robert L
• Ward, Michael P

• eDNA

Statement dc:rights

• © 2022 Amanda N. Curtis

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/116038

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F116038