Isolating and studying degraded DNA from preserved organismal remains and environmental samples allows new inferences about past ecosystem compositions, population dynamics, and, in the context of archaeological remains, human interactions with their environment. In this dissertation, I addressed how sequencing depth and stochasticity of metabarcoding PCR influences various measures of biodiversity. I found that sequencing depth and stochasticity between PCR replicates significantly influence estimates of alpha but not beta diversity. In my second chapter, I used eDNA isolated from permafrost cores spanning the last 50,000 years in the Klondike, Canada to characterize community composition and turnover of plant and mammalian communities. In this chapter, I characterized floral and faunal change over the last 50,000 years, with clear shifts from steppe to boreal forest habitat delineated with the presence and absence of arctic ground squirrels and woody plants. Finally, I isolated ancient DNA from archaeological moccasins to observe hunting patterns of Bison used by occupants of the Promontory Caves of Utah, an archaeological site occupied 1240-1290 AD. I found the majority (87%) of moccasins were constructed from female bison, supporting prior hypotheses of hunting strategies targeting cow-calf herds at the end of fall preparing for overwintering. My dissertation highlights some of the many questions that degraded DNA present in soil, bone, and preserved hides can contribute towards answering.

Climate change is leading to habitat shifts that threaten species persistence throughout California’s unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term environmental change. Aiming to provide biodiversity data, the UC Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program to be a citizen and community science biomonitoring initiative that uses environmental DNA (eDNA, DNA shed from organisms such as from fur, feces, spores, pollen or leaves). Now with results from 1,000 samples shared online, California biodiversity patterns are discoverable. Soil, sediment and water collected by researchers, undergraduates and the public reveal a new catalog of thousands of organisms that only slightly overlap with traditional survey bioinventories. The CALeDNA website lets users explore the taxonomic diversity in different ways, and researchers have created tools to help people new to eDNA to analyze community ecology patterns. Although eDNA results are not always precise, the program team is making progress to fit it into California’s biodiversity management toolbox, such as for monitoring ecosystem recovery after invasive species removal or wildfire.