I am a post-doc in Dr. Beth Shapiro's lab (Paleogenomics Lab) at the University of California Santa Cruz in the Ecology and Evolutionary Biology Department. I use contemporary and ancient (aDNA) and environmental DNA (eDNA) to answer multi-scalar ecological and evolutionary questions and to inform conservation of several threatened and endangered vertebrate and invertebrate species. I also teach an undergraduate biology course using eDNA as a framework for STEM education.
I completed my PhD in Ecology, Evolution, and Behavior in December 2018 at the University of Texas at Austin, supervised by Dr. Shalene Jha. My dissertation research focused on how urban landscapes shape wildlife communities, plant-animal interactions, and affect dispersal, using wild native bees as a model system. I hope my research can inform conservation efforts of this vital group of pollinators.
RECENT AND UPCOMING EVENTS
American Genetic Association Annual Meeting
UCSC Class BIOE-19: Biodiversity in the Age of Humans
CURRENT RESEARCH AND ACTIVITIES
Informing restoration using eDNA
Simone Pond, Coachella Valley Nature Preserve, Palm Desert CA
In this study, we use eDNA to measure biodiversity and detect invasive species within two desert oases in the Coachella Valley Nature Preserve, CA. One of the oases was targeted to restore the endangered desert pupfish (Cyprinodon macularis), but had two invasive species (tilapia, Oreochromis aureus and red swamp crayfish, Procambarus clarkii) introduced in the 1960’s. Previous restoration efforts of pupfish were unsuccessful due to invasive presence. An eradication program of these two species was completed in July 2019. We collected a total of 238 eDNA sediment and water samples at 4 time points in both the invaded and non-invaded oases: immediately before eradication and every 6 months post-eradication for two years.
We found nearly 6000 total taxa in the pre-eradication samples, with a significant difference in biodiversity between the invaded and non-invaded oases. Crayfish presence is notoriously difficult to detect with eDNA, and indeed crayfish were not detected in any other samples known to contain crayfish. However, we detected a unique microbial community of around 90 species in the invaded oasis, that was absent in the non-invaded oasis and control tanks. Many of these species have previously been associated with crayfish in other studies. Analysis of the subsequent sampling time points is ongoing, but preliminary results indicate community turnover of microbial, plant, and animal species. We hope that these results can inform restoration of other invaded aquatic systems.
Landscape genomics of endangered California species
I have recently gained funding for two collaborative conservation genomics projects funded by the California Conservation Genomics Project (CCGP). Both of these projects will create full genomes for for important and threatened species, which will aid research of these and related taxa.
Examining the impacts of a century of decline on genomic diversity of the Tricolored Blackbird
In collaboration with PhD Candidate Kelly Barr at UCLA, we are using DNA extracted from 100+ year old museum specimens as well as contemporary samples to compare genetic composisiton through time of this iconic California species. Once one of the most abundant birds in California, it has undergone rapid decline after the 1930's as 90% of its preferred wetland habitat has been lost to urbanization and agricultural development. By comparing genomic diversity and structure in different individuals across its contemporary and historic range, we can understand potential ecological features that represent long-term barriers to gene flow, and help develop management strategies for this species.
Conservation genomics of California bumblebees
In collaboration with Drs Hollis Woodard (UCR) and Neal Williams (UCD), we are using contemporary specimens from across the state to assess genetic structure and diversity in two declining (B. crotchii, B. sonorus) and one stable (B. vosnesenskii) species. Bombus crotchii is considered endangered by the IUCN, and will likely soon be listed in the California Endangered Species Act. B. sonorus appears to be declining significantly, but has not yet been proposed for listing. In contrast, B. vosnesenskii is the most abundant bumblebee species in California and we will compare genomic diversity between species to explore drivers of decline by examining associations between land use, environmental factors, and genetic diversity, including both landscape and finer-scale patterns of habitat diversity and connectivity between sites. Understanding these factors will help management of these beautiful and economically important pollinators.