Utilizing CRISPR-based SHERLOCK for Rapid Species Identification


We have developed a novel ecological monitoring approach using CRISPR technology, which is widely utilized in the biomedical field for viral diagnostics, but is only starting to expand into other disciplines such as conservation biology. This CRISPR-Cas13a-based SHERLOCK (Specific High-sensitivity Enzymatic Reporter unlocking) platform is a highly sensitive, specific, and rapid method to discriminate between species in the field.

Developing Parentage-Based Tagging to Improve White Sturgeon Conservation Hatchery Methods

Kootenai River White Sturgeon: Parentage-based tagging

Parentage-based tagging (PBT) involves genotyping hatchery broodstock and using parentage assignment to identify exact parents of a hatchery origin fish of unknown parentage. This technique has been successfully utilized in other river spawning fishes but has yet to be validated and optimized for use in sturgeon. Previous research in other species indicates that the release of hatchery fish at earlier life stages improves overall survival and performance in the wild.

Estimating the Number of Parents Contributing to Wild Sturgeon Year Classes

Project Background

Sturgeon species across the globe face many threats to their continued survival in the wild including pollution, habitat degradation resulting from impoundments and water diversions, insufficient river flows, historical overfishing, and lack of access to spawning grounds. White sturgeon (Acipenser transmontanus, hereafter WS), are not federally listed in the United States, however, several population segments are state-listed as threatened and the Kootenai River population is listed as endangered.

Genome Assembly & Sex Marker Identification

For my Ph.D. research, I intend to create a reference quality genome assembly for Hypomesus transpacificus (delta smelt). A high-quality reference genome is a useful tool in many areas of modern biology. It will allow for fine scale resolution of population genetic analyses and may help to elucidate genetic and genomic sex-determining regions in delta smelt, which are currently unknown.

Population Genetics of Lamprey in California

Project Summary:

Lampreys, a group of jawless, eel-like fishes, are extant representatives of the first known vertebrates. Survival to modern times depended on lampreys’ parasitic strategy; however, multiple non-parasitic species have evolved. One current complication to lamprey population genetic research is the difficulty in determining an accurate species identification based on morphological features at the larval and juvenile life stages. At least six species of lamprey (Entosphenus spp.

Environmental DNA Metabarcoding in the San Francisco Estuary

Environmental DNA Metabarcoding in the San Francisco Estuary Multi-year, multi-institution collaborative project funded by CA Department of Fish and Wildlife and CA Proposition 1   Project Summary

Environmental DNA (eDNA) refers to DNA originating from skin/scales, mucus, gametes, or feces that can be isolated from water and used to detect target species or reconstruct whole communities (metabarcoding) (Figure 1). In this project we are developing an eDNA metabarcoding protocol to complement existing monitoring surveys.

Vernal pool fairy shrimp conservation and biodiversity

Background and Significance of Study

Vernal pools in California support diverse assemblages of species, including waterfowl, amphibians, endemic plants, insects, and at least 67 species of crustaceans (most of which are endemic and rare). Among the crustaceans are vernal pool branchiopods, known commonly as “fairy shrimp”. There are approximately 25 species of branchiopods in California, eight of which are endemic to California.