Publications: Google Scholar 

The fish ladder at Ice Harbor Dam on the Snake River.

Columbia River Basin Steelhead migration

Columbia and Snake River Steelhead are listed as Threatened under the U.S. Endangered Species Act. During their pre-spawn adult migration, they exhibit complex migration behaviors which are believed to be influenced by environmental and hydrosystem factors; many of these migration behaviors have been shown to be detrimental to spawning success. To inform the recovery of these populations, we are developing a multistate model to investigate the impact of various factors on movement patterns, and thus eventual spawning success. This GitHub repository contains the code for our ongoing project.

Stock Assessment review (STAR) Panel at the Northwest Fisheries Science Center in June 2023.

Fisheries stock assessment and management

I was the lead author on the assessment of Rex Sole along the U.S. West Coast in 2023. The stock assessment document can be found here.

I also serve on the Pacific Fishery Management Council's Ecosystem Advisory Subpanel.

Sunset over Puget Sound.

ESA-listed rockfishes in Puget Sound

As part of my research at SAFS, I worked with the NOAA Office of Protected Resources and WDFW on the 5-year status review of Endangered Species Act (ESA)-listed rockfishes in Puget Sound. Our analysis focused on the Puget Sound/Georgia Basin Distinct Population Segment (DPS) of Yelloweye Rockfish, which is listed as Threatened under the U.S. Endangered Species Act. To inform the recovery of this DPS, we reconstructed historical catches of this species within Puget Sound, collated historical and contemporary demographic data, and fit a data-limited stock assessment model to generate estimates of population status. You can find our data, code, and paper here and press release for this project here.

This paper was published in Marine and Coastal Fisheries.

Here's a great five-minute video put together by NOAA Fisheries on recovering ESA-listed rockfishes in Puget Sound:

A CTD/Niskin rosette on the deck of the R/V Rachel Carson.

Environmental DNA data analysis

During my time with the Biological Oceanography Group at MBARI, I analyzed DNA sequencing data from environmental DNA (eDNA) samples. Over the course of many projects, I worked on bioinformatics, statistical analyses, and data visualization. While I was involved in a number of studies through field sampling efforts and computational analysis, I led analyses for three projects.

The first of these projects was the analysis of eDNA data from an in situ mesocosm experiment in Peru, during which the response of a marine community to simulated upwelling (via injection of water collected in the oxygen minimum zone) was monitored using eDNA. Using multiple metabarcoding primer sets to target different taxonomic groups (from bacteria to vertebrates), we detected a strong response of the community to upwelling and subsequent stratification, showing the potential of eDNA for monitoring changes in mesocosm experiments and improving our mechanistic understanding of these systems. This paper was published in Biogeosciences.

The second project was the meta-analysis of all eDNA samples collected by the Biological Oceanography Group at MBARI and collaborators through the Marine Biodiversity Observation Network project (>1,000 samples from locations including Monterey Bay, the Florida Keys, Hawaii, the Santa Barbara Channel Islands, and Peru). This project involved the management and analysis of an enormous amount of data, and provided insight into the differentiation of marine communities by depth, location, and seasonality. This paper was published in Oceanography.

The third project was a comparison of eDNA samples collected using traditional shipboard methods (such as the Niskin rosette pictured in the picture on the left) and autonomous underwater vehicles. We found that while each sampling method had some biases as to which taxa were well-represented in samples, ecological patterns were not obscured by the choice of sampling method. This paper was published in Environmental DNA.

The poster for my rockfish metabarcoding primer set, presented at UCLA Undergraduate Research Poster Day.

Rockfish metabarcoding primers

Rockfishes (Sebastes spp.) are a critical part of ecosystems in the Northeast Pacific, comprised of 110 commercially and ecologically important species. Many of these populations are also threatened due to a history of heavy fishing pressure and a slow time to reproductive maturity, making them a critical group to monitor. However, the recent radiation of many species in this genus has limited the application of genomic monitoring tools; many exhibit high sequence similarity at standard barcoding loci, prohibiting their identification from eDNA samples using commonly used universal fish primers. Using a set of programs in Python and Unix to analyze genomic data and determine the optimal metabarcoding primer set for this genus, I developed new metabarcoding primers that allow for the first time the detection of many of these species from eDNA samples. This paper was published in Conservation Genetics Resources.

Left: A section of an ovary mounted on a slide and stained with hematoxylin and eosin for histological  analysis.
Right: Rockfish ovaries being examined visually. Photo by Sheryl Flores, ODFW.

Maturity analyses of U.S. West Coast groundfishes

Maturity data for marine fishes is collected in two primary ways: through histology or by visual characteristics of gonads. Histology, the examination of these gonads under a microscope, is more accurate than the visual determination of maturity, but is also far more expensive and time-consuming. In this project, I worked with the Northwest Fisheries Science Center to compare these two methods for three west coast groundfish species: arrowtooth flounder (Atheresthes stomias), canary rockfish (Sebastes pinniger), and sablefish (Anoplopoma fimbria). We found that for arrowtooth flounder and canary rockfish (but not for sablefish), visual maturity assignments were fairly accurate when determining if fish were capable of spawning, but lacked the resolution to determine if fish were actually spawning in that year. These results will help inform the collection and use of visual maturity data along the U.S. West Coast. This paper was published in Environmental Biology of Fishes.