Research

Sunset over Puget Sound.

ESA-listed rockfishes in Puget Sound

As part of my research at SAFS, I will be working with the NOAA Office of Protected Resources on the 5-year status review of Endangered Species Act (ESA)-listed rockfishes in Puget Sound. This work will involve determining historical population levels via catch reconstruction from older datasets and evaluating the current population status from recent ROV (remotely operated vehicle) and hook-and-line survey data.

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 two primary 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.

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.

The manuscripts for both of these projects are in preparation.

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.

The pre-print of this work can be found here.

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 manuscript is in internal review at NOAA.