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.
This paper was submitted to Marine and Coastal Fisheries.
Here's a great five-minute video put together by NOAA Fisheries on recovering ESA-listed rockfishes in Puget Sound:
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 is in review at 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 is published in Environmental DNA.
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.
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.