Advancing eDNA methods to inform ecological and conservation questions
The use of eDNA methods is a new and exciting area of research. Tania Valdivia, a post-doctoral student in the Whale and Dolphin Ecology Lab, is working on a large marine project under the guidance of Amy Van Cise from SAFS, and Ryan Kelly from the School of Marine and Environmental Affairs (SMEA).
The project focuses on the application of eDNA methods to detect and identify the spatial distribution of marine mammals and their prey in the California Current. Moving southward along the West Coast of North America, the California Current is a cold water Pacific Ocean current. The goal of the project is to advance eDNA methods for use in a variety of ecological and conservation questions that are relevant now and in the future.
Found in environmental samples, different aspects of eDNA can be investigated, each with complex behavior depending on the environment and the study scale. Tania’s interest is in using marine eDNA for the study of marine biodiversity and applying its potential in conservation studies.
Using eDNA to detect different species across the California Current system, she is working on samples from hake surveys from 2019, 2021 and 2023. This marine monitoring project takes place along the West Coast of the US at depths up to 500m. For several years, scientists have been collecting seawater samples during these oceanographic campaigns to extract eDNA. These samples are used to assess the presence of marine mammals throughout the US West Coast, covering a wide geographical and temporal range.
Detecting marine mammals can be a challenging task using acoustic, visual, or eDNA methods. Therefore, the project also focuses on identifying potential prey such as fish and cephalopods, as they play a crucial role in predicting the distribution of marine mammals. After the identification of the presence of marine mammals, Tania’s research combines marine mammal and prey detections with statistical models and environmental variables, with which she can gain valuable insights into marine mammal distribution. One unique contribution of incorporating eDNA methods is its ability to detect both marine mammals and their prey simultaneously at various depths, which is difficult to achieve using traditional methods alone.
How is the eDNA data used in projects like this collected? By deploying an array of Niskin water sampling bottles from a vessel, which go to different depths to retrieve samples. The water samples are then filtered and stored to prevent eDNA degradation, until eDNA extraction takes place back at the NOAA Northwest Fisheries Science Center (NWFSC) laboratory. Processing involves extracting and quantifying the eDNA obtained per sample. These samples are precious and must be stored correctly, as each sample takes a lot of effort and funding to collect and can be used for other research.
After obtaining eDNA in good enough concentration, polymerase chain reactions (PCRs) are conducted with specific primers. Different primers are selected depending on the taxonomical feature you want to focus on in the eDNA mixture. In this research, primers have been chosen specifically for cetaceans, fishes, and cephalopods.
After the PCR reaction, numerous copies of eDNA molecules are produced, sequenced, and analyzed using bioinformatics. Part of Tania’s research concentrates on analyzing millions of sequences using various pipelines to obtain a catalog of sequences that can be identified taxonomically using genetic reference databases. This data enables researchers to indirectly determine the species presence and abundance in the area where the samples were collected.
At this moment in time, many different species such as the Pacific white-sided dolphin, the Northern right whale dolphin, Risso’s dolphin, Dall’s porpoise, humpback whale, orca and the Baird’s beaked whale have been detected using eDNA collected from the Washington Coast above the Columbia River – the Northern portion of the California Current. These detections will then be used to create distribution models of marine mammal species at different depths. This project is particularly notable as it may be one of the first attempts to 3D map the distribution of marine mammals across such a vast area.
One of the end goals of collecting and working with eDNA is to transform this information and its complexities in different ways, into informative ecological data. This can be then used in conservation assessments and applied to real-world management of species of interest. For Tania, one of the highlights of this work is despite not physically being out in the field and on the vessels collecting eDNA data, she is a crucial part of detection efforts through working with complex code to detect marine mammals through eDNA.