Detection and Identification of Environmental DNA from Beaked Whales on the Navy’s Atlantic Undersea Test and Evaluation Centre (AUTEC) Range Using Droplet Digital PCR

Dr. Charles Baker | Oregon State University



Detection and identification of species, subspecies, or stock of whales, dolphins, and porpoises at sea remain a challenging obligation for monitoring activities by the Department of Defense (DoD), particularly for cryptic or elusive species like beaked whales. The project's objective is to improve detection and identification of cetacean species using environmental (e)DNA. Specifically, the project aims to:

  • determine the temporal and spatial distribution of cetacean eDNA in habitats of relevance to DoD;
  • enhance the body of knowledge necessary to improve confidence in cetacean species identification by eDNA ‘barcoding’; and
  • advance the body of knowledge necessary to improve confidence in species presence and absence determinations by eDNA quantification.

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Technical Approach

The project will investigate the potential for detection and identification of eDNA from beaked whales on the Navy’s Atlantic Undersea Test and Evaluation Centre (AUTEC) using droplet digital (dd) Polymerase Chain Reaction (PCR). ddPCR is a powerful new technology for quantifying low levels of eDNA by fractionating a PCR reaction into thousands of droplets using an oil emulsion. Amplification of a target-specific eDNA ‘barcode’ is quantified by measuring the ratio of target-positive to target-negative droplets. Previously, the project team has used ddPCR to detect eDNA from the passage of killer whales (Orcinus orca) in the inshore waters of Puget Sound over a period of at least 2 hours, despite movement of the water mass by several kilometers due to tidal currents (Baker et al. in review). This project will extend these methods to the detection and identification of eDNA from beaked whales in the open ocean. To enhance the likelihood of experimental success, the project will take advantage of the acoustic array on the AUTEC range for detection and localization of Blainville's beaked whales (Mesoplodon densirostris) (Moretti et al. 2010) and the extensive information from the long-term study of abundance and distribution of this population (Claridge 2013). The team will use real-time localization from the acoustic array to direct a small vessel to collect seawater from the proximity of beaked whales using two sampling strategies: 1) serial sampling from the terminal dive of beaked whales, with visual confirmation of location; and 2) localized spatial sampling from the estimated location of the acoustic signals, without visual confirmation. Using ddPCR, the limits of detection for these whale-positive samples can then be compared to a collection of whale-negative samples from locations where the acoustic monitoring shows the whales to be absent.

Baker, C.S., M.L. Dalebout, S. Lavery and H.A. Ross. 2003. www.DNA-surveillance: applied molecular taxonomy for species conservation and discovery. Trends in ecology & evolution 18:271-272.

Claridge, D.E. 2013. Population ecology of Blainville's beaked whales (Mesoplodon densirostris). PhD thesis, University of St Andrews, Scotland. University of St Andrews, Scotland, St Andrews.

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The benefits of this project are two-fold. First, it will refine methods for routine species identification of beaked whales using eDNA barcoding to improve confidence in the taxonomy and knowledge of stock structure (Baker et al. 2003). Second, it will quantify the temporal persistence and spatial distribution of beaked whale eDNA to improve confidence in determination of species presence and absence. With the result of this project, it will be possible to design a large-scale survey to integrate the eDNA detection function with the estimates of density/occupancy of beaked whales based on acoustic detection (Moretti et al. 2010). This approach can be extended to other species and to other Navy ranges with acoustic support, including the Pacific Missile Range Facility (PMRF) and Southern California Offshore Range (SCORE), and, eventually to areas without acoustic arrays.

Moretti, D., T.A. Marques, L. Thomas, N. DiMarzio, A. Dilley, R. Morrissey, E. McCarthy, J. Ward and S. Jarvis. 2010. A dive counting density estimation method for Blainville's beaked whale (Mesoplodon densirostris) using a bottom-mounted hydrophone field as applied to a Mid-Frequency Active (MFA) sonar operation. Applied Acoustics 71:1036-1042.

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Points of Contact

Principal Investigator

Dr. Charles Baker

Oregon State University

Phone: 541-867-0255

Program Manager

Resource Conservation and Resiliency