DNA from dives: Species detection of humpback whales (Megaptera novaeangliae) from flukeprint eDNA

Environmental DNA (eDNA) is an increasingly utilized tool in the conservation world that helps us identify the presence or absence of a species. Our Conservation genetics laboratory scientist Dr. Adam Warner was part of a recently published study that demonstrated the ability to detect humpback whales in as little as 500 ml of seawater. In “DNA from dives: Species detection of humpback whales (Megaptera novaeangliae) from flukeprint eDNA” published in the journal Environmental DNA, methods were established to collect seawater from the “fluke-print,” or area of water that was impacted by a whale’s fluke when diving, and then filter the water to collect biological material and DNA on filter paper. DNA was then extracted and tested for the presence of humpback whale DNA, with 1/3 samples containing sufficient humpback whale eDNA to be detected. Notably, the same samples were also tested for the presence of several other cetacean species, but none were detected leading to confidence that the technique was specific for humpback whales. Further work is being carried out in our conservation genetics lab to improve on species detection and look at a broader view of DNA in a sample to detect more than just one species, but all species present in DNA form in a water sample.

Methods like this are important in conservation biology because they allow us to monitor species non-invasively and also detect species that we may not be able to observe easily using traditional methods. This can include sampling water in the open ocean, where eDNA can detect species from a water sample and negate the need for costly monitoring using a dive team. Our genetics lab is currently working with a number of outside organizations to do this very type of work, including a large study with Project Watershed Society where we are helping them identify species of forage fish present in water samples taken at a number of key locations in the pelagic zone.

Useful methods also include using eDNA to assess the diet of individuals in a species. This is difficult using camera traps or microscopic analysis of fecal material, but using the DNA found in a fecal sample, our lab is working with UVic to identify the prey consumed by coastal black bears in their study. We also use this technique to assess the prey consumed by coastal wolves as part of a large study in our coastal carnivores program here at Raincoast. Better understanding of what individuals are eating, and how that changes over the course of the year are important when considering the conservation impact of policy decisions.

As we move into 2025, our conservation genetics lab is gearing up for new studies and collaborations to help achieve a better future for our natural world through study, analysis, and action by our Raincoast teams.

Citation

Robinson CV, Dracott K, Glover RD, Warner A, Migneault A. 2024. DNA from dives: Species detection of humpback whales (Megaptera novaeangliae) from flukeprint eDNA. Environmental DNA. 6(2): e524. https://doi.org/10.1002/edn3.524

Abstract

Northern British Columbia has been identified as an important habitat for several coastal cetacean species, including humpback whales (Megaptera novaeangliae). This species is listed as being of “Special Concern” under Canada’s Species at Risk Act, partly due to data deficiencies concerning genetic population structure and demographics in British Columbia. Anthropogenic activities threaten North Coast humpback whale populations, with particular concern for the impact of vessel noise, entanglement, and ship strikes. Current methodology (i.e., biopsy sampling) for obtaining cetacean genetic data is invasive, challenging, and costly; therefore, there is an urgency to develop effective and minimally invasive methodologies for efficiently collecting this data. Environmental DNA (eDNA) has been identified as an ideal tool for monitoring the presence and distribution of numerous species within marine ecosystems; however, the feasibility for cetaceans is not yet well established. In this study, we opportunistically collected targeted 1 L seawater eDNA samples from flukeprints when individual humpback whales were observed diving between the years of 2020 and 2022. A total of 93 samples were collected from individual humpback whales identified using a photographic identification catalogue. We successfully detected humpback whale eDNA in 28 samples using novel species-specific qPCR primers (~500 mL of sample), with relatively equal successful detection between immediate (0 days) and delayed (up to 10 days) sample filtration. Here, we have validated a qPCR assay for detecting humpback whale DNA from flukeprints and highlighted the future optimizations required to improve the potential application of flukeprint eDNA for conservation management.

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Raincoast’s in-house scientists, collaborating graduate students, postdoctoral fellows, and professors make us unique among conservation groups. We work with First Nations, academic institutions, government, and other NGOs to build support and inform decisions that protect aquatic and terrestrial ecosystems, and the wildlife that depend on them. We conduct ethically applied, process-oriented, and hypothesis-driven research that has immediate and relevant utility for conservation deliberations and the collective body of scientific knowledge.

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