ESR 35:101-111 (2018)  -  DOI: https://doi.org/10.3354/esr00880

Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations

Margaret E. Hunter1,*, Gaia Meigs-Friend1, Jason A. Ferrante1, Aristide Takoukam Kamla2, Robert M. Dorazio1, Lucy Keith Diagne3, Fabia Luna4, Janet M. Lanyon5, James P. Reid

1U.S. Geological Survey, Wetland and Aquatic Research Center, Sirenia Project, 7920 NW 71st Street, Gainesville, Florida 32653, USA
2Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32608, USA
3African Aquatic Conservation Fund, BP 449, Ngaparou, Mbour 33022, Senegal, West Africa
4The National Center for Research and Conservation of Aquatic Mammals (ICMBio/CMA), Santos, SP, Brazil
5The University of Queensland, School of Biological Sciences, St. Lucia, Queensland 4072, Australia
*Corresponding author:

ABSTRACT: Environmental DNA (eDNA) detection is a technique used to non-invasively detect cryptic, low density, or logistically difficult-to-study species, such as imperiled manatees. For eDNA measurement, genetic material shed into the environment is concentrated from water samples and analyzed for the presence of target species. Cytochrome b quantitative PCR and droplet digital PCR eDNA assays were developed for the 3 Vulnerable manatee species: African, Amazonian, and both subspecies of the West Indian (Florida and Antillean) manatee. Environmental DNA assays can help to delineate manatee habitat ranges, high use areas, and seasonal population changes. To validate the assay, water was analyzed from Florida’s east coast containing a high-density manatee population and produced 31564 DNA molecules l-1 on average and high occurrence (ψ) and detection (p) estimates (ψ = 0.84 [0.40-0.99]; p = 0.99 [0.95-1.00]; limit of detection 3 copies µl-1). Similar occupancy estimates were produced in the Florida Panhandle (ψ = 0.79 [0.54-0.97]) and Cuba (ψ = 0.89 [0.54-1.00]), while occupancy estimates in Cameroon were lower (ψ = 0.49 [0.09-0.95]). The eDNA-derived detection estimates were higher than those generated using aerial survey data on the west coast of Florida and may be effective for population monitoring. Subsequent eDNA studies could be particularly useful in locations where manatees are (1) difficult to identify visually (e.g. the Amazon River and Africa), (2) are present in patchy distributions or are on the verge of extinction (e.g. Jamaica, Haiti), and (3) where repatriation efforts are proposed (e.g. Brazil, Guadeloupe). Extension of these eDNA techniques could be applied to other imperiled marine mammal populations such as African and Asian dugongs.


KEY WORDS: Marine mammal · Multi-scale occupancy model · Salt water · Trichechus · Non‑invasive detection · Quantitative PCR · eDNA · Sirenia


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Cite this article as: Hunter ME, Meigs-Friend G, Ferrante JA, Takoukam Kamla A and others (2018) Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations. Endang Species Res 35:101-111. https://doi.org/10.3354/esr00880

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