[MARMAM] New Publication: Manatee environmental DNA (eDNA) detection and occurrence estimates

Hunter, Margaret mhunter at usgs.gov
Thu Apr 19 13:02:28 PDT 2018


Dear colleagues,
Our paper on the development of a manatee eDNA assay for digital PCR and
its use to estimate occurrence and detection probabilities is now available
from Endangered Species Research (open access):
http://www.int-res.com/abstracts/esr/v35/p101-111/


Hunter, M.E., Meigs-Friend, G., Ferrante, J.A., Takoukam Kamla, A.,
Dorazio, R.M., Keith Diagne, L., Luna, F., Lanyon, J.M., and Reid, J.P.,
2018, Surveys of environmental DNA (eDNA): a new approach to estimate
occurrence in vulnerable manatee populations: Endangered Species Research,
v. 35, p. 101-111, https://doi.org/10.3354/esr00880.

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.


Margaret E. Hunter, PhD, Research Geneticist
U.S. Geological Survey, Wetland and Aquatic Research Center
7920 NW 71st Street
Gainesville, Florida 32653

Office: (352) 264-3484
Mobile: (303) 817-5792

*https://www.usgs.gov/staff-profiles/margaret-hunter
<https://www.usgs.gov/staff-profiles/margaret-hunter>*
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