Abstract
Coastal areas globally are experiencing changes in viable habitat and food
availability for many aquatic species, driving subsequent shifts in migration patterns,
and distributions. In the northern Gulf of Mexico, an increasing number of tropical
species have recently become established, leading to the hypothesis that these
waters will continue to tropicalize, significantly impacting ecosystem functions. This
research used a multidisciplinary approach to investigate the anticipated effects of
climate change on the distribution and habitat use patterns of the West Indian
manatee (Trichechus manatus), a sentinel megafauna species that is of ecological
and cultural importance to Alabama, supporting stewardship of Alabama’s coastal
resources. This project 1) analyzed existing long-term and high-resolution datasets
to build predictive models for distribution and habitat use of the West Indian
manatee, a locally endangered and globally threatened sentinel megafauna species,
under current and future climate scenarios, and 2) tested and calibrated
environmental DNA techniques as a novel alternative to direct monitoring for
conservation of large and often hard to study animals in Alabama waters.
Purpose
The purpose of this dataset was to assess the feasibility and utility of incorporating
environmental DNA surveys as part of long-term species monitoring programs for
megafauna such as manatees in Alabama and similar freshwater-influenced
systems.
DOI: 10.57778/bqv3-0140
Suggested Citation
Phillips, N., & Carmichael, R. (2025). Environmental DNA survey data for the West Indian Manatee, Trichechus manatus, in Alabama waters [Data set]. Dauphin Island Sea Lab. https://doi.org/10.57778/BQV3-0140
Related Publication Citation
Methodology
Environmental DNA surveys were conducted in two years (2022, 2023) during peak
periods of manatee occurrence in Alabama. Water samples were collected and
filtered from up to 24 sites in each year at locations where manatees were known to
be present in real-time and at locations estimated to have higher and lower manatee
occurrence, based on existing sighting and tagged animal data. At each sampling
site, benthic water samples (3L) were collected and filtered, and environmental data
(e.g., sampling depth in m, DO in mg/L, temperature in °C, salinity, turbidity in cm)
were recorded.
Total eDNA was extracted from half of each filter using the QIAGEN DNeasy Blood
and Tissue Kit incorporating QIAshredder spin columns. DNA extracts were
screened for manatee DNA using a previously published and validated Droplet
Digital PCR (ddPCR) eDNA assay. Data were analyzed using a three criteria
approach to guard against false positives. Positive samples had: 1) droplets above
the manual threshold of the assay, 2) droplets within the known positive range for
the species/assay, and 3) a concentration of target DNA greater than or equal to the
Limit of Detection for the assay. DNA concentrations (copies/µL) were quantified
using the Rare Event Detection analysis in the Bio-Rad QuantaSoft software.
Attribution
This project was paid for [in part] with federal funding for the Alabama Center of Excellence from the Department of the Treasury under the Resources and Ecosystems Sustainability, Tourist Opportunities, and Revived Economies of the Gulf Coast States Act of 2012 (RESTORE Act) in cooperation with the State of Alabama Department of Conservation and Natural Resources under the Alabama Center of Excellence Program at the MESC/Dauphin Island Sea Lab.
