Environmental DNA Detection: New Method for Monitoring Manatees

Researchers use new wildlife sampling technique to identify site occupancy of Manatees in a more accurate, less intrusive, cheaper manner.

Listed by the IUCN as a vulnerable species, the West Indian Manatee is a prime candidate for conservation efforts[1]. However, designating protected areas for manatees can be difficult if you don’t know where they are. Aerial surveys currently conducted by the Florida Fish and Wildlife Conservation Committee are successful at near-shore population counts[2], but have trouble identifying manatees in murky waters, like brackish streams, and rivers obstructed by foliage.

In response to this, scientists from the United States Geological Survey have developed a new method for detecting the presence of manatees- environmental DNA (eDNA) detection.

The pipeline for eDNA detection is as follows:

  1. a species of interest sheds tissue in their environment
  2. these tissues contain DNA
  3. The DNA contains unique signatures that can identify the existence of the species of interest


In this case, researchers identified regions in the cytochrome b gene (involved in the electron transport chain) as a unique marker for the manatee genus (Trichechus), and developed a corresponding primer. Subsequent amplification via digital droplet PCR and  its corresponding results were fed through a site-occupancy model to determine the statistical probability that a manatee had been through the sampled water based on the amount of target DNA amplified.

A common problem in the field of ecology is the link between detecting a species and a species occupying a particular area. For instance, just because you did not find a species at a site, does not mean that it is absent there. Instead of modelling a site as a binary presence/absence label, site-occupancy models estimate a fluid probability that a species occupies a site based on repeated surveying.

In this case, the researchers found the West Indian Manatee occupyting a variety of habitats including Wakulla River, Lake Wimico, and Guantanamo Bay. More importantly, in my opinion, they established eDNA detection as an effective method for surveying wildlife populations.


IUCN 2017. The IUCN Red List of Threatened Species. Version 2017-3.  available from: http://www.iucnredlist.org

Florida Fish and Wildlife Conservation Commission. Manatee Aerial Surveys. Population Monitoring. Available From: http://myfwc.com/research/manatee/research/population-monitoring/aerial-surveys/

Original Study

Hunter M, et al. Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations. Endangered Species Research.  March, 2018. https://doi.org/10.3354/esr00880.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s