Marine Mammal Molecular Genetics Laboratory

Using molecular genetic tools and techniques to study marine mammals and gather information essential for their successful conservation and management in the Southeast Region.

Southeast

Five common bottlenose dolphins — Common bottlenose dolphins swimming just below the surface. ESA/MMPA Permit No. 779-1633.

We utilize various genomic techniques to study marine mammals and answer questions concerning population structure, species identification, species occurrence, prey preference, health, habitat use, phylogenetics, and taxonomy. Importantly, our research aims to meet the objectives of the Marine Mammal Protection Act and Endangered Species Act and helps to inform decisions for marine mammal management, conservation, and restoration planning. Although much of our work is focused on marine mammals inhabiting U.S. waters of the western North Atlantic and Gulf of Mexico, we also work with collaborators worldwide to study species ranging well beyond the waters of the southeastern U.S. The Marine Mammal Molecular Genetics Lab is located in Lafayette, Louisiana and is part of the NOAA Fisheries Southeast Fisheries Science Center’s Marine Mammal and Turtle Division.

Population Structure and Stock Assessment

Our research is used to inform stock assessment reports for the 34 species of whales, porpoises and dolphins that are known to inhabit the U.S. waters of the western North Atlantic and Gulf of Mexico. The more we learn about the different populations and their interconnectedness, the better NOAA Fisheries is able to protect and conserve marine mammals and maintain the overall health and productivity of our marine ecosystems. We use first-generation (e.g., Sanger sequencing), next-generation (e.g., restriction-site associated DNA sequencing or RADseq) sequencing, and genotyping techniques to investigate:

how many populations are present,
where populations occur,
and how genetically distinct populations are from one another.

Knowing where distinct populations of different species occur allows us to assess how each is impacted by natural occurrences such as harmful algal blooms and human-caused events like the Deepwater Horizon oil spill. The lab has active projects investigating genetic population structure of species such as common bottlenose dolphins, pantropical spotted dolphins, short-finned pilot whales, and sperm whales (also see ‘Omics section below) and has previously published population research on common bottlenose dolphins and Atlantic spotted dolphins.

Scientist Lynsey Wilcox loads marine mammal DNA samples onto a DNA sequencer for genetic analysis.

Genetic Species Identification

The Lab provides information about marine mammals that wash up on shore or strand along beaches and waterfronts, and works with many collaborators and partners throughout the northeastern and southeastern U.S. including regional stranding networks, state wildlife offices, conservation groups, research laboratories, and aquaria. Occasionally, animals are found stranded on beaches and field biologists are unable to identify the species or sex. This often happens when stranded animals are in an advanced state of decomposition, or sometimes animals of different species are very similar in body shape and coloration, especially when they are young, and can be hard to identify in the field. When this happens, a small bit of tissue (e.g., skin, muscle) from the stranded animal is sent to the lab for genetic identification to provide the missing information. Information like sex and species identity is important to understand what and how different marine mammals are being impacted by natural (e.g., bacterial and viral outbreaks) and human-caused (e.g., ship-strikes, fisheries interactions) events. Also, characterizing where species strand helps scientists to learn about where different marine mammals live and what kind of habitat ranges they have.

eDNA Research

A relatively new technique that can be used to get DNA from an organism without having to get a piece of tissue from a biopsy is to gather the DNA that is naturally shed by animals (and plants) into their surrounding environment; this is called environmental DNA, or eDNA.

Scientist Nikki Vollmer collects sea water for eDNA analysis.

Utilizing eDNA is an ideal method to non-invasively study the genetics of an organism. The Lab has developed techniques to collect eDNA from different marine mammal and fish species by taking samples of the water that the animals swim through. Back in the lab, scientists use genetic markers that are unique to different species in order to identify what species are present without ever having to see them. Current projects include collecting eDNA from the endangered Rice’s whale to help learn more about where they live, and we are also collecting eDNA where these whales are feeding to study their trophic ecology and identify what types of prey they may be targeting (also see ‘Omics section below).

Omics

One of NOAA’s newest strategies is to utilize emerging science and technology such as ‘omics research. ‘Omics is a suite of advanced techniques used to analyze DNA, RNA, or proteins and often incorporates advances in next-generation sequencing techniques and complex computational and analytical processes. At the Lab, we are incorporating ‘omics techniques to study multiple marine mammal species, including short-finned pilot whales, common bottlenose dolphins, and sperm whales to investigate fine-scale levels of population structure, and also to help clarify higher-level taxonomic relationships among common bottlenose dolphins within the western Atlantic Ocean. Additionally, we are using eDNA sampling (see eDNA section above) along with metabarcoding techniques to study trophic ecology and identify the potential prey species that are present in the Rice’s whale core habitat. This research will help to better characterize the prey preference of this endangered animal.

Taxonomy and Systematics

In addition to studying the population-level genetic differences within marine mammal species (intraspecific comparisons), the Lab also investigates higher-level taxonomic and systematic relationships among subspecies or species (interspecific comparisons). This type of information ensures that we are accurately recognizing all the marine mammal species in our waters and provides an accurate depiction of their evolutionary histories. For example, we are combining data from the morphology and genetics of the Rice’s whale to examine how closely related they are to not only Bryde’s whales in other parts of the world but also to other whale species. We have also been gathering extensive genetic and morphological datasets to research the systematic relationships among species within the dolphin genus Tursiops throughout the western Atlantic Ocean.