Population Biology & Behavioral Ecology Research Labs


Protect Wild Dolphins plate


A portion of this research is funded by proceeds from Florida's Protect Wild Dolphins specialty license plate.


Ancient DNA

The Population Biology & Behavioral Ecology program’s state-of-the-art Ancient DNA Laboratory is a three-chambered clean room designed specifically for DNA/RNA extractions from samples of limited quantity whose quality has often been compromised by the passage of time and exposure to the elements. Our initial project focus is the extinct Steller sea cow, a giant sirenian that plied the frigid waters of the Commander Islands to the west of the Aleutian chain in the North Pacific Ocean. Discovered in 1742 by Vitus Bering’s expedition, the gentle leviathans were hunted to extinction within a few decades. We are collaborating with Russian colleague Dr. Alexander Burdin to investigate the ecology and behavior of Steller sea cows using aDNA techniques. This includes looking for clues in the DNA that may explain why the Steller sea cow population was small and its range -- from the time of first Russian contact to its demise -- very restricted. What we learn may be applicable to similarly small and restricted populations of marine mammals today.


Genetic studies by the Population Biology & Behavioral Ecology program span a diverse range: from dispersal patterns and population structures of beluga whales across the Arctic to community and group structures of bottlenose dolphins in estuarine systems in Florida, and from colonization and mating systems in Steller sea lions in the north Pacific Ocean to the demographic history and population structure of harbor seals in Alaska. We use numerous types of markers, tools and methods including mitochondrial DNA, microsatellite loci and MHC genes, high-throughput sequencing and genotyping and the latest likelihood and coalescent methods to infer demographic history, as well as past and contemporary patterns of behavior and life history. Much of our research is applied, assisting in resolving management of stocks of marine mammals and investigating possible genetic explanations for the failure of depleted populations to recover despite the implementation of robust protection and conservation measures.

Established in 2011, the Harbor Branch Ancient DNA Laboratory expands our ability to investigate the population biology, genetic diversity and species composition of past ecosystems. The facility is designed to accommodate several projects simultaneously, and since opening has yielded new insights into areas including the genetic causes of Steller sea cow extinction and biodiversity in marine systems during the neoglacial period, some 3,000 years BP.



IRL Dolphins

Population biology, behavioral ecology and genetic structure of estuarine bottlenose dolphins. Estuarine systems are among the most dynamic and biodiverse aquatic systems. Their shores are often centers of urban development and their waters the terminus of rivers and canals. As such, estuaries bear the brunt of anthropogenic (man-made) activities both urban and rural. As these ecosystems struggle to adapt to increasing anthropogenic threats, climate change and other ecosystem-wide impacts so too do their apex predators.

We are conducting a comprehensive study of the bottlenose dolphin population in the Indian River Lagoon estuarine system. This 150-mile ribbon of water that spans fully one third of Florida’s east coast and traverses a patchwork of dense urban centers, high agricultural runoff and near-pristine habitats. This long term study of a top predator residing in a high human use coastal ecosystem focuses not just on bottlenose dolphins themselves but also on their role in the larger ecosystem, an approach that fosters informed species management and greater understanding of ecosystem function. Now in its 17th year, the study is based on systematic boat-based photo-ID surveys that monitor over 600 individually identified dolphins, providing an unprecedented level of detail on behavior, ecology and individual life histories. We combine these methods with a diverse array of research technologies, including molecular genetics, telemetry, acoustic monitoring and GIS to estimate population abundance, gene flow, dispersal patterns and stock ID. We investigate the genetics of individual and population health, fitness and viability, and learn about group structure, predator-prey interactions and foraging ecology.



Epidermal lesions can often be an indicator of the health of an individual dolphin. Lacaziosis is an epidermal disease that has been shown to be endemic in the IRL dolphin population. Our study of lacaziosis in the IRL dolphins:

  • determined the sensitivity and specificity of photo-identification
    for diagnosis of lobomycosis in free-ranging dolphins,
  • determined the spatial distribution of lobomycosis in the IRL; and
  • assessed temporal patterns of occurrence.

We found the prevalence of the disease to be 6.8% across the population, which is higher than the prevalence in other populations across the globe. This study proved that photo-identification is a useful tool to monitor the course of individual and population health. Following the lacaziosis study in the IRL population, we used the same methods to determine the prevalence of lacaziosis (2.1%) in the adjoining Atlantic Ocean population. Currently, researchers are exploring the prevalence, distribution and causes of other epidermal lesions occurring throughout the population.
photos, left: Figures 1 & 2 - Lacaziosis in IRL dolphins.



A radio tracking study of bottlenose dolphins in the Indian River Lagoon, Florida was conducted in collaboration with HUBBS Sea World Research Institute during the summer of 2010. Dolphins were chosen based on known individuals within the HBOI Photo-Identification catalogue that portrayed high sightability and local home ranges. All dolphins were observed immediately after release with no unusual behavioral observations noted. Tracking was conducted primarily by boat-based surveys but additional data were acquired via aerial surveys. Sixty-eight hours were spent on survey, tracking all four individuals over the three-month study period. All individuals were tracked within their respective known home ranges, but specific locations were predominantly in the shallows (>81%), off the track line from ongoing photo-identification studies. The shortest transmission duration was 36 days, and longest was 62 days. The tags are designed to fall off, and to date, all dolphins have been sighted without attached tags and appear to be in good health. Future tracking studies will focus on behavioral interactions, male coalitions, and on equipment and attachment placement.

photos, right:
Figure 1. – Radio tag attachment before release.
Figure 2. – Hole made from designed disassembly of radio tag (disregard roto tag mid fin).
Figure 3. – Migration of intact radio tag.




IRL dolphins are provisionally listed as a strategic stock, and the effects of naturally-induced mortality on abundance are uncertain. This study investigated year-round predator-prey interactions between bottlenose dolphin (Tursiops truncatus) and bull shark (Carcharhinus leucas) by documenting the attack rate and spatial prevalence of shark/dolphin interactions . Thirty-two percent (223 of 704) of the distinct dolphin population had evidence of shark encounters, defined as fresh wounds (n=9) or healed scars (n=214). Wounds were found primarily on the dorsal surface of the animal (91%), but were equally dispersed anterior versus posterior, illustrating both fight and flight responses. Spatially disproportionate attack rates were found and may indicate more competition for limited, shared resources in the north-central lagoon. The high rate of shark bite scars from unsuccessful attack or interspecific competition indicates that risk of attack is substantial, and therefore fatal shark attacks may have a significant impact on dolphin survival within discrete communities existing within the estuary.


Vessel-based anthropogenic impacts on bottlenose dolphins (Tursiops truncatus) in the Indian River Lagoon (IRL), Florida were investigated by quantifying visible physical injuries to dorsal fins from photo-identification data collected from 1996-2006.

Our objectives were to:
1. identify boat-injured dolphins within the IRL using a photo-identification database;
2. determine the spatial distribution of boat-hit dolphins by segment and county;
3. determine whether dolphin injury rates are correlated with boater registration statistics; and
4. determine whether the behavioral patterns of IRL dolphins are disturbed by the presence of boats.

Forty-three dolphins, 6.0% of the distinctly-marked population, had injuries related to vessel impact. Segment 4, consisting of St. Lucie and Martin Counties, had the highest prevalence (9.9/100 distinct dolphins) of boat injured dolphins and had the highest number of registered boaters per square kilometer of habitat. These preliminary data suggest that vessel impacts on dolphins occur disproportionally in the IRL and should be considered a high priority management issue for local governments. Behavioral data collected during photo-identification surveys support the possibility of a low tolerance and sensitization to vessel interactions.



Last Modified 5/2/14