Trophic Interactions and Habitat Requirements of Gulf of Mexico Rice’s Whales

As part of the RESTORE Science Program-funded Gulf of Mexico Rice’s Whale Trophic Ecology Project, we worked with Scripps Institution of Oceanography and Florida International University on a multi-year study to develop a comprehensive ecological understanding of the endangered Rice's whale. In 2018 and 2019, we collected data on the physical, oceanographic, and biological features that may influence Rice’s whale distribution in the Gulf of Mexico. We surveyed mostly within the species’ current core distribution area using a multifaceted approach to collect data. 

During the study we integrated: 

• Animal photo-identification
• Kinematic (motion) and acoustic tagging
• Biological sampling of the whales and their potential prey
• Visual and passive acoustic monitoring and
• Environmental measurements and prey distribution mapping

Rice’s whales—recently recognized as a new species—are rare and range-restricted. They are the only baleen whale to reside in the Gulf of Mexico year-round and may be one of the most endangered baleen whales in the world, with the population estimation of fewer than 100 individuals. 

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Repercussions of the Deepwater Horizon Oil Spill

Rice’s whales—like many marine mammals—are subject to various human threats. Vessel collisions and noise, and activities related to energy exploration, development, and production are high on that list. These whales suffered substantial impacts at population-level as a result of the 2010 oil spill, as described in the comprehensive Deepwater Horizon Trustee Council’s Final Programmatic Restoration Plan. It is estimated that 48 percent of the whale’s core habitat was exposed to surface oil, 17 percent of the population died, 22 percent of females had reproductive problems, and an additional 18 percent suffered adverse health effects. Scientists estimate the population declined approximately 22 percent from their pre-spill population size and it will take 69 years for the population to recover from these losses. 

The information gathered during these trophic ecology surveys will help us improve management and recovery efforts for this endangered species by identifying the whales’ preferred habitats, prey types and distribution, and ecological role all aimed at recovering these species in the Gulf of Mexico.

Photo-Identification and the Creation of their First Catalog

Photo-identification (Photo-ID) techniques use unique patterns on the dorsal fin and body of cetaceans to characterize and identify individuals using photographs. Over time, as we photograph whales multiple times, we add new records thus creating the sighting history for that animal. Different whales and their respective sighting histories constitute a Photo-ID catalog. 

During this project, we constructed the first photo-ID catalog for the Rice’s whale. Currently we have 33 whales with sightings of some individuals spanning more than 15 years. 

We use photo-ID data to estimate population size, learn about movement patterns, and better understand population structure and group associations. These data may also be used to estimate survival rates. “Witchhazel” (catalog ID 7003), a male whale that was first documented in November 2018 was matched a few months later, using markings on his dorsal fin, to the whale that stranded in the Florida Everglades. Following a necropsy, the skeleton was preserved and archived and then used in studies to determine that this population is in fact a new species.

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Photo-ID catalogs allow us to document the health of whales. In the 2019 survey, researchers from the Northeast Fisheries Science Center joined us to observe the animals using small uncrewed aerial systems (sUAS). Our highly trained scientists are authorized through permits to operate sUAS at a prescribed altitude directly above the whales. By using high-resolution images, we are able to obtain measurements (photogrammetry) to assess body condition and potential changes in the health of this population over time.

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Animal Telemetry

During our surveys, we also tagged whales with Acousonde^TM tags for recording whale acoustics and kinematics to measure their dive behavior and movements and record their sounds. These tags are about the size of a 16 ounce water-bottle and attach to the whales’ back via suction cups. The tags remain on the whales anywhere from hours to a few days. Once they detach from the whales, we use satellite and VHF transmitters to locate and recover them and access the data recorded.

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Acousonde tags record sounds as well as temperature, depth and animal orientation as the animal moves through the water. This information provides a complete and extensive dataset on the whales’ diving and movement behaviors and environmental conditions.

Rice's Whale Dive: Double Lunge for Lunch (0:20)

Dive plot created by Melissa Soldevilla in TrackPlot software developed by Colin Ware. Note this software uses a humpback whale symbol to represent the tagged Rice's whale. Credit: NOAA Fisheries (Permit # 14450 and 21938)

Our research has identified that Rice's whales make foraging dives near the sea floor, especially during the day. At the beginning of a dive, the whales slowly go under and once close to the bottom make lunges that are circular in pattern while searching for food. Here a Rice’s whale surfaces after we attached an Acousonde™ tag with suction-cups on its back.

Biological Sampling

Another way to study population structure and whale health is by collecting a biopsy sample. Our trained scientists are authorized through permits to collect a small sample of skin and blubber—roughly the size of a pencil eraser—using a modified crossbow with a sharp sampling tip. Biopsy samples can be used to determine sex, sequence DNA, assess hormone levels, and analyze for contaminants. Combined with other data, these samples offer insights into the overall health of individual whales within the population. 

A method that helps us determine the presence of whales in the environment is by testing seawater for environmental DNA, or eDNA. All organisms naturally shed DNA into their environment through dead skin cells, feces, and breathing. During this project we collected seawater in the ‘flukeprint’—right after whale dives—  and were able to detect whale eDNA in these samples through the use of species-specific genetic primers.

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Prey Classification and Distribution

From our past research, we know that Rice’s whales dive and feed near the seafloor during daylight hours. 

We still have much to learn though. We do not know:

• What they are preferentially feeding on at these depths 
• How they find their prey 
• If prey found in their core habitat are present in sufficient numbers year round and are nutritiously-rich to meet the daily energetic demands

Understanding the prey requirements for these endangered whales is vital to protecting the habitat they need to survive. To understand their food chain, we look at many different factors.

One tool we use is a scientific echosounder, similar to fishfinders. They allow us to study marine organisms without removing them from the water. The echosounders on our ships use high frequency vibrating transducers set to a specific frequency to emit sound into the water column. As the sound wave travels through the water and encounters objects, it is reflected back. We record these “echos” continuously and are able to identify the types of organisms and to quantify biomass. This helps us understand how potential prey are distributed throughout the whales’ core area.

So far, using the echosounder, we have found  that during the day, some fish and invertebrates (e.g. squid) concentrate near the seafloor and sometimes form large patches, or aggregations. Usually, when we find feeding whales, we find these high density aggregations near the bottom. They are patchy in space and don’t stay put for very long. This makes us wonder how the whales find the right aggregations to feed on.  

Similarly to collecting water samples in a whale’s ‘flukeprint’, we also use eDNA to study potential prey aggregations. Using conductivity, temperature, and depth (CTD) casts we collect water samples from where an aggregation was detected. The water is then analyzed to identify the organisms in the sampled area based on genetic data.

Trawling for Answers

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We aim to identify the most likely prey types and put together a picture of the food web that supports these whales in the Gulf of Mexico. In 2019, we towed a net that was 90 feet across and 12 feet deep at the opening to target potential prey seen on the echosounder images. We conducted several successful trawls within the core habitat at various depths. We caught mostly small, schooling fish that are found near the bottom during daylight hours and that migrate upward closer to the surface at night. With the trawl data in hand we can compare what was caught, and how much there was, to the signals from the echosounders. 

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To draw the last link in the food web, we are working with our partners at Florida International University to analyze tissue samples that we collected from the fish, squids, and crustaceans caught in the trawls. By analysing the ratio of stable isotopes like carbon and nitrogen we can assess the trophic relationship among organisms and identify their position in the food web.

Call of the Whale

Baleen whales produce low-frequency calls to communicate over distances more than 60 miles away. Studying animals by listening to the sounds they produce is known as passive acoustic monitoring. By listening for sounds the whales make, we are able to study their call types and calling behavior, as well as locate whales. 

To hear and locate calling whales, we use specialized instruments called Directional Frequency Analysis and Ranging (DIFAR) sonobuoys. These instruments allow us to use sound to find distant whales to approach for focused studies such as tagging, photo-ID, and small uncrewed aerial vehicle (sUAS) work.

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When whales produce the same sound many times that has consistent frequency and duration characteristics, it is referred to as a “stereotyped call”. While most baleen whales produce stereotyped calls that are specific to the species or population, the vocal repertoire of the Rice’s whale is not well known. Several stereotyped sounds have been detected on instruments deployed in the study area and these have been proposed as possible Rice’s whale calls. They include pulsed calls—a series of low thump-like sounds and downswept pulse sequences, which often occur in pairs of pulses or longer sequences (up to 25 pulses).

Link to Audio file of Downsweep Sequence

Note: The audio has been sped up 1.25x to enable the listener to better hear the very low-frequency sounds.

There are also tonal calls including long-moans and shorter repetitive segments of constant-frequency tones, called tonal-sequences, that sometimes follow long-moans. The downswept pulse pairs have been localized to specific sightings of the Rice’s whales, and are a validated species-specific call type produced by Rice’s whales.

Link to Audio file of Long-Moan Call

Note: Audio has been sped up 1.25x to enable the listener to better hear the very low-frequency sounds.

During these trophic ecology surveys, sonobuoys were deployed to help validate whether the other possible call types are in fact produced by Rice’s whales to characterize species-specific call types. When species-specific call types are known, long-term passive acoustic recordings using hydrophone-equipped instruments moored on the seafloor can detect calls produced by animals, such as Rice’s whales over long periods of time. We can then use these data to better understand the whales’ distribution and seasonal movements in the absence of visual surveys.

Environmental Measurements

Combining environmental datasets with whale sightings allows us to develop predictive habitat models that explain what environmental features may be driving whale distribution. Understanding the ecology of Rice’s whales requires understanding short term fluctuations and trends in environmental conditions where they occur. We collect In-situ environmental data during all our ship-board surveys. We look at temperature, salinity, fluorescence (a measure of primary productivity), sea surface height, and other environmental parameters to understand their effects on whale habitat-use and their prey. Remotely-sensed environmental data from satellites, such as sea surface height (which provides the location of major features like the Loop Current), can also be incorporated during data analysis. 

We are analyzing the echosounder data, trawl catch, eDNA, and stable isotope data together to help us better understand the key components that are important for sustaining this endangered whale population. Once we have a better understanding of the whale's preferred prey in the core habitat, we can survey other regions in the western and southern Gulf of Mexico to see whether they contain these prey and could support the whales. This will help us better understand where whales could potentially live in the entire Gulf of Mexico.

Data Products and Information Transfer to Stakeholders

A primary goal of our RESTORE-funded research is to ensure that project outcomes will be integrated into effective actions to contribute to the recovery and conservation of these endangered whales. To date, we have held three workshops with stakeholders and managers to share our progress and preliminary results and to get their feedback. 

Multiple data products and publications are currently being developed and will be available on this page soon. 

More Information

• RESTORE ACT Science Program 
• Rice’s Whale Species Page 
• Frequently Asked Questions—Rice’s Whales
• Rice’s Whales Core Habitat Map and Data 
• Video: Researchers Identify Endangered Rice’s Whales' Habitat Requirements to Inform Recovery Effort by the National Centers for Coastal Ocean Science.

Management Documents

• Status Review of the Gulf of Mexico Bryde’s Whale 
• Final Rule to List Rice’s Whale under the Endangered Species Act 
• Gulf of Mexico Bryde’s Whale Recovery Outline  
• Marine Mammal Stock Assessment Reports

Blog and Web Stories

• RESTORE research mission Blog
• New Species of Baleen Whale in the Gulf of Mexico 
• DNA Confirms Rare Bryde’s Whale Off Florida is Gulf of Mexico Species 
• NOAA Lists Gulf of Mexico Bryde’s Whales as Endangered
• The Expert is in! Gulf of Mexico Bryde’s Whale 
• How the Gulf of Mexico Bryde's Whale Became the Rice's Whale: A brief timeline of these whales' history, from their first specimen to their official new name.

Research Documents produced by Southeast Fisheries Science Center staff and collaborators

Soldevilla M. S., A. J. Debich, L. P. Garrison, J. A. Hildebrand, S. M. Wiggins. 2022. Rice’s whales in the northwestern Gulf of Mexico: call variation and occurrence beyond the known core habitat. Endang Species Res 48:155-174.

Soldevilla, M.S., K. Ternus, A. Cook, J. A. Hildebrand, K. E. Frasier, A. Martinez, and L. P. Garrison. 2022. Acoustic localization, validation, and characterization of Rice's whale calls. The Journal of the Acoustical Society of America 151, 4264-4278

Rosel, P. E., L. A. Wilcox, K. Y. Tadasu, and K. D. Mullin. 2021. A new species of baleen whale (Balaenoptera) from the Gulf of Mexico, with a review of its geographic distribution. Marine Mammal Science. Volume 37, (2): 577-610.   

Garrison, L. P., and L. Aichinger Dias. 2020. Distribution and Abundance of Cetaceans in the Northern Gulf of Mexico. NOAA Technical Memorandum NMFS-SEFSC-747,40 p.

Soldevilla, M. S., J. A. Hildebrand, K. E. Frasier, L. Aichinger Dias, A. Martinez, K. D. Mullin, P. E. Rosel, L. P. Garrison. 2017. Spatial Distribution and Dive Behavior of Gulf of Mexico Bryde's Whales: Potential Risk of Vessel Strikes and Fisheries Interactions. Endang Species Res 32: 533– 550, 2017.

Rosel, P. and L. A. Wilcox. 2014. Genetic Evidence Reveals a Unique Lineage of Bryde's Whales in the Northern Gulf of Mexico. Endangered Species Research, 25(1): 19-34.

Garrison, L. P., J. Ortega-Ortiz, and G. Rappucci. Abundance of Marine Mammals in Waters of the U.S. Gulf of Mexico During the Summers of 2017 and 2018. Southeast Fisheries Science Center Reference document PBRD-2020-07.

Mullin, K. D. 2007. Abundance of Cetaceans in the Oceanic Northern Gulf of Mexico from 2003 and 2004 Ship Surveys. Southeast Fisheries Science Center Reference document PBRD-2016-03.