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Top Updates from the FIM Program


June 20, 2024

A man and woman are pulling in a large net while standing in waist-deep water. A third person off the edge of the image is holding a tall pole.

Net Surveys in Sarasota Bay
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Our team recently spent the day conducting net surveys in Sarasota Bay to monitor fish populations and record vital information on captured species. The vast majority of fish captured in these samples are counted, measured and carefully released alive, while a few specimens are occasionally retained for further life history and fish health analysis. These data help us better understand and evaluate impacts to fisheries over time and are particularly valuable for evaluating fisheries impacts after environmental disturbances like red tide, hurricanes, temperature anomalies, and chemical/oil spills. On this trip, we pulled three 600’ seines and eleven 70’ seines, and recorded many species, including redfish, sheepshead, grey snapper, pinfish, pig fish, and needle fish.

We were lucky to be joined on this trip by Dave Tomasko, Executive Director of the Sarasota Bay Estuary Program (SBEP) – a long-time partner of ours. Since 2009, The SBEP has been working with our Fisheries Independent Monitoring (FIM) team to assess and monitor fish populations in Sarasota Bay. Thanks for joining us, Dave!

Photos by Sarasota Bay Estuary Program

February 26, 2024

A woman sitting outside on a dock next to a large white cooler. The cooler is opened to show a sturgeon on ice.

Atlantic Sturgeon Collection

Last month, our Fish Kill Hotline received a report of a dead sturgeon along the banks of the St. Johns River outside of Jacksonville. Our researchers arrived on the scene and identified the specimen as an Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus), a unique, prehistoric, and federally endangered species, which makes it a rare find!

The Atlantic sturgeon inhabits both salt and freshwater habitats, cycling between the two. Some migrate into brackish and saltwater during the fall and feed there throughout the winter months before heading back into freshwater rivers during the spring, while others may remain at sea for years. Sturgeon spawn in rivers and typically return to their native spawning grounds when they mature. In Florida, the Atlantic sturgeon can be found in the St. John’s River, but the species can be found along the east coast all the way north to Canada!

Sturgeons are benthic feeders, which means that they feed on organisms located in or on the bottom of waterways, with a diet primarily consisting of crabs, grass shrimp, lancets, brachiopods, and marine worms. They have barbels located on the underside of their snout, no teeth, rubbery lips, and a mouth used for suctioning food off the bottom.

Similar to sharks and rays, sturgeons have a skeleton made of cartilage. But, unlike most other fish, they have lines of hard dermal scutes (bony plates) along their body. These plates keep them safe from predators, serving as an important set of armor. Atlantic sturgeons have five rows of these plates that run along the top, sides, and bottom of the body. Typically, these scutes run all the way along the body, but in the case of this specimen, decay has already caused a few near the tail to fall off.

If you find a stranded, injured, or dead sturgeon, please report it to NOAA Fisheries at (844) 788-7491 or send them an email at If you observe a fish kill, please report it to our Fish Kill Hotline at 800-636-0511 or online.

Learn more about the Atlantic Sturgeon.

View these original posts online:

December 7, 2023

November 24, 2023

Freaky Flounder Friday!

Close up view of heads of two flounder fish with dark brown coloration on both the top and bottom of the fish.

No, you're not seeing double. This is a rare instance of a flounder with full pigment on both the “eye” side and the “blind” side, known as “complete ambicoloration”. Typically, larval flounder start out swimming upright in the water column with an eye on each side, and then they undergo metamorphosis in the first few weeks of their life. One eye moves to the opposite side of their head, their body flattens out as they start swimming parallel to the bottom, and pigment develops on the “eye” side, while the “blind” side that rests on the bottom remains white. These adaptations are thought to help the flounder have a wider field of view as they burrow in the sand to hide from predators and ambush their prey. Pigment mutations in flounder are common in aquaculture, but extremely rare in the wild.

p>A local fisherman, Jeremy Goodrich, caught this Southern Flounder (Paralichthys lethostigma) near Oak Hill in the Mosquito Lagoon over the Veteran's Day weekend, and gave it to Rick Riley an FWC scientist at the Indian River Lagoon Field Lab in Melbourne. Cool catch!


The Fisheries Independent Monitoring (FIM) program at FWRI strives to provide timely, fisheries-independent data and analysis to fisheries managers for the conservation and protection of Florida’s fisheries. The FIM sampling program was designed to track annual trends in abundance, as well as changes in size and age composition over time. The program supports single-species assessment and management, multi-species and ecosystem-based modeling and management, as well as emerging issues. Because the FIM program uses a multi-gear approach (many different types and sizes of capture gear) to collect information on a suite of species and size/age classes, FIM data have many applications.

Read more about the FIM program in the October 2023 feature article.

Two women are standing at a metal lab counter wearing gloves and each holding a large shark jaw that has been removed from inside of a shark.

New Flickr Album: Shark Jaw Removal
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Deceased fish and sharks are often reported by the public to FWC and through our FISH KILL HOTLINE (800-636-0511), website or social media. These specimens are often retrieved by FWC scientists for further examination. Recently, two such specimens were reported to FWC, a Tiger Shark (~ 10.5 ft TL) and a Great Hammerhead Shark (~12 ft TL), both of which are prohibited from harvest in Florida waters. Scientists can gather a variety of valuable information from such specimens - collecting a series of external measurements and gathering genetic tissue samples that can be analyzed and added to our Florida Biodiversity Collection, where they serve as a valuable resource for researchers who can use them as guides for identifying species and a source for research material. Other tissue samples are often taken to evaluate fish age, fish health, reproductive state, and tissue toxicology (i.e., mercury levels). After these sharks had served their purpose for research, scientists from the Fish and Wildlife Research Institute (FWRI) helped give them a new purpose as an educational outreach tool that can be displayed and continue to help the public learn more about these interesting species.

FWRI scientists removed the jaws from both the Great Hammerhead Shark and the Tiger Shark specimens. Removal of the jaws from a shark is a laborious and tedious hands-on process. Scientists use special knives and dissection instruments to extract the jaws and remove all muscle and connective tissue. This process can be dangerous as rows of razor-sharp teeth are exposed and dissected around. In this instance, sharp teeth was not all that was found; during the jaw removal, our biologists unveiled a sting ray barb lodged in the jaw of the hammerhead shark! Although we don’t know the exact events that led to this barb getting stuck in the shark’s jaw, we do know that hammerhead sharks are known to enjoy stingrays as part of their diet. So, we’ll let you draw your own conclusions.

A woman stands at the back of a large vessel traveling in the ocean. Her handing is resting on the edge of a metallic frame surrounding an underwater camera.

Greater Amberjack Research Cruise
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Join us as we set sail with our Fisheries Independent Monitoring (FIM) team and staff from Florida International University aboard Florida Institute of Oceanography's R/V Hogarth working on grant-funded research estimating Greater Amberjack abundance in the Gulf of Mexico and U.S. South Atlantic. Amidst an array of cutting-edge tools deployed to aid our research, today’s spotlight shines on our Stereo Baited Remote Underwater Video (SBRUV) Cameras. With the swift yank of a rope, these heavy-duty underwater cameras plunge to the ocean floor where they record a 360-degree view of marine life and activity – capturing crucial data for our researchers. Watch until the end for a look at the underwater footage!

In the Gulf, Greater Amberjack are overfished and are currently undergoing overfishing. To learn more about the population’s abundance, movement and distribution data are being collected as part of the Greater Amberjack Count – a congressionally funded project and multi-agency effort worked on by a team of researchers throughout the Southeastern United States, including our very own here at FWRI. Learn more about the project.


A man wearing an FWC hat and thick brown gloves is standing in waist-deep water and holding a sawfish at the base of the rostrum.

Sawfish Comeback?
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Check it out! Dr. Gregg Poulakis, a biologist from our Fisheries Independent Monitoring (FIM) team, is featured in a Florida Sportsman article discussing signs of a smalltooth sawfish (Pristis pectinata) comeback. Historically, sawfish were a common sighting off Florida’s coastline, but over the last century, their numbers declined from unintentional overfishing due to entanglement in fishing gear and habitat degradation due to coastal development. In 2003, the species was officially listed as endangered under the Endangered Species Act.

Today, the overall sawfish population in the US is thought to be stable or possibly increasing, and our team has identified nurseries off Southwest Florida in areas such as the Peace and Caloosahatchee rivers. Juveniles have returned to the southern Indian River Lagoon decades after their disappearance, and the core population in Southwest Florida may be increasing too. Some positive news in a sea of negative headlines regarding many marine species lately. Our team is currently conducting vital research on sawfish to understand aspects of biology and ecology that will inform conservation and management decisions.

Help support sawfish research! Sawfish are protected from harvest, but if you catch a sawfish while fishing for other species, or see one while you are near the water, please report it by calling 844-472-9347 (1-844-4SAWFISH) or via email to

When reporting a sawfish sighting or encounter, please include the date and time of the encounter, location, and the estimated length of each sawfish including the saw, and any other relevant details. If you catch a sawfish, keep it in the water, try to untangle it if necessary and safe to do so, and cut the line as close to the hook as possible before release.

Pick up a copy of the August/September 2023 Edition of Florida Sportsman magazine at a newsstand or online for more details.

Sawfish research was conducted pursuant to NMFS ESA Permit No. 25864


Sampling along Tampa Bay’s Mangrove Forests – FIM
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Join our team of biologists from FWC’s Fisheries Independent Monitoring (FIM) program in Tampa Bay as they conduct surveys along a thriving mangrove forest. Mangroves and their intricate root structures are an ideal nursery habitat for young and smaller fish who find shelter and food among the roots. Similarly, mangroves also provide ideal habitat for ambush predators (such as Common Snook) that conceal themselves under the mangroves waiting patiently for their next meal to swim by.

In this clip, the two varieties of mangroves present are the red mangrove (Rhizophora mangle) and black mangrove (Avicennia germinans). Red mangroves are commonly found close to the water’s edge, often growing in it, and can be easily identified by their red arching prop roots. In contrast, black mangroves tend to grow closer to land and are characterized by their dark, woody appearance and finger-like projections that extend vertically from the soil, which earned them their nickname ‘Dead Man’s Fingers.’

Biologists from our FIM team conduct sampling to monitor the health of our fisheries and collect important data on fish, their associated habitats, and water quality. Most fish are captured in nets, counted, measured, and carefully released, but some are occasionally retained for further life history and fish health analysis.

Learn more about mangrove forests.

A researcher is holding a fish in the water.

Scientists with the Fisheries-Independent Monitoring (FIM) program have been working on a grant-funded research project to track the movement of juvenile sport fish within and around Robinson Preserve, a fish-focused habitat restoration site located on the south shore of Tampa Bay in Manatee County, Florida Government. The goal of the study is to investigate how juvenile sport fish navigate through the protected waters of the fish nursery habitats created within the restoration site and estimate how many move out into sub-adult and adult habitats of Tampa Bay and surrounding waters, thereby potentially contributing to the fisheries. To do this, scientists are using acoustic telemetry to monitor fish movements. Staff have placed acoustic listening devices (receivers) in and around the Preserve, which are listening for up to 80 tagged juvenile sport fish. These tags emit a sound that is picked up when the fish pass by the receivers, allowing scientists to track individual fish for 2-3 years. Data from this study can be used to inform future restoration habitat design features.

“Track” this research at the project website.

This research is supported by a Tampa Bay Environmental Restoration Fund grant through the Tampa Bay Estuary Program and Restore America's Estuaries.


Two people on either end of a large net are standing in knee deep water along mangroves.

It’s #NationalEstuariesWeek!

Estuaries are important natural places, often called the “nurseries of the sea”. Numerous animal species rely on estuaries for nesting and breeding, and for juvenile sportfish, estuaries mean plenty of food and places to hide from predators!

Charlotte Harbor is the second largest estuary in Florida and home to one of FWRI’s field labs.

Our Fisheries-Independent Monitoring (FIM) biologists in Charlotte Harbor conduct monthly sampling surveys within the estuary recording water quality, habitat types and fish community data.

FIMs sampling techniques tend to target juvenile and sub-adult fishes, the abundance trends are a valuable forecasting tool for future adult stocks. Fisheries managers use these FIM data as well as other fisheries data to assess the overall well-being of fish populations.


Several people in deep water pull together a large net floating in the water.

Through support from the National Park Service, researchers from FWC’s Fisheries Independent Monitoring (FIM) program have been monitoring the coastal waters of the Everglades National Park (ENP). The project began in 2019 to provide information on ecosystem changes in response to Everglades restoration efforts. Using multiple seine and trawl nets, FIM’s sampling design allows scientists to gather data on the entire fish community at different life stages in diverse habitats, providing a comprehensive picture of marine life within the ENP. Last April, the FIM program sampled within the ENP for 21 days deploying 244 nets, identifying and counting 30,429 individuals from 139 distinct taxa!

Monitoring activities are conducted under permit number EVER-2021-SCI-0019


Common Snook and Gray Snapper have been observed using freshwater springs in rivers to keep warm during winter, much like manatees. As their range expands northward, these thermal refuges are critical for survival, but we have limited information on how snook and snapper use the rivers and springs over time and space.

Recently, FWRI’s Fish Biology and Fisheries Independent Monitoring sections partnered with Southwest Florida Water Management District, UF IFAS Nature Coast Biological Station, Florida Sea Grant and UF IFAS Tropical Aquaculture Laboratory to tag snook and snapper in rivers along the springs coast. During a 3.5 day blitz, biologists tagged 70 snook and 30 snapper in the Crystal, Chassahowitzka, and Pithlachascotee (Cotee) Rivers. Acoustic tags (which ping a unique ID recorded onto a receiver) were surgically implanted in each fish and an array of acoustic receivers was deployed within each river. This work will document how fish use the rivers year-round and specifically how much area fish use to congregate around springheads during cold snaps.

Each fish has an external tag (yellow or orange) by their dorsal fin. If you catch a tagged snook or snapper and plan to release it, please leave the external tag in place and report the tag #, date, location, and total length to our Tag Return Hotline at 1-800-367-4461 or

If you catch and keep a tagged fish, please retrieve the acoustic tag from the body cavity and call 1-800-367-4461 with the same information. A biologist will arrange to collect the acoustic tag which can be implanted in another fish.

For more information on the Crystal River project, check out this great article by the Citrus County Chronicle.