Category Archives: Fisheries-Independent Monitoring

Fine Tuning Reef Fish Surveys through the Incorporation of Hydroacoustic Technology

By Ryan Munnelly and Brett Pittinger

Stereobaited remote underwater video arrays (S-BRUVs) have become a standard gear used to sample fish distributions in aquatic systems around the world.  Over the past decade, the Fisheries-Independent Monitoring (FIM) program of the Florida Fish and Wildlife Conservation Commission (FWC) has used S-BRUVs like the array shown in Fig. 1 to study fish populations associated with natural and artificial reef habitats of the West Florida Shelf (WFS).  This effort has involved thousands of 30-minute deployments in waters 10–180 m deep, from Pensacola to the Florida Keys.

An example of some of the sampled artificial habitat of the West Florida Shelf.

Some advantages of S-BRUVs are that they are minimally invasive to the fish community and habitat, they are less selective than other gears, and they provide behavioral information.  However, despite these advantages, it is difficult to determine the distance from which fishes are attracted to the bait during a deployment.  This complicates fish-habitat relationships observed in the video by adding uncertainty regarding the total area sampled and whether fishes observed were in fact associated with the habitat targeted.  Improving our current understanding of the range of attraction of fishes to an S-BRUV is an important step toward determining absolute species abundances.

Hydroacoustics use sound to detect fish in the water column in the same way that a typical fish finder works.  Hydroacoustics can be used to rapidly survey a large area and are even less invasive than S-BRUVs in that they do not influence fish distributions.  These features make hydroacoustics a complementary method to the S-BRUV surveys conducted by the FIM program.  Figure 2 shows the results from one survey designed to evaluate spatial redistributions of fishes that take place during an S-BRUV deployment relative to before the gear entered the water.  At this site located in 61 m water depth offshore of Panama City, fish abundance increased near the S-BRUV during deployment and decreased to the northwest of the site, where the current was oriented.  This information will be used to improve assessments of commercially targeted fishes, sportfish, and other ecologically valuable species throughout WFS waters.

Fig. 2. Mean volume backscatter in the lower 5 m of the water column from a hydroacoustic survey over several patches of low-relief habitat before (left panel) and during (right panel) deployment of an S-BRUV video array.  The dots represent data points that were interpolated throughout the 375 x 375 m survey grid, hashed areas are patches of previously identified habitat, and brighter colors indicate higher fish abundances.  The S-BRUV was deployed in the center of the survey grid and an arrow in the right panel shows the direction of the prevailing bottom current distributing the odor plume from the bait.

A Fond Farewell to Ed Matheson, FIM’s Top Taxonomist

By Sean Keenan and Theresa Warner, with much assistance from coworkers

Dr. Richard “Ed” Matheson Jr., an Associate Research Scientist at the Fish and Wildlife Research Institute (FWRI), is retiring after 32 years with the Institute. A Masters from the College of William & Mary and a Ph.D. from Texas A&M University provided Ed with the basis for a career focused on the systematics and ecology of fishes. Over the years, his research interests have included Gerreid systematics, seagrass-associated fishes, fishes of tidal-rivers, fish community structure in Florida Bay, seagrass die-offs, Everglades restoration, and fishes of the West Florida Shelf.

Starting with FWRI St. Petersburg in 1987, Ed has seen the Institute transition through several agencies and name changes to become what it is today. Initially hired into the Coastal Zone Management group with the Fish Biology program, Ed became the chief ichthyologist for the Fisheries-Independent Monitoring (FIM) program in the late 1990s. With FIM’s statewide, comprehensive sampling, rare or difficult to identify species are frequently encountered and they invariably come to Ed for verification.

Ed is seen here field sampling in Florida Bay.

The accurate identification of specimens is vital to evaluating distribution and abundance trends of native and exotic species. Ed has been instrumental in developing, maintaining and ensuring the near perfect fish identification proficiency of FWRI staff. He regularly creates and presents fish identification training sessions that focus on key sportfish and difficult to identify species groups like gobies, mojarras and sunfishes. His sessions always include a presentation, access to slides and identification keys, and typically include a ‘hands-on’ component that reinforces what staff learned in the presentation. Ed’s fish identification contributions beyond FWRI have been equally important. He frequently confirms identifications of specimens being cataloged in the Ichthyology Collection of the Florida State Board of Conservation and receives requests for assistance from other groups such as FWC Law Enforcement.

The professional impact of Ed’s work at FWRI is immeasurable. He has been the lead author on five peer-reviewed manuscripts and he has co-authored over 20 manuscripts and over 10 reports. He has served as adjunct faculty at the University of South Florida (USF) and as a graduate committee member for students at USF and the University of Central Florida. Ed has participated in innumerable one day estuarine sampling trips, eight multiday research cruises, and dove in the Johnson Sea-Link submersible to 1,100 feet. He is a member of the American Society of Ichthyologists and Herpetologists, American Fisheries Society and Sigma Xi. Ed has served as a reviewer for scientific journals including Bulletin of Marine Science, Estuaries, Southwestern Naturalist and Fishery Bulletin.

Ed is one of the friendliest and most approachable scientists at FWRI. His sense of humor, pleasant demeanor, and professional expertise have made him an invaluable and irreplaceable asset to FWC.

Best Fishes, Ed! We will miss you.

Recruitment of Juvenile Gag Grouper in the Eastern Gulf of Mexico

By Ted Switzer

Gags (Mycteroperca microlepis) support extensive commercial and recreational fisheries in the eastern Gulf of Mexico. A 2016 stock assessment did not support earlier assessments that indicated that gags are currently overfished and continue to undergo overfishing (South East Data Assessment and Review 33 update). Considering the status of Gag in the eastern Gulf of Mexico, it is especially important to improve understanding of its juvenile recruitment processes.

Study area of polyhaline seagrass habitats sampled in estuarine systems in the panhandle (St. Andrew Bay, Apalachicola Bay), Big Bend region (St. Marks, Econfina, and Steinhatchee), and peninsula (Tampa Bay and Charlotte Harbor) of Florida, USA (Schrandt et al. 2018).

Past research has shown that juvenile Gags generally occupy structured polyhaline (18-30 practical salinity units) habitats such as seagrass beds and oyster reefs for several months before emigrating to nearshore reefs (Figure 1). The reliance of Gags on estuarine nurseries, combined with a brief period of estuarine occupancy, greatly facilitates the accurate characterization of the strength of juvenile recruitment.

A comprehensive examination of long-term (10+ years) FWC/FWRI fisheries-independent data was conducted to characterize habitat selection and recruitment of juvenile Gags. Results from Apalachicola Bay, Tampa Bay and Charlotte Harbor habitat suitability analyses indicated that juvenile Gags selected polyhaline habitats with sloping bottoms and extensive seagrass coverage. These analyses indicated that the near shore, deeper water polyhaline seagrass habitats had been under sampled (Switzer et al. 2012).

A multi-gear survey (183-m haul seine and 6.1-m trawl) was designed to supplement long-term, fisheries-independent survey data on estuarine-dependent reef-associated fishes. The supplemental survey design specifically considered juvenile Gag recruitment ecology and thus targeted the deep, polyhaline (>18 psu) seagrass habitats that are used by age-0 Gags. Potential sampling sites were limited to generally polyhaline waters that contained at least 50% bottom coverage of seagrass, had a measurable slope and were between 1.0 and 7.6 m deep.

Gag begin their life offshore in a pelagic environment where they spend their first 30-60 days. Eventually they settle out onto shallow water seagrass beds, where they spend the summer months feeding and growing. In the fall they migrate to nearshore hard-bottom habitat. As they mature, they eventually migrate to deeper water reefs and as mature adults they form spawning aggregations and spawn during the winter months. Gag are hermaphrodites. They are born as females and as they grow eventually transition to be male.

This supplemental sampling was initiated in 2008 and polyhaline seagrass beds were sampled by bottom trawls (6.1-m otter trawl) and haul seines (183-m haul seines) in seven estuaries along Florida’s Gulf coast (Figure 2). Apalachicola Bay, Charlotte Harbor and Tampa Bay have been routinely sampled since the late 1990s; St. Andrew Bay and three estuaries in the Big Bend region between Cedar Key and Cape San Blas (St. Marks, Ecofina, and Steinhatchee), where Gag recruitment had been documented, were added for this study and have become part of the continuing survey.

Analyses of the data collected in the long-term and supplemental surveys (2008-2012) demonstrated the effectiveness of this sampling approach. The size ranges of Gags collected in both studies were similar, but age-0 individuals were captured more frequently and the catch-per-unit-effort (CPUE) was significantly higher in the supplemental surveys (Switzer et al 2015). These analyses will not only enhance our understanding of recruitment processes for juvenile Gags in the eastern Gulf but will also provide valuable insight into observed patterns of habitat use and the relative importance of various habitat types. Nevertheless, additional information on habitat availability, combined with a better understanding of the estuarine systems’ relative contributions to nearshore Gag populations, will be required to maximize the utility of these data in predicting fisheries productivity.

Strong Gag year-classes have been documented as persisting as the fish grow and enter the fishery. Accordingly, accurate estimation and prediction of juvenile recruitment is critical to the effective assessment and management of at-risk fisheries. Variability of estuarine nekton assemblages is valuable as an indicator of environmental quality.  Therefore, the patterns discerned from the supplemental sampling have important implications for fisheries managers.

FIM Data and the Southeast Data, Assessment and Review Process

By Dr. Ted Switzer

The Southeast Data, Assessment, and Review (SEDAR) is the cooperative process by which stock assessments of federally-managed species are conducted in the Southeast Region of NOAA Fisheries. SEDAR was initiated to improve planning and coordination of stock assessment activities and to improve the quality and reliability of stock assessments.  SEDAR strives to provide an open and transparent approach for development and review of the scientific information on fish stocks that is critical to effective management and decision making, and includes participants from various sectors, including researchers, stock assessment scientists, managers, and stakeholders.

Figure 1. Indices of abundance (least square means ± SE) for age-0 and age-1 Gray Snapper collected during FWRI long-term and polyhaline seine and trawl surveys in northeastern Gulf of Mexico estuaries

Many research groups at the institute provide data critical to the SEDAR process, including data on landings and discards from the commercial and recreational fishery, discard mortality, and life history including age and growth, reproduction, and stock identification. Data provided by the FIM program typically include trends in relative abundance through identification. Data provided by the FIM program typically include trends in relative abundance through time as well as annual estimates of size/age composition. Because these data are meant to characterize fluctuations in managed fish populations through time, several years of data are often required before fishery-independent indices become useful. Nevertheless, FIM data are increasingly being used for the assessment of managed fishes, including the ongoing SEDAR 51: Gulf of Mexico Gray Snapper.

Data from long-term seine-surveys (initiated in 1996 – 1998, depending on estuary) and recently-implemented polyhaline seagrass seine and trawl surveys (initiated in 2008) were analyzed separately to generate indices of abundance for age-0 (≤ 100 mm SL) and age-1 (101 – 250 mm SL) Gray Snapper; a single index was developed for each by combining data from multiple estuarine systems. In general, indices for each age class were similar between surveys (Figure 1); index results documented strong interannual variability in age-0 recruitment, but a generally increasing trend in the relative abundance of age-1 Gray Snapper. Although the SEDAR Data Workshop recommended incorporation of the long-term index only to avoid duplication, future efforts to incorporate data fromboth surveys into unified age-0 and age-1 indices should dramatically increase the statistical power of these indices.

Figure 2. Relative standardized index (solid red line) with 2.5% and 97.5% confidence intervals (black dotted lines) and the nominal index (blue hashed line) for Gray Snapper in the FWRI West Florida Shelf Video Survey.

In addition, data from the FWRI video survey off Tampa Bay and Charlotte Harbor were analyzed to generate and index of abundance for subadult/adult Gray Snapper (generally ≥ 300 mm FL) from 2010 – 2015. Model results generally corroborate the increasing trend in abundance of Gray Snapper in recent years. Although useful, this model was ultimately not recommended for incorporation, as an additional model, it was developed utilizing data from FWRI, NMFS – Panama City, and NMFS – Pascagoula video surveys.

Recovery Act: Hardbottom mapping and community characterization of the west central Florida Gulf coast

by Ryan Maloney and Sean Keenan

Habitat classification and mapping are a crucial part of fisheries conservation and ecosystem-based management.  Essential fish habitats act as nurseries, feeding, and breeding grounds for many commercially and recreationally important species. Technological advances like side scan sonar and satellite imagery allow researchers to gain a better understanding of where these habitats are located, their aerial extent, and what the habitat and fish community looks like.

The distribution and composition of benthic habitats on the west Florida shelf including submerged aquatic vegetation (SAV) and submerged marine carbonate reef outcroppings (hard bottom) are poorly understood. While these habitats serve as nursery and forage areas for many economically-important reef-fish species (e.g. gag, red snapper, gray snapper and hogfish), benthic mapping and characterization of the benthic communities are nonexistent for a majority of the West Florida continental shelf.

Mapping habitat in such a large area is a daunting task, which requires an extensive amount of time, and can be very costly.  Current methods for characterizing marine habitats include acoustic (side scan sonar) and optical (satellite) imagery.  Side scan sonar provides high resolution (~0.1 m) imagery through processing of acoustic backscatter or echo strength (Figure1). While commercial grade side scan systems have become more cost effective, time and resource requirements for data collection and post-processing still add up. Satellite imagery, in comparison, has a substantially lower cost per unit area and is much more time efficient. Satellite imagery, however, is restricted by water depth and clarity and is more difficult to acquire and has a limited resolution of ~3 m (Figure2).

imagery comparisons
Figure 1. This slide illustrates some or our more commonly used habitat classifications. By utilizing camera ground truthing images, we can better define the corresponding side scan imagery.

satellite imagery
Figure 2. The image to the left represents raw satellite data, while the image to the right shows the delineated habitat defined based on the parameters mentioned.

For this project, the Fisheries Independent Monitoring (FIM) group is compiling past and present side scan sonar surveys contained within two designated study areas.  The areas are divided into a 790 km² area off of Clearwater, FL and 820 km² area just off of Sarasota, FL.  Within each study area, surveys are being scanned and read for the presence of essential fish habitats.  In conjunction with scanning, a drop camera is deployed at each survey site as a ground truthing technique.  All side scan and ground truth data will be compared to preexisting satellite imagery, processed and classified by grant collaborators.  By comparing and contrasting side scan sonar with satellite imagery, this project is exploring different methods to map essential fish habitats at varying scales (Figure 3).

side scan sonar mosaic
Figure 3. A side scan sonar mosaic, with defined habitat outlined, shows that brighter imagery returns, correspond to hard harder substrates. These returns are inversely related to satellite imagery, where we see dark returns representing hard bottom.

With a more economical way of characterizing nearshore marine habitats, scientists and fisheries managers can 1) establish the exact locations and spatial extent of these habitats; 2) monitor any changes in habitats and fish communities; and 3) implement habitat-based fisheries independent surveys.

Expansion of Juvenile Snook Sampling in Tampa Bay, Charlotte Harbor and the Indian River Lagoon

by Brent Winner, Tim MacDonald and Dave Blewett

men and woman in water holding net
Photo: Chris Johnson (volunteer), Brittany Hall, Ryan Jones, and Brad Lenhart. FIM scientists gather the catch into the bag of the seine. The fish are then transferred to the boat where they are identified, counted, and measured for length.

Snook are one of Florida’s most popular sportfish. In 2013, the Stock Assessment group at the Florida Fish and Wildlife Conservation Commission’s (FWC) Fish and Wildlife Research Institute (FWRI) evaluated available juvenile snook data sources to determine the feasibility of incorporating age-1 juvenile snook information into the snook stock assessment. These data were found to be insufficient and FWRI’s Fisheries Independent Monitoring (FIM) program was tasked to develop a sampling program to improve estimates of abundance and size-at-age for age-1 snook.

In July of 2013, a “Snook Team” consisting of FIM staff from the Tampa Bay, Charlotte Harbor, and Indian River field labs was formed.  Team members looked at historical datasets to define the size range of age-1 snook, to examine temporal and spatial trends of age-1 snook, and to determine how mesh and gear size related to selectivity.  Preliminary gear testing and reconnaissance trips were conducted to establish gear specifications, sampling universes, and sampling design.  Methods were developed for site selection, gear deployment and retrieval, sample work-up and culling of specimens for age determination.  In July 2014, gear testing in Tampa Bay, Charlotte Harbor, and the Indian River Lagoon began with two sizes of center-bag seines (21.3-m with 3.2-mm mesh and 40-m seine with 25.4-mm mesh) being deployed by boat at each randomly selected site. A total of 1,872 seine hauls were conducted during the 12-month gear testing period, yielding 2,315 snook; of these, 1,285 were young-of-the-year (< 99 mm SL) and 714 were presumed age-1 (100-300 mm SL).

man's hands holding fish
Scientist measures a snook prior to release. Based upon its size this individual is approximately 1 year old.

To adequately assess potential habitats used by juvenile snook, the gear testing study design included habitats and geographic areas (i.e., backwater and tidal creek habitats; small seines sampling in the southern IRL) that had not been included in previous FIM program sampling.  This sampling also provided data on a wide variety of other estuarine fish and invertebrate species. In Tampa Bay 278,763 specimens were collected representing 108 taxa.  Charlotte Harbor collected 59,013 specimens (73 taxa) and Indian River Lagoon caught 183,225 specimens (162 taxa).

fish in net
Seine sample collected in the lower Manatee River by FIM scientists. Catches often include many species of fishes, crabs, and shrimp. Notice the young of the year snook in the lower center of the picture by the ruler.

The gear testing data were analyzed to determine habitat selectivity, spatial and temporal distributions, and catch rates of snook by gear.  The 21.3-m seine provided the most consistent assessment of all sizes of juvenile snook as well as other fishes and macroinvertebrates in the habitats where juvenile snook were prevalent.  Based on this information, the FIM program added a standardized sampling design for juvenile snook using the 21.3-m seine into its monitoring program in January 2016.  This sampling design included several rivers and many tidal creeks previously not sampled with this gear in Tampa Bay, Charlotte Harbor, and the Indian River Lagoon.  These data have already been used in the 2016 snook stock assessment.

On January 13, 2016 the most recent snook stock assessment and some ongoing snook research studies being conducted at FWRI were presented at the FWC hosted Snook VI Symposium in Orlando, Fl.  The objective of this meeting was to initiate a discussion and process that could result in new management goals for snook.  The symposium was attended by several hundred fishermen, industry stakeholders, and members of the academic and scientific community from throughout the state.  Following updates on research and the status of the stocks, the public was offered an opportunity to share their opinions and concerns on the status of snook in Florida.  One of the top concerns of the attending stakeholders was the lack of information on juvenile snook habitats. They were also concerned about and the vulnerability of juvenile habitat to anthropogenic alteration.  Many of these habitats are directly addressed by the new juvenile snook sampling design initiated by the FIM program.  This new data stream will continue to be valuable for the management of snook, and many other species, in future years.

For more information on the Snook VI Symposium, visit the FWC website  (

Searching for Juvenile Red Snapper Along Florida’s Atlantic Coast

by Russel Brodie and Ted Switzer


The Fisheries-Independent Monitoring program recently completed the first year of field sampling for a study funded by NOAA Marine Fisheries Initiative (MARFIN) to evaluate the utility of trawls and small fish traps to provide data on/regarding juvenile (age 0-1) red snapper and other managed fishes in the U.S. South Atlantic (SA). Surveys were conducted using a 12.8-m semi-balloon trawl and Antillean Z-traps within nearshore waters (10 – 70 m) off central and northeast Florida from July-October. Trawl surveys targeted low-relief soft-bottom/shell habitats which are underrepresented in current fisheries-independent surveys in the SA despite having been documented as red snapper nursery habitat in the Gulf of Mexico (GOM). Small-mesh fish traps targeted low- to high-relief hard bottom and artificial reef habitats not accessible by trawls to investigate whether SA juvenile red snapper are exploiting different habitats from what has been documented in the GOM. In 2015, 86 trap stations (400 individual trap sets) were sampled, and 110 red snapper ranging in size from 124 – 329 mm standard length were captured. At the same time, 93 trawl stations were sampled (68,693 fish and invertebrates collected) over 18 sampling days aboard the R/V Georgia Bulldog. A total of 83 red snapper were collected ranging in size from 42 – 119 mm fork length. Combined, these two surveys captured in one year as many juvenile red snapper as had been reported in over four decades of research in the region.  Data from this three-year pilot study will be used to develop recommendations for a fisheries-independent monitoring survey designed to provide valuable life history data as well as recruitment indices for juvenile red snapper and other juvenile reef fishes in the SA.

Return to Marine Fisheries Research

Fish Feeding Ecology (Gut) Lab

by Brittany Hall and Gabriel Ramos-Tafur

Scientists in the gut lab process stomachs from fish of all sizes, collected both inshore and offshore, in order to compile comprehensive diet information that is used in various models.  Digestion is the biggest obstacle when processing these guts.  Our main goal is to identify everything to the lowest taxonomic level possible (this includes amphipods, shrimps, crabs, mysids, and the list goes on and on), and generally we are looking for identifiable parts that are more resistant to digestion.  Crabs and shrimps have external hard parts that are a little more resistant to digestion, but fish have fewer of these external parts.  Most of the time, things like color, fin-ray counts, pores, and scales are needed to work your way through an identification key, but when a fish is a prey item, these clues are often missing.  One of the last parts of a fish to disappear during digestion is its jaws, and we often use jaws to identify fish in stomach contents.  Careful study has revealed that jaws are like fingerprints – very distinct teeth and bones that allow us to identify many prey species to family and even species.

Because there are currently no identification keys for the jaws of fish species found Gulf of Mexico and Tampa Bay, scientists have been diligently developing a reference key to be used to identify digested fish prey.   This task involves removing the tissues from the jaw bones of fresh specimens, staining the jaws, taking pictures, and writing descriptions of each intricate bone.  Although tedious, much headway has been made, and results of this one of a kind project were presented at the upcoming national meeting of the American Fisheries Society in August 2015!

Testing mercury levels in Florida’s marine fishes

by Derek Tremain and Doug Adams

Fish dissection
Removing muscle tissue from a Spanish mackerel for mercury testing.

Mercury, a toxic metallic element, has been shown to bioaccumulate in fish tissue, and if humans eat contaminated fish, they can potentially consume significant levels of mercury. Testing fish flesh for mercury content began in 1989, the same year the Fisheries-Independent Monitoring (FIM) program began and continues today. In the early years, fish samples were sent to the Florida Department of Environmental Protection for testing, but in 2006 the FIM program purchased a new state-of-the-art instrument (DMA-80 Direct Mercury Analyzer) that now allows fisheries scientists from FIM’s Indian River field laboratory to analyze more fish samples for mercury content and reduce the processing time. To date, FIM staff have collected, processed, and documented mercury information from more than 80,000 individual fish yielding almost 300 species, all of which were collected through the statewide sampling program.  These individual specimens represent all major groups from primary consumers and prey species to apex predators at the top of the food web and include many popular sport fish such as seatrout, red drum, snappers, groupers, common snook, mackerels, and tunas to name just a few. The majority of marine and estuarine fishes examined contained low levels of mercury, but several important recreational and commercial fishery species such as sharks, tunas, mackerels, and cobia have shown elevated levels. Many of the samples processed by FIM scientists are provided to the Florida Department of Health (FDOH) to develop and update fish consumption advisories. These advisories provide specific guidelines regarding Florida marine fishes, and recent updates can be found on the FDOH website.

The venom in lionfish spines remains active, so fisherman are urged to clean their catch with an abundance of caution. Photo by John Stevely Florida Sea Grant Extension Emeritus

One species of recent interest, with almost no previous mercury information available, is the invasive Indo-Pacific lionfish (Pterois spp). Given the recent management strategy to encourage divers and fishers to harvest and eat this species, FIM scientists analyzed mercury levels in this species from throughout Florida’s coastal waters and published the research in a recent paper. The results suggest that lionfish contain very low levels of mercury, similar to species that currently fall under the FDOHs least restrictive consumption guidelines. However, lionfish populations are in the relatively early stages of establishment in Florida and larger and older individuals, with potentially higher mercury levels, will likely become available to consumers. Therefore, a routine part of the FIM program is to continue to monitor this species, and others, to identify any changes in mercury levels that may occur over time.

In the past few months, FIM staff and partners at the Florida Department of Environmental Protection have analyzed nearly 3,000 samples that include many fishery species such as mangrove snapper, red snapper, red porgy, common snook, black sea bass, spotted seatrout, and red drum. Future research relating mercury levels to fish age, feeding ecology, and the trophic structure (food web) of Florida’s marine and estuarine ecosystems will help us better understand concentrations of this element in marine fishes.