All about that bait: Pinfish population dynamics in the eastern Gulf of Mexico

By Meaghan Faletti, USF MS Student

If you’ve ever gone fishing in the Gulf of Mexico – or anywhere around Florida, for that matter – you’ve probably used Pinfish (Lagodon rhomboides) as bait. They work well because many predators consume them as part of their natural diet. This includes nearshore species such as Tarpon, Snook, and Redfish, as well as offshore species such as groupers and snappers. In addition to being used in the recreational fishery, a commercial market exists for Pinfish and extracted over 100,000 pounds of Pinfish from Florida waters in 2016 (NMFS 2018). Furthermore, recreational and commercial landings in the Atlantic and Gulf coasts of the United States show a general increasing trend since 2000 (NMFS 2014). Despite their importance to fisheries, a formal stock assessment has not been conducted for Pinfish.


Figure 1. Pinfish (Lagodon rhomboides)

With Florida’s ever-growing fishing industries, efforts to protect these important food sources are needed to sustain higher trophic-level species that are targeted by the recreational and commercial fisheries, and maintain a natural ecological balance. Not only are Pinfish providing food for predatory fishes, but they also act as a major source of nutrient transfer from nearshore to offshore foodwebs when they migrate to spawn. The nitrogen contribution from Pinfish migration offshore is on the same order of magnitude as trichodesmium, a major nitrogen-fixing bacteria, and one of the most significant contributors of nitrogen to marine systems (Nelson et al. 2013).  Due to the importance of Pinfish and other forage (“bait”) fishes, the Florida Fish and Wildlife Conservation Commission (FWC) adopted a resolution in 2017 encouraging further research on these species. The Florida Forage Fish Coalition was then formed to fund this research, and the USF Fish Ecology Lab was chosen as one of the first recipients.

We chose to study the population dynamics of Pinfish in the eastern Gulf of Mexico (eGOM) due to our lab’s familiarity and previous work with this system (Chacin et al. 2016; Stallings et al. 2015) as well as the extensive monitoring previously conducted by FWC’s Fisheries Independent Monitoring program. We chose to focus on four eGOM estuaries that have been sampled monthly with standardized seining methods since 1998: Apalachicola Bay (AP), Cedar Key (CK), Tampa Bay (TB), and Charlotte Harbor (CH). We analyzed density, biomass, and instantaneous growth rates (basically – how many, how big, and how fast are they growing?), and conducted time series analyses to see if these parameters were in synchrony with one another on an intra- and inter-annual basis. We then conducted a Zero-Altered Negative Binomial (ZANB) Model – don’t worry about the name, all you need to know is that it is used to assess what environmental factors may be driving these population patterns.

Pinfish estuaries

Figure 2. Four eGOM estuaries of interest where FWC Fisheries Independent Monitoring has conducted seine surveys since 1998. AP: Apalachicola Bay, CK: Cedar Key, TB: Tampa Bay, CH: Charlotte Harbor

We found density and biomass to be highest in CH, followed by TB, AP, then CK. Our time series analysis indicated that AP & CK (two northernmost estuaries) are in sync with one another, and TB & CH (two southernmost estuaries) are in sync with one another. On an intra-annual basis, all four estuaries are in sync with one another, with densities peaking around March-April, and biomass peaking in April-May. This makes sense from a life history standpoint, as Pinfish recruit to seagrass in the spring, and after feeding for a period of time, we expect to see an increase in mass lagging slightly behind the recruitment period.

The ZANB model indicated that density and biomass are significantly related to submerged aquatic vegetation (SAV; e.g. seagrass) for all estuaries. This is likely because seagrass plays an important role for Pinfish by offering protection for juveniles (Chacin & Stallings 2016) and substrata for food as they grow older and begin foraging on epiphytic algae. Pinfish abundance is related to salinity and temperature, which also affect seagrass, so this could either be through direct or indirect effects.

interannual density

Figure 3. Mean inter-annual Pinfish A) density and B) biomass for 1998-2016. Light gray dotted line represents the overall mean.

annual density

Figure 4. Intra-annual Pinfish A) density and B) biomass for 1998-2016. Biomass peak lagged ~1month behind density peak.


Figure 5. Pinfish growth plots. A) Instantaneous Growth Rate (IGR) for each estuary. B) Mean Pinfish standard length (SL) by month. Month 0 represents the average size of the smaller cohort present in month 12 of the previous year.

It is important to understand baseline population dynamics of fisheries species, including forage fish, so that we can better understand the effects of commercial and recreational fishing. This is especially true for species that do not have formal stock assessments such as Pinfish. This information has been shared at the Florida Chapter Meeting of the American Fisheries Society (Haines City, March 2018), the 2nd Florida Forage Fish Workshop (St. Petersburg, April 2018), and will be presented to the FWC Commissioners during a 2018 Commission Meeting. The project has also attracted a wealth of media coverage due to the importance of Pinfish and concerns from stakeholders about potential overharvest. We plan to publish a peer-reviewed article on these data in the summer of 2018 and intend for this information to be used to help better manage Pinfish populations.



Chacin, D. H., T. S. Switzer, C. H. Ainsworth, and C. D. Stallings. 2016. Long-term analysis of spatio-temporal patterns in population dynamics and demography of juvenile Pinfish (Lagodon rhomboides). Estuarine Coastal and Shelf Science 183:52-61.

Nelson, J. A., C. D. Stallings, W. M. Landing, and J. Chanton. 2013. Biomass Transfer Subsidizes Nitrogen to Offshore Food Webs. Ecosystems 16:1130-1138.

NMFS 2018 Commercial landings species locator.

NOAA NMFS Marine Recreational Information Program,; National Marine Fisheries Service, accessed 4 March 2014

Stallings, C. D., A. Mickle, J. A. Nelson, M. G. McManus, and C. C. Koenig. 2015. Faunal communities and habitat characteristics of the Big Bend seagrass meadows, 2009–2010. Ecology 96:304-304.



Florida Forage Fish Research Program funded by the Florida Forage Fish Coalition ( We thank the Florida Fish and Wildlife Research Institute Fisheries Independent Monitoring Program for field collections, and Ian Williams, Aleksandra Cison, and Kiara Barbarette for lab assistance. We also thank Ethan Goddard for assistance with the mass spectrometer.


Funding Sources:



“Don’t go into the light!” – Using Light Traps to Sample Ichthyoplankton

By Amanda Croteau, UF PhD Student

The Original Light Trap

Meroplankton are animals that spend a portion of their lives (larval and early life stages) as plankton. These organisms eventually grow larger and become part of the nekton (animals that are able to swim and move independently of water currents) or benthic communities. Ichthyoplankton are the eggs and larvae of fish. Eggs are passive and dispersed by currents. Initially most larval fish have no or minimal swimming ability. As they develop, they become active swimmers.

It is important to study meroplankton and ichthyoplankton because they are indicators of the spawning population of adults, and the survival or mortality of meroplankton have a direct effect on adult population numbers. Species composition at a given location depends on the spatial distribution and reproductive habits (periodicity, fecundity, etc.) of adults, growth and larval stage duration, and abiotic factors that affect transport (currents, tides, salinity, etc.). Mortality depends on many factors such as predation, disease, food availability, and habitat. Habitat is important because individuals who fail to make it to their correct settlement or juvenile habitat are unlikely to survive. In estuarine environments, freshwater and tidal cycles play key roles in species distribution.

Mangroves and salt marshes provide vital juvenile habitat for many inshore, nearshore, and offshore marine species. Florida’s coastal habitats have been severely impacted by coastal development, and Tampa Bay has lost over 44% of its mangrove and salt marsh habitats (Lewis et al. 1985). Robinson Preserve is one of the largest (197 hectare) mangrove and salt marsh restoration efforts in Tampa Bay. Robinson Preserve was originally a coastal wetland that was ditched and drained in the 1920s for agricultural use. In 2006, tidal flow was restored through connections with Perico Bayou, Palma Sola Bay, and the Manatee River. Restoration also involved the planting of native upland and salt marsh vegetation. However, no efforts were made to supplement the aquatic flora and fauna, rather it was expected that they would colonize the preserve from neighboring populations. Ichthyoplankton and meroplankton abundances were selected as one metric to evaluate the quality of the restored ecosystem as nursery habitat.

Meroplankton and ichthyoplankton can be sampled in a variety of ways including light traps, benthic sleds, Miller high-speed samplers, push nets, tow nets, and light traps. As with any sampling gear, each method has its pros and cons and gear selection should be informed by target taxa, gear bias, and site constraints. Light traps utilize organisms’ natural attraction to light (photopositive) as bait. Photopositive taxa approach and enter the trap and are then funneled into a collection chamber. Light traps also allow you to sample continuously over an entire night at multiple locations.  Robinson Preserve is shallow (generally <2 m), with complex habitat types and obstructions. It is also a no motor zone. Due to these study site constraints, light traps were selected as the most efficient gear to sample ichthyoplankton and meroplankton within the preserve. The light trap designed by Jones (2006) was redesigned for deployment from shore and scaled down for use in shallow, estuarine systems (Figure 1 and 2).


Figure 1. Design of modified light trap. The trap is powered by a battery located on-shore. Fish are attracted by the light source in the entrance chamber. The size of the openings, restrict the size of the organisms that can enter the chamber. Organisms are then funneled into the collection chamber where a mesh screen allows water to exit, but prevents organisms from escaping. Floats keep the trap vertical in the water column, and it is anchored in place. In shallow tidal systems, the depth changes due to incoming and outgoing tides must be considered when placing the trap.


Figure 2. Light trap deployed along mangrove shoreline in Robinson Preserve.

Among the larger organisms (≥3 mm) collected, 18 major taxonomic groups have been identified to date. Overall community composition was dominated by isopods (19%), caridean shrimp (18.2%), fish (15.7%), and parasitic copepods (13.1%), though species assemblages varied by site and season (Figure 3). The greater taxonomic richness in sites 1 and 3 is likely related to their locations. Both of these sites were located in areas with slower currents than in sites 2 and 4, which may have allowed some less mobile species to enter the light traps than in the latter two sites. Larval and settlement stage fish were collected in nearly every sample (Figure 4), including fish from at least 8 families. This is similar to the degree of diversity noted in other light trap studies in similar habitats (Hernandez and Shaw 2003; Strydom 2003). Juvenile mullet (likely Striped Mullet Mugil cephalus) were always present in winter samples, while juvenile clupeids (likely menhaden Brevoortia spp.) were present in the winter and spring, which corresponds well with their respective peak spawning periods within this region.


Figure 3. Ichthyoplankton and meroplankton community composition for each site (1.DK in Mixing Zone, 2.B1 in Palma Sola Bay and Perico Bayou zone, 3.W in Upland Freshwater Drainage zone, and 4.PD in the Manatee River zone) by season.


Figure 4. Ichthyoplankton community composition for each site (1.DK in Mixing Zone, 2.B1 in Palma Sola Bay and Perico Bayou zone, 3.W in Upland Freshwater Drainage zone, and 4.PD in the Manatee River zone) by season.

The use of a modified light trap in Robinson Preserve proved to be an effective method for sampling ichthyoplankton and meroplankton, as well as some other groups. Several fish parasites were collected in large numbers during this study. Juveniles of the parasitic isopod family Cymothidae were by far the most dominant form of isopod present in the light trap samples. Parasitic copepods of the genera Argulus and Caligus were also collected in large numbers. The high abundance of external fish parasites collected with this method may provide a new and efficient means of surveying such taxa in estuarine systems.


Hernandez, F.J., and R. F. Shaw. 2003. Comparison of plankton net and light trap methodologies for sampling larval and juvenile fishes at offshore petroleum platforms and a coastal jetty off Louisiana. American Fisheries Society Symposium 36: 15-38.

Jones, D.L. 2006. Design, construction, and use of a new light trap for sampling larval coral reef fishes. NOAA Technical Memorandum NMFS-SEFSC-544.

Lewis, R. R., R. G. Gilmore, Jr., D. W. Crewz, and W. E. Odum. 1985. Mangrove habitat and fishery resources of Florida. Pages 281-336 in W. Seaman, Jr., editor. Florida aquatic habitat and fishery resources. Florida Chapter, American Fisheries Society, Kissimmee, Florida.

Strydom, N.A. 2003. An assessment of habitat use by larval fishes in a warm temperate estuarine creek using light traps. Estuaries 26(5): 1310-1318.

How to catch a Koi: A failed extraction adventure

By Allison Durland Donahue

UF PhD Student

What do you do when you receive a request from a concerned citizen asking for assistance rescuing her Koi from her neighbor’s pool? You excitedly accept the challenge and begin planning the best way to catch a Koi. You are the expert. You will know how to catch the darn fish when others have not been able to. Enter real life.

Last month, UF’s Aquatic Research Graduate Organization (ARGO) received a request to remove a Koi from a pool. This seemed like an excellent outreach adventure – catching a Koi and teaching citizens about fishing techniques, exotic species, and other fish things.

First question: How did the Koi get in the pool in the first place? Irma. During Irma, this area had major flooding (a creek became a lake). The Koi was moved over a mile with the flood waters. The owner assumed her prized Koi was lost, but her neighbor called with news that there was a Koi in his pool.

Next question: How many avid fisher people does it take to catch a Koi? More than three (plus a shellfish person). The four of us attempted to use our advanced degree trained minds and fishing expertise to design a plan to get the elusive Koi.

The challenge: An oddly shaped, 12-foot deep pool, a Koi that hangs out on the bottom, and three feet of water visibility.


Analyzing the challenge

Extraction method, take one: Deploy a seine with the hopes that the Koi will startle into the net. The seine was stretched across the width of the pool and drug through the water column, catching nothing but leaves.

Extraction method, take two: Use the seine on the surface and an ingeniously crafted seine on the bottom to cover the entire water column. The owners had built their own seine out of bamboo poles and chicken wire. Combined, the two seines could cover the entire water column. Or so we thought.

Extraction method, take three: Tie a weight to the seine to (hopefully) ensure that the net is reaching and staying on the bottom. The trick is to make sure the net is not ever dragging the weight. One person stood on the opposite end of the pool and pulled the weight on the bottom of the pool as the other two pulled the seine. Alas, no fish.

Conclusion: Either that Koi is the smartest Koi ever or it was removed from the pool via natural methods (i.e. an eagle ate it).


The only fish we caught

Even though the extraction failed, we were able to educate the owner about fish health requirements and various fishing methods. We left her with our last method idea: build a seine that is fourteen feet high with limited slack. And with that we hung our fishers’ heads in shame and swore at that elusive Koi.


Natalie Simon


Natalie Simon is from New Jersey and received her BS in Marine Sciences from Stockton University. While working at Rutgers’s Haskin Shellfish Research Laboratory as a hatchery technician, she found her love for oysters. Not long after, Natalie moved to Gainesville to attend the University of Florida (UF) for a Master’s degree in Fisheries and Aquatic Sciences and has since stayed to continue her academic career for a PhD. Her research interests include cryogenics, germplasm preservation, and molluscan aquaculture.


Vice President

Allison Durland Donahou

Allison Durland Donahou is from Seattle, but ran away to warmer, sunnier weather ten years ago and has never looked back. She received her BA from the University of San Diego in Marine Biology and her MS from Nova Southeastern University in Marine Biology and Coastal Zone Management. While working with Alaskan fishing communities as a research assistant with NMFS, she discovered her interest in the human dimensions of fisheries. For her PhD, Allison is trying to tackle the challenge of managing invasive species, specifically examining the effects climate change will have on non-native fish distributions. When she finds “free” time, Allison loves partaking in water sports with her puppies and husband, as well as exploring what Gainesville restaurants have to offer.

University Liason

Lauren Kircher


Lauren is from western New York and received her BS in Marine Biology from University of New Haven. Lauren participated in several fellowships at University of New Haven and University of Southern California, nurturing her love of research. Following her BS, Lauren started a Ph.D. in Integrative Biology at Florida Atlantic University. Her dissertation focuses on natural and anthropogenic environmental influences on the movement of a tropical sportfish (common snook) in St. Lucie estuary. Lauren’s research interests include fisheries, movement ecology, behavioral ecology, and physiology.

Raising Funds to Support Dominican Fisherfolk

As a result of Hurricane Maria most Dominican fisherfolk lost their homes and gear. Please help us sponsor a fisher! $100 will purchase enough gear to get the Dominican fisherfolk back on the water, be able to restart their business and feed their fellow citizens! Each fisher sponsored will receive a kit of line, hooks, gloves etc. 100% of funds raised will go towards purchasing of these kits and I will use my own personal funds to travel to Dominica and manage distrubution.

Dominican fishers are the most helpful, resilient, giving people I have met. Right now they are acting as first responders post Maria and the least we can do is get them back to fishing!

Roger Rottmann Memorial Scholarship

At the 37th Annual Chapter Business meeting of The Florida Chapter of the American Fisheries Society two students recieved the Roger Rottmann Memorial Scholarship.

Award recipients:

  • PhD: Katie Lawson
  • MS: Natalie Simon

The Roger Rottmann Memorial Scholarship was established in memory of Roger Rottmann, one of the first fisheries biologists ever hired by the State of Florida University System. Roger conducted fisheries and aquaculture research for more than 20 years at the University of Florida, producing numerous scientific journal and educational publications and videos.

This scholarship was established to recognize outstanding students enrolled in Florida universities and colleges. Congratulations to our award recipients! #AFS147