S.C. Sea Grant Consortium
Underwater camera image of red snapper.

The South Atlantic Red Snapper Research Program

What is the Issue with Red Snapper?

Red snapper (Lutjanus campechanus) is an economically valuable and ecologically important reef fish.

Red snapper has been estimated to be overfished in U.S. Atlantic waters since the early 1980s.

Regulations aimed at rebuilding the Atlantic red snapper stock have not met the necessary requirements to declare the stock no longer overfished, which causes challenges for natural resources managers, as well as commercial and recreational fishers.

What is the South Atlantic Red Snapper Research Program?

The South Atlantic Red Snapper Research Program was created to address unknowns such as the population size, distribution, and density of red snapper.

Fishery stock assessments are statistical models used to estimate fish population size and how it is affected by fishing. The most recent South Atlantic red snapper stock assessment showed the South Atlantic red snapper stock is overfished and undergoing overfishing.

This project will increase scientific understanding of red snapper populations across the entire South Atlantic region to better inform future stock assessments and management.

What is the Research Team Studying?

The research team will produce an independent estimate (separate from the SEDAR stock assessment) of the population size of red snapper age 2 years and older from North Carolina to Florida.

The estimates will be produced using two separate approaches:

  1. Genetic close-kin mark recapture (CKMR).
  2. Bayesian integrated modeling to estimate red snapper population size from the Southeast Reef Fish Survey (SERFS) trap-camera and remotely operated vehicle (ROV) sampling.

The research team will also assess the occurrence and estimate the density of red snapper in areas that have not been surveyed (known as unknown and unconsolidated habitats), including areas outside the current SERFS sampling frame.

The research team will work cooperatively with for-hire recreational and commercial fishers for this portion of sampling efforts to accomplish research goals.

An underwater measuring device inside a metal cage.

The SeaBird 16plus CTD measures temperature, dissolved oxygen, salinity, and turbidity throughout the water column.

University of Florida VideoRay Pro4 mini remotely operated vehicle (ROV) system.

VideoRay Pro4 min ROV with tether and tether deployment system on deck of ship.

Maps of the Study Area

A map of the coast of North Carolina, South Carolina, and Georgia marked with dozens of red snapper project ROV sites.

Sites surveyed with a remotely operated vehicle in 2021 (green) and 2022 (yellow).

A map of the coast of North Carolina, South Carolina, and Georgia marked with dozens of red snapper project trap video sites.

Reef sites sampled with camera-trap gear by the SERFS survey in 2002. Annually, the SERFS program samples 1,800-2,000 reef sites on the US Atlantic shelf from North Carolina to Florida.

How Long is the Project?

Research began in the Fall of 2020 and will finish in the Fall of 2025.

Who is Involved?

The South Atlantic Red Snapper Research Program is led by a team of researchers spanning the following research institutions: University of Florida, Texas A&M Corpus Christi, N.C. State University, NOAA Fisheries, S.C. Department of Natural Resources, NOAA NOS Center for Coastal Fisheries Habitat Research, Florida Fish & Wildlife Conservation Commission, and GA Department of Natural Resources.

The South Atlantic red snapper Research Program is financially supported by the Sea Grant programs of Florida, Georgia, South Carolina and North Carolina with support provided by the NOAA National Marine Fisheries Service.

The project is led by the S.C. Sea Grant Consortium and overseen by a steering committee made up of Sea Grant directors and extension specialists as well as state fisheries staff from Florida, Georgia, South Carolina and North Carolina, industry members and South Atlantic Marine Fishery Management Council staff.

Frequently Asked Questions

What does “absolute abundance” mean?

Congress indicated in the legislation that established the South Atlantic Red Snapper Research Program that age-2+ Atlantic red snapper “absolute abundance” needed to be estimated. However, “absolute abundance” simply means total abundance or population size in the study region. The word “absolute” distinguishes this concept from “relative abundance,” which only tracks population trends (increases or decreases) over time, without providing information on the actual population size.

Difference between a stock assessment and an absolute abundance estimate?

There are many approaches in population ecology that can be used to estimate fish population size. A fishery stock assessment is a statistical model that utilizes landings data, fishery catch rate trends, life history data (e.g., growth, natural mortality, reproductive biology parameters, etc.), and fishery-independent relative abundance trends to track year classes or cohorts across time, estimate fishing mortality rates, and estimate spawning stock biomass. Notably, mark-recapture studies can also be utilized to estimate population size, including genetic mark-recapture like the CKMR approach in the SARSRP study.

Yet another approach to estimating population size is estimating the density (individuals per area) of fish in specific habitats and then scaling those density estimates to a population estimate based on estimates of the habitat distribution in the study region. This latter approach is the general approach of the Hierarchical Bayesian Integrated Modeling component of the SARSRP study on the Atlantic shelf from North Carolina to the Florida Keys, as well as the approach previously taken in the Gulf of Mexico Great Red Snapper Count study. It should be stressed that in neither study was there (or will there be) an attempt made to actually count each individual, or census, red snapper in the study regions.

What are “independent estimates”?

There are two approaches being undertaken by the study team to estimate age-2+ red snapper population size (i.e., abundance or “absolute abundance”) in the US Atlantic Ocean. Both approaches will produce population size estimates independent of the SEDAR stock assessment for Atlantic red snapper. The word independent in this case means separate from the assessment, which will be done with approaches other than stock assessment modeling. However, to make the estimates meaningful for fishery management, they will eventually need to be integrated into the stock assessment model itself, which is the final objective of the overall study.

What is Close-Kin Mark Recapture (CKMR)?

Mark-recapture is a population estimation technique in which an artificial mark is applied, or a natural mark is detected, on individuals within a population of interest. Then, the marked individuals are allowed to mix with unmarked individuals. In a subsequent sampling event, marked as well as unmarked fish are captured and the proportion of recaptured marks in this second sample of individuals is assessed. If 100 fish were originally captured and tagged, and then during the second sampling event 10 tagged fish were recaptured among 100 total fish (i.e., 90 did not have marks), then 0.1 is the proportion of tagged fish in the second sample.

Dividing the number of tagged fish originally released in the population by this recapture proportion (i.e., 100/0.1) produces an estimate of population size (N = 1,000). This is a simple example and omits various assumptions that need to be met (e.g., tagged fish are well-mixed in population, fish survive after being tagged, tags are retained, tags are recognized and reported when recaptured, etc.), but it illustrates the general concept of mark-recapture. The lower the proportion of tags recaptured in the second sample, the higher the estimated population size.

In the case of CKMR, the tag is a natural tag, namely DNA markers (microhaplotypes) within individual red snapper, and the statistical modeling approach involves the number of genetically related individuals observed relative to the number of individuals captured. This is accomplished by collecting tissue samples (fin clips) from many individuals (>10,000) in the Atlantic red snapper population, sequencing DNA for each individual, and assessing how similar each individual is to every other individual at the DNA sequence level. In simplest terms, the larger the number of related individuals observed for a sample containing a given number of individuals (say, 10,000), the smaller the population size would be estimated to be.

This generally is how CKMR analysis works. In the current study, the research team is spending considerable effort sampling adult red snapper fin clips throughout the study region from North Carolina through the Florida Keys over multiple years to ensure as robust a sample as possible to produce a reliable estimate of Atlantic red snapper population size.

What is Bayesian integrated modeling?

Bayesian modeling is a type of statistical analysis in which information known ahead of time can be utilized to fit models to data. This information is called prior information, and it is included in the model by defining a distribution (aka, a prior) for each parameter that reflects our current knowledge.

If we have strong information on a given parameter before fitting a model to data, then the distribution for that parameter’s prior will often be narrow or informative. Likewise, parameters for which we have little information will be given loose or uninformative priors, which allows the model more solution space to estimate the posterior distribution for those parameters. In the model-fitting exercise, the goal is to fit a model that has the highest likelihood or best fit to the data, and in the process of fitting a Bayesian model, posterior distributions (i.e., posterior to or after model fitting) on all parameters are estimated. In this way, the posterior distributions, which are ultimately the quantities of interest, combine information from the priors and from the data being fitted by the model.

The integrated part of the modeling for the SARSRP study describes a modeling approach in which several different processes (e.g., habitat-specific fish density, detection probabilities, capture rates, etc.) are incorporated into a single model to produce an estimate of population size. Because the study team will include priors on certain parameters in some components of the model, it is therefore a Bayesian analysis.

What is meant by “unknown” or “unconsolidated habitats” and why is sampling taking place there?

There are vast areas of the US Atlantic shelf that have not been surveyed, thus the habitat in those areas of the shelf is unknown. In some cases, we have a general idea that hardbottom or reef habitat broadly exists in a given region, but those habitat types are often interspersed with sand habitat. Other areas are thought to be almost exclusively open sand habitat.  The term “unconsolidated” generally refers to this sand habitat, which gets that name because it is not consolidated into sedimentary rock or reef habitat.

The reason the study team needs to conduct remotely operated surveys in those unconsolidated areas is 1) to estimate what percentage of sand habitats actually contain some hardbottom habitat mixed in with the sand habitat, and 2) to estimate the occurrence and density of red snapper in open sand habitat. In the Gulf of Mexico Great Red Snapper Count study, a substantial percentage of adult red snapper in the western Gulf of Mexico was estimated to occur on unconsolidated habitats, while the fish were mostly associated with hardbottom habitat in the eastern Gulf of Mexico.

A key difference in the bottom type between those two regions is the predominance of muddy sediments in the western Gulf of Mexico, while quartz silica or carbonate sands predominate in the eastern Gulf of Mexico off Florida. While the Atlantic shelf in the SARSRP study region is more similar to the eastern Gulf of Mexico, it is still important to test the habitat association of red snapper in the Atlantic.