A stratified random survey, tagging study (conventional and telemetry), fish health evaluation and genomics study of red snapper in the northern Gulf of Mexico

End Date: 12/5/16


  1. We will apply two abundance estimate methods: mark-recapture and hydroacoustics. We will estimate the abundance of red snapper by releasing conventionally tagged red snapper on both artificial and natural reefs with newly developed cage release methods. We will use standard Peterson mark-recapture estimates of fish abundance on each individual reef. We will use telemetry based estimates of residency and emigration rates, and telemetry based estimates of tagging artifact mortality, fisher non-reporting, tag retention and natural mortality. 
  2. We will use hydroacoustics and video camera surveys to estimate red snapper abundance. These estimates will provide a second and completely independent estimate of red snapper abundance on each reef.
  3. We will estimate age frequency distributions and growth rates of red snapper. We will use fish traps, hook-and-line, commercial bandit rigs, hydroacoustic surveys, and camera video surveys for all fish collections.
  4. We will collect fish health data on red snapper and codify it in such a way so that qualitative results can be compared as numerical values across study sites and geographical locations.
  5. We will use eDNA metabarcoding for the assessment of red snapper abundance in the Gulf of Mexico.


Additional PIs: Zhanjiang Liu, Auburn University; Edward Chesney, Louisiana Universities Marine Consortium and William Heyman, LGL Ecological Research Associates

It is well recognized that there are many difficulties with conventional mark-recapture studies, including fisher non-reporting, unknown tag loss, unknown predation rates, emigrations, unknown tagging mortality artifacts and unknown natural mortality. The major advantage of the present study is that we will address these known difficulties by also applying telemetry methods. Previous telemetry studies were successful in obtaining estimates of mortality (M, F and Z) as well as documenting movement patterns, non-reporting, tag retention, and tagging mortality artifacts in red snapper. The present proposal will apply these telemetry based estimates to conventional mark-recapture estimates of red snapper abundance. The advantage of the conventional tagging is that we can substantially increase the sample size of tagged fish and increase the geographical coverage of tagged fish. These combined methods (conventional and telemetry tagging) will then provide the most accurate abundance estimates to date, that can then be applied and compared to traditional stock assessments (SEDAR) to help managers in their critical and difficult task of sustaining this important fishery.

This study will also test for significant differences between red snapper health among habitats (e.g., natural hard bottom substratum and artificial reefs, including oil platforms). This fundamental objective is completely novel as no such study exists presently. For example, we will test if fish collected near oil platforms present gill and hepatic lesions indicative of chronic toxicological exposure when compared to controls captured from natural hard bottom sites far from any oil platform.

Two main approaches using eDNA will be applied for red snapper assessment. We will use red snapper-specific eDNA barcoding for accurate assessment of red snappers in the Gulf, and eDNA metabarcoding to assess the biota of the ecosystem including vertebrates, invertebrates, and bacterial communities that affect the red snapper populations.


Accurate stock assessment is critical to the management of marine "reef" fish populations in the northeast Gulf of Mexico. However, this assessment task often proves difficult because of the inherent difficulty of sampling reef fishes with complicated life history patterns and cryptic habitats. Red snapper support a large and wide ranging sport and commercial fishery in the northern Gulf of Mexico. Critical to management are accurate stock assessments. Recently these stock assessments have received extensive public criticism from both sport and commercial fishers declaring that federal stock assessments are inaccurate and there are many more red snapper in the northern Gulf of Mexico that are not being counted. To address this criticism the present study will make a direct count of red snapper in the northern Gulf of Mexico using conventional mark-recapture, telemetry studies, hydroacoustic surveys, fishery independent collection surveys, and assessment using both modern genomics (eDNA analysis) and fish health approaches (pathobiology).