Artificial reefs have been deployed throughout the world’s oceans to act as habitat and fishing enhancement tools. To expand current research on the role of artificial reefs in the marine community, ordination and multivariate regression methods were used here to analyze survey data of natural and artificial reefs. The reefs, located in the Northern Gulf of Mexico (NGOM) and on the West Florida Shelf (WFS), had been previously surveyed from 2004 to 2015 using remote operated vehicle and stationary video techniques. This study tested the hypothesis that similar functional roles are accounted for at both natural and artificial reef sites even if species composition varies. Secondly, it examines the role of environment and fisheries in determining the assemblages. Artificial reefs tended to host communities that were as biodiverse as natural reefs, although not necessarily composed of the same species. Results of an ordination confirmed that as the classification was broadened from the level of species, to family, to functional group, the assemblages on each reef type (natural vs. artificial and NGOM vs WFS) appeared more similar. Dominant groups were present at all levels of classification and included the families Lutjanidae and Carangidae, as well as functional groups Red Snapper and Small Reef Fish. Both natural and artificial reefs tended to be dominated by one of the following: Lutjanidae, Carangidae, or Small Reef Fish, although a continuous gradient was found across the extremes of natural versus artificial reefs. Generalized Additive Models were developed to examine the influence of reef type, location, environment and fishing intensity covariates. Results indicated that for both natural and artificial reefs, the abundance of families and functional groups can be influenced by environmental factors. In both cases, there is strong spatial autocorrelation suggesting connectivity with neighboring reefs.

The assemblage structure, abundance, biomass, and vertical distribution of juvenile reef fishes in the offshore pelagic habitat of the northern Gulf of Mexico are described as part of the NOAA-supported Offshore Nekton Sampling and Analysis Program. The results presented here are from a 3-month, continuous sampling series in 2011 in which discrete depth strata from 0 to 1500 m were sampled using a 10-m2 MOCNESS midwater trawl. This is the first study to examine pelagic juvenile reef fish distributions across the entire oceanic northern Gulf of Mexico seaward of the continental shelf break after the Deepwater Horizon Oil Spill. During this series, 87,407 specimens were collected, of which 838 were reef fishes, representing seven orders, 30 families and 119 species. The faunal composition of pelagic juvenile reef fishes was diverse and well mixed, with no discernable spatial structure with respect to water masses and solar cycle. Seventy-nine percent of the pelagic juvenile reef fishes were collected in the epipelagic and the dominant families were Congridae, Carangidae, Tetraodontidae, and Acanthuridae. Species richness, biomass, and frequency of occurrence of pelagic juvenile reef fishes was greatest between 0-200 m and decreased with depth. Data from the assemblage structure, abundance, biomass, and vertical distribution of pelagic juvenile reef fishes collected from this cruise series will contribute to the lack of knowledge regarding the dispersal dynamics and coastal-connectivity of these fishes in the northern Gulf of Mexico.

Largespot pompano, Trachinotus botla, is a surf zone carangid with a cosmopolitan distribution in subtropical and tropical waters. Within South Africa, the species occurs along the KwaZulu-Natal coastline where it is a popular recreational fishing target. Recreational fishing in southern Africa has developed significantly in recent years, and is now regarded as an industry with huge economic potential. The long-term contribution of South African recreational fisheries to local economies is reliant upon sustainable exploitation through effective management. Trachinotus botla was found to grow rapidly with maximum observed age of six years. Otolith growth zone deposition was validated using edge analysis. Growth was similar between males and females until ~350 mm FL after which females continued to grow while growth in males slowed. The resulting overall sex ratio was slightly female-biased (1 male: 1.3 females). Trachinotus botla matures early with all fish considered to be mature at 290 mm FL, which corresponds to an age of three years. A protracted spawning season was observed ranging from November to February and there was evidence to suggest that T. botla is a serial spawner. Dietary analysis indicates that T. botla is an opportunistic predator with a catholic diet. The opportunistic utilization of “superabundant” prey items is a fundamental characteristic of the species feeding habits. An ontogenetic dietary shift was observed at approximately 300 mm FL that was linked to a shift in habitat preference. This thesis provided the first evidence that infection by the tongue-replacing isopod, Cymothoa borbonica, reduces the growth rate of wild host fish populations despite not affecting the diet, feeding habits and feeding frequency of their hosts. These results also highlighted the inadequacy of condition factor as a proxy for quantifying the effects of cymothoids on their hosts, and identified the need to incorporate host age when assessing the effects of parasite infection. Information on the life-cycle of C. borbonica, including estimates of the hypothesized “infectious” period and its longevity were obtained through analysis of parasite infection patterns as a function of host age and length. An assessment of the T. botla shore fishery of KwaZulu-Natal using historical catch data revealed that the fishery is stable. Productivity of the T. botla fishery increased towards the north of KwaZulu-Natal. Distinct seasonal variations in the T. botla fishery were also noted with catches peaking in summer months and lowest during winter. A per-recruit assessment revealed that the species is currently underexploited (SBR = 62% of pristine levels), and fishing mortality rate could be doubled before reaching the spawner biomass-per recruit target reference point of FSB₄₀. A combination of the life history characteristics of species, the nature of the recreational shore fishery together with the current management regulation of 5 fish person⁻¹ day⁻¹ has ensured the sustainable utilization of the T. botla resource in KwaZulu-Natal.