Little is known about the population structure and genetic variability of blackfin tuna despite catch increases over the past 25 years. In this thesis, levels of genetic variation contained in 323bp of the mitochondrial DNA (mtDNA) control region-I (CR-I) and in six microsatellite loci were characterized for two regions: the Gulf of Mexico (GoM) and the Northwest Atlantic. Large amounts of mtDNA diversity (h>0.99; =0.047) were observed in both regions. Mismatch distribution analysis of the CR-I sequence data, using a mutation rate of 1.6% Ma-1for scombroid fishes, indicate blackfin tuna underwent population expansion about 1.4 Ma, a timeline concordant with the expansion of other tunas and billfishes. Estimates of female effective population size were very large at 7.8 million and 12.8 million individuals for the NW Atlantic and the GoM, respectively. Both mtDNA and six microsatellite loci were used to determine blackfin tuna population structure. Microsatellite and mtDNA AMOVAs revealed significant differentiation (msat st=0.01, p=0.006 and mtDNA st=0.01, p=0.049) between the GoM and the NW Atlantic samples. Migration estimates using mtDNA data indicate that twice as many females enter the NW Atlantic from the GoM (346 individuals/generation) than the opposite direction (150 individuals/generation). Migration estimates using microsatellite data were substantially smaller, with the Gulf receiving 7 individuals/generation and the NW Atlantic 4 individuals/generation. Finally, low levels of genetic differentiation using microsatellite data have been reported in other highly abundant marine fishes, which have been attributed to homoplasy in allele size. To test this hypothesis, the allele frequency distributions of blackfin and yellowfin tuna at six microsatellite loci were compared. The distances between species were surprisingly small (Da=4.0%, (delta mu)squared=1.08), with a large degree of similarity in frequency distributions at four loci. The comparison of bigeye tuna at two microsatellite loci revealed additional inter-specific similarities. A mutation rate for these loci was estimated by modifying an equation used to estimate time since divergence. Microsatellites in tunas appear to evolve at a rate (4.3x10-7 Ma-1) that is two orders of magnitude slower than other fishes (1x10-5 Ma-1). Accordingly, microsatellite allele size similarities are plesiomorphic and not due to homoplasy.

Estuarine marshes are generally considered to be productive but not necessarily diverse ecosystems. During 24 consecutive months, I collected 65,000 fishes and decapods comprising over 65 species from the New Orleans Land Bridge, an estuarine salt marsh. My research details the distribution of nekton across five contiguous but geomorphically different regions, which I defined as “Areas”. This factor “Area” was significant in explaining community composition differences in 11 of the 24 months I evaluated. That is, during those 11 months community structure was different among the Areas. Specific “month” was also found to be a significant factor as community structure was found to differ among the months. No consistent abiotic factors were associated with community structure. These observations imply that a different set of factors are associated with community structure at the Area level than at the microhabitat level. Sampling of nekton in shallow estuarine salt marsh habitats was difficult. The cast net is a useful gear type for this type of sampling and can be readily standardized for each operator. Standardization of the area covered by the net allows density of collected nekton to be calculated. Little is known about the life cycle of one important estuarine dependent sport fish, tarpon (Megalops atlanticus), in southeastern Louisiana. This research details the presence of the major life stages of the species in Louisiana and suggests that it is capable of completing its life cycle in State waters. The presence of a spawning capable female and male tarpon is documented.

Understanding the life history of a species is essential for fully understanding its role within an ecosystem. However, many of the fish species of high ecological value have not been studied due to their less prominent roles in local recreational and commercial fisheries in comparison to other targeted species. This study describes the age and growth patterns of three small tuna species inhabiting South Florida waters: blackfin tuna Thunnus atlanticus, little tunny Euthynnus alletteratus, and skipjack tuna Katsuwonus pelamis. Tuna specimens were collected via donations obtained from various fishing tournaments and charter captains in the areas of the Florida Straits as well as hook-and-line by the Nova Southeastern University Oceanographic Center. Age was described via sagittal otolith deposition patterns. They were removed, dried, sectioned, and rings were counted as well as measured. Validation of the timing of ring deposits was done by marginal increment analysis. Growth parameters were determined by comparison of fish fork length to count measurements. This comparison via the Von Bertalanffy growth equation produced a growth rate for each species: blackfin, L∞ = 95.34 cm, K = 0.28, and t0 = -1.53; little tunny, L∞ = 77.93 cm, K = 0.69, and t0 = -0.69; and skipjack, L∞ = 112.76 cm, K = 0.24, and t0 = -1.70. The curves indicate an average size of an individual of a given species at a certain age. They also give an estimation of a maximum length (L∞) of each species, in addition to specific growth rate, which is indicated by the slope. Parameters of each resulting Von Bertalanffy equation were compared among species. Results were also compared with growth rates currently used in stock assessments by fisheries management organizations, such as the International Commission for the Conservation of Atlantic Tunas (ICCAT).