The intensive harvesting of sardines has raised major concerns among Omani artisanal fishers regarding the future of tuna fisheries. As tuna serve as a vital economic resource and play a crucial ecological role in the marine ecosystem, this thesis investigates the dietary composition and prey diversity of two commercially significant species, yellowfin (Thunnus albacares) and longtail tuna (Thunnus tonggol), in Omani waters using morphological analysis and DNA metabarcoding techniques. The analysis of diet composition revealed that fish constitute the predominant prey group for both tuna species, while cephalopods and crustaceans represent important secondary contributors to dietary components. DNA metabarcoding significantly enhanced prey identification, overcoming the limitations of visual stomach content analysis by detecting a broader range of species and improving taxonomic resolution. A total of 40 prey species from 23 families were identified within tuna stomach samples, comprising 16 fish, 12 crustaceans, and 12 cephalopods. Despite expectations that sardines (Sardinella longiceps) would dominate the diet, carangids (jacks and trevallies) and squids were the most frequently detected prey groups. The study found genetically seasonal variations in prey community composition, with secondary prey (prey of prey) playing a role. Secondary prey influenced species composition changes, reflecting trophic interactions and prey availability rather than prey diversity. In contrast, the analysis of prey diversity revealed diversity was significantly higher in Seeb compared to Ash Sharqiyah, likely due to regional differences in habitat productivity and prey availability. Seasonally, dietary diversity was lower in winter than in spring, suggesting potential fluctuations in prey availability driven by oceanographic and climatic conditions. Metabarcoding also detected cases of secondary predation—that is, the presence of prey DNA originating from the digestive contents of the prey consumed by the predator, rather than from direct predation. This distinction is essential for accurately interpreting trophic interactions and avoiding misidentification of actual predator-prey relationships. Importantly, secondary predation should not be confused with the consumption of prey of secondary importance, which refers to prey species that are directly consumed but contribute minimally to the overall diet. Despite these complexities, the integrated methodologies confirmed that both yellowfin and longtail tuna are opportunistic predators, capable of adjusting their diets based on prey availability. The substantial presence of forage fish supports the broader ecological understanding that Oman’s upwelling-driven marine environment sustains a diverse and abundant small pelagic community, forming a critical prey base for top predators. These findings have important implications for fisheries management, particularly in light of increasing fishing pressures and environmental changes.
