| Summary: | The skipjack tuna (<i>Katsuwonus pelamis</i>) is a mesopredator fish species with seasonal abundance in waters off Taiwan. Regional ecological and life-history information has been historically lacking for this species. In recent years, stable isotope analysis (SIA) of carbon and nitrogen has been used to assess predator feeding ecology and broader ecosystem trophic dynamics. This study evaluated comparative skipjack feeding ecology in distinct regions off Taiwan, combining traditional stomach content analysis with SIA of individuals off western (<i>n</i> = 43; 2020) and eastern (<i>n</i> = 347; 2012–2014 and <i>n</i> = 167; 2020) Taiwan. The stomach content analysis showed the most important prey to be ponyfish (<i>Photopectoralis bindus</i>) in western Taiwan and epipelagic squids (<i>Myopsina</i> spp.) and carangids (<i>Decapterus macrosoma</i>;) in eastern Taiwan from 2012 to 2014 and epipelagic carangids (<i>Decapterus</i> spp.) and flying fishes (<i>Cheilopogon</i> spp.) in eastern Taiwan in 2020, suggesting that the skipjack tuna is a generalist predator across regions. In contrast, time-integrated diet estimates from Bayesian mixing models indicated the importance of cephalopods and crustaceans as prey, potentially demonstrating more mesopelagic feeding in less productive waters during skipjack migrations outside the study regions. Skipjack off western Taiwan had a slightly higher estimated trophic position than in the waters off eastern Taiwan, potentially driven by the varying nutrient-driven pelagic food web structures. Skipjack SI values increased with body size off eastern Taiwan but not in western waters, suggesting that opportunistic predation can still result in different predator–prey size dynamics between regions.
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