Combining otolith chemistry and genetics to infer the population structure of yellow snapper Lutjanus argentiventris

Abstract Developing a metapopulation framework contributes to the understanding of spatial processes and structures in populations, providing basic information for conservation biology. However, the extent to which the metapopulation structure differs geographically and across life history stages is unexplored for most fishes. Here, we compared the population structure and connectivity patterns of juvenile yellow snapper Lutjanus argentiventris in mangroves of the Eastern Tropical Pacific Ocean. In both the Gulf of California and Galápagos, these fish experience an array of environmental and oceanographic conditions that produce unique otolith microchemistry signatures and genetic population structures. In the Galápagos Archipelago, we used otolith microchemistry and microsatellite DNA, while for the Gulf of California, we only used otolith microchemistry. We observed relatively small differences in the otolith microchemistry at the ecoregion spatial scale (10–100 km 2 ) for the Galápagos and the Gulf of California (classification accuracy of 57% and 64%, respectively). At the finer mangrove spatial scale (~1 km 2 ), we found larger differences in the otolith microchemistry among the Gulf of California mangroves (classification accuracy ~90%) than in Galápagos (classification accuracy ~24%), potentially related to a stronger environmental gradient in the former. Based on otoliths, 75% of juveniles were migrants among mangroves in the Galápagos, in contrast to only around 10% of juveniles being migrants among the Gulf of California mangroves, suggesting a metapopulation structure characterized by high rates of self‐recruitment for snappers in the Gulf of California. For Galápagos, both otolith microchemistry and genetics supported the presence of a source–sink metapopulation structure for the yellow snapper, with high levels of connectivity in mangroves within the Eastern and Western ecoregions ( F ST = 0.003, p < 0.05). By combining tools that assess connectivity at multiple timescales (microchemistry and genetics) at different life stages and ecosystems, we provide a more complete elucidation of metapopulation structure for L. argentiventris . The approach employed here can be applied to other tropical fishes with broad distribution ranges and ontogenetic changes across complex habitats such as mangroves, seagrasses, and coral reefs.