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Meeting the objectives of sustainable fisheries management requires attention to the complex interactions between humans, institutions and ecosystems that give rise to fishery outcomes. Traditional approaches to studying fisheries often do not fully capture, nor focus on these complex interactions between people and ecosystems. Despite advances in the scope and scale of interactions encompassed by more holistic methods, for example ecosystem-based fisheries management approaches, no single method can adequately capture the complexity of human-nature interactions. Approaches that combine quantitative and qualitative analytical approaches are necessary to generate a deeper understanding of these interactions and illuminate pathways to address fisheries sustainability challenges. However, combining methods is inherently challenging and requires understanding multiple methods from different, often disciplinarily distinct origins, demanding reflexivity of the researchers involved. Social-ecological systems' research has a history of utilising combinations of methods across the social and ecological realms to account for spatial and temporal dynamics, uncertainty and feedbacks that are key components of fisheries. We describe several categories of analytical methods (statistical modelling, network analysis, dynamic modelling, qualitative analysis and controlled behavioural experiments) and highlight their applications in fisheries research, strengths and limitations, data needs and overall objectives. We then discuss important considerations of a methods portfolio development process, including reflexivity, epistemological and ontological concerns and illustrate these considerations via three case studies. We show that, by expanding their methods portfolios, researchers will be better equipped to study the complex interactions shaping fisheries and contribute to solutions for sustainable fisheries management., (© 2022 The Authors. Fish and Fisheries published by John Wiley & Sons Ltd.)

Understanding patterns of larval dispersal is key in determining whether no-take marine reserves are self-sustaining, what will be protected inside reserves and where the benefits of reserves will be observed. We followed a multidisciplinary approach that merged detailed descriptions of fishing zones and spawning time at 17 sites distributed in the Midriff Island region of the Gulf of California with a biophysical oceanographic model that simulated larval transport at Pelagic Larval Duration (PLD) 14, 21 and 28 days for the most common and targeted predatory reef fish, (leopard grouper Mycteroperca rosacea). We tested the hypothesis that source-sink larval metapopulation dynamics describing the direction and frequency of larval dispersal according to an oceanographic model can help to explain empirical genetic data. We described modeled metapopulation dynamics using graph theory and employed empirical sequence data from a subset of 11 sites at two mitochondrial genes to verify the model predictions based on patterns of genetic diversity within sites and genetic structure between sites. We employed a population graph describing a network of genetic relationships among sites and contrasted it against modeled networks. While our results failed to explain genetic diversity within sites, they confirmed that ocean models summarized via graph and adjacency distances over modeled networks can explain seemingly chaotic patterns of genetic structure between sites. Empirical and modeled networks showed significant similarities in the clustering coefficients of each site and adjacency matrices between sites. Most of the connectivity patterns observed towards downstream sites (Sonora coast) were strictly asymmetric, while those between upstream sites (Baja and the Midriffs) were symmetric. The best-supported gene flow model and analyses of modularity of the modeled networks confirmed a pulse of larvae from the Baja Peninsula, across the Midriff Island region and towards the Sonoran coastline that acts like a larval sink, in agreement with the cyclonic gyre (anti-clockwise) present at the peak of spawning (May-June). Our approach provided a mechanistic explanation of the location of fishing zones: most of the largest areas where fishing takes place seem to be sustained simultaneously by high levels of local retention, contribution of larvae from upstream sites and oceanographic patterns that concentrate larval density from all over the region. The general asymmetry in marine connectivity observed highlights that benefits from reserves are biased towards particular directions, that no-take areas need to be located upstream of targeted fishing zones, and that some fishing localities might not directly benefit from avoiding fishing within reserves located adjacent to their communities. We discuss the implications of marine connectivity for the current network of marine protected areas and no-take zones, and identify ways of improving it.