Fisheries sustainability is inherently linked to an understanding of the population-level effects of fishing. With an accurate characterization of historical fish and fishery dynamics, management agencies are more equipped to create regulations that sustain fishery resources over the long term. The overarching goal of this dissertation is to contribute to the advancement of fisheries stock assessment and promote resource sustainability. My research focused on highly migratory species (HMS), particularly fishes that reside in the open ocean. These species constitute some of the highest valued global fisheries; however, numerous factors compromise HMS stock assessment and management. These challenges are fully described in Chapter 1, which also includes corresponding research and management recommendations. A key limitation in HMS assessments underlying my research is the lack of independent scientific monitoring programs. In the absence of research surveys, HMS stock assessments must rely on fishery catch and effort data. Therefore, special care is required to infer population dynamics from entities that were not established to monitor populations. In particular, the habitat in which fishing occurs largely dictates the amount and composition of fishes captured. Unfortunately, habitat effects on fishery-dependent data are not commonly accounted for in HMS assessments. Chapter 2 presents the results of a performance evaluation of methods used for estimating HMS abundance trends, including traditional generalized linear models (GLMs), an existing method that considers habitat (statHBS), and a proposed method that hybridizes traditional and habitat-based approaches (HabGLM). I demonstrate that HabGLM was most accurate of those evaluated, while exhibiting minimal sensitivity to errors in input data. I recommend the use of HabGLM in future HMS stock assessments; however, despite being most accurate, there were scenarios where HabGLM still did not sufficiently capture the true abundance pattern. In Chapter 3, the HabGLM was applied to 35 HMS in the Atlantic Ocean using fisher logbook data from the US pelagic longline fishery. This comprehensive analysis portrays an HMS community in the Atlantic as generally depleted, with current abundances of 76% of the species at less than half of their 25-year observed maxima. However, despite these depletions, 26% of the species exhibited population growth, suggesting recent fishing intensities may be adequate for sustaining or rebuilding certain populations. While interpretations of abundance trends can be informative, fisheries management is more often guided by the output of stock assessments. Thus, in Chapter 4, I present the results of a study that evaluated the effects of abundance index quality on the performance of a stock assessment model (Stock Synthesis), with a focus on Atlantic blue marlin (Makaira nigricans). In general, assessment model performance was superior when based on abundance indices estimated using HabGLM; however, the management quantities derived from this best case scenario were still overly optimistic, and when the fisheries were regulated accordingly, population biomass was projected to be well below the management target level. Overall, my research emphasizes that (1) habitat should be directly incorporated into HMS stock assessments, and (2) independent stock monitoring programs are essential for effective fisheries management.

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