The biological characteristics of fisheries stocks that are assessed for management considerations are rarely homogeneous over time or space. However, stock assessment scientists largely ignore this heterogeneity in their models. This thesis addresses the effects of spatial and temporal heterogeneity on stock assessment models using Atlantic Weakfish (Cynoscion regalis) as a case study. First, spatial and temporal variation was incorporated into length-, weight-, and maturity-at-age estimates using mixed-effects models (Chapter Two). The resulting heterogeneous weight and maturity parameters then were applied to per-recruit analyses to examine the sensitivity of biological reference points to spatial and temporal variation in life history attributes (Chapter Three). Mixed-effects life history models incorporating spatial and temporal variation revealed distinct regional and annual trends that were not visible from standard homogeneous models. In several instances, the homogeneous modelling approach produced life history estimates that varied significantly from the spatial and temporal means produced by the heterogeneous models. In some cases, this difference was so great that the homogeneous means were much higher or lower than the heterogeneous means for all regions or years. Minimized AIC statistics revealed that spatially and temporally integrated mixed-effects models were more robust and descriptive of Atlantic Weakfish life history than the standard homogeneous models. Per-recruit and biological reference points derived from these life history estimates in Chapter Three were found to be highly sensitive to spatial and temporal variations in weight parameters. In several cases, reference points used as management targets were so significantly different that ignoring spatial and temporal heterogeneity in Atlantic Weakfish life history would likely cause overfishing and decline of Weakfish in certain regions and years. / Master of Science

Globally, the status of many fish stocks remains unknown, of which the majority fall under data-limited small-scale fisheries. Management decisions in most of these fisheries are difficult due conflicting objectives and views from fisheries managers and scientists. In South Africa, the traditional boat-based ‘linefishery’ provides such an example of a small-scale, multi-species fishery with a long history. The historical de facto open access nature of this fishery resulted in continuous declines in catches of many linefish species, and in 2000 the fishery was declared to be in a state of emergency. This led to a reduction of up to 70% within the fishery, among other measures, such as introductions of size and bag limits. Assessing the status of linefish species is difficult due to a lack of reliable long-term data for the majority of species. The aims of this study were therefore: (1) to quantify the stock status for all linefish species with available life history and size composition information, (2) compare current and historical stock levels to ascertain if the reduction in effort facilitated any recovery in linefish species and (3) correlate the current stock status estimates to life history traits to identify simple indicators of resilience to exploitation. For this purpose, length frequency data from 1988-1990 and 2008-2010 and biological parameters sourced from literature were used to conduct per-recruit analysis to estimate spawner biomass depletion (SBD) for both time periods. The majority of the 26 species analyzed, (68%) showed improvements in spawner biomass between the two time periods, with 12 species undergoing a change in stock status (i.e. improving from collapsed or overexploited). Specifically, increases in length-at-capture (Lc) as well decreases in fishing mortality (F) facilitated recovery for many species. Asymptotic length (L∞), as well as the ratio between Lc / L∞ and Lc / Lopt (where Lopt is the optimum length) were found to be significantly correlated to spawner biomass depletion. Kruskal Wallis analyses revealed that only movement pattern had a significant relationship to SBD, more specifically, migratory species were significantly more depleted than resident ones. This study identifies simple indicators that, in the absence of conventional stock assessments, provide fisheries managers with a fundamental understanding of a species’ susceptibility to overexploitation – offering another decision making tool for use in data poor fisheries such as the South African linefishery.