This thesis is presented as a collection of five papers and one report, each of which has been either published after peer review or submitted for publication. It covers a broad range of applied statistical methods, from deterministic modelling to integrated Bayesian modelling using MCMC, via bootstrapping and stochastic simulation. It also covers a broad range of subjects, from analysis of recreational fishing diaries, to genetic mark recapture for wombats. However, it focuses on practical applications of statistics to the management of wild populations. The first chapter (Hoyle and Jellyman 2002, published in Marine and Freshwater Research) applies a simple deterministic yield per recruit model to a fishery management problem: possible overexploitation of the New Zealand longfin eel. The chapter has significant implications for longfin eel fishery management. The second chapter (Hoyle and Cameron 2003, published in Fisheries Management and Ecology) focuses on uncertainty in the classical paradigm, by investigating the best way to estimate bootstrap confidence limits on recreational harvest and catch rate using catch diary data. The third chapter (Hoyle et al., in press with Molecular Ecology Notes) takes a different path by looking at genetic mark-recapture in a fisheries management context. Genetic mark-recapture was developed for wildlife abundance estimation but has not previously been applied to fish harvest rate estimation. The fourth chapter (Hoyle and Banks, submitted) addresses genetic mark-recapture, but in the wildlife context for estimates of abundance rather than harvest rate. Our approach uses individual-based modeling and Bayesian analysis to investigate the effect of shadows on abundance estimates and confidence intervals, and to provide guidelines for developing sets of loci for populations of different sizes and levels of relatedness. The fifth chapter (Hoyle and Maunder 2004, Animal Biodiversity and Conservation) applies integrated analysis techniques developed in fisheries to the modeling of protected species population dynamics - specifically the north-eastern spotted dolphin, Stenella attenuata. It combines data from a number of different sources in a single statistical model, and estimates parameters using both maximum likelihood and Bayesian MCMC. The sixth chapter (Hoyle 2002, peer reviewed and published as Queensland Department of Primary Industries Information Series) results directly from a pressing management issue: developing new management procedures for the Queensland east coast Spanish mackerel fishery. It uses an existing stock assessment as a starting point for an integrated Bayesian management strategy evaluation. Possibilities for further research have been identified within the subject areas of each chapter, both within the chapters and in the final discussion chapter.

The Roe’s abalone (Haliotis roei) fishery near Perth, Western Australia, is uniquely accessible, and highly vulnerable to overexploitation. The sustainability of this intensively utilized fishery requires robust assessment. To facilitate an assessment, this research aimed to provide rigorous and detailed biological information with appropriate interpretation. Four critical aspects of the species’ biology and population dynamics were investigated: (1) the stock structure; (2) the recreational catch; (3) an appropriate growth curve and description of size at age; and (4) abundance measures against which to assess the impact of fishing mortality. Allozyme electrophoresis was used to investigate stock structure across the species’ distribution. Standardized variance in allelic frequencies between 10 sites in south-western Australia indicated high levels of gene flow across the 3000 km sampled (mean FST = 0.009). An isolation-by-distance was evident when pairwise measures of GST were related to geographic distance (r=0.45, P<0.001). The area of complete genetic mixing was estimated from samples within the Perth fishery to be less than the distance between the two nearest sites, or 13 km. Consequently, the Perth fishery comprises numerous discrete stocks, each requiring independent assessment. A possible mechanism for this population structure is the retention of larvae in the wind driven currents oscillating in the near-shore lagoons, with rare pulses of long distance dispersal via the southerly Leeuwin current, running further offshore. The presumed impact of intensive recreational fishing, combined with substantial commercial quotas for the Perth fishery, had led to tight restrictions on fishing effort, without any quantitative measure of the recreational catch. A stratified creel survey was adapted to estimate the effort, catch rate and mean weight of abalone harvested by the recreational sector. Catches were estimated for reef complexes, or stocks, of less than 10 nautical miles (18.5 km) of coast. Between 1997 and 2000 the recreational catch varied from 30 to 45 tonnes whole weight, approximately equivalent to the commercial quota of 36 tonnes. On average 88% of the recreational catch came from two stocks, while 98% of the commercial catch came from these two, and one additional, stocks. The incidental mortality from recreational fishing, measured as the number of abalone left dead on the reef as a proportion of the estimated catch, was approximately 7% and 20% at two sites surveyed. Spatial and temporal patterns of growth were examined on the west coast of Western Australia. Growth increments were measured for abalone larger than about 30 mm from tagging studies at five sites in the Perth fishery, a site at the northern extent of the species’ distribution and a site in the southwest. Mean annual growth increments of the 0+ year class were obtained by fitting components to length frequencies from five sites in the Perth fishery, and combined with growth increments from each Perth tag site for model fitting. A von Bertalanffy growth curve provided a slightly better fit to the tag data, but a Gompertz growth curve was a much better fit when the mean increment from the 0+ to 1+ cohort was included, with the inflection occurring at about 40 mm, the size at sexual maturity. There was no difference in annual growth between the two years studied. There was significant variation in growth between the reef platform and adjacent sub-tidal reef, but this variation was site specific and faster growth rates were not consistently associated with either habitat. There was no latitudinal trend in growth rate. Growth at the Perth sites was the fastest and similar at all five sites with growth increments greater in summer than in winter. Size and abundance of abalone were measured using fixed transects and quadrats. Abalone densities were highest on the outer edge of the platform, intermediate in the middle of the reef platform, and lowest on both the inner platform and the sub-tidal reef. The pattern of mean lengths of abalone was the inverse of the density. Mean length and abundance were driven by the presence of post-settlement juveniles on the outer and middle reef habitats. There was a high spatial variation in abundance, with densities varying between transects at the same site, but the trend between years for each transect at a site was not significantly different. Abalone abundances, by size class, were examined from sites sampled between 1996 and 2002. A low density of post-settlement juveniles at all sites in 1997 was reflected in low densities of the 1+ and 2+ year classes in subsequent years. Abalone abundances at an unfished site were steady over the seven years. Two sites were located within each of the main stocks utilised by the recreational fishery. Abundance was stable or increasing in one stock, corresponding to a stable total catch. In the second stock the total catch increased over time and abundances declined. Perth is the focus of the Roe’s abalone fishery, with recreational and commercial fishers take about equal shares of the annual catch. Stocks are highly subdivided, with most of this catch coming from only 3 stocks occupying about 20 nautical miles of coast. Growth rates were found to be lower than previous estimates, and more similar to other commercial species of abalone. All life history stages are highly habitat specific, particularly the recruits, and the distribution and abundance through time indicate that the main stocks are near, or slightly over, the limit of sustainable fishing.