Ten stations were sampled in Exmouth Gulf (7 on the eastern side and 3 on the western). At each station water temperature and salinity were measured at 1m depth intervals and secchi depth recorded. Values for Chlorophyll a, particulate carbon and nitrogen were determined.

Egg production rates by 4 of the dominant copepod species were measured by bottle incubations (Acartia fossae, Parvocalanus crassirostris) and the egg-ratio technique (Oithona attenuata and Oithona simplex). Egg production data was used to calculate adult females grazing rates of the total particulate carbon each day.

Plankton abundance and biomass did not differ greatly within the gulf; however, highest values of chlorophyll a, particulate carbon and nitrogen, and copepod egg production rates occurred in the south-east of the gulf. Though egg production rates were low and apparently severely food-limited, resuspension of bottom sediments or export of material from adjacent salt flats may fuel production in shallow inshore areas of the gulf. P. crassirostris appeared to be omnivorous and 0. attenuata primarily herbivorous, but the trophic resources used by 0. simplex and A. fossae could not be identified. From the egg production data, it was calculated that adult females of the four dominant copepod species graze 12% of the total particulate carbon each day.

A total of 1737 Pinctada maxima samples were collected from eight distinct populations, six in Australia and two in Indonesia. The Australian populations were sampled from Darwin in the Northern Territory and the Lacepede Islands, 80 Mile Beach - shallow water, 80 Mile Beach - deep water, Port Hedland and Exmouth Gulf in Western Australia. The Indonesian populations were sampled from Madura Island and Sumbawa Island.Samples of both adductor muscle and mantle tissue were collected from Pinctada maxima oysters of various sizes aboard pearling industry vessels in Western Australia and the Northern Territory, between February 1998 and November 1999. Whole shell samples from the Indonesian sites, collected in November 1999, were delivered by road to Gondol Fisheries Station and held in flowing sea water tanks prior to dissection. The entire soft tissues from small spat were removed from the shell. Samples were either snap frozen in liquid nitrogen or preserved in 70% ethanol immediately following collection.Assays were developed for eight highly variable microsatellites markers and an mtDNA marker for rapid assessment of genetic variation in pearl oysters. These assays were used to screen the eight populations of P. maxima (including different juvenile age classes for the Western Australian and Northern Territory populations). It was demonstrated that the Western Australian populations belong to one stock with large effective population sizes and have little or no recruitment from Indonesia and a reasonable degree of exchange with Northern Territory. A basic technology for assessment of genetic variation in spat and for future use in improving cultured pearl oyster stocks was developed.Successful description of the population genetic structure for different age classes of Pinctada maxima in Western Australia and Northern Territory has provided a basis for improved maintenance of a productive and valuable fishery through improved stock definition and determination of levels of dispersal among populations. The development of highly variable DNA markers provides a base technology to assist the choice of sources of broodstock for hatcheries and future management of cultured populations as the Pearling Industry increasingly relies on hatchery produced spat. The objectives of this research were:1. To develop assays for regions of highly variable DNA (microsatellites) and mtDNA markers for rapid assessment of genetic variation in pearl oysters.2. To survey up to eight populations of P. maxima throughout the Western Australian coast, including different juvenile age classes, using up to ten highly variable markers.3. To infer the level of dispersal between populations and the effective population size contributing to the next generation from the genetic data and identify the management implications of these data.4. To develop the basic technology for assessment of genetic variation in spat and for future use in improving cultured pearl oyster stocks. Initially two sites were collected in each of 80 Mile shallow and 80 Mile deep populations. The 80 Mile shallow collections were made almost continuously between ten and eighteen mile beach and the subsets were fused into one sample. The 80 Mile deep collections were made from Cape Bossut and Compass Rose sites, the latter being more offshore than the former. These two sites showed no significant microsatellite frequency differences and were also fused.In 1998, samples were collected from Australian waters only and consisted of animals from three different year classes defined by dorso-ventral shell length, 0+ spat (1-60mm), 1+ spat (61- 120mm) and adults (>120 mm). In 1999 a second set of 0+ and 1+ spat were collected from four of the Western Australian populations (the Lacepede Islands, 80 Mile Beach, Port Hedland and Exmouth Gulf) to allow a comparison of gene frequencies for a single cohort over two successive years.

To determine a minimum estimate of dugong population (relative dugong density) in Shark Bay, Ningaloo and Exmouth Gulf.