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Macroalgae, hard corals, octocorals, and fish were surveyed on 10 to 13 inshore coral reefs of the Great Barrier Reef, along a water quality gradient in two regions with contrasting agricultural land use. A water quality index was calculated for each reef based on available data of particulate and dissolved nutrients, chlorophyll and suspended solids. Strong gradients in ecological attributes occurred along the water quality gradient. Macroalgae of the divisions Rhodophyta and Chlorophyta increased with increasing nutrients, while Phaeophyta remained similar. Octocoral richness and abundances of many hard coral and octocoral taxa decreased, and none of the hundreds of species increased. At reefs in higher nutrient environments, hard coral and octocoral assemblages were composed of subsets of the many species found in lower nutrient environments, whereas fish and macroalgal assemblages consisted of contrasting suites of species. The study identifies species groups that are likely to increase or decrease in abundance with changing water quality.

The age, growth and mortality of Lutjanus carponotatus and L. vitta were determined from sectioned otoliths of fishes from the central Great Barrier Reef. The periodicity of annulus formation was validated by oxytetracycline labelling of tagged fishes in a separate study. Growth in length was variable between sexes for both species, males tending to grow larger than females. The von Bertalanffy growth function (fork length-at-age) for L. carponotatus was Lt=313.0 (1−exp {−0.449[t+0.016]}), and Lt=245.3 (1−exp {−0.853[t+0.179]}) for L. vitta. The oldest individuals found were an L. carponotatus individual of unknown sex, 20 years of age (FL=335 mm) and a female L. vitta 12 years of age (FL=257 mm). Otolith weight was strongly correlated with age for both species. The annual instantaneous rate of natural mortality (M) was estimated to be 0.199 for L. carponotatus and 0.342 for L. vitta, representing an annual survivorship of approximately 82 and 71%, respectively. The longer life span and lower rate of natural mortality for L. carponotatus indicates that this species will be more vulnerable to overfishing than L. vitta.

Otoliths of L. erythropterus, L. malabaricus and L. sebae from the central Great Barrier Reef contain a well defined series of opaque and translucent increments known to be deposited annually. These three species are relatively long-lived, and grow slowly after becoming reproductively mature. Age estimates up to 32 years for L. erythropterus, 20 years for L. malabaricus and 22 years for L. sebae were much higher than those previously reported from other northern Australian waters. Age estimates obtained from counts of increments on whole otoliths were consistently much lower and more imprecise, at all ages compared with counts from sectioned otoliths. Precision of counts from whole otoliths declined significantly with increasing fish age. The regression of sectioned age on otolith weight revealed consistent linear relationships among all three species. To explore the fishery research and management implications of these biases, age estimates from the two ageing methods were used to construct comparative growth and mortality parameters and model yield-per-recruit values under contrasting harvest strategies. While the von Bertalanffy growth functions were not significantly different for the two methods, the underestimates of age from whole otoliths caused serious over-estimation of natural mortality. Serious overfishing could occur if these estimates were applied for fishery management purposes.

Fish traps were used to quantify the distribution and abundance of the Lutjanidae and Lethrinidae on reefs across the central Great Barrier Reef. The assemblages of fishes on inshore reefs were distinctive from those on midshelf and outershelf reefs. There were significantly fewer individuals of the Lutjanidae and Lethrinidae inshore and all species examined displayed significant cross-shelf changes in abundance. These significant cross shelf changes in abundance were due to an absence or low abundance of individuals of a species at one or more cross shelf locations, with many species present in only one location on the continental shelf. The genera Aprion, Lutjanus, Macolor, Symphorichthys, Symphorus, Gnathodentex, Gymnocranius, Lethrinus and Monotaxis were all characteristic of the shallow shelf waters less than 100 m. In contrast, species of the genera Paracaesio, Pristipomoides and Wattsia were characteristic of the intermediate depths (100–200 m) and the deeper outer reef slope waters in excess of 200 m were characterised by species of the genus Etelis.

The effect of mesh size and diel variability in fish trap catch was investigated on the central Great Barrier Reef in order to select an optimal mesh size for ecological studies of lutjanids (snappers) and lethrinids (emperors). Four mesh sizes, 12.5 mm square, 30 mm hexagonal, 40 mm hexagonal and 50 mm hexagonal were examined over two sampling periods (day versus night) yielding a total of 1571 fish representing 70 species from 451 trap hauls. Mesh size had no significant effect on the total catch rate of fish traps. The 40 mm hexagonal mesh size was, however, the preferred mesh size because the size range of target species (Lutjanus and Lethrinus) caught in this mesh was greater than that in the 50 mm hexagonal mesh and the mean catch rate tended to be greater than the 30 mm hexagonal mesh. The mean catch rate in the 12.5 mm square mesh was low relative to the mean catch rates of the other mesh sizes tested and the size range of target species caught in the mesh size were not significantly different from that caught in the 30 mm hexagonal mesh. Diel sampling period had a significant effect on the catch of fish traps. More fish were captured at night, with the lutjanids (78% of total catch) and lethrinids dominating night and day catches, respectively. Mesh selectivity in fish traps was probably not a simple function of the ability of a given mesh aperture to retain individuals of a certain body depth. The behaviour and activity patterns of reef fish in response to the visual outline of the traps was considered of prime importance in the mesh selectivity.

The distribution of fish larvae around Myrmidon Reef in the central Great Barrier Reef was examined on four cruises using a Tucker trawl. On the first cruise, the abundance of reef fish larvae upstream of a coral reef and inside a topographically generated eddy system was compared. No evidence was found of retention of larvae of coral reef species within the eddy. On the second and third cruises, no evidence of significant retention of larvae was found at the site where the eddy had previously been demonstrated. On the fourth cruise, no significant difference was found in the concentration of larvae in sites adjacent to the reef or up to 5 km away, but a large synchronous increase in densities of reef fish larvae across a number of stations was inferred as the arrival of a mixed-species patch of larvae of at least 6 km (two reef diameters) across. These findings support the existence of large, multi-specific patches of larvae of reef fishes previously only inferred from recruitment studies.

Visual censuses were used to survey shallow-water assemblages of the Lutjanidae and Lethrinidae among three mid-continental shelf reefs, and fish traps were used to survey deeper water assemblages below diveable depths. Significant differences were found in visual censuses of the Lutjanidae and Lethrinidae among reefs. Trap catches of the Lutjanidae and Lethrinidae varied more between depths and diel sampling periods than among reefs or over time. Lutjanus carponotatus, L. fulviflamma and Lethrinus miniatus were more abundant in shallow trap sets, whereas Lutjanus adetii, L. russelli, L. sebae, L. vitta, Gymnocranius audleyi, Lethrinus sp.2 and Abalistes stellaris were more abundant in deeper sets. Additionally, Lutjanus adetii, L. fulviflamma, L. quinquelineatus, L. russelli, L. sebae, L. vitta and Lethrinus miniatus were more abundant at night, whereas Lethrinus sp. 2, Abalistes stellarisand Plectropomus leopardus were more abundant during the day. The absence of significant temporal variation in the observed spatial patterns both among reefs and between depths indicates that these patterns may persist through time. The use of both visual censuses and fish traps to assess reef fish assemblages may provide an objective way of repeatedly censusing reefs for monitoring purposes, especially where differences among reefs and regions are important.

Visual censuses were used to quantify the distribution and abundance of the Lutjanidae, Lethrinidae and Serranidae in three reef zones (windward reef slope, lagoon, back reef) of three reefs on the mid shelf and three reefs on the outer continental shelf in the central region of the Great Barrier Reef. Significant spatial variability was identified in the abundances of many species between locations (outer-shelf and mid-shelf communities), between reefs (high-abundance v. low-abundance reefs), and within reefs (characteristic communities within zones on individual reefs). Species of the Lutjanidae, Lethrinidae and Serranidae were found to occur in assemblages that were characteristic of major zones (windward reef slopes, lagoons and leeward back reefs), this pattern being consistent within and among shelf locations. Care will need to be taken in determining the appropriate spatial scales of sampling in any future experiments (e.g. manipulations of fishing pressure) to ensure that the effects of smaller-scale spatial differences are not confounded when larger-scale comparisons are made.

Otolith microstructure was used to characterize growth in five cohorts of larval Herklotsichthys castelnaui from Townsville, north eastern tropical Australia in spring/summer of 1987. Ontogenetic development of larval H. castelnaui is described, and is correlated with changes in otolith microstructure. Development of fin rays coincided with a period of rapid otolith and somatic growth. Otolith increment width and water temperature series were modelled for each cohort using time series analysis. Cross-correlation functions showed no detectable dependencies between increment widths and temperature. Length-at-age relationships were significantly different among cohorts. Repeated-measures analysis of variance was used to establish differences in increment spacing among cohorts. Measurement of otolith radii allowed back-calculation of absolute growth rates of cohorts over the first 30 d of larval life. Significant differences in growth trajectories were detected among cohorts. Data presented here suggest that growth may vary among cohorts separated by as little as 2 wk, and that these differences are detectable by otolith increment analysis.

Coral reef fishes almost universally disperse over relatively great distances during a pelagic larval phase. Barlow (1981) suggested that this dispersal is adaptive because adult fishes inhabit a patchy, uncertain environment. This reiterated an older idea that the random extinction of local populations necessarily favours dispersal, since ultimately all populations of non-dispersers will disappear. Whereas this view is based on adult survival, we emphasize a less frequent view that substantial larval dispersal may be adaptive when offspring experience patchy and unpredictable survival in the pelagic habitat. We do not address the question of why these animals ‘broadcast’ rather than ‘brood’, but suggest that species committed to pelagic offspring will be under selection to disperse siblings to spread the risk of failure among members of a cohort. Our arguments are supported by a heuristic computer simulation.

1. 1. The ocular tissues from 52 species (19 families) of tropical marine fish from the Great Barrier Reef were found to contain variable levels of specific pigments which absorb u.v. light in the spectral region 300—380 nm. 2. 2. These pigments have been identified as the mycosporine-like amino acids: palythine ( λ max 320 nm ), asterina-330 ( λ max 330 nm ), palythinol ( λ max 332 nm ) and palythene ( λ max 360 nm ). 3. 3. Interspecific variations in total lens concentrations ranged from 0.00796 nmol/mg protein (white-tip reef shark) to 2357 nmol/mg protein (scarlet-breasted Maori wrasse); intraspecific variations are small. 4. 4. Several active diurnal surface-feeders had only small concentrations in their lens tissues suggesting that possession of these pigments is not an obligate adaptation to protect ocular tissues from u.v. damage.