Thesis (Ph.D.) -- McMaster University, 1998. / Includes bibliographical references (leaves 161-170). Also available via World Wide Web.

Thesis (Ph.D.) - James Cook University, 2004. / Typescript (photocopy) Bibliography: leaves 110-130.

Thesis (Ph.D.) - James Cook University, 2004. / Typescript (photocopy) Bibliography: leaves 127-154.

Most of the reef's biodiversity remains undiscovered due to its complex tridimensional structure and the small size of the organisms that compose most of its biodiversity. To better understand the biodiversity of the major biological component of the reef environment (the cryptobiome), artificial cubic-like tools called Autonomous Reef Monitoring Structures (ARMS) were created to mimic the tridimensional nature of coral reefs. Here, I deployed 16 ARMS within four distinct benthic habitats on Tahla reef in the Red Sea (Saudi Arabia) to investigate how changes in reef habitats reflect changes in associated biodiversity of the cryptobiome. The following habitat types were selected after reef surveys and based on benthic coverage prevalence: i) Algae Pavement; ii) Rubble; iii) Plating corals; and iv) Branching corals. Habitats were located at the same depth contour (~10m), under similar exposure conditions and separated by at least 35m. The rugosity of the habitats was estimated based on the chain method, whereas monthly measurements of the physicochemical characteristics of the water were assessed by water collections (nutrients and chlorophyll a) and Conductivity-Temperature-Depth (CTD) instrument deployments (temperature, salinity). A fixed quadrat of approximately 15m2 was marked within each habitat type and four ARMS were deployed randomly within it. Units were retrieved after a period of approximately seven months for analysis of pioneer eukaryotic assemblages through traditional taxonomy identification of organisms larger than 2000μm, and through molecular metabarcoding using COI and 18S markers for the remaining ARMS fractions: sessile, 500μm-2000μm, and 106μm-500μm. To compare two distinct current methodologies to assess cryptobenthic taxa, water collections next to each ARMS unit were conducted right before retrieval. These samples were used to investigate the environmental DNA using the same COI and 18S markers. The biodiversity of the pioneer cryptobiome assemblage was analyzed through a combination of univariate and multivariate statistical methods. Overall, the habitats that showed greatest significantly distinct cryptobenthic community composition were Algae Pavement and Plating Corals, the ARMS and eDNA were defined as complementary techniques to assess the cryptofauna, and the use of a multi-marker approach increased the resolution of the cryptofauna characterization across different reef habitats.

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Patterns of settlement of larvae and population dynamics of juveniles are poorly known for coral reef fishes. During 1987 to 1989, I studied these phenomena in the domino damselfish (Dascyllus albisella), a species endemic to the Hawaiian Islands. Larvae settle onto branching coral heads as new recruits (10-15 mm in length), usually with conspecific groups, and remain on the coral heads through juvenile life until maturity (70 mm total length). By conducting experiments on natural patch reefs and on an artificially distributed grid of coral heads, I found that most larvae settle at night, and that they settle preferentially on corals supporting large conspecific groups compared to small groups or empty corals. Within a group, juveniles form a linear dominance hierarchy based on fish size; aggressive interactions are mainly directed by larger fish towards smaller fish. Tagging studies demonstrated that growth was retarded in larger groups and for fish of low social status, but that survival, especially of new recruits, was enhanced in larger groups. Therefore, I identified both a growth cost and a survival benefit to group living. I derived a measure of net benefit of group living by combining size-specific growth and survival data into an estimate of the probability of reaching mature size. This estimate increased with group size in 1988 but not in 1987. I developed a simulation model which used my field data on settlement rate, settlement preferences, and juvenile growth and survival to predict demography of juvenile groups. The model successfully predicted seasonal fluctuations in mean group size, and estimated the number of fish maturing in 1987 and 1988, as a function of settlement rate and preferences and of juvenile growth and survival. Numbers maturing were directly related to settlement rate in both years, except at high rates in 1987, suggesting that primary recruitment limitation of adult numbers could be occurring. Settlement preferences also influenced numbers maturing. At all settlement rates, numbers maturing differed between years, suggesting that secondary recruitment limitation of adult numbers may also occur. / Graduation date: 1991

Thesis (Ph. D.)--University of Queensland. / Includes bibliographical references.

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