This study showed that population differentiation in P. damicornis varied over spatial scales and that this variability occurred at both evolutionary and ecological time scales. This paradox is discussed in light of stochastic recruitment and small scale population structures found in other species of coral. The study also identifies potential source reefs, such as those within Mnemba Conservation area near Zanzibar and genetically isolated reefs such as those within Malindi Marine National Park and Reserve in northern Kenya.

Considering the rapid degradation of coral reefs, it is becoming increasingly important to assess factors such as levels of intraspecific genetic diversity and degree of connectivity between populations and reefs. In this study, five DNA microsatellite markers were used to infer migration patterns and levels of genetic diversity in ten populations of the faviid coral Platygyra daedalea along the coast of East Africa. Populations from reef-slopes and offshore islands had significantly greater genetic diversity, measured as expected heterozygosity and allelic richness than those of inshore lagoonal reefs. A combination of F-statistics and individual assignment tests indicated moderate to high levels of gene flow among lagoonal populations, and less migration between lagoonal sites and the reef-slope and island sites. These results suggest that reef-slope and island reefs could be important reservoirs of genetic diversity for this coral species.

The work presented in this thesis is a study of the spatial genetic structure of two species of scleractinian corals, Pocillopora damicornis and Platygyra daedalea. The overall objective was to investigate the current capacity of MPAs to preserve and restore coral reefs and to contribute information to improve management decisions. Samples were taken from 11 sites along the coast of Kenya. In addition P. daedalea was sampled from one site on each of the islands of Unguja (Zanzibar archipelago) and Mafia in Tanzania.

Populations of P. daedalea were largely panmictic within two lagoonal clusters. Samples obtained from two off-shore sites were more similar to the samples from the island samples in Tanzania than they were to proximal lagoonal samples. Off-shore and island samples were also significantly more genetically diverse in both the level of heterozygosity and allelic richness. Migration predominantly occurs from off-shore and island reefs toward the lagoonal reefs. The investigated populations of P. damicornis exhibited limited genetic neighbourhoods and highly localised recruitment and a significant pair-wise differentiation was found between a majority of the sampling sites. These results are probably a cause of the genetic bottleneck caused by the high mortality of this species during the 1998 coral bleaching event and reflects subsequent founder events and variable recruitment patterns, causing genetically distinct populations.

P. damicornis also displayed plastic reproduction, with some sites being dominated by large numbers of identical multilocus genotypes. The clonal colonies showed signs of being genotypcially distinct as they were all found to be homozygotes for a specific allele at one of the microsatellite loci. Due to the decreased genotypic diversity, associated with the high rate of clonal reproduction, the level of genetic diversity and allelic richness tended to be lower at unmanaged reefs. Also, the probability of encountering clonally produced individuals was significantly greater on unprotected reefs compared with protected reefs.

Canonical discriminant analysis of measurements of ten skeletal characters identified two distinct morphological types of P. daedalea. Analysis of molecular variance showed that morphotype explained a larger proportion of the genetic divergence than did the geographic distribution of sites sampled within MMP. However, phylogenetic analysis of rRNA sequences showed no evidence of sequence divergence, neither between morphotypes nor between samples of P. daedalea from MMP and samples of Platygyra sinensis from Hong Kong.

In summary, these data demonstrate the importance of incorporating multiple species and aspects when addressing the issue of connectivity and its implications for management. P. damicornis would benefit from localised management efforts to preserve its genotypic diversity, whereas P. daedalea would benefit from larger reserves to minimise the risk of loosing rare alleles through genetic drift which would further reduce its genetic diversity on lagoonal reefs. It also brings the subject of morphological characteristics and local adaptation into focus by revealing possible genetic divergence between two morphotypes of P. daedalea and two reproductive modes in P. damicornis.

High intraspecific variability and lack of adequate field descriptions or distinguishing skeletal features has made identification of the scleractinian coral Platygyra daedalea challenging. This species displays a number of distinct morphological types that co-occur on lagoonal reefs in Kenya and which often cannot be separated by field observations. To better understand how morphological and genetic variations are related, morphometric and molecular techniques were used to examine phenotypic variation in P. daedalea. A canonical discriminant analysis of measurements of 10 skeletal characters confirmed the existence of 2 morphotypes. No single diagnostic trait could be used to distinguish the 2 morphotypes, though a combination of 4 characters separated them. A mathematical equation is presented to separate colonies into the 2 morphotypes, where field identification is not possible. Genetic differentiation was studied using 5 microsatellite loci and sequence analysis of the internal transcriber spacer (ITS1 and ITS2) and 5.8S region of the nuclear ribosomal RNA gene. AMOVA of the microsatellite and ITS sequence data showed significant genetic differences between the 2 morphotypes. However, phylogenetic analysis of the ITS sequences showed no evidence of sequence divergence between morphotypes, which suggests that they share a gene pool, or that the genetic divergence is recent. We conclude that the occurrence of distinct morphotypes is a characteristic of P. daedalea and that there does appear to be a genetic basis for separating morphotypes. However, genetic differences in P. daedalea could only be detected when combined with morphometric data.

Here we report the isolation of 44 microsatellites from the brooding, pocilloporid coral, Seriatopora hystrix, developed from a partial genomic DNA library using a repeat enrichment protocol. A further eight previously published microsatellites were also tested; five of these were developed for S. hystrix, whereas three were isolated from corals of the closely related genus Pocillopora. Out of these, we incorporated nine and 10 primer pairs into two multiplex reactions that reliably amplified polymorphic microsatellites in populations from the west and the east coast of Australia, respectively. Number of alleles ranged from three to 22 per locus.

A hierarchical sampling study of the distribution of the large foraminiferan Discobotellina biperforata (Collins, 1958) was conducted along the west shore of Moreton Island, at Shark Spit and Tangalooma, in Moreton Bay, Queensland, between March and June 1995. D. biperforata is disc-shaped, with a test made up of organic matter, reinforced with sand grains. The species exhibits different test morphologies, the most abundant type being the biperforate which has two holes, or lunules, through its test. A less common type is the non-lunulate form, and the multiperforate and crescent-shaped types are rare. Possible abundance-substratum correlations were studied and the results indicated that D. biperforata is strongly correlated to a band of siltier and more organic-rich sediment found at the bottom of sand slopes running off Moreton Island. There was a significant difference in abundance between Tangalooma, where the mean abundance was 11.11 individuals per square meter (SD = 3.63) and Shark Spit, where it was found to be 7.73 individuals per square meter (SD = 3.06). No patchiness was apparent within the areas of siltier and organic-rich sediments. There was no significant difference in the ratio between the different forms within the areas sampled, but a size difference was apparent between locations, with larger specimens found at Tangalooma. The mean size of the specimens found was 27.7 mm in diameter. D. biperforata is the most abundant macrofaunal species in the area studied.