Within landscapes, spatial heterogeneity is common and specific landscape features can influence propagule dispersal by wind or water, affecting population connectivity and dynamics. Coastline topographic features, such as bays and headlands, have a variety of biophysical effects on nearshore oceanography, larval transport, retention and supply, and the processes of larval settlement and recruitment. Although this has been demonstrated in several parts of the world, engendering a perception of a general ‘bay effect’, few studies have investigated this generality in a single experiment or region, by replicating at the level of ‘bay’. The Agulhas biogeographic region of the south coast of South Africa is a useful system within which to test for such generality. Using the intertidal mussels Mytilus galloprovincialis and Perna perna as model organisms, patterns of adult distribution were surveyed across four large ‘halfheart’ bays and intervening stretches of open coast, providing replication at the level of ‘bay’ and duplication of ecologically similar species. In support of a general, pervasive influence of bays on intertidal populations, mussel cover was found to be greater in bays than on the open coast for both species, although the effect was strongest for M. galloprovincialis. To explain this adult distribution, settlement, post-settlement mortality and recruitment were examined over 12mo at the same sites, with the prediction that rates of each would favour larger bay populations. Contrary to this, an interaction between month and bay-status was found, with greater settlement and recruitment on the open coast than in bays reflecting extreme settlement and recruitment events at 3 westerly open coast sites during summer. Re-analysis excluding these outliers, revealed the expected effect, of greater settlement and recruitment in bays. While this indicates the broad generality of the bay effect, it highlights exceptions and the need for replication in time and space when examining landscape effects. Measuring post-settlement mortality required testing small-scale settlement behaviour on established and newly deployed settler collectors. It was found that all settlers preferred collectors with biofilm, but that primary settlers avoided conspecific settlers, while secondary settlers were attracted to them. With discrepancies in settler attraction to new and established collectors accounted for, initial (over 2d) and longer-term (over 7d) post-settlement mortality rates were found to be substantial (ca 60 %) for both species. No topographic effect on p-s mortality was evident. Finally, recruit-settler, adult-recruit and interspecies correlations were examined at regional and local scales. Synergistic (or neutral) effects maintained the initial settlement pattern in recruit and adult populations regionally, but not at local scales; striking interspecies correlations suggested the influence of common regional transport processes. Ultimately, the results emphasize the importance of the direction of effects in different life stages and at different spatial scales, and the possibility that antagonistic effects may mask even strong patterns.

Epibiosis is an ecological relationship that has been described as one of the closest possible associations in marine ecosystems. In the space limited rocky intertidal, mussel beds provide important secondary space for barnacles. The epibiotic relationship between mussels and barnacles on the south-east coast of South Africa was considered at different scales, from large-scale, natural patterns of epibiosis on the rocky shore, to fine-scale settlement choices of barnacles and the effects on the condition and growth rates of individual mussels. Mussel and barnacle assemblages were generally stable over a 12-month period. The tracking of individual mussels with and without barnacle epibionts resulted in a significant increase in mortality rate of mussels with epibionts over 12 months (two-way ANOVA, p = 0.028). Barnacles on rocks, as well as on mussels, were also tracked with no significant effect of substratum on mortality of barnacles (two-way ANOVA, p = 0.119). Prevalence and intensity of barnacle infestations was also examined in relation to coastline topography on two co-occurring mussel species, the indigenous Perna perna and invasive Mytilus galloprovincialis. The results were complex, but bay status had significant effects on prevalence and intensity for both mussel species, depending on the time and zone. The effect of bay in relation to time was particularly relevant for M. galloprovincialis (four-way nested ANOVA, Season X Site(Bay): p = 0.0002), where summer prevalence was higher than that of winter in bays, regardless of zone, while in open coast sites, the effect of season was only significant in the mid zone. Patterns of intensity generally showed higher values in summer. Substratum preference by barnacles was investigated by recording settlement, survival and mortality of Chthamalus dentatus barnacles on various treatments. There was a strong preference for the rock-like plastic substratum by primary settlers (pair-wise tests of PERMANOVA: Dead < Rock mimic (p = 0.0001); Replica < Rock mimic (p = 0.019) and Live < Rock mimic (p = 0.0001)). This indicates that barnacles settle on mussel shells only as a secondary choice and that micro-topography is an important variable in barnacle settlement. The effect of barnacle epibiosis on condition index and growth of P. perna and M. galloprovincialis was also examined as a direct indication of the health of mussels subjected to the biological stress of epibiosis. Although not significant (PERMANOVA: P. perna: p(perm) = 0.890; M. galloprovincialis: p(perm) = 0.395), growth for both mussel species was slower for barnacle-infested individuals in summer, which is the main growing season for mussels in the region. Results from condition index calculations, however, showed no negative impacts of epibiotic barnacles (three-way ANCOVA: P. perna: p = 0.372; M. galloprovincialis: p = 0.762). Barnacle epibionts create a new interface between the mussel and its environment and this interaction can affect other members of the community. The possibility of the barnacle epibiont causing increased drag also needs further investigation. Biological processes operating within a wide range of physical stressors drive the interactions on the rocky shore, such as epibiosis. Overall, the results of this study suggest that the epibiotic relationship between mussels and barnacles on the south-east coast of South Africa does not significantly affect the mussel species present and that barnacles only use mussel shells as a secondary choice of substratum.

Mussels play an important supplementary role in the diet of local communities on the Transkei coast in the Eastern Cape province of South Africa. The exploitation of mussels date back to about 1350 years ago, but in the last 3 decades, exploitation of the brown mussel Perna perna has become unsustainable with mussels collected as small as 30-40mm when they are only just sexually mature. Dye and Dyantyi (2002) developed a technique to rehabilitate areas denuded of adult mussels. The government sponsored Mussel Rehabilitation Project (MRP) to use this technique but only some sites have been successfully rehabilitated, reaching c. 80 % cover within a year whilst others only reach about 5%. At an unexploited site (Riet River), I tested the effects of mussel size and wave strength on the effectiveness of the rehabilitation technique, hypothesizing that different size classes may respond differently due to differences in their energy allocation (growth vs reproduction), while wave action determines food supply. Small (1-2cm) and large mussels (3-4cm) were deployed for rehabilitation at 2 exposed and 2 sheltered sites, separated by 100s m. A similar study was repeated in Coffee Bay where shores are exploited. Six sites were selected, 3 sites that had been successfully rehabilitated and 3 that were unsuccessful according to the MRP. Again, two size classes were used but these differed from the first experiment. Mussels of 3-4cm size were now rated as small and 5-6cm as large. Two methods were used to re-attach mussels, the original and the same method with the addition of mesh bags during mussel deployment. Treatments were examined on three occasions at approximately one month intervals. At Riet River, the sites chosen did not show differences in wave strength (measured using dynamometers) or water flux (measured using erosion of cement balls) so that water motion was excluded from the analyses. Small mussels grew faster and had weaker attachment than large mussels. There was no difference in condition index between small and large mussels, or in the numbers of recruits settling among the byssus threads of deployed mussels of the two size classes. In Coffee Bay, there was no relationship between rehabilitation success and maximum wave force, and no difference in bulk water flux among sites. Small mussels deployed using mesh bags survived better than non-meshed or large mussels of either treatment. There was no difference in condition index (CI) between mesh and no-mesh, or between small and large mussels. As in the case of Riet River, small mussels grew faster than large mussels, but large mussels attached stronger than small mussels, with no effect of mesh. Although the factors that improve reseeding of mussels can be identified (use of mesh, use of small mussels, choice of sites with high recruitment rates), successful long-term rehabilitation requires appropriate subsequent management of re-seeded sites.

Landscape ecology helps in predicting the influence of habitat fragmentation on populations. Marine protected areas (MPAs) are expected to create areas of good quality patches and so improve connectivity among shores. MPAs are believed not only to protect adult populations, but also to enhance recruitment both within MPAs and on surrounding exploited shores, therefore improving their ability to recover from overexploitation. As such, MPAs are a preferred management tool for the conservation of natural populations. Although MPAs have been demonstrated to enhance adult abundances, little work has been done on their ability to provide so called "spill-over" of recruits nor has the generality of the influence of MPAs been investigated in a single region with multiple control sites. The Transkei region, on the east coast of South Africa, and the intertidal mussel, Perna perna, offer an ideal system to test the generality of the influence of MPAs on surrounding shores, due to the presence of multiple MPAs and exploited control sites. Patterns of adult abundance were surveyed at four MPAs and two comparably sized exploited control sites. Adult abundances were, in general, found to be higher within MPAs than at exploited control sites, with adult abundances decreasing towards the edge of MPAs and decreasing even more on the outside shores. To simplify the sorting procedure for samples of mussel recruits, a new method using fractionated elutriation was devised and tested. This new method was found to be more accurate, although not statistically significant but also substantially more time consuming. The increase in accuracy although not statistically significant could be biologically significant, especially when looking at low numbers. This new method could, therefore, be very useful especially when [...] is low. Recruitment was estimated over three months during the main reproductive season at two of the MPAs and at appropriate control sites. I predicted that recruitment patterns would mirror the patterns found in adult abundances and that there would be directionality in patterns of recruitment, with northern sites having greater recruitment due to the direction of near-shore ocean currents. Contrary to this, there were no correlations between adult abundance and recruitment for any of the months or sites, with no clear spatial pattern of recruitment in any of the three months. There was, however, a slight trend of greater recruitment at northern sites. To explain the lack of consistency in recruitment and adult abundances, wind data were used to examine the near-shore surface currents in this area, with theoretical surface currents showing similar patterns to those observed for recruitment. From a landscape perspective, the good patches created by MPAs supply recruits to the surrounding matrix but the low quality of habitat in the matrix prevents rehabilitation. The quality of the matrix must therefore be first improved by reseeding these shores. These results emphasise that while MPAs may function in protecting adult abundances, their influence on supplying recruits and hence recovery of near-by exploited shores may be overestimated. This lack of influence on near-by exploited shores highlights the need for reseeding of shores in conjunction with suitable management plans.

Organisms inhabit environments that have many dimensions, each of which can vary temporally and spatially. The spatial-temporal variations of environmental stressors and disturbances may have major but different effects on indigenous and invasive species, favouring either of them at different times and places. The invasive mussel Mytilus galloprovincialis invaded the South African coast 30 years ago and, on the south coast of South Africa, it now competes and co-exists with the indigenous Perna perna in the lower eulittoral zone (referred to here as the mussel zone) The invasive and indigenous species dominate the upper and the lower mussel zones respectively, while the two co-exist in the mid-zone. My results show that intertidal mussels experience, and respond to, spatial and temporal fluctuations of several biotic and abiotic stressors. The invasive and the indigenous species adopt different strategies when reacting to environmental factors and their physiological and behavioural responses vary in time and in different habitats as different pressures become of overriding importance. Attachment strength of both species decreased in summer and increased in winter, and was higher on the open coast than in bays for both species, showing a strong positive correlation with wave force in time and space. P. perna had significantly higher attachment strength than M. galloprovincialis but, contrary to previous studies, the difference in gonad index between the two species varied according to the habitat. In bay habitats, M. galloprovincialis had a higher maximum reproductive effort than P. perna, however, on the open coast, there was no significant difference between the two species, suggesting that for the invasive species wave action is a limiting factor not only in terms of the attachment strength but also of energy availability for reproductive tissue development. Major spawning events occurred during periods of low wave action while minor spawning coincided with periods of intense hydrodynamic stress. On the open coast, gonad index was negatively correlated with attachment strength for both species while, in bays, there was no correlation between these two factors for either. The two species also showed different behaviour. In the field, M. galloprovincialis moved significantly more than P. perna over a period of six months. The higher mobility of the invasive species was also confirmed in the laboratory where, in general, M. galloprovincialis formed clumps more readily than P. perna. Taken collectively, these results suggest that channelling more energy into attachment strength limits reproductive tissue development and that, while the indigenous species invests more in byssal production, the invasive species adopts a more dynamic strategy looking for aggregation or a safer arrangement. Higher endolithic infestation and a greater expression of heat shock proteins (Hsps) in mussel populations on the open coast than in bays indicate that this habitat is a more stressful environment not only in terms of wave action. Endolith damaged mussels had significantly lower attachment strengths and condition indices than clean mussels, probably due to the need to channel energy into shell repair. The constant shell repair and expression of Hsps typical of open coast populations are energetically demanding processes. These observations suggest that on the open coast, mussels are subjected to more severe energetic constraints than in bay habitats. Wave and sand stress fluctuated seasonally with the former having a greater effect on mussel mortality on the open coast and the latter a higher impact on bay populations. Overall, mussel mortality rates were higher on the open coast than in bays. My results show that populations on the open coast had fewer private haplotypes and less genetic endemism than those inside bays. Gene flow analysis showed the relatively stable bay habitats act as source populations with greater genetic migration rates out of bays than into them. These differences in genetic structure on scales of las of kilometers show that coastal configuration strongly affects selection, larval dispersal and haplotype diversity. Environmental gradients that are key factors in species distribution over large geographical scales can also be responsible for micro-scale distributions. My results show that M. galloprovincialis colonizes the upper mussel zone where temperature is high, but is less tolerant to this stressor and has to maintain a high expression of Hsps. This suggests that temperature is probably a limiting factor in its invasion towards the sub-tropical east coast. There are inter- and intra-specific differences in responses to the environment which highlight the efforts of M. galloprovincialis and P. perna to optimize resource utilization for survival and reproduction. Determining these differences is crucial to understanding patterns of co-existence between competing indigenous and invasive species.