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South Africa has taken an iterative approach to marine ecosystem mapping over 18 years that has provided a valuable foundation for ecosystem assessment, planning and decision-making, supporting improved ecosystem-based management and protection. Iterative progress has been made in overcoming challenges faced by developing countries, especially in the inaccessible marine realm. Our aim is to report on the approach to produce and improve a national marine ecosystem map to guide other countries facing similar challenges, and to illustrate the impact of even the simplest ecosystem map. South Africa has produced four map versions, from a rudimentary map of 34 biozones informed by bathymetry data, to the latest version comprising 163 ecosystem types informed by 83 environmental and biodiversity datasets that aligns with the IUCN Global Ecosystem Typology. Data were unlocked through academic and industry collaborations; multi-disciplinary, multi-realm and multi-generational networks of practitioners; and targeted research to address key gaps. To advance toward a more transparent, reproducible and data-driven approach, limitations, barriers and opportunities for improvement were identified. Challenges included limited human and data infrastructure capacity to collate, curate and assimilate many data sources, covering a variety of ecosystem components, methods and scales. Five key lessons that are of relevance for others working to advance ecosystem classification and mapping, were distilled. These include (1) the benefits of iterative improvement; (2) the value of fostering relationships among a co-ordinated network of practitioners including early-career researchers; (3) strategically prioritizing and leveraging resources to build and curate key foundational biodiversity datasets and understand drivers of biodiversity pattern; (4) the need for developing, transferring and applying capacity and tools that enhance data quality, analytical workflows and outputs; and (5) the application of new technology and emerging statistical tools to improve the classification and prediction of biodiversity pattern. South Africa’s map of marine ecosystem types has been successfully applied in spatial biodiversity assessment, prioritization to support protected area expansion and marine spatial planning. These successes demonstrate the value of a co-ordinated network of practitioners who continually build an evidence base and iteratively improve ecosystem mapping while simultaneously growing ecological knowledge and informing changing priorities and policy.

This thesis investigates the impacts of the demersal trawl fishery on infaunal, epifaunal and fish assemblages in the southern Benguela upwelling system for the first time. In the absence of representative areas of similar habitat protected from trawling in the southern Benguela region, infaunal and epifaunal assemblages were compared between heavily and lightly trawled areas to assess the impacts of the otter-trawl fishery. Infauna were sampled at four sites, from southern Namibia to near Cape Town by means of five replicate grab samples at each paired heavily and lightly trawled area. Invertebrate epifauna were sampled at two sites in heavily and lightly trawled areas using a finemeshed otter trawl. Sites ranged in depth from 350-450 m in unconsolidated sediment habitat. Epifaunal assemblages showed greater differences at heavily trawled areas with significantly reduced species diversity, average number of species and individuals. Several epifaunal species were absent from heavily trawled areas highlighting their vulnerability to impacts of trawling. Multivariate analyses show significant differences in composition of both infaunal and epifaunal assemblages among the sites and between trawling treatments at all sites. The results of this study suggest that intense trawling activities are at least partially responsible for significantly altering benthic community composition, affecting epifauna to a greater measurable extent than infauna. Biological Traits Analysis (BTA) was used to explore potential changes in ecological functioning of benthic assemblages, comparing areas exposed to heavy and light trawl intensities in the Benguela system. BTA incorporates biological traits (life-history, morphology and behaviour) of infaunal and epifaunal species with biomass, capturing a broad range of information of marine benthic assemblages. Seventeen percent of the infaunal traits analysed showed a significant difference between heavily and lightly trawled areas. Twenty-four percent of epifaunal biological traits investigated were significantly different between areas of heavy and light trawling. This study suggests that more intense trawling modifies some trait constituents of the benthic assemblage in the southern Benguela region, confirming the sensitivity of functional traits analysis in detecting changes induced by trawling disturbance. Biological traits analysis of benthic invertebrates shows promise as a practical technique for incorporation into monitoring programmes and for developing indicators of benthic ecosystem health, needed for implementation of an ecosystem approach to fisheries management in South Africa. A lack of representative untrawled areas in the trawl grounds of southern Africa precluded investigations comparing trawl impacts with unfished reference sites. A bilateral agreement between South Africa and Norway (NORSA) provided the opportunity to conduct experiments in an untrawled area of Oslofjord, Norway, where a shrimp trawl fishery for Pandalus borealis operates nearby. Infauna Abstract 2 were sampled at four untrawled sites in Oslofjord with five replicate grabs after which an Agassiz beam sled was dragged across two of the sites (impact sites) four times, simulating a trawl disturbance. Infauna were re-sampled at all four sites immediately after trawling (post-impact), 14 days and 64 days after the impact to monitor recovery of infaunal populations. Multivariate analyses comparing the impact sites with paired control sites for each sampling occasion showed no significant differences in infaunal assemblages at any stage of the experiment. Whilst it is considered possible that the trawl simulation was not a sufficient impact to represent that of a commercial trawl effect, it is considered more likely that trawl activities in Oslofjord do not inflict measurable impacts on infaunal assemblages. However, the impact of trawling on epifaunal assemblages in Oslofjord was not investigated in this study. Annual research survey data collected over the past 24 years (1986-2009) provide an opportunity to explore long-term demersal fish assemblage composition changes on the west coast of South Africa. Differences in spatial (latitude and depth) and temporal (seasonal and annual) factors were examined using multivariate analyses. Possible long-term changes were investigated using the Sequential T-test Algorithm to detect Regime Shifts (STARS). Results indicate geographic differences in fish assemblage composition from the northern to the southern region on the west coast of South Africa. The fish community composition is also clearly influenced by depth with a distinct change in fish assemblages in the shelf break region between 300 m and 400 m. Multivariate analyses also show two clear temporal changes in assemblage composition, firstly, in the early 1990s and secondly, in the mid- 2000s. STARS analyses detect long-term shifts in 27% of demersal species with the majority of speciesâ shifts detected either in the early- to mid-1990s or in the past decade (2002 to 2009). Multivariate analyses among year groups reveal an increase in three fast-growing, early maturing species and decreases in two slow-growing, long-lived species. STARS analysis detected increases in two of the same fast-growing species, decreases in an additional four slow-growing, long-lived species, but four other slow-growing, long-lived species showed the opposite trend (i.e. increases). The hypothesis of an increase in fast-growing, early maturing species and a decline in slow-growing, longlived species in fished systems is therefore only partially supported by these findings. Shifts in demersal fish assemblages coincide temporally with spatial shifts observed in small pelagic species and west coast rock lobster. The shifts in the demersal fish assemblage composition detected in this study are probably a reflection of long-term indirect effects of fishing in combination with environmental changes. Abstract 3 The response of benthic invertebrate assemblages to two levels of fishing intensity in the southern Benguela region justifies regular monitoring of epifauna during existing annual demersal research surveys and infaunal monitoring through dedicated, periodic sampling initiatives. Demersal fish assemblage data should be regularly assessed for changes in community composition. Representative protected areas can serve as reference areas against which fishing impacts could be assessed and improve our understanding of ecosystem effects of demersal fishing.

Bibliography: leaves 93-100., The primary focus of this thesis was to investigate the movement patterns of the South African West Coast rock lobster, Jasus lalandii, using a diverse range of techniques. These were (1) an examination of long-term data from an ongoing tag-recapture program, (2) observations on rock lobsters in a mesocosm aquarium, (3) surveys that monitored the seasonal fluxes in activities and abundance of rock lobsters in the field, (4) video recordings of movement behaviour in small aquaria and (5) acoustically tracking the movements of four individual rock lobsters.

Few studies of rock-lobster diet have included analyses of mature females or juveniles of either sex. This study focused on the diet of male and female West Coast rock lobsters (Jasus lalandii) in three size classes (viz.: 10 - 35 mm CL (carapace length) - small, 40 - 59 mm CL - medium and 70 - 85 mm CL - large), using visual analyses of stomach contents. The principle aims were to examine potential differences in diet between: (1) male and female rock lobsters; (2) changes in diet with size and (3) a comparison of rock-lobster diet between areas of known fast- and slow-growth rates. The primary prey items of rock lobsters are shown to be the black mussel (Choromytilus meridianalis), ribbed mussel (Aulacomya ater), barnacle (Notomegabalanus algicola), sea urchin (Parechinus angulosus), sponge and crustacean remains. There was no difference in diet between male and female rock lobsters within any size class. Bray-Curtis similarity dendograms and Multi-Dimensional scaling plots revealed differences between small, medium and large rock-lobster diets. Small rock lobsters consumed mainly ribbed and black mussels, whereas medium rock lobsters consumed higher percentages of barnacle and sponge. Sea urchins comprised a substantial percentage of large rock-lobster diet. ANOSIM (Primer v 4.0) established significant differences (p < 0.05) among diets of the three size classes. Differences in diet were also observed between areas of fast- and slow-growth rates, but these were limited to the small and medium size classes. Key prey items responsible for this difference in diet were black mussel and rock-lobster remains. The gut fullness index decreased with increasing rock-lobster size. In conclusion, there appears to be no difference in diet between male and female rock lobsters, regardless of their size. However, rock-lobster diet does appear to vary with size. The inverse relationship between gut fullness indices and size, suggests that small rock lobsters, which have a higher moult frequency, feed relatively more frequently than larger rock lobsters. Diet composition plays a role in determining the growth rate of rock lobsters from different areas.

Long-term monitoring of marine benthic communities provides data which are essential for effective ocean management. However, long-term monitoring is limited by the difficulty and expense of sampling deep seafloor areas comprehensively enough to represent the whole benthic community. This has led to the development of a wide array of seafloor sampling methods. Consequently, the integration and prioritisation of data collected using different methods remains an area of concern. Demersal research trawling and grab sampling are two methods employed to sample the marine benthos in South Africa, targeting different habitats and fauna, at different scales and with different sampling efficiencies. Both datasets inform the national marine ecosystem classification, yet the consistency between biodiversity patterns detected by each sampling method has not yet been explored. The aim of this thesis is to determine the influence of sampling method on the detection of benthic biodiversity patterns. This was explored using demersal trawl and grab datasets collected from twenty-four pairs of stations within the Southern Benguela Shelf ecoregion on the west coast of South Africa (70 – 600 m) between the years 2009 and 2020. Differences in benthic structure, univariate diversity indices, and multivariate assemblage structure were compared between demersal trawl and grab datasets using both taxonomic and trait-based approaches. This study utilised the rarely applied co-correspondence analysis (CoCA) to test for congruency in multivariate assemblage patterns sampled by trawls and grabs. Furthermore, the use of Biological Traits Analysis (BTA) allowed for the assessment of functional diversity patterns which is often a missing link when measuring biodiversity relative to ecosystem functioning. The epifaunal community was dominated by Asteroidea, Decapoda and Gastropoda, whereas Polychaeta, Amphipoda and Bivalvia dominated infaunal communities. BTA found trawl samples to be dominated by epifauna exhibiting large sizes, dorso-ventrally flattened body forms, free-living and surface-crawling life habits, moderate mobility, predatory feeding, planktotrophic larval development and medium-long lifespans. Grab samples were dominated by infauna with small sizes, vermiform or laterally flattened body forms, low mobility, surface deposit feeding strategies, planktotrophic larval development and short lifespans. Demersal trawl and grab sampling detected significantly similar patterns in species abundance, species richness, species diversity, and functional richness values across the west coast. Species evenness, functional evenness, functional diversity, and functional redundancy gave no evidence of a significant relationship between the two sampling methods. CoCA found infaunal assemblage patterns to be highly correlated with epifaunal assemblage patterns across the study area using both taxonomic and trait-based approaches. Environmental and spatial gradients, including depth, longitude, and sediment characteristics, played key roles in structuring broad scale biodiversity patterns. The results of this thesis have implications for how biological datasets from trawl and grab surveys should be prioritised or weighted at different ecological scales when incorporated in the South African marine ecosystem classification and mapping process. This is the first step in transitioning the current ecosystem classification from a data informed, expert driven approach to an expert informed, data driven approach through the use of quantitative multivariate statistical techniques. Furthermore, multi-method biodiversity studies are crucial to represent the entire benthic community and understanding the extent to which the choice of sampling method affects the biodiversity patterns detected is an integral component of accurate ecosystem delineation. The findings from this thesis can be applied to future assessments of South Africa's marine ecosystem classification, increasing its accuracy, and therefore contributing to improved ecosystem-based sea-use management.

Deep-sea benthic ecosystems remain poorly studied in South Africa, limiting understanding of community biodiversity patterns and their environmental drivers. This is one of the first studies to (i) visually investigate marine epifaunal community patterns and their environmental drivers along the Agulhas ecoregion outer shelf, shelf edge and upper slope to support marine ecosystem classification and mapping, and (ii) to determine the conservation targets for selected national marine ecosystem types to inform improved management of the marine environment, through Marine Spatial Planning processes. Visual surveys of the seabed were conducted to quantify epifauna during the ACEP Deep Secrets Cruise in 2016, using a towed benthic camera system. Twenty-nine sites were sampled, ranging from 120-700 m in depth and spanning the shelf-slope transition from the western edge of the Agulhas Bank to offshore of the Kei River mouth. A total of 855 seabed images were processed, and 173 benthic taxa quantified. Corresponding environmental variables were used to determine potential drivers of observed biodiversity patterns. Data were analysed using multivariate analyses, including CLUSTER, MDS and DistLM, in PRIMER v6 with PERMANOVA. Ten different epifaunal communities were classified and described with key characteristic taxa identified. Communities found in habitats that comprised mostly hard rocky substrata generally exhibited higher in species richness and were most commonly characterized by stalked crinoids, various corals and bryozoans, whereas communities found in habitats comprising unconsolidated sediment were lower in species richness and commonly characterized by polychaetes, cerianthids and brittle stars. Communities found in habitats comprising both hard and soft substrata had a mix of the above-mentioned epifauna. The distribution of these communities was mostly influenced by substratum type, longitude, trawling intensity, depth, and presence of visible particulate organic matter. The combined interactions of topography, substratum and the unique hydrodynamic conditions along the Agulhas ecoregion shelf-slope transition are likely responsible for the observed patterns. The observed community patterns were also compared to the existing classification of marine ecosystem types from the 2018 National Biodiversity Assessment. Fine-scale heterogeneity was revealed within the examined marine ecosystem types, particularly with substratum type and associated community variability and should be recognized and incorporated into future iterations of the national marine ecosystem classification and map. Species-area curves were used to calculate conservation targets for three ecosystem types, defined by the 2018 National Biodiversity Assessment, namely the Agulhas Coarse Sediment Shelf Edge, South West Indian Upper Slope, and the Agulhas Rocky Shelf Edge. Considering the epifaunal species richness (using the bootstrap estimator) and area, per image and per ecosystem type, the rate of accumulation of species was calculated and used to estimate the percentage of species expected to be represented by any given percentage of protected ecosystem type area. Between 20 and 30% of the area within these ecosystem types will need to be protected to represent 80% of the species. This study has shown that an integration of environmental parameters together with biodiversity measures to better understand and classify offshore benthic ecosystems has worked well. However, to improve the resolution of the national marine ecosystem classification and map, there needs to be greater input of fine-scale biological and environmental sampling and mapping of substratum types across the Agulhas ecoregion shelf-slope transition zone. This work is contributing to improvements in the national marine ecosystem classification and map and hence the spatial assessment and planning processes that rely on these products.

Marine unconsolidated sediments, such as sand, gravel and muds, constitute the most extensive benthic ecosystems globally. Biological data for these ecosystems are frequently sparse which can hinder the success and implementation of marine management strategies for benthic ecosystems. There are limited studies in South Africa on benthic epifauna. This study investigates the composition and distribution of epibenthic invertebrate assemblages along the west and south coast of South Africa (sampled using depth-stratified demersal trawls) to inform marine environmental management. Sample depth varied from 36m to 899m. Multivariate tools (PRIMER and PERMANOVA+) were used to analyse spatial (west vs south coast) and temporal (2011 vs 2017) patterns in epifauna. This study also investigated an overlap region between the west and south coast. A group average linkage cluster analysis defined biotopes using significant branching (p< 0.05). Biotopes were compared against the 2012 National Biodiversity Assessment (NBA) benthic habitat map to investigate whether epifaunal biotopes identified, align with the existing classification. A significant difference among epifauna between region and depth was found, where the west coast had a higher average number of individuals and species per station. Sympagarus dimorphus and Pelagia noctiluca were characteristic species for west and south coast respectively. Epifauna was found to be significantly different between 2011 and 2017, with a notable increase in the abundance of Crossaster penicillatus in 2017. The majority of the biotopes aligned with the current NBA classification, in particular the Agulhas Sandy Shelf Edge ecosystem type on the south coast and South Atlantic Upper Bathyal and Namaqua Muddy Inner Shelf ecosystem types on the west coast. This thesis contributes to the mapping and description of offshore ecosystem types to inform marine environmental impact assessments, marine spatial planning and marine protected area expansion.

The habitat associations between the caridean shrimp Nauticaris marionis and sessile epibenthic assemblages and substratum types of the Sub-Antarctic Prince Edward Islands were investigated. Twenty five stations, varying in substratum type, depth and location on the shelf and slope around the islands were sampled photographically with a towed benthic camera sled. At each station the substratum type was classified, sessile epibenthic cover was quantified through the use of digital quadrats and shrimp density was estimated. Results add to the broadly described distribution patterns of N. marionis by identifying specifically the habitat characteristics they generally utilize. The distribution of N. marionis was found to be influenced by a combination of substratum and sessile epibenthic assemblages, but not substratum type alone. Shrimp inhabited stations with >50 % biogenic cover on mud and gravel substrata, but were not found at stations with rocky-sand or rocky-mud substrata. Their distribution appears to also be influenced by depth, as shrimp were only found within a depth range of 50 - 160 m in this study. A strong correlation was found between N. marionis density and depth. Shrimp were found both inshore around the islands, and on the relatively shallow saddle between the islands. In comparison with previous studies, N. marionis was found at similar, if not higher, densities in this study, although they occupied a narrower depth range.