Browsing by Author "Griffiths, Charles"

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    A taxonomic revision of the squat lobsters (Anomura: Chirostyloidea and Galatheoidea) of South Africa
    (2025) Botha, Thomas; Griffiths, Charles
    South African squat lobsters (Chirostyloidea and Galatheoidea) are a severely understudied group. They have never been the subject of a formal monographic study and the last additions to the fauna were made almost 20 years ago. Thus, a revision of these superfamilies is long overdue. This study relied on examination of historic material housed in the Natural History Collections of the Iziko South African Museum, as well as ad-hoc sampling to carry out morphological analyses and molecular barcoding where possible. These methods were used to add to, revise and update the regional fauna. The thesis is presented in the form of six chapters, four of which each revise one of the families of squat lobsters present in South Africa and provide an illustrated key to the known regional species in that family. These chapters are supported by an introduction and synthesis chapter and a reference list. The first revisory chapter covers the Chirostyloidea (Chapter 2), and includes redescriptions of four species, reports on one species (and genus) from South Africa for the first time and expands the distribution and depth range for Uroptychus simiae. The third chapter describes two new species of Galatheidae, adds three species (and a genus) to the regional fauna list and resolves several dubious records. Galathea labidolepta Stimpson, 1858 is also redescribed and a neotype assigned, as the holotype was lost in the 1871 Chicago fire. The Munididae are revised in the fourth chapter, wherein two new species are described, seven species (four of which are new generic records for South Africa) are added as new distribution records, while five species are redescribed, two of which were previously only known from brief descriptions. The fifth chapter revises the deep-dwelling Munidopsidae and redescribes two species. This study marks the largest ever contribution to the South African squat lobster fauna with 15 species being added, comprising four new species and 11 new distribution records, while two species are removed due to synonymy. This increases the number of South African squat lobster species from 32 to 45. In the process, six genera are also reported on for the first time. Illustrated redescriptions are given for 12 species that were known from outdated or inadequate descriptions. Where possible, DNA sequences were produced as part of an integrative approach to delineate species, and this is the first study to provide such genetic data on South African squat lobsters, with 28 barcodes provided for eight species. Though this study adds valuable knowledge to this important group, it also highlights the need for more rigorous sampling, as more than half of the species are known from just a single sampling event and almost certainly more species remain to be discovered from the region.
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    Aspects of population biology and behaviour of mobulid rays
    (2023) Carpenter, Michelle; Griffiths, Charles
    Manta and devil rays (Mobula spp.) are charismatic yet threatened species that remain poorly understood. The Inhambane Province in Mozambique is known to be home to the largest populations of manta rays in Africa, including the reef manta ray (M. alfredi) and the oceanic manta ray (M. birostris). However, research on other mobulid species, and in the region south of Tofo, including Závora in Mozambique and South Africa, has been limited. This thesis identifies critical sites and describes their characteristics, including habitat use, population abundance, and behaviour, for three species of mobulids: M. alfredi, M. birostris, and the shortfin devil ray, M. kuhlii. Chapter 1 comprises a literature review on the status and knowledge on mobulids in a global context, and within the southern African region, with focus on M. alfredi and M. birostris, due to the increased amount of information available on these species. Chapter 2 provides detailed information on the methodologies used throughout the thesis, some of which overlap. Chapter 3 utilises an 11-year photographic mark-recapture dataset spanning from 2010-2021 to investigate the size and structure of the M. alfredi population that aggregate at 'Red Sands' (RS), a reef cleaning station located at Závora, Mozambique. A total of 583 individual M. alfredi were identified using photographic mark recapture (photo-ID) of the unique ventral spot patterning. Pollock's Robust Design models were used to estimate annual abundances, emigration, annual apparent survival, and capture probability at RS during peak season, July-November, between 2016-2021. The resulting abundance estimates varied each year, with a range of 35 individuals (95% CI 30-45) up to 233 individuals (95% CI 224-249). Lagged Identification Rates were additionally used to describe the residency patterns of M. alfredi at Red Sands, revealing that despite site affinity to RS, individuals were overall transient within a given season, with an average residency of four days. Chapter 4 applies the methods used in Chapter 3 to report on South Africa's first photo-ID dataset for manta rays, including both M. alfredi and M. birostris, spanning from 2020-2022. Through the use of citizen science photographic donations and opportunistic snorkelling and diving, were used to document manta ray aggregation sites in the KwaZulu-Natal (KZN) Province. These same data were used to further document connectivity of M. alfredi between Mozambique and South Africa, revealing that at least 20% of all photographed individuals in South Africa had made international migrations to or from Mozambique. The distances travelled ranged from 435 km and 1,000 km, between the Aliwal Shoal Marine Protected Area (MPA), KZN and Závora, the second longest known migration for this species. Additionally, previously undocumented aggregations were found, including M. alfredi at the iSimangaliso Wetland Park and possibly M. birostris at Ballito. Aggregations in KZN were primarily related to surface feeding, with cleaning and courtship behaviours also documented. Chapter 5 analyses a 41-year catch dataset (1981-2021) provided by the KZN Sharks Board bather protection programme to investigate broad spatial-temporal trends in catch for manta rays (M. alfredi, M. birostris). Using Generalised Additive Models and the probability of encounter, the effects of annual and seasonal factors, moon phase, and location on catch rates are assessed. The size composition and demographics of the caught manta rays and the catch per unit effort at different beaches are also examined. The results revealed a significant decline in overall catches around 2000 (p<0.0001). Catches increased in summer, indicating seasonal visitation to South African waters. Moon phase had an effect on manta ray presence, with more catches during new and full moon phases. Over half of the catches included juveniles, whereby a total of 841 individuals (52% of total catch) of confirmed juvenile size class (1400-2500 mm disc width) were caught, particularly in the southernmost sampled area, from Hibberdene in the north to Mzamba in the south. Chapter 6 investigates a previously undocumented aggregation of M. kuhlii in the Aliwal Shoal MPA, and their cleaning behaviour by the bluestreak cleaner wrasse, Labroides dimidiatus. The study documented M. kuhlii sightings, behaviours, and associated environmental conditions during recreational snorkelling/diving. Generalised additive models (GAMs) were used to assess predictors of M. kuhlii presence and cleaning behaviour duration. The results showed that M. kuhlii were present in 56% of the survey days, with up to 150 individuals observed. The study recorded a total of 4.04 hours of M. kuhlii cleaning behaviour which was processed using frame by frame analysis. Sea surface temperature was found to be a significant predictor for M. kuhlii presence, while the absence of current and estimated horizontal visibility were significant predictors for longer cleaning durations. During recreational diving in the Aliwal Shoal MPA, first-time observations of M. kuhlii courtship were unexpectedly encountered and videoed in November 2020 and January 2021, which are detailed in Chapter 7. The common behaviours associated with mobulid courtship were documented: multiple males following a single female, rapid speed bursts, avoidance of the female, and swerving, which confirmed that M. kuhlii mating occurs in KZN waters. The collective results are concluded in Chapter 8, which indicate that both Závora and KZN waters provide important seasonal habitat for mobulid species along the southern African coastline. The findings of this work support other studies that show manta rays to use an expansive area, with seasonal affinities to certain locations, and transience during periods when conditions are not favourable for visitation. This demonstrates the importance of understanding site use within the larger home range of a given mobulid population. Therefore, this thesis has filled critical knowledge gaps and improved the overall understanding of mobulids in southern Africa, providing valuable information for conservation management efforts.
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    Between a bass and a hard place: the fragmented distribution of an endangered redfin in the Heuningnes River System of the Cape Fold Ecoregion
    (2024) Morch, Casper; Griffiths, Charles; Cunningham Susan
    Native freshwater fish are globally in decline due to anthropogenic impacts, including changes to water quality, over-abstraction, climate change, and introduction of nonnative species. The Cape Fold Ecoregion (CFE) of South Africa is recognised as a hotspot for freshwater fish endemism. It is also recognised as one of six hotspots for freshwater fish invasions. Hence, 36% of native and 66% of endemic freshwater fish are considered threatened (vulnerable, endangered, or critically endangered). The Heuningnes redfin (Pseudobarbus sp Burchelli Heuningnes) is one such fish. It is considered endangered (SANBI Red List of Threatened Species) and currently occupies a small number of tributaries within the Heuningnes River System (HRS). The Heuningnes redfin co-occurs with Cape kurpers and Cape galaxias, some of which are currently being described as new and unique lineages. As such, the HRS is of critical conservation significance. This study analysed a data set collected by Keir Lynch in March of 2018, that consists of 22 water quality, geographic, and habitat-related environmental variables. The goal was to determine whether the distribution of native fish is independent of the distribution of non-native fish, as well as what environmental variables best predict the presence and abundance of Heuningnes redfin in the HRS. The data suggest non-native species appear to be excluding native species from invaded reaches. Moreover, redfins prefer warmer, more acidic water with complex habitats in the form of woody debris and gravel substrate, allowing them to hide from predators. Their abundance is negatively correlated with phosphorous, which may indicate that they are affected by pollution from agricultural runoff. Moving forward, conservation practitioners should consider non-native eradication projects, through either chemical or mechanical removal. Additionally, they should also consider creating a buffer of indigenous vegetation, which could mitigate the impacts of agricultural effluents and provide benefits for the currently endangered renosterveld. Additional surveys are necessary to determine the exact extent bass have invaded the system, as well as to obtain an accurate measure of how different land uses are affecting the distribution of native fishes.
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    Ecological impacts of invasive mussels (Mytilus galloprovincialis) colonising the canopy of kelp forests in False Bay, South Africa
    (2018) Lindberg, Colleen; Griffiths, Charles; Anderson, Robert
    Kelp forests are amongst the most productive, diverse and dynamic ecosystems on earth and kelp are ecosystem engineers, which provide a structurally-complex habitat for many marine plants and animals. The Mediterranean mussel (Mytilus galloprovincialis) is an aggressive invader that has been in South Africa since the late 1970s, and does not normally occur in the subtidal zone, however in 2016 this mussel was first observed growing on the heads and stipes of kelp plants (Ecklonia maxima) in False Bay, South Africa. The overall aim of this project was to gain a better understanding of the ecological impacts of the invasive mussel colonising the canopy of kelp forests in False Bay. It was found that M. galloprovincialis were more likely to occur on the outer edge of kelp beds, where there is more water movement, and mussel masses are much more frequently found on kelp heads than on stipes. In addition, mussels infecting the kelp beds were likely younger than three years, indicating that colonisation has been a recent event. While the buoyancy of kelp plants was reduced by the invasion of mussels, it was not enough to sink most kelp plants. The mussel masses created habitat that increased species richness on both infected heads and stipes, and six species that are alien to the Western Cape were identified on the infected kelp plants. As detached kelps can raft vast distances, there is thus potential to spread not only alien species, but also native South African species to locations where they could become invasive. Lastly, a new species of amphipod that burrows into the primary blades of kelp heads was discovered during the course of the study. Further investigation is required to determine if the infection rate of kelp forests in False Bay is increasing and whether this phenomenon occurs in other locations.
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    Marine ecosystem classification and conservation targets within the Agulhas ecoregion, South Africa
    (2022) Nefdt, Leila; Karenyi, Natasha; Griffiths, Charles; Sink, Kerry; Atkinson, Lara
    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.
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    Molecular and morphological factors contributing to the resolution of the taxonomy of Octopus vulgaris Type III
    (2024) Fee, Gareth; Griffiths, Charles
    Cryptic species are common in the marine environment, particularly among invertebrates. The genus Octopus Cuiver, 1797 is considered a ‘catch all' genus due to the lack of morphological traits available to distinguish closely-related species. In recent years, the Octopus vulgaris species complex has received much attention with many cryptic species ‘Types' being identified, most of which have now been re- or newly described as separate species. The last remaining Type currently known within this complex which requires taxonomic resolution is the Southern African lineage, Octopus vulgaris Type III. This taxon was not included in a recent global morphological assessment of the complex and few specimens were included in phylogenetic studies. Mitochondrial barcodes failed to distinguish O. vulgaris Type III from O. vulgaris sensu stricto (ss), but nuclear genes did. This dissertation aims to resolve the taxonomy of O. vulgaris Type III using both genetic and morphological lines of evidence. Chapter 1 gives a broad background to the cryptic species problem within cephalopods and discusses the significance of resolving the taxonomy of O. vulgaris Type III. Chapters 2 and 3 sequence and annotate the first complete mitochondrial genomes (mitogenomes) of O. vulgaris ss and O. vulgaris Type III respectively. Chapter 2 also includes a phylogenomic assessment and found O. vulgaris Type III to be a sister taxon to O. vulgaris ss, separated with high statistical support. Chapter 4 presents a detailed morphological assessment of O. vulgaris Type III, which successfully delimit it from all other species within the species complex. Finally, Chapter 5 summarises these findings. These results have significant implications, considering the growing octopus fishery in South Africa, as management should consider the population as an isolated species, distinct from O. vulgaris ss, which is found in the Mediterranean and Northeast Atlantic.
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    Particle size and biotic composition on Western Cape shores, including first description of the unique fauna of pebble and cobble beaches
    (2021) Robbins, Amanda; Griffiths, Charles
    Intertidal ecology research has focused primarily on sandy (grain size < 2mm), granule (2 –< 4mm), pebble (4 –< 64mm) or cobble (64 –< 256mm) shores, and only one on the biota of boulder (256+mm) shores. This study samples intermediate shore types (1 – 256mm) within the Western Cape for the first time and compares these with published data on other Western Cape shores to determine how many distinct habitat types occur across the full spectrum of particle sizes with a focus on describing the unique fauna of pebble and cobble shores. Chapter 1 reviews the literature to date on well-studied shore types including sandy and rocky shores, and explores the limited ecological research on shore types ranging from 1 – 256mm, while both data chapters use sample data to complete the study aim. Sampled shores were surveyed using a 20 x 20cm quadrat placed at eight tidal levels along a transect from low to high shore and species collected were identified, counted and wet-weighed. Chapter 2 also used extractions from previously sampled data which included species presence, biomass and abundance per site (where available). All biomass records were converted to wet weight using published conversion factors. Chapter 2 analyzes data from 58 sites in the South-Western Cape, with data for 42 sites derived from eight previous studies, while 16 sites were sampled as part of this study. Three main groupings of sandy shores (1 – 256mm) and boulder and rocky shores (>256mm) occur. Similar to other shores within the spectrum, shores of intermediate particle grain sizes (1 – 256mm) are affected by heavy wave action, among other driving factors. Heavy wave action against intermediate grain sizes which do not have the stability of larger boulders or rocks, or the compacted nature of smaller grain sizes which can be burrowed into to protect biota, results in rough living conditions only few species can endure, as such these shores have a similar biotic composition. A polarization of species presence occurs amongst the two ends of the spectrum with mobile taxa occurring across particle grain size shores between 0.125 – 256mm, but concentrating on smaller grain sizes (256mm. Chapter 3 examines a total of 12 sites in the South-Western Cape, composed of seven pebble and five cobble shores. Of 39 taxa collected on these shores only 14 species occurred more than once and were thus considered typical of pebble and cobble shores. These were mostly air-breathing species, primarily Arthropoda and a single species of pulmonate Gastropoda. Macroalgae were notable in their absence. Unlike the burrowing species of sandy shores, or the attached species of rocky and boulder shores, pebble and cobble shore species all tended to be motile, no doubt to avoid the rolling grains. Unlike most other intertidal shores, the fauna was also concentrated towards the high shore, where food was available in the form of drift kelp, although, as some airbreathing species were found in the low shore, it is presumed some such species migrated well into the intertidal at low tide, presumably retreating back above the high-water mark at high tide.
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    Residency, habitat use and sexual segregation of white sharks, Carcharodon carcharias in False Bay, South Africa
    (Public Library of Science, 2013) Kock, Alison; O'Riain, M Justin; Mauff, Katya; Meÿer, Michael; Kotze, Deon; Griffiths, Charles
    White sharks ( Carcharodon carcharias ) are threatened apex predators and identification of their critical habitats and how these are used are essential to ensuring improved local and ultimately global white shark protection. In this study we investigated habitat use by white sharks in False Bay, South Africa, using acoustic telemetry. 56 sharks (39 female, 17 male), ranging in size from 1.7-5 m TL, were tagged with acoustic transmitters and monitored on an array of 30 receivers for 975 days. To investigate the effects of season, sex and size on habitat use we used a generalized linear mixed effects model. Tagged sharks were detected in the Bay in all months and across all years, but their use of the Bay varied significantly with the season and the sex of the shark. In autumn and winter males and females aggregated around the Cape fur seal colony at Seal Island, where they fed predominantly on young of the year seals. In spring and summer there was marked sexual segregation, with females frequenting the Inshore areas and males seldom being detected. The shift from the Island in autumn and winter to the Inshore region in spring and summer by females mirrors the seasonal peak in abundance of juvenile seals and of migratory teleost and elasmobranch species respectively. This study provides the first evidence of sexual segregation at a fine spatial scale and demonstrates that sexual segregation in white sharks is not restricted to adults, but is apparent for juveniles and sub-adults too. Overall, the results confirm False Bay as a critical area for white shark conservation as both sexes, across a range of sizes, frequent the Bay on an annual basis. The finding that female sharks aggregate in the Inshore regions when recreational use peaks highlights the need for ongoing shark-human conflict mitigation strategies.
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    Testing the use of port biological baseline surveys to support relevant marine alien species management applications in Africa
    (2018) Awad, Alexander Adnan; Griffiths, Charles
    The prevention of non-native marine species introductions is the first line of defense in the management of alien invasive species problems occurring on coastlines around the world. Ports and the shipping industry have been targeted as a sector requiring increased attention and regulation to reduce the significance of the ballast water and biofouling pathways. Ballast water management (BWM) processes have matured significantly at international levels over recent decades, with the support of the International Maritime Organization (IMO) and its BWM Convention. The development of baseline species and environmental data for port areas is increasingly recognized as a foundational step in managing ports and ships with respect to potentially harmful species transfers. Several countries have been conducting port biological baseline surveys using protocols developed at the Centre for Research on Introduced Marine Pests (CRIMP) in Australia, which has become the recommended approach at the IMO for developing countries tackling this issue. This study applies the CRIMP methodology for conducting comprehensive baseline surveys in three key African ports to examine the relevance for practical and effective management outcomes. Lessons learned through survey implementation were consolidated into a set of guidelines for conducting port surveys in developing regions. The generation of species and environmental data allowed for investigation of methodologies for shipping-focused risk assessment for new species introductions. Furthermore, the ability of risk assessment processes to support decisions for Port State Control measures related to BWM was tested though the development of a ship-specific decision support system. Where the presence of a potentially problematic species has been recorded, the role of species-specific risk assessment was also considered. The European Green Crab Carcinus maenas, presently found in isolated bays of South Africa was assessed with respect to the validation of management concerns related to the likelihood for further spread and impact, especially to the valuable aquaculture sector.
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    The Burrowing Barnacles (Cirripedia, Acrothoracica) of South Africa
    (2019) Botha, Thomas Petrus Arnoldus; Griffiths, Charles
    The Acrothoracica of South Africa are reviewed for the first time, 50 years after the last publication on this group appeared. A new host category for acrothoracicans is described in Chapter 1, as Weltneria spinosa was collected from coralline red algae. This finding was not an isolated event, as this species was found inhabiting four different species of coralline algae across a range of sites up to 900 km apart. These are the first unequivocal records of living acrothoracicans burrowing into coralline red algae. Further inspections of coralline algae in this and other regions will likely reveal many more new host records and possibly new acrothoracican species. In Chapter 2 a systematic account and key to all known South African acrothoracicans are given, with each description accompanied by scanning electron microscopy, light microscopy and a distribution map. The number of known South African acrothoracicans is increased from four to eight species, as three new records and two undescribed species are added to the fauna, while one existing record is determined to be a nomen nudum. Chapter 3 examines patterns of distribution and host specificity. All species except one saw a range extension, some of which were > 500 km, while all species had additional hosts described. The species with the most hosts was W. spinosa, which was reported from 13 hosts that included gastropods, chitons and coralline red algae. South Africa thus now includes 11.27% of the world’s acrothoracican species, with 62.50% of these endemic. Moreover, 75% of South African acrothoracicans were endemic to specific provinces. However, these values are likely to change substantially as more sites are sampled both within the region and in neighbouring countries. In conclusion this dissertation shows that South Africa has more acrothoracican species, occupying more hosts across wider distributional ranges than previously thought. Although this study serves as a valuable baseline it should be expanded on through future sampling, specifically focusing on areas (Delagoa, Namaqua and offshore bioregions) and hosts (especially corals) not yet sampled in South Africa.
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    The chiton fauna (Mollusca: Polyplacophora) of South Africa
    (2025) Erasmus, Karlien; Griffiths, Charles
    Chitons are a diverse class of molluscs inhabiting marine waters and constitute a significant, yet relatively underexplored group of invertebrates in South Africa. Over the past three decades, taxonomic research has resulted in a pronounced increase in the description of regional chiton species, with the result that the most recent (1985- 2006) series of global monographs on chitons by Kaas and Van Belle now cover only 22 of the 50 chiton species currently recognised from the region, highlighting the need for a new synthesis of the fauna. This dissertation documents all the known chiton species inhabiting South African waters and adds new records of species that were previously undocumented. The study identifies an additional eight species new to the region from South African museum collections. A remarkable endemism is found in this group, with 46% of chiton species in South Africa found nowhere else. Of these endemics, 34% can be found only on the South Coast. The dissertation also includes a complete species list of the region and a user-friendly field guide that highlights key taxonomic features of the region's chiton species, with an accompanying binomial key for identification of species. It includes photographs and illustrations to aid in species identification, as well as a distribution map for each species. Chitonida is the largest order found in the region, with Acanthochitonidae, Chaetopleuridae, Chitonidae and Ischnochitonidae as four of the largest families in the region. Leptochiton is the most diverse genus in the region, also indicating a relatively high species richness in deeper waters. Chiton species of the region exhibit a greater species richness to the east and a higher endemicity to the South, with 56% of the species found on the South Coast endemic, though there seem to be a low intensity of collection on the Eastern coast. Although this dissertation adds significantly to the regional chiton fauna, further sampling and research is needed to comprehensively resolve and describe all the species and to assess their conservation status, given the anthropogenic threats these species face, including habitat destruction and possible unethical and unregulated collections.
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    The effects of microplastic and natural particles on the invasive mussel Mytilus galloprovincialis (Lamarck, 1819) and the native Choromytilus meridionalis
    (2021) Germishuizen, Matthew; Griffiths, Charles; Pfaff, Maya; Lenz, Mark
    Mussels living in coastal environments are often exposed to natural inorganic particles and hence may be well adapted to dealing with high sediment loads. The mechanisms by which they deal with particle loads do, however, cause stress and alter metabolic processes. An increasingly common anthropogenic addition to particle loads in the ocean are microplastic particles. Numerous recent experiments have addressed the impacts of microplastics on metabolic performance, but few of these have used natural reference particles to control for the concurrent effects of particle load itself. This study aims to compare the effects of microplastic and of natural particle exposure on the mussel Mytilus galloprovincialis, an invasive species which has become the dominant mussel in the mid- to low-shore of the south and west coasts of South Africa, but is absent from areas prone to sand inundation. These effects will be compared to those on the native mussel Choromytilus meridionalis, which resides on the low shore, and unlike M. galloprovincialis often occurs in areas prone to sand inundation. Respiration rates, byssus production, clearance rate, body condition (BCI) and survival of mussels exposed to four concentrations of two particle types, polyvinyl chloride (PVC) and red clay were measured. A significant concentration effect was found in the respiration rates of Mytilus galloprovincialis, while C. meridionalis respiration rates were largely unaffected by both particle type and particle concentration. The byssus numbers of M. galloprovincialis were significantly reduced by microplastic exposure, whilst no particle type effects were found in C. meridionalis. Clearance rates of C. meridionalis, on the other hand, were significantly affected by particle concentration, while no effects were found on M. galloprovincialis. The BCI of C. meridionalis was also found to be affected by particle concentrations, while M. galloprovincialis was unaffected. All C. meridionalisindividualssurvived the experiment, while 29 M. galloprovincialis died. Mortality of M. galloprovincialis exposed to the two particle types was not significantly different, although more mortality was suffered in PVC treatments than in red clay treatments. The results reveal that there was indeed a difference in the response of M. galloprovincialis to the different particle types, and that the two species did exhibit different strategies to both particle type, and concentration. Experimental studies of this nature are imperative in order to disentangle microplastic effects from those of particles in general, and to develop a better understanding of potential impacts of plastic debris on marine ecosystems.
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    Trajectories of Change in South Africa's Freshwater Fish Fauna
    (2025) Kajee, Mohammed; Griffiths, Charles; Shelton, Jeremy; Dallas, Helen; Pegg, Josephine
    In South Africa, freshwaters are the most threatened ecosystems in the country, facing pressure from water abstraction, land-use change, pollution, invasive species and climate change. These anthropogenic pressures are directly impacting the diversity, abundance, and survival of freshwater fauna and flora across the country. Freshwater fishes are recognised as South Africa's most threatened species group, with one third of species classified as threatened (Vulnerable, Endangered, Critically Endangered) by the International Union for the Conservation of Nature (IUCN). Understanding patterns of diversity, threat, invasion, and protection status are vital for management. However, access to reliable and comprehensive long-term data on fish distributions, are limited. This thesis aims to collect, collate, and analyse historic and current freshwater fish records for all fish species (native and non-native) known to occur in South Africa, to better understand distribution, diversity, and threat patterns in space and time. A comprehensive freshwater fish occurrence dataset for South Africa was compiled and uploaded to the Freshwater Biodiversity Information System (FBIS, freshwaterbiodiversity.org). An 18-month historic-data collation effort resulted in the accrual of 35 955 records of freshwater fish from South Africa spanning 194 years (1828–2022), that have since also been uploaded to the Global Biodiversity Information Facility (GBIF). Together with pre-existing GBIF records (24 861), a total of 60 837 freshwater fish records are thus now available for South Africa. The data show a marked decline in the number of native fish occurrence records over the last decade relative to the previous five decades. Conversely, the number of occurrences for non-native fishes increased over the past three decades. A breakdown of the data is provided for all native (n = 105) and non-native (n = 24) species as well as for all endemic (n = 40) and threatened (n = 27) species. Using occurrence records collected for this thesis, spatial patterns in distribution, diversity, threat, invasion, and protection status of freshwater fishes in South Africa were analysed. Few studies have undertaken such analyses at ecologically and politically appropriate spatial scales, largely because of limited access to comprehensive biodiversity data sets. Results show that record density varies spatially, at both primary catchment and provincial scales. The diversity of freshwater fishes also varied spatially: native species hotspots were identified at provincial level in the Limpopo, Mpumalanga and KwaZulu-Natal provinces, endemic species hotspots were identified in the Western Cape, and threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Non-native species distributions mirrored threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Some 47% of threatened species records fell outside of protected areas, and 38% of non-native species records fell within protected areas. Concerningly, 58% of the distribution ranges of threatened species were invaded by non-native species. A data breakdown is provided for each of South Africa's nine provinces including total number of records, and the numbers of native, non-native, endemic and threatened species. These data provide a much-needed update of the known status and distribution of freshwater fishes in the country. To support future spatial modelling of South Africa's freshwater fish species distributions, a robust and repeatable method for applying Species Distribution Models (SDMs) to freshwater fishes was developed. Specifically, this thesis sought to investigate whether SDMs could be applied to a wide range of freshwater fishes in South Africa and whether the inclusion of invasive species spatial data would result in improved model accuracy and performance. Using a Bayesian Additive Regression Trees (BART) algorithm, the distributions of three black bass (Micropterus salmoides, M. dolomieu, and M. punctulatus) species and two native species (Clarias gariepinus and Pseudobarbus burgi) were modelled. A total of 148 hydrological and 16 biological predictor variables were specifically developed for this chapter, along with the collation of 75 environmental predictor variables. The results demonstrated that, with appropriate data cleaning and using a statistically robust method for selecting predictor variables, model outputs performed well, with the resulting modelled distributions congruent with known distributions and historic descriptions of the species' presence. All models for invasive, native, and threatened species performed well, with AUC values ranging from 0.923–0.994 and TSS ranging from 0.701–0.940. Furthermore, model performance for P. burgi was not improved by the inclusion of biological predictors (invasive species). The AUC for the original P. burgi model (including only climatic, environmental, and hydrological predictors) was 0.994, whereas the adapted model (including both climatic, environmental, and hydrological predictors as well as biological predictors) was marginally lower, with an AUC value of 0.993. This indicates that the inclusion of invasive species as biological predictors may not be necessary to produce accurate predicted species distributions. This thesis also presents a case study demonstrating how the FBIS system was used to provide freshwater fish spatial data products to a national conservation decision-support tool – The Department of Forestry, Fisheries, and the Environment (DFFE) National Environmental Screening Tool. The Tool uses empirical and modelled biodiversity data to guide Environmental Impact Assessments of proposed developments. Occurrence records for 34 threatened freshwater fishes occurring in South Africa were extracted from the FBIS and verified by taxon specialists, resulting in 6 660 records being used to generate modelled and empirical national distribution layers. This represents the first inclusion of freshwater biodiversity data in the Screening Tool, and future iterations of the Tool will incorporate additional freshwater taxa. This case study demonstrates how systems like the FBIS can play a pivotal role in the data-to-decision pipeline through supporting data-driven conservation and management decisions at a national level. The collective findings of the thesis are concluded in Chapter 6, which highlight the importance of collecting, collating, and consolidating biodiversity data at a national level. The dataset presents the largest (by number of records) collection of freshwater fish records in Africa to date, with data spanning 194 years. This thesis also presents an updated version of South Africa's Species List for Freshwater Fishes, which includes all known native (n = 107) and non-native (n = 27) species occurring in the country, and key species attributes like species origin, endemism, and threat status. By consolidating historical data for all known freshwater fishes, this thesis presents the first comprehensive assessment of the status of South Africa's freshwater fish fauna, providing valuable insights into spatial patterns of richness, endemism, threat status and non-native species, as well as assessing how effective the country's protected area network is for protecting freshwater fishes. This thesis addressed the critical need for a deeper, data-driven understanding of spatial and temporal variation in South Africa's freshwater fishes – an essential foundation for sound management of these species and their habitats into the future.