South African Institute for Aquatic Biodiversity

Schistosomiasis is a vector-borne disease transmitted by freshwater snails and is prevalent in rural areas with poor sanitation and no access to tap water. Three snail species are known to transmit schistosomiasis in South Africa (SA), namely Biomphalaria pfeifferi , Bulinus globosus and Bulinus africanus . In 2003, a predicted prevalence of 70% was reported in tropical climates in SA. Temperature and rainfall variability can alter schistosomiasis-transmitting snails’ development by increasing or decreasing their abundance and geographical distribution. This study aimed to map the historical distribution of schistosomiasis from 1950 to 2006 in SA. The snail sampling data were obtained from the historical National Snail Freshwater Collection (NFSC). Bioclimatic variables were extracted using ERA 5 reanalysis data provided by the Copernicus Climate Change Service. In this study, we used 19 bioclimatic and four soil variables. The temporal aggregation was the mean climatological period pre-calculated over the 40-year reference period with a spatial resolution of 0.5° x 0.5°. Multicollinearity was reduced by calculating the Variance Inflation Factor Core (VIF), and highly correlated variables (> 0.85) were excluded. To obtain an "ensemble" and avoid the integration of weak models, we averaged predictions using the True Skill Statistical (TSS) method. Results showed that the ensemble model achieved the highest Area Under the Curve (AUC) scores (0.99). For B . africanus , precipitation-related variables contributed to determining the suitability for schistosomiasis. Temperature and precipitation-related variables influenced the distribution of B . globosus in all three models. Biomphalaria pfeifferi showed that Temperature Seasonality (bio4) contributed the most (47%) in all three models. According to the models, suitable areas for transmitting schistosomiasis were in the eastern regions of South Africa. Temperature and rainfall can impact the transmission and distribution of schistosomiasis in SA. The results will enable us to develop future projections for Schistosoma in SA based on climate scenarios.

Apex predators can both suppress mesopredators, causing behavioral changes such as temporal avoidance, and facilitate mesopredators via carrion provision. Thus, responses to apex predators may vary depending on the local context. We investigated the differences in the temporal activity of two mesopredators, the black-backed jackal (Lupulella/Canis mesomelas) and caracal (Caracal caracal), in response to the presence of human and non-human apex predators, using camera trap data. We compared mesopredator temporal overlap in the Eastern Cape province, South Africa, across a range of sites with and without lethal predator control (culling). We also assessed mesopredator activity across sites with varying apex predator (i.e., lions Panthera leo, leopards P. pardus, brown hyaenas Parahyanea brunnea, spotted hyaena Crocuta crocuta) presence, and between the mesopredator and apex predator species present. Jackals decreased diurnal activity at sites where culling occurred, increased nocturnal activity at sites with apex predators, and showed temporal overlap with apex predators, providing support that jackals avoid human activity, and apex predators may facilitate scavenging. Caracals remained crepuscular regardless of culling practices, were marginally more diurnal where apex predators were present, and showed low to moderate temporal overlap with these species, providing at least some support that apex predators may suppress caracals. Our results indicate that these mesopredators exhibit flexible behavioral responses to humans and apex predators which may promote their persistence across the landscape. Significance statement While the activity patterns of mesopredators in response to apex predators are frequently assessed, the investigation of how mesopredator behavior differs in response to human and non-human apex predators has seldom been studied. Here, we present novel findings comparing the activity patterns of two mesopredators in response to human and non-human apex predators. We demonstrate that (1) both species avoid peak periods of human activity, (2) black-backed jackals also partially align their activity patterns with the activity patterns of apex predators, and (3) caracals show some temporal avoidance of apex predators. Ultimately, black-backed jackals likely improve their foraging success by balancing the energetic gain from scavenging with the increased costs associated with interference competition by apex predators. Whereas caracals likely reduce interference competition by temporally avoiding dominant apex predators.

Aquatic macrophytes are a key component of freshwater ecosystems, providing habitats for aquatic organisms, and play an integral role in food webs and nutrient cycles. Understanding the factors that influence macrophyte growth, distribution, structure and community composition is indispensable for their integrated management, which are explored in this chapter. Among these are biotic (herbivory, macrophyte properties and competition and pathogens and diseases) and abiotic (water chemistry including temperature, substrate composition/embeddedness and hydrological conditions) factors. Anthropogenic stressors further drive these biotic and abiotic factors individually or in combination, causing either the extinction of important native macrophytes or the uncontrolled proliferation of macrophytes, usually invasive alien species, which has been recognised as an important issue of aquatic ecosystem management in freshwater systems globally. Among the notorious aquatic macrophytes of global concern are the invasive water hyacinth (Pontederia crassipes) and giant salvinia (Salvinia molesta), which have detrimental impacts in invaded freshwater systems. The global problem of nuisance macrophytes needs to be holistically handled at all levels to prevent ecological and socioeconomic impacts associated with their proliferation. Solutions to curb the nuisance growth of aquatic macrophytes include mechanical removal, biological control and chemical treatment although integrated control is the most cost-effective control option. The control efforts need to be integrated at catchment and regional scales, facilitating the integration and partnerships of institutions to ensure functional aquatic systems and conservation of global biodiversity.

A dense Ecklonia radiata (Laminariales) kelp forest extending at least 35 km has been found between 45 and 60 m depth range within the mesophotic zone inside the iSimangaliso marine-protected area (MPA) at the iSimangaliso Wetland park World Heritage Site on the east coast of South Africa. This is the first visual confirmation of the occurrence of E. radiata beds in subtropical South Africa, in an area situated between the tropical and subtropical bioregions, in an area that spans the Natal and Delagoa bioregions of the south-western Indian Ocean, more than 350 km north of its previously documented South African range. The kelp was found to be present across the length of the MPA, but dense beds were present only in the southern Natal bioregion, with sparse occurrences observed elsewhere on soft-coral and sponge-dominated reefs in the upper mesophotic zone. The footage was collected in November 2020, May 2021 and November 2022 during remotely operated vehicle and drop camera surveys of the mesophotic zone inside the MPA. This discovery adds to the body of knowledge on the global distribution of Laminariales populations in deep tropical and subtropical settings and the diversity of habitats within South Africa's largest coastal MPA.

The literature currently recognizes four guilds of estuarine resident fish species, namely solely estuarine, estuarine & marine, estuarine & freshwater, and estuarine migrant. In this review the life cycles of actual representatives from these four guilds is assessed to determine whether the current definitions, which have never been formally tested, are appropriate to fish species resident in South African estuaries. Detailed information and diagrammatic life cycles are provided for the selected species covered by this review. A potential new estuarine resident guild category is also identified, viz. those taxa that are primarily estuarine but also have subpopulations recorded in both adjacent marine and freshwater habitats. The full range of reproductive characteristics employed by estuary resident species is examined, ranging from live bearers, pouch and nest brooders, to a suite of oviparous taxa that attach their ova to estuarine rocks, shells and submerged vegetation, all of which assists with larval retention within the estuarine environment. The small size and early reproductive maturity of most estuarine resident species is highlighted, with reduced vulnerability to predation in shallow, sheltered, often turbid estuary waters offering considerable protection during spawning events when compared to the open ocean. In addition, these small fish would not have to move considerable distances at any stage of their life cycle, since egg, larval, juvenile and adult stages all occur in the same place. The existence of contingent subpopulations within many estuarine resident species is noted, physico‐chemical stresses on these species are highlighted, and the eurytopic nature of these small fish taxa emphasized. This article is protected by copyright. All rights reserved.

Acoustic telemetry is a popular approach used to track many different aquatic animal taxa in marine and freshwater systems. However, information derived from focal studies is typically resource‐ and geography‐limited by the extent and placement of acoustic receivers. Even so, animals tagged and tracked in one region or study may be detected unexpectedly at distant locations by other researchers using compatible equipment, who ideally share that information. Synergies through national and global acoustic tracking networks are facilitating significant discoveries and unexpected observations that yield novel insight into the movement ecology and habitat use of wild animals. Here, we present a selection of case studies that highlight unexpected tracking observations or absence of observations where we expected to find animals in aquatic systems around the globe. These examples span freshwater and marine systems across spatiotemporal scales ranging from adjacent watersheds to distant ocean regions. These unexpected movements showcase the power of collaborative telemetry networks and serendipitous observations. Unique and unexpected observations such as those presented here can capture the imagination of both researchers and members of the public, and improve understanding of movement and connectivity within aquatic ecosystems.

The Cape Fold Ecoregion (CFE) is one of southern Africa’s unique aquatic ecoregions and its freshwater fish fauna is characterized by high levels of endemism. As with many other Mediterranean-type ecosystems, the region is also a hotspot for threatened and range-restricted freshwater fish. Many of the CFE’s endemic species are at risk for extinction, with declines in population sizes and distribution ranges. The Clanwilliam sandfish Labeo seeberi is an example of such a species and is considered one of South Africa’s most endangered large migratory cyprinids. This species is endemic to the Olifants/Doring river system in the CFE and has been subject to a major population decline, mainly as a result of invasive alien fish and adverse climate events. Little is known of the genetics of the Clanwilliam sandfish, thus this study aimed to provide basic population genetic parameters to inform future conservation interventions. Both microsatellite and mitochondrial DNA (mtDNA) markers were used to assess populations from three sites within the Olifants/Doring river system. Genetic diversity was moderate to low and did not reflect the drastic decline expected on the basis of previous relative abundance data. This is likely due to a lag effect between ecological/life history demographics (due to juvenile recruitment failures) and population genetic composition. Furthermore, there was limited genetic differentiation between the sampling locations, suggesting a single breeding population, but mtDNA haplotype distribution and slight divergence of the smaller populations does suggest that the population might have become recently fragmented. The results show that the effective population size of the current breeding population might still be sufficient to maintain evolutionary potential in the short term, which could act as a buffer until conservation strategies focusing on protecting breeding animals and maximizing juvenile survival can restore population numbers.

Microplastic (MP) prevalence has been well documented, however, knowledge gaps exist for African mangrove forests. This research is the first to compare MP pollution (using FT-IR analysis) in an urban (Durban Bay) and peri-urban (Mngazana Estuary) mangrove forest in South Africa, across different compartments. MP pollution (typology, abundance, and distribution) was quantified in estuarine surface water, sediment and the soft tissue of three keystone species (Austruca occidentalis, Chiromantes eulimene and Cerithidea decollata) in relation to disturbances acting on these systems. MP averages ranged from 99 to 82 MPs/kg sediment, 177 to 76 MPs/L water and 82 to 59 MP/g − 1 DW in biota. Overall fibres were the dominant MP type across all compartments. The three invertebrate species exhibited MP bioaccumulation, however, significant differences were observed between MP concentrations in the soft body tissue of invertebrates and abiotic compartments, providing evidence that they are not effective biomonitors of MP pollution.

A universal paradigm describing patterns of speciation across the tree of life has been debated for decades. In marine organisms, inferring patterns of speciation using contemporary and historical patterns of biogeography is challenging due to the deficiency of species-level phylogenies and information on species' distributions, as well as conflicting relationships between species’ dispersal, range size and co-occurrence. Most research on global patterns of marine fish speciation and biogeography has focused on coral reef or pelagic species. Carangoidei is an ecologically important clade of marine fishes that use coral reef and pelagic environments. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a time-calibrated phylogeny of Carangoidei and its parent clade, Carangiformes. Age-range correlation analyses of the geographical distributions and divergence times of sister species pairs reveal widespread sympatry, with 73% of sister species pairs exhibiting sympatric geographical distributions, regardless of node age. Most species pairs coexist across large portions of their ranges. We also observe greater disparity in body length and maximum depth between sympatric relative to allopatric sister species. These and other ecological or behavioural attributes probably facilitate sympatry among the most closely related carangoids.

Ethnoherpetology improves our understanding of the conservation implications of nature-based cultural practices through investigations of the influence of traditional culture on frog and reptile species (herptiles). Improved understanding of the implications of human activities on these taxa is especially important as herptiles are experiencing global population declines. Furthermore, improved understanding of nature-based cultural practices can better inform conservation planning that includes cultural practices as defined by South African legislation. The herptile-based cultural practices recorded from a sample of 275 online questionnaire respondents and 68 publications show some cultural practices to compel or inspire protection of herptiles. Conversely, other practices were found to pose a conservation risk as they either involve killing herptile species or they perpetuate negative perceptions towards them. Leveraging protective cultural practices as a conservation tool and mitigating culture-motivated threats requires integrating cultural aspects into modern law. Such an integrative approach is possible under South African legislation’s provisions for socially inclusive conservation planning and recognition of customary law. Integrative conservation approaches are also in line with international policy such as the Kunming-Montreal global biodiversity framework. In addition to an inventory of herptile-based cultural practices, the study also assesses their feasibility as conservation tools. Furthermore, this study highlights a need for quantification of their conservation implications (both positive and negative) and aligning protective traditional cultural practices with modern means of law enforcement.

The study investigated the spatial distributions of selected metals, semi-metals and non-metals within a floodplain pan ecosystem in the Ramsar declared Makuleke Wetlands within the Makuleke Contractual National Park, in the northern Kruger National Park (South Africa), along varying soil depths (0-120 cm) at 20 cm intervals. The study identified significant differences in metal concentrations (i.e. Ca, Mn, Fe) and non-metals (i.e. C, S) across sediment depths. Metal and non-metal concentrations in surface sediments (0-40 cm) were generally high. Compared with the sediment quality guidelines, all measured metals were within the 'no effect' level across different sites and depths, except for one site (i.e. Mambvumbvanyi pan). In contrast, enrichment factors showed that K, Ca and Mg were enriched in sediments across all the floodplain pans and depths. Principal component and cluster analyses indicated that various metals originated from different sources. Although a high concentration of metals was found in the topsoil, no potential detrimental effects on the aquatic systems could be observed. Based on the findings, this study provides a baseline overview of sediment metal pollution that can inform effective management of these floodplain wetlands systems. ARTICLE HISTORY

Previous literature suggests that Indigenous cultural practices, specifically traditional medicine, are commonplace among urban communities contrary to the general conception that such practices are restricted to rural societies. We reviewed previous literature for records of herptiles (frog and reptile species) sold by traditional health practitioners in urban South Africa, then used visual confirmation surveys, DNA barcoding and folk taxonomy to identify the herptile species that were on sale. Additionally, we interviewed 11 IsiZulu and SePedi speaking traditional health practitioners to document details of the collection and pricing of herptile specimens along with the practitioners' views of current conservation measures for traditional medicine markets. The 34 herptile species recorded in previous literature on traditional medicine markets included endangered and non‐native species. Spectrophotometry measurements of the DNA we extracted from the tissue of herptiles used in traditional medicine were an unreliable predictor of whether those extractions would be suitable for further experimental work. From our initial set of 111 tissue samples, 81 sequencing reactions were successful and 55 of those sequences had species‐level matches to COI reference sequences on the NCBI GenBank and/or BOLD databases. Molecular identification revealed that traditional health practitioners correctly labelled 77% of the samples that we successfully identified with DNA barcoding in this study. Our mixed methodology approach is useful for conservation planning as it updates knowledge of animal use in Indigenous remedies and can accurately identify species of high conservation priority. Furthermore, this study highlights the possibility of collaborative conservation planning with traditional health practitioners.

Globally, there is growing concern on the occurrence of multiple non‐native species within invaded habitats. Proliferation of multiple non‐native species together with anthropogenic‐driven habitat modifications raise questions on the mechanisms facilitating the co‐occurrence of these species and their potential impact within the recipient systems. Using the Great Fish River system (South Africa) which is anthropogenically‐modified by inter‐basin water transfer (IBWT), as a case study, this research employed trait‐based approaches to explore patterns associated with the co‐occurrence of multiple non‐native fish species. This was achieved by investigating the role of functional diversity of non‐native and native fishes in relation to their composition, distribution and environmental relationships. Nineteen functional traits that defined two broad ecological attributes (habitat use and feeding) were determined for 13 fish species that comprised eight native and five non‐native fishes. We used these data to, firstly, evaluate functional diversity patterns and to compare functional traits of native and non‐native fishes in the Great Fish River system. Secondly, we employed multivariate ordination analyses (factor analysis, RLQ and fourth‐corner analyses) to investigate interspecific trait variations and potential species‐trait‐environmental relationships. From a functional diversity perspective, there were no significant differences in most functional diversity indices between native and non‐native species. Despite interspecific variation in body morphology‐related traits, we also found no clear separation between native and non‐native species based on the ordination analysis of the functional traits. Furthermore, while RLQ ordination showed broad spatial patterns, the fourth‐corner analyses revealed no significant relationships of species distribution, functional traits and environmental variables. The weak species‐trait‐environment relationship observed in this study suggests that environmental filtering was likely a poor determinant of functional trait structure within the Great Fish River. Modification of the natural flow regime may have weakened the relationship between species traits and environment as has been shown in other systems. This article is protected by copyright. All rights reserved.

Floodplain wetlands remain important habitats for most macrophytes, macroinvertebrates, birds, fish, amphibians, wildlife and in particular large mammals. They are dynamic in nature and provide many ecosystem services even to humans. The present study was undertaken to assess water and sediment chemistry as drivers of macroinvertebrates and fish communities in Makuleke floodplain wetlands in north Kruger National Park, South Africa. Water, sediments, macroinvertebrates and fish samples were collected across different hydroperiods (i.e., Low water period and high water period) from six floodplain pans. Macroinvertebrates were dominated by (Notonectidae, Libellulidae, Gerridae, Chironomidae larvae, Belostomatidae, gomphidae, dytiscidae and Baetidae, while fish were dominated byTilapia sparminii, Gambusia affinis, Coptodon rendali, Oreochromis hybrid, Oreochromis mossambicus, Enteromius palludinosus and Clarais gariepinus. Generally, fish and macroinvertebrate abundances and diversity were elevated during high water levels as compared to low water levels, suggesting that hydroperiod plays a significant role in structuring aquatic faunal communities. Redundancy and canonical– correlation analysis identified salinity, TDS (water) and Zn, C and B concentrations (sediment) as the major drivers of macroinvertebrate community structure, while pH, TDS (water), and K, Ca and Mg concetrations (sediment) were the major drivers of fish communities. In addition, pelagic chlorophyll –a was strongly positively associated with fish, particularly Gambusia affinis, during the high water level period. The results of this study provide important baseline information on the ecology of the Makuleke pans.

The dependence on connectivity and use of estuaries by two major groups of fishes, namely estuary-associated marine and diadromous species, are reviewed. The former group comprises marine estuarine–opportunists and marine estuarine–dependents, and the latter anadromous, catadromous, and amphidromous species. Examples of ingress to estuaries by larvae and juveniles of species from each group illustrate the importance of freshwater-estuarine-marine connectivity to the life cycles of those species. Factors that threaten estuarine connectivity, including the potential/possible consequences of global climate change on the contribution of these key taxa to coastal fish assemblages at pristine or recent historical levels, are highlighted. The implications of reduced connectivity on the current and future status of these major groups in estuaries are also discussed. Finally, it is noted that the abundance of fishes in the above guilds has already declined substantially and that there are no clear prospects for a reversal of this trend. Possible future research on fishes and coastal connectivity include applications of environmental DNA and otolith microchemistry, and the assessment of fish responses to the removal of dams to restore connectivity in catchment rivers.

Migratory sharks play a key ecological role through movements within and among marine ecosystems, yet many populations are declining. Addressing the decline is especially challenging for wide-ranging species, as they may undertake movements between countries with disparate conservation priorities. To investigate the transboundary migrations of threatened sharks between neighbouring South Africa and Mozambique, we tracked 4 commonly occurring carcharhinid species (bull, blacktip, tiger and grey reef sharks). A total of 102 individuals were fitted with long-life acoustic transmitters and monitored for 4 yr (2018-2022) on an acoustic receiver network of 350 receivers. During this period, 63% of tagged bull sharks (n = 19), 87% of blacktips (n = 13), 94% of tiger (n = 16) and 25% of grey reef sharks (n = 3) undertook transboundary movements. The frequency of mean transboundary movements per year ranged between 1.3 ± 1.5 (SD) for grey reef sharks and 81 ± 35.6 for tiger sharks. Blacktip, bull and tiger sharks all undertook long-distance transboundary migrations ranging from 980 to 2256 km. These data confirm high connectivity between neighbouring countries by threatened sharks undertaking persistent transboundary movements. This study emphasizes the need for collaborative transboundary cooperation between the 2 countries and the alignment of regional management plans and interventions to address declining shark populations in this region of the Western Indian Ocean.

Given a growing global population and shift to embrace the blue economy, a need for marine spatial planning (MSP) has emerged in South Africa to sustainably resolve the rising conflicts over the use of marine and seabed resources and services. A well-developed marine spatial plan yields numerous ecological, social and economic benefits. These are achieved through mediating between spatially conflicting economic drivers’ interests (e.g. commercial fishing, tourism, mining), preventing their activities from compromising thresholds of an environment’s sustainability. Within the MSP framework, high-resolution geospatial datasets are required to document and describe the seabed in the highest possible detail. At any scale, integrated analysis of seabed geomorphology and habitats is anticipated to greatly improve the understanding of ecosystem functioning from a multidisciplinary perspective, whilst improving MSP procedures and management of marine space. South Africa is the first of few African countries to have an approved and implemented MSP framework, but is still somewhat behind globally in implementing large-scale regional hydroacoustic surveys to cover the country’s vast offshore territory. The deficiency of hydroacoustic surveys is perhaps due to a relative lack of funds and poor communication about the value of multibeam echo-sounder (MBES) derived data, whilst marine geoscience remains a scarce skill in the country. This review paper presents a geological perspective of MSP and explores (1) the value that seabed mapping offers MSP specifically and (2) the need to increase seabed mapping with MBES, using a recently initiated project from the South African east coast as a case study.

Seagrass habitats provide structural complexity in coastal estuarine and marine environments, which offer fish optimal foraging grounds and refuge from predation. However, seagrasses are some of the most threatened ecosystems globally, with anthropogenic activities such as population growth and environmental degradation leading to the fragmentation, thinning and loss of these habitats. Rhabdosargus holubi is one of only a few vegetation‐associated marine fish species in South African estuaries. Although field studies have shown a strong association with seagrass over other aquatic vegetation for the juveniles of this species, habitat choice has never been empirically tested. Here, we used artificial vegetation units (AVU) to test habitat choice (different structural complexities) for this species. We also tested whether habitat choice is influenced by a predatory threat, with fish preferentially selecting dense habitat in the presence of a predator and whether this effect may be more apparent in smaller individuals. We found that R. holubi significantly prefer greater structural complexity over less complex habitats, in both the absence and presence of a predator and for both small and large juveniles, showing that R. holubi actively chose more complex structure and are attracted to the structure per se irrespective of the threat of predation. This study highlights the importance of dense seagrass as nursery areas for this species and demonstrates how the loss of these habitats could impact the nursery function of estuaries. This article is protected by copyright. All rights reserved.