The number of African penguins Spheniscus demersus breeding in South Africa collapsed from about 56 000 pairs in 2001 to some 21 000 pairs in 2009, a loss of 35 000 pairs (>60%) in eight years. This reduced the global population to 26 000 pairs, when including Namibian breeders, and led to classification of the species as Endangered. In South Africa, penguins breed in two regions, the Western Cape and Algoa Bay (Eastern Cape), their breeding localities in these regions being separated by c. 600 km. Their main food is anchovy Engraulis encrasicolus and sardine Sardinops sagax, which are also the target of purse-seine fisheries. In Algoa Bay, numbers of African penguins halved from 21 000 pairs in 2001 to 10 000 pairs in 2003. In the Western Cape, numbers decreased from a mean of 35 000 pairs in 2001-2005 to 11 000 pairs in 2009. At Dassen Island, the annual survival rate of adult penguins decreased from 0.70 in 2002/2003 to 0.46 in 2006/2007; at Robben Island it decreased from 0.77 to 0.55 in the same period. In both the Western and Eastern Cape provinces, long-term trends in numbers of penguins breeding were significantly related to the combined biomass of anchovy and sardine off South Africa. However, recent decreases in the Western Cape were greater than expected given a continuing high abundance of anchovy. In this province, there was a south-east displacement of prey around 2000, which led to a mismatch in the distributions of prey and the western breeding localities of penguins.
Coastal urban environments have high plastic pollution levels, and hence interactions between plastic debris and marine life are frequent. We report on plastic ingestion by mullet Mugil cephalus in Durban Harbour, KwaZulu-Natal, South Africa. Of 70 mullet (13.0-19.5 cm total length), 73% had plastic particles in their guts, with a mean of 3.8 particles per fish (SD 4.7). Plastic ingestion showed no relation to digestive tract content or fish length. White and clear plastic fibres were ingested most commonly. This urban population of M. cephalus had a higher incidence of plastic ingestion than has been reported in studies on fish from other coastal areas or the oceanic environment.
The region located in the far northeast of the Gulf of Guinea (NEGG), eastern tropical Atlantic, remains poorly documented due to a lack of available in situ ocean data. Heavy rainfall and intense river discharges observed in this region induce a strong salinity stratification that may have a significant impact on the mixed layer depth and on sea surface temperatures, through the so-called barrier-layer effect. By using recent in situ data and climatological outputs from a numerical simulation, we reveal the existence of a barrier layer in the NEGG and describe its seasonal occurrence. In the NEGG, the barrier layer limits the mixed layer depth. From January to March, significant values for the barrier-layer thickness are observed mostly due to the horizontal advection of fresh water. From April, vertical mixing along with vertical advection increase the sea surface salinity; hence, the barrier-layer thickness decreases and reaches its minimum in July. During the rest of the year, values for the barrier-layer thickness are again high, mostly under the influence of the Niger River discharge and precipitation, with the highest values recorded in October, when the river discharge and precipitation are at a maximum.
Kelp forests are believed to host a large biomass of epiphytic fauna and flora, including diatoms, which constitute the base of aquatic food webs and play an important role in the transfer of energy to higher trophic levels. Epiphytic diatom assemblages associated with two common species of South African kelps, Ecklonia maxima and Laminaria pallida, were investigated in this study. Primary blades of adult and juvenile thalli of both kelp species were sampled at False Bay in July 2017 and analysed using scanning electron microscopy. Our findings showed that both kelp species hosted relatively low densities of diatoms (ranging from 7 [SD 5] cells mm −2 on adult specimens of L. pallida to 43 [SD 66] cells mm −2 on blades of juvenile E. maxima), with Amphora and Gomphoseptatum reaching the highest absolute abundances. Although non-metric multidimensional scaling showed overlapping and largely scattered sample sets, a significant relationship between the diatom communities and the species and age of the host macroalga was detected by two-way PERMANOVA. In general, more abundant and diverse diatom communities were observed on juvenile thalli than on adult thalli, with species belonging to Navicula and Rhoicosphenia contributing significantly to the observed dissimilarity. Due to a significant interaction between species and age effects, however, the overall ability of kelp species, their age, and their interaction to explain the variation in diatom community structure was limited. We suggest that the low densities of epiphytic diatoms were directly related to the sloughing of epithelial cells observed in both kelp species. We further speculate that on such unstable substrata some diatom taxa might adapt to an endophytic life to avoid the antifouling mechanisms developed by their hosts.
Namibia's most important commercial fisheries resource, the shallow-water Cape hake Merluccius capensis, is currently assessed using statistical catch-at-age analysis. Age data obtained from otoliths constitute an important data component of this model. Recent age-validation studies of M. capensis showed that growth was previously underestimated. We investigated this new fast-growth hypothesis (FGH) by using measurements and counts of translucent zones (T1 to T14, from otolith core to edge) on two survey otolith samples covering the entire range of fish lengths. We compared three hypotheses of periodicity of otolith zone formation and show that, if all zones are counted, T2 (at 9.0 mm otolith length), T5, T8, T11 and T14 are most likely to be annuli. A conversion from the slow-growth-hypothesis (SGH, currently used) age data was calculated as: FGH age group = round (0.41[SGH age group] + 0.25), and this formula should be applied to compute and test updated catch-at-age data in a future hake stock assessment. Additional adjustment for the hake stock assessment following the FGH, such as the timing of recruitment in winter and catches in summer, should be considered in future assessments.
This study investigated multiple mating in three species of intertidal klipfishes (family Clinidae): super klipfish Clinus superciliosus, bluntnose klipfish Clinus cottoides, and nosestripe klipfish Muraenoclinus dorsalis. These species display the rare reproductive mode of female vivipary with superfetation, a phenomenon where offspring at various stages of development are found within the female. Three or four microsatellite loci were used to genotype 25-30 adults of each species, as well as embryos of 131 C. superciliosus from six broods, 103 C. cottoides from six broods, and 63 M. dorsalis from five broods. The presence of multiple mating by females was assessed by maximum-likelihood sibship reconstruction implemented in the program COLONY, and the non-random distribution of reproductive success among individuals (reproductive skew) within broods was tested using the binomial skew index. Multiple mating by females was pervasive and observed in 83%, 100% and 80% of the broods of C. superciliosus, C. cottoides and M. dorsalis, respectively. The mean number of sires per brood was 4.3, 3.0 and 3.2, and, correspondingly, 5/5, 5/6 and 1/4 of multiply-sired broods showed significant reproductive skew in C. superciliosus, C. cottoides and M. dorsalis, respectively. The presence of pronounced reproductive skew may indicate post-copulatory processes taking place that bias paternity. We compared our results on multiple mating within the klipfish family, and with four other fish families that have vivipary with superfetation, and found the klipfish patterns were among those of live-bearing vertebrate groups with the highest average numbers of sires per brood.
Efforts to conserve and manage shark populations are often hampered by a lack of basic data, such as species-specific landings and distribution ranges. We bridge this gap in coastal East Africa by providing data on the distributions, catch rates, morphometrics, and exploitation status of shark species in Kenyan coastal waters. Data were collected from artisanal fishers and from bycatch taken by shallow-water (10-50 m) prawn trawlers from Malindi-Ungwana Bay and demersal research trawlers (10-150-m depth) along the ∼640-km coastline, over a 12-month period (June 2012 to May 2013). A total of 1 893 individual sharks (representing 20 species and 11 families) were sampled from the artisanal fishery (n = 1 610) and the trawlers (n = 283). The demersal trawl bycatches were dominated by the African angelshark Squatina africana (2.39 kg h -1 ), shortnose spurdog shark Squalus megalops (1.48 kg h -1 ) and African spotted catshark Holohalaelurus punctatus (0.11 kg h -1 ). Catches of the scalloped hammerhead shark Sphyrna lewini (0.73 kg h -1 ), smooth hammerhead shark Sphyrna zygaena (0.60 kg h -1 ) and grey reef shark Carcharhinus amblyrhynchos (0.77 kg h -1 ) dominated in the prawn trawlers. Only a few species (S. lewini, C. amblyrhynchos, and blacktip reef shark Carcharhinus melanopterus) showed a coast-wide distribution in the artisanal fishery. Artisanal fishers harvested mostly immature specimens of S. lewini, C. melanopterus and blacktip shark Carcharhinus limbatus, suggesting that the fishery might be unsustainable in the long-term. The Endangered S. lewini is the most vulnerable to overexploitation on the Kenyan coast, with most specimens landed (>90%) being below the size at maturity. Data are also presented on morphometric relationships and observed or estimated exploitation reference points (maximum observed length L max , asymptotic length L∞, mean length at first maturity L m , and optimum length L opt ) for the commonly landed species. A more comprehensive coast-wide National Plan of Action is recommended for the management of shark populations in Kenya.
Studies of water-particle flow dynamics in shallow estuarine systems show that tidal currents control water exchange, salt flux and residence time. We used the 3D Estuary, Lake and Coastal Ocean Model (ELCOM) to estimate the dynamics of tidal currents, salt flux and residence time in the Macuse Estuary, central Mozambique. The model was calibrated using data acquired from field-data measurements obtained in 2014 with an acoustic Doppler current profiler and conductivity-temperature-depth (CTD) casts and a tide-gauge. The water flow dynamics that were tracked indicated that tidal currents of 100 cm s −1 were dissipated by friction caused by bathymetric morphology during both the spring and neap tides. The water dissipation was translated into a phase-difference delay of ∼15 min between the catchment zone and the outlet during flood and ebb tides. The study showed that tidal currents and river discharges controlled the salt flux (2.07 × 10 5 g kg −1 m 3 s −1 ) and the variation in residence time from hours to 40 days. The water ages were mostly driven by U-velocity tidal currents, bathymetric gradients and seasonal river discharges of ∼500 m 3 s −1 . River discharges seasonally affected salinity changes between 15 and 30, and changes in the concentration of suspended sediments of ∼300 mg l −1 . In addition, it was shown that ELCOM was able to track the water-particle dynamics well, indicating the model's suitability. These results contribute to our understanding of the effect of water-exchange dynamics on residence time and salt flux in shallow coastal inlet systems.
The east and south coasts of South Africa are characterised by a transition from subtropical to warm-temperate conditions. This transition in environmental temperatures may shape the physiological tolerance of ectothermic species inhabiting harsh environments, such as the intertidal zone. A subtropical (Mngazana Estuary) and a warm-temperate (Knysna Estuary) population of the truncated mangrove snail Cerithidea decollata were selected to investigate thermal tolerance (LT 50 ) and performance (oxygen consumption) across increasing and decreasing air temperatures (at a rate of 2 °C h −1 ) under controlled laboratory conditions. Animals from both populations showed a considerable thermal tolerance, surviving temperatures of over 50 °C. The thermal performances of the two populations under temperature change showed similar trends, with individuals from the Mngazana Estuary displaying higher rates of metabolism than those from the Knysna Estuary. Both thermal tolerance and performance in increasing/decreasing temperatures suggested that this snail shows intraspecific differences in thermal physiology. We discuss the importance of including the effect of microhabitat variability and behavioural thermoregulation when investigating the effect of climatic transition on the thermal physiology of intertidal species. This would enhance our knowledge of the interactions between organisms and their environment, helping to evaluate the likelihood that a species can maintain itself in a changing landscape.
Due to the presence of few dominant predators on South African rocky shores, this coastline could be vulnerable to invasion by predatory crabs. This study applied horizon scanning to create an ordered watch list of alien crab species that could establish along this coastline under present-day and future temperature scenarios. This was done by: (i) identifying the species with both an invasion history and a possible pathway to South Africa; (ii) comparing the temperature ranges of the species' native and introduced distributions to those of each of the four South African ecoregions; and (iii) ranking the species based on their potential ecological impacts. Of the 56 alien predatory crab species known worldwide, 28 species have pathways to South Africa. Incompatible temperature ranges excluded only two species from each ecoregion. Negative ecological impacts in their invaded ranges placed Japanese shore crab Hemigrapsus sanguineus, brush-clawed shore crab H. takanoi and Chinese mitten crab Eriocheir sinensis at the top of the watch list. This study highlights that many alien crab species have the potential to reach South Africa, with most likely to survive. This watch list should be used to support targeted monitoring and so facilitate early detection of these species, should they reach South Africa.
Understanding ecological structures and the dynamics of reef fish assemblages is a fundamental step in current conservation biology. Patterns of abundance and biomass of reef fish communities of the tropical Cabo Verde Archipelago (eastern central Atlantic Ocean) have not been assessed previously. We studied general patterns of reef fish trophic groups and benthic cover at 11 sites around Santa Luzia Island, employing underwater visual census (UVC) and benthic photo-quadrats. Fish assemblage attributes were plotted against several descriptors, such as fishing intensity, water surge, and complexity and type of substrate, using multivariate analysis. The 15 most abundant species accounted for 94.12% of all fishes censused by UVC; nine of these were also among the 15 species with the highest biomass. The families Muraenidae, Pomacentridae and Labridae were the most speciose, while Chromis spp. (Pomacentridae) and Labridae were the dominant groups in terms of both density and biomass. In terms of trophic groups of fishes, planktivores dominated fish density (69%, with 4 species), followed by mobile invertebrate feeders (17.9%, with 13 species), with other groups such as carnivores (3.6%) and roving herbivores (2.7%) being less prevalent. The benthic community was partially dominated by crustose coralline algae and macroalgae (more than 25% of total coverage). The low densities of large piscivorous and carnivorous fishes in the reserve might be directly linked to overfishing. The highest fish and benthic biodiversity were detected in the northwestern Santa Luzia reef sites, indicating this area as a priority for establishment of a no-take zone in the future.
Morphometric variation can be very useful for discriminating 'phenotypic stocks' as groups with similar life-history traits. Such groups are of great importance for accurate population-dynamics modelling for purposes of fishery stock assessment and management, independent of their genetic differences or similarities. This study is a contribution to the stock identification of the sardine Sardina pilchardus off the Moroccan Atlantic coast. The objectives were to (i) assess whether specimens from stocks defined by the FAO correspond to different morphotypes, and (ii) compare the obtained results with those recently published on the genetic variability of the studied populations. Morphometric analyses, using truss variables and landmarks data from sardine sampled from four widely spaced ports of landing along the Moroccan Atlantic coast (from north to south: Larache, Safi, Tantan and Dakhla), were carried out using multivariate and geometric approaches. Principal components analysis of truss variables and cluster analysis of the average shape of the sardine revealed the existence of three distinct morphotypes: 'Larache,' 'Safi-Tantan' and 'Dakhla.' These correspond well with the FAO's stock subdivision. The morphometric variation might be related to the mesoscale hydrodynamic characteristics of the study area. However, these morphometric results do not fully accord with recently published data on genetic variability of the species. Those data indicated the genetic singularity of the Safi population, which could have led to the historical collapse of that sardine stock in the 1970s. Additional work is needed to validate the obtained results by taking into account seasonal variations and transitional areas between stocks.
Most of the Southeast Atlantic Ocean is abyssal, and global bathymetries suggest that only ∼3.2% of the areas beyond national jurisdiction (ABNJ; also known as the high seas, as defined in the United Nations Convention on the Law of the Sea [UNCLOS]) are shallower than 2 500 m. This study mapped bathymetry and characterised substrates in selected seamount summit areas, including several that have been or may become fishing areas. The southernmost location, the Schmitt-Ott Seamount, has exposed volcanic bedrock with surrounding flats covered by thin biogenic sediments and/or coral rubble that appears ancient. At Wüst, Vema, Valdivia and Ewing seamounts the basaltic base appears to be overlain by coral caps and other coral substrates (sheets, rubble). Adjacent summit plains have biogenic sediments of varying thickness. Vema has a flat, roughly circular summit, <100 m deep, with the shallowest point being a 22-m-deep summit knoll; the upper slopes have ancient coral framework, but the summit has a mixture of coralline and volcanic rock and coarse sediments, including extensive areas with coralline algae and kelp forests. Valdivia Bank is a 230-m-deep, flat, rocky area (∼11 × 5 km), protruding steeply from the extensive multi-summit Valdivia subarea of the Walvis Ridge. The distribution of past fisheries in the Convention Area of the South East Atlantic Fisheries Organisation (SEAFO) was considered in relation to the new information on bathymetry and substrate.
In a descriptive study of megafauna of several Southeast Atlantic seamounts, multiple video-transects on upper slopes and summits documented the occurrence of benthic invertebrate taxa, primarily corals, regarded as indicators of vulnerable marine ecosystems (VMEs) as defined in international guidelines. At Schmitt-Ott Seamount there was a pronounced dominance of gorgonian corals (seafans, Alcyonacea). In all other study areas the diversity was greater, and more scleractinians (stony corals, Scleractinia) were observed. Scleractinian corals were mainly dead, and much of the coral framework and rubble may have been ancient. In the Valdivia complex and on Ewing Seamount, which are open to fisheries, scleractinians seemed restricted to some slopes of knolls, and on Valdivia Bank and the subarea denoted Valdivia West the summit substrate was mostly bare rock. Pelagic armourhead Pseudopentaceros richardsoni and splendid alfonsino Beryx splendens (two targets of commercial fisheries in the area) were observed at a few sites, but did not appear to be abundant in the main former fishing areas of the Valdivia area. Orange roughy Hoplostethus atlanticus was common in video records around the summit at Ewing Seamount. The deep-sea red crab Chaceon erytheiae was abundant in the Valdivia area and at Ewing Seamount, and crabs were distributed across a more extensive depth range than the fishes. In areas with high densities of live coral, the video records suggested that the benthic communities were intact and not impacted by fishing. Evidence of past fishing activities included observations of lost pots and rope at Vema Seamount and in the Valdivia area.
A previous study that explored the age and growth of red steenbras Petrus rupestris (Valenciennes, 1830), a large sparid (family Sparidae, seabreams or porgies) endemic to South Africa and reported to approach 2 m in length, provided estimates as a moderately slow-growing species with a maximum age near 30 years. The stock is considered collapsed and a fishing moratorium was imposed in 2012, resulting in this species being assessed as Endangered by the IUCN. One consideration in addressing population status is validation of life-history traits. In this study, estimates of age for red steenbras from thin-sectioned otoliths were reassessed visually in terms of both the original ages and revised estimates using a different age-reading pattern. The revised ages exceeded the original ages by up to 30 years, with a maximum estimated age of 55 years from a well-defined otolith section that provided a basis for the revised age-reading procedure. Bomb radiocarbon ( 14 C) dating revealed there was an offset in the timing of the 14 C rise on the Agulhas Bank that, when coupled with considerations for regional oceanography, provided support for the revised age-reading pattern and an estimated longevity that exceeds 50 years. These findings were further supported by the fortuitous recapture of a tagged red steenbras that was at liberty for 22 years.
Large physical changes that alter reef macrobenthos and fish assemblages occur with increasing depth, so the biological processes that regulate communities at different depths are expected to diverge. We used analyses of stable isotopes (δ13C and δ15N) and fatty acids to establish whether shallow (11-25 m) and deep (45-75 m) warm-temperate reef communities within a South African marine protected area differ in their trophic organisation and nutritional condition. We found evidence of enhanced nutritional condition in plankton from the deeper reef as compared with the shallow reef based on the essential fatty acid content, but this effect was generally not observed in the macrobenthos or the fish communities. Community-based indices derived from the stable isotope data indicated that the shallow-reef community had significantly greater niche diversification (greater diversity of carbon sources at the base of the food web) and more niche space occupied than the deep-reef community. One obvious difference in available carbon sources between reef communities was the absence of benthic primary production on the deep reef, where light is limiting. Our results highlight that the decreased trophic diversity, and to an extent functional redundancy, associated with the simplification of food webs at depth may translate into greater vulnerability of deep reefs to disturbance.
The coastal population of common bottlenose dolphins Tursiops truncatus found in Namibia is regionally isolated and unique. This population faces several potential anthropogenic threats, especially in Walvis Bay, including boat-based tourism, a commercial harbour undergoing expansion, and aquaculture for oysters and mussels. Between 2008 and 2012, 238 boat-based surveys were conducted, resulting in 170 encounters with bottlenose dolphins. Overall, group sizes varied from 1 to 45 individuals (mean 10.7). Encounter rates, group sizes and total numbers of animals identified were higher in winter than in summer field seasons. The number, and survival and immigration parameters, of bottlenose dolphins using Walvis Bay was investigated using robust design and Huggins closed-population mark-recapture models. The highest numbers estimated were in the first and last years of the study, with estimates of 74-82 in 2008 and 76-77 in 2012 (numbers identified and upper 95% confidence limits). The only previously available data, from an incomplete study in the early 1990s, suggested that the population was between 100 and 150 individuals at the time. Although no linear trend in population size was obvious during the current study, the clear evidence of isolation, small population size, low annual birth rate, and potential long-term decrease in numbers since the early 1990s is concerning. Further work to collect data on demographic parameters is urgently recommended with a view to obtaining increased protection for this species.
Genomic data can be a useful tool in the management and conservation of biodiversity. Here, we report the development of genomic resources for the spotted ragged-tooth shark Carcharias taurus using genome-wide DNA data from Illumina next-generation sequencing. We explored two commonly used genetic marker types: microsatellites and mitochondrial DNA. A total of 4 394 putative microsatellites were identified, of which 10 were tested on 24 individuals and found to have ideal properties for population genetic analyses. Additionally, we reconstructed the first complete mitochondrial genome of a South African spotted ragged-tooth shark, and highlight the most informative gene regions to facilitate future primer design. The data reported here may serve as a resource for future studies and can ultimately be applied in the sustainable conservation and fisheries management of this apex predator.
Shorebirds, as migratory aquatic birds and top predators in intertidal ecosystems, can be affected by global environmental changes and escalations in local impacts on coastal lagoons and estuarine trophic networks. Many shorebirds winter in North African Atlantic coastal sites, most likely because these locations provide constant and reliable food supplies with less energy costs in comparison with the wintering sites of northern Europe. Although more information is available for other important southern coastal sites (e.g. Saharan Atlantic coastal desert and Guinean mangroves coast), very little information is available for the North African Atlantic coast. Here, we focus on the impact of shorebird predation on benthic macroinvertebrates in a major wintering site in this area-Sidi Moussa coastal lagoon, Morocco-using an exclosure experiment. For most of the macroinvertebrate species there was no significant effect of the exclusion of shorebird predation. Overall, our results do not show evidence that predation by shorebirds influenced the overall standing biomass of the benthic community. This may indicate that the benthic productivity is high enough to provide constant and reliable food supplies for non-breeding shorebirds.
Spatial dependence can obscure relationships between response and explanatory variables because of structuring within the residuals reducing variance and biasing coefficient estimates. Here, we highlight the influence of the spatial component, in the presence of spatial dependence, on abundance trends. This is illustrated using abundance data for a Critically Endangered reef fish, dageraad Chrysoblephus cristiceps, which were obtained from a long-term monitoring programme in the Tsitsikamma National Park marine protected area, South Africa. Correlograms illustrate distinct spatial structuring in the abundance data, and spatial variables were determined as more important than temporal variables when ranked according to predictive power using a random forest analysis. A generalised additive model (GAM) that did not account for spatial dependencies was compared to a generalised additive mixed model (GAMM) that incorporated a spatial residual correlation structure. Results derived from the spatially explicit GAMM differed considerably from the GAM lacking a spatial component, with the latter deemed to produce over-precise and partially biased abundance trends. The study emphasises the importance of space in accurately modelling abundance estimates, particularly temporal trends, and provides an introduction to the minimal statistical requirements necessary to address the violations associated with spatial autocorrelation.