Private Bag X2

South Africa

Private Bag X2

South Africa
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Roberts M.J.,Private Bag X2 | Mullon C.,Institute Of Recherche Pour Le Developpement Ird
African Journal of Marine Science | Year: 2010

Present knowledge of ocean currents based on in situ observation and models suggests that passive biological material such as eggs and larvae can be advected offshore away from the Agulhas Bank, South Africa, and hence removed from the ecosystem on which their survival and recruitment depends. Such losses have been cited as the root cause of the sudden drop in annual squid catches experienced in 2001. In this study, a Lagrangian IBM (individual-based model) coupled to a ROMS (regional ocean model system) model was used to investigate this hypothesis. Three simulations were performed for 12 model months using neutrally buoyant particles released from the seabed (120 m) every second day on the mid-shelf of the eastern, central and western regions of the Agulhas Bank. Boundary effects and resolution precluded the release of virtual particles on the inshore spawning grounds. Particles were given lifespans of 40 days. Results demonstrated large particle losses from the eastern Agulhas Bank (76%) and the western Agulhas Bank (64%). In contrast, few particles were lost from the central Agulhas Bank (2%), making this, in terms of the model, the most suitable place on the Agulhas Bank for spawning. Visualisation of the ROMS outputs revealed that leakage on the eastern Agulhas Bank was caused by a cyclonic eddy resident in the Agulhas Bight. Similarly, leakage from the western Agulhas Bank was caused by deep-water cyclonic eddies in the adjacent Atlantic Ocean.


Grote B.,Leibniz Center for Tropical Marine Ecology | Grote B.,University of Bremen | Ekau W.,Leibniz Center for Tropical Marine Ecology | Stenevik E.K.,Norwegian Institute of Marine Research | And 5 more authors.
ICES Journal of Marine Science | Year: 2012

Larval mortality in marine fish is strongly linked to characteristic traits such as growth and condition, but the variability in these traits is poorly understood. We tried to identify the variability in growth in relation to conditions leading to greater survival chances for early stages of Cape hake, Merluccius paradoxus and M. capensis, in the Benguela upwelling ecosystem. During two cruises in 2007 and one cruise in 2008, hake larvae and juveniles were caught. Otolith microstructures revealed a larval age ranging from 2 to 29 days post-hatching (dph), whereas juvenile age was 67152 dph. RNA:DNA ratios, used to evaluate nutritional condition, were above the relevant threshold level for growth. No strong coupling between growth and condition was detected, indicating a complex relationship between these factors in the southern Benguela ecosystem. Merluccius paradoxus juveniles caught in 2007 (the surviving larvae of 2006) had significantly higher larval growth rates than larvae hatched in 2007 and 2008, possibly indicating selection for fast growth in 2006. High selection pressure on growth could be linked to predation avoidance, including cannibalism. © 2012 International Council for the Exploration of the Sea. Published by Oxford University Press. All rights reserved.


Jaquemet S.,University of Reunion Island | Jaquemet S.,Rhodes University | Ternon J.F.,IRD Montpellier | Kaehler S.,Rhodes University | And 5 more authors.
Deep-Sea Research Part II: Topical Studies in Oceanography | Year: 2014

The Mozambique Channel (western Indian Ocean) is a dynamic environment characterised by strong mesoscale features, which influence all biological components of the pelagic ecosystem. We investigated the distribution, abundance and feeding behaviour of seabirds in the Mozambique Channel in relation to physical and biological environmental variables, with a specific interest in mesoscale features. Seabird censuses were conducted in summer and winter during 7 cruises in the southern and northern Mozambique Channel. Tropical species accounted for 49% of the 37 species identified and 97% of the individuals, and species from the sub-Antarctic region constituted 30% of the identifications. The typically tropical sooty tern (Onychoprion fuscata) was the dominant species during all cruises, and overall accounted for 74% of the species observations and 85% of counted birds. Outputs of Generalised Linear Models at the scale of the Mozambique Channel suggested that higher densities of flying and feeding birds occurred in areas with lower sea surface temperatures and lower surface chlorophyll a concentrations. Most of the flocks of feeding birds did not associate with surface schools of fish or marine mammals, but when they did, these flocks were larger, especially when associated with tuna. While tropical species seemed to favour cyclonic eddies, frontal and divergence zones, non-tropical species were more frequently recorded over shelf waters. Sooty terns foraged preferentially in cyclonic eddies where zooplankton, micronekton and tuna schools were abundant. Among other major tropical species, frigatebirds (Fregata spp.) predominated in frontal zones between eddies, where tuna schools also frequently occurred and where geostrophic currents were the strongest. Red-footed boobies (Sula sula) concentrated in divergence zones characterised by low sea level anomalies, low geostrophic currents, and high zooplankton biomass close to the surface. Our results highlight the importance of mescoscale features in structuring the tropical seabird community in the Mozambique Channel, in addition to segregating tropical and non-tropical species. The mechanisms underlying the segregation of tropical seabirds seem to partially differ from that of other tropical regions, and this may be a consequence of the strong local mesoscale activity, affecting prey size and availability schemes. Beyond characterising the foraging habitats of the seabird community of the Mozambique Channel, this study highlights the importance of this region as a hot spot for seabirds; especially the southern part, where several endangered sub-Antarctic species over-winter. © 2013 Elsevier Ltd.


PubMed | French Research Institute for Exploitation of the Sea, Private Bag X2, GENOSCREEN and IRD Montpellier
Type: Journal Article | Journal: PloS one | Year: 2015

Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers (neutral) and 9 non-neutral markers. The variability of neutral markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 non-neutral markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87-90%), and assignment index. ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24-27%), low assignment index and significant inbreeding. Finally, the 34 neutral and 3 non-neutral microsatellites markers were tested on four economically important Scombridae species-Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.


Kirkman S.P.,Private Bag X2 | Kirkman S.P.,University of Cape Town | Meyer M.A.,Private Bag X2 | Thornton M.,University of Pretoria
African Journal of Marine Science | Year: 2010

A mass stranding of false killer whales Pseudorca crassidens at Long Beach near the village of Kommetjie (34°8.18′ S, 18°9.77′ E) on the Cape Peninsula, South Africa, in May 2009 is described. The estimated size of stranded group was 55 animals, which is close to the median size of P. crassidens groups that have stranded previously in South Africa (58). Five of the stranded individuals succumbed, 36 were euthanised and 14 were rescued. This was the eighth known mass stranding of this species to occur in South Africa, with all these events occurring on the irregular south-west coast of the Western Cape province. © NISC (Pty) Ltd.


Crichton M.,University of Cape Town | Hutchings L.,University of Cape Town | Lamont T.,Private Bag X2 | Jarre A.,University of Cape Town
Journal of Plankton Research | Year: 2013

An index of upwelling and temperature profiles (indicating the dynamics of the upper mixed layer) gave a good qualitative prediction of the dominance of either small (4-10 μm) or intermediate-to-large (10-74 μm) phytoplankton cells in surface waters of St Helena Bay, a semi-enclosed bay in the Southern Benguela upwelling region on the west coast of South Africa. Phytoplankton cell size was determined with particle volume estimates obtained with a Coulter Counter. Predictions were made using a decision tree incorporating size-based theory and requiring wind and temperature data. Overall, the dominant phytoplankton cell size was correctly predicted 84% of the time. Successful prediction was higher in winter than in summer and higher for water offshore of the upwelling front. The transport of phytoplankton cells from adjacent water masses, variable re-seeding mechanisms and undetected non-phytoplankton cells hampered the achievement of full prediction success. The results of this study are of relevance to the assessment of the monthly feeding habitat available to zooplankton and juveniles of small pelagic fish, and a step towards understanding the trophic functioning of the Southern Benguela at the sub-annual scale. © 2013 The Author.


Distiller G.,University of Cape Town | Altwegg R.,South African National Biodiversity Institute | Altwegg R.,University of Cape Town | Crawford R.J.M.,Private Bag X2 | And 2 more authors.
Marine Ecology Progress Series | Year: 2012

Marine systems are under pressure from both climate change and exploitation. While many of these ecosystems are inherently variable and hard to monitor, seabirds can be used as ecological indicators that provide early warning signals of deeper environmental change. The Agulhas-Benguela marine ecosystem around southern Africa has exhibited long-term changes in sea surface temperature, and the distribution of pelagic fish in this system has shifted. The Cape gannet Morus capensis is a seabird endemic as a breeding species to the Agulhas-Benguela ecosystem. Cape gannets breed at just 6 locations and are listed by the IUCN as Vulnerable. Knowledge of the survival and movements of a species is important for understanding of factors influencing its conservation. A random effects multistate capture-recapture model was used to estimate the annual survival probabilities and movement between colonies for adult birds at the 3 South African colonies of the species. The effects on survival of environmental and fisheries-related covariates were explored. Survival over the 20 yr period did not exhibit any long-term trend at the 2 southern colonies (Malgas and Bird Islands) but decreased at Lambert's Bay between 1996 and 2007. At all 3 colonies, adult birds showed a high degree of site fidelity. It may be that for Cape gannets, the primary effects of climate and fishing are on recruitment rather than on survival. The continued use of sub-optimal conditions by the west coast colonies has been referred to as an 'ecological trap' and necessitates the introduction of spatial considerations into fisheries management. © Inter-Research 2012 · www.int-res.com.


Jackson J.M.,University of Cape Town | Rainville L.,University of Washington | Roberts M.J.,Private Bag X2 | McQuaid C.D.,Rhodes University | Lutjeharms J.R.E.,University of Cape Town
Continental Shelf Research | Year: 2012

The Agulhas Current on the east coast of South Africa is a major western boundary current that exchanges heat and salt between the Indian and South Atlantic Oceans. The current retroflects as it deflects away from the African continent at the southern tip of the Agulhas Bank, a biologically productive extension of the continental shelf south of the South African coast. The less energetic Benguela Current borders the Agulhas Bank to the west. Little is known about mesoscale interactions between the Agulhas Current and the shelf waters of the Agulhas Bank or how these processes influence the biology of the bank. In this study, physical and biological data collected during a dedicated cruise in September 2010 allowed the identification of several mesoscale features that indicate a strong effect of the current on the bank, including a Natal Pulse that forced the Agulhas Current onto the Agulhas Bank. While on the bank itself, the current entrained particles that were then transported offshore. We also found evidence of upwelling on the southeast edge of the Agulhas Bank, which is thought to be a source of water for a cold ridge that characterizes the eastern region of the bank. Large fluctuations of the thermocline, consistent with internal waves, were observed inshore of the Agulhas Current, with high phytoplankton concentrations at their crests. We suggest that this is a physical effect, with doming of the waves concentrating plankton at their crests, thereby creating episodic biological hotspots. © 2012 Elsevier Ltd.


Boat ADCP surveys and an eight-month deployment of a 1 200 kHz ADCP were used to study the nearshore (5-25 m depth) current and temperature patterns along the eastern coastal region of Algoa Bay, on the south-east coast of South Africa. The boat surveys showed three distinct alongshore current patterns: all eastward, all westward, and a complex mix of flows. High variance in the upper layers of the water column, possibly caused by rip currents, eliminated the use of ADCP mooring data between 0-9 m, but analysis of the remainder of the data (10-19 m) indicated a dominant alongshore current alternating between eastward and westward flows, with velocities of up to 75 cm s-1 at a depth of 10 m and 65 cm s-1 at 19 m. Average velocities for these depths were 17.6 cm s-1 and 10.8 cm s-1 respectively. The frequency of eastward flow almost equalled westward flow (56% vs 47% respectively) over this period. A good correlation between wind and current direction indicated wind to be the primary driving force of the nearshore currents in eastern Algoa Bay. Net monthly displacement in the midwater layer (10 m) ranged between 60 km and 260 km, with eastward advection in seven of the eight months under study. Net monthly displacement in the bottom layer (19 m) was eastwards for all study months, and ranged from 8 km to 296 km. These results imply a strong likelihood that neutrally buoyant, passive material such as eggs and larvae of fish and invertebrates will be exported beyond the boundaries of a proposed marine reserve (the Greater Addo Marine Protected Area) in eastern Algoa Bay and onto the Transkei shelf. Bottom temperature data from the mooring and SST satellite imagery indicated that a warm-water plume from the Agulhas Current entered Algoa Bay and influenced the coastal current and unusually increased water temperature over a period of three days. Similarly, cold water from the adjacent Port Alfred upwelling area also entered the eastern sector of Algoa Bay, more commonly than warm-water intrusions. © NISC (Pty) Ltd.


Samaai T.,Private Bag X2 | Gibbons M.J.,University of the Western Cape | Kerwath S.,Forestry and Fisheries Fisheries Branch | Yemane D.,Private Bag X2 | Sink K.,South African Institute For Aquatic Biodiversity
Marine Biodiversity | Year: 2010

A total of 96 species of sponge were recorded in a bathymetric survey conducted within the iSimangaliso Wetland Park. Non-random processes are hypothesised to account for the decline in species richness with increasing depth, and the data add support to Rapoport's rule. Morphological and colour diversity were strongly correlated and decreased with depth. Five communities could be identified at the 30% level of similarity using cluster analysis, and these correspond to intertidal and shallow subtidal (to 10 m), deep sub-photic zone (coral reefs: 10-30 m), deep reefs (40-90 m), canyon margin (100-140 m) and canyon (140-360 m). The data add support to recently hypothesised bathymetric zones around South Africa. © 2010 Senckenberg, Gesellschaft für Naturforschung and Springer.

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