Eureka and beyond: mining's impact on African urbanisation

This collection brings separate literatures on mining and urbanisation together at a time when both artisanal and large-scale mining are expanding in many African economies. While much has been written about contestation over land and mineral rights, the impact of mining on settlement, notably its catalytic and fluctuating effects on migration and urban growth, has been largely ignored. African nation-states’ urbanisation trends have shown considerable variation over the past half century. The current surge in ‘new’ mining countries and the slow-down in ‘old’ mining countries are generating some remarkable settlement patterns and welfare outcomes. Presently, the African continent is a laboratory of national mining experiences. This special issue on African mining and urbanisation encompasses a wide cross-section of country case studies: beginning with the historical experiences of mining in Southern Africa (South Africa, Zambia, Zimbabwe), followed by more recent mineralizing trends in comparatively new mineral-producing countries (Tanzania) and an established West African gold producer (Ghana), before turning to the influence of conflict minerals (Angola, the Democratic Republic of Congo and Sierra Leone)

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Trends in fishery resource utilisation on the Great Fish Estuary

Potts, W.M., Cowley, P.D., Corroyer, B. & Næsje, T.F. 2005. Trends in fishery resource utilisation on the Great Fish Estuary. - NINA Report 50. 34pp. The Great Fish Estuary, located in the Eastern Cape Province, is becoming an increasingly popular fishing venue. A resource utilisation study consisting of a series of roving creel interview surveys was conducted in the estuary between March 200 I and February 2002 and between October 2003 and September 2004. During interviews with resource users, demographic informat ion as well as catch, effort, bait, duration of the fishing trip and number of rods/lines were obtained. Recreational shore fishers dominat ed during both study periods (54 %, both periods), followed by subsistence fishers (40 % - 1st st udy period, 23 % - 2nd study period) and recreat ional boat fishers (5 % - 1st study period, 23 % - 2nd st udy period). The increase in recreational boat fishers between the two study periods, was most probably attributed to the increased sampling on weekend days during the second study period and to the improved infrastructure at the Fish River Diner Caravan Park. Spotted grunter (Pomadasys commersonnii) and dusky kob (Argyrosomus japonicus) dominated the catches during both st udy periods. The overall catch per unit effort was lower during the second (0.19 fish/angler-hour) than during the first (0.22 fish/angler-hour) study period, while the distribution of fishing effort was more widespread during the second study period than in the fi rst . The total fishing effort during the second study period was twice as high (122 044 hrs), while the total catch was only o ne third higher (18 978 fish) than in the first study period (60 436 hrs and 12 752 fish, respectively). Results from the two study periods were used to make recommendations for the design of future estuarine fishery surveys. While the study showed a variety of short -term fluctuations, long term monitoring studies are recommended to examine trends in the Great Fish Estuary fisheries and other estuarine fisheries in South Africa. Subsistence fishery, recreational fishery, bait fishery, datacollection protocols, managemen

Preface: Linefish resilience in the Anthropocene

No Abstrac

Assessing trophic adaptability is critical for understanding the response of predatory fishes to climate change: a case study of Pomatomus saltatrix in a global hotspot

There is a growing need to incorporate biotic interactions, particularly those between predators and their prey, when predicting climate-driven shifts in marine fishes. Predators dependent on a narrow range of prey species should respond rapidly to shifts in the distribution of their prey, whereas those with broad trophic adaptability may respond to shifts in their prey by altering their diet. Small pelagic fishes are an extremely important component of the diet of many marine predators. However, their populations are expected to shift in distribution and fluctuate in abundance as the climate changes. We conducted a comparative study of the seasonal diet of adult Pomatomus saltatrix over two periods (June–December 2006 and 2012) and examined the available data on small pelagic fishes biomass in a global hotspot (the coastal region of southern Angola, southern Africa) to gain an understanding of the tropic adaptability of the species. Despite a drop (630 000 t to 353 000 t) in the abundance of their dominant prey (Sardinella aurita) in the region, it remained the most important prey item during both study periods (Period 1 = 99.3% RI, Period 2 = 85.3% RI, where %RI is a ranking index of relative importance). However, the diet during Period 2 was supplemented with prey typically associated with the nearshore zone. The seasonal data showed that P. saltatrix were capable not only of switching their diet from S. aurita to other prey items, but also of switching their trophic habitat from the pelagic to the nearshore zone. These findings suggest that P. saltatrix will not necessarily co-migrate if there is a climate-driven shift in the distribution of small pelagic fishes (their dominant prey). Accordingly, understanding the trophic adaptability of predators is critical for understanding their response to the impacts of climate change.Keywords: bluefish, diet, feeding, predator, shad, small pelagic fishe

Can long-term content analysis of print media be used to examine species composition, population demography and changes in distributional range of recreational fishery species?

Although marine recreational fisheries are socially and economically important, there is often limited funding for their monitoring and assessment. With South African anglers reporting catch declines for almost all targeted species and little long-term monitoring data available, novel methods need to be explored to provide managers with additional information. This study aimed to evaluate the efficacy of content analysis of print-media records for detecting long-term trends in species composition, size composition and distribution of selected recreational fishery species. Information for eight fishes captured in the marine shore-based fishery was collected from South Africa’s most popular recreational fishery magazine, between 1960 and 2009. During the five decades, there were shifts in the catch composition, from being dominated by slow-growing, large predators to faster-growing, large predators and lower-trophic-level species. There were no significant trends in the mean and maximum sizes of the dominant species, except for dusky kob Argyrosomus japonicus, which increased significantly in the maximum size reported during the study period. The distributional range of A. japonicus and leervis Lichia amia significantly increased, and that of galjoen Dichistius capensis significantly decreased. However, it was uncertain whether these trends could be attributed to population changes, changes in angler technology and/or behaviour, or climate signals. Overall, this type of content analysis may provide a cost-effective method to examine changes in species composition and fish distributions over time, but, without detailed knowledge of shifts in angler behavioural patterns, it may not be as useful for understanding changes in the population dynamics of recreational fishery species. It is suggested that fishery-independent monitoring programmes are most suited for this type of complex fishery.Keywords: angling magazine, Argyrosomus japonicus, catch trends, citizen science, Dichistius capensis, Lichia amia, recreational fish stocks, shore-based fishin

Preliminary observations of the reproductive biology of the Frenchman seabream Polysteganus baissaci (Sparidae) from Mauritius

The Frenchman seabream Polysteganus baissaci is an important commercial fish species found on the slopes of the fishing banks of the exclusive economic zone of Mauritius. Exploitation of this species started in 2007, and it is targeted using hydraulic reels with baited hooks. The introduction of suitable management measures is important for this fishery and a sound understanding of the biology is required. Monthly biological data were collected over a 2-year period from fish landed in the commercial catch, to investigate aspects of the biology. A total of 698 females and 1 129 males (sex ratio 1:1.6) were collected from commercial fishing vessels operating on the Nazareth Bank. Females dominated smaller size classes (30–36 cm total length [TL]), whereas males were mostly present at larger sizes (37–44 cm TL). Although ripe and spent female gonads were found throughout the study period, the gonadosomatic index (GSI) revealed a peak in spawning between April and September, coinciding with the cooler sea temperatures in the region. Male GSI (0.169 [SD 0.0443]) during its peak month (August) was more than 14-times lower than the female GSI (2.470 [SD 1.0185]) during its peak month (July), and this, together with male and female length frequencies and adult sex ratios, provides strong supporting evidence for protogyny in this species. Although this fishery appears to harvest adults exclusively, which is positive in terms of sustainability, the potential hermaphroditism in this species necessitates implementation of a conservative harvest strategy, including effort limitation and a closed fishing season over the peak spawning period.Keywords: condition factor, gonadosomatic index, gonad staging, Nazareth Bank, protogyny, sex ratio, western Indian Ocea

Localised intermittent upwelling intensity has increased along South Africa’s south coast due to El Niño–Southern Oscillation phase state

The El Niño–Southern Oscillation (ENSO) phase state is reported to drive interannual variability in sea temperatures along South Africa’s south coast through its influence on wind-induced upwelling processes. Whether ENSO drives the intensity of localised, abrupt, intermittent upwelling is less well known. To explore this relationship, we used an index of localised, extreme (>2 °C anomaly), intermittent upwelling intensity, derived from in situ sea temperature data within the Tsitsikamma National Park Marine Protected Area, and quantified the relationship between annual cumulative upwelling intensities (1991–2013) with an annual ENSO index, namely the Southern Oscillation Index. We found that ENSO phase state modulates the cumulative intensity of extreme intermittent upwelling events during an annual period, with more and greater events during La Niña phases compared with El Niño phases. Furthermore, these extreme upwelling events have increased with time along South Africa’s south coast as ENSO phase state becomes more intense and variable. Our findings support the emerging notion that the biological effects of climate change may be manifested through increased environmental variability rather than long-term mean environmental changes as ENSO is predicted to remain the dominant driver of local climate patterns in the future.Keywords: coastal climate change, environmental variability, La Niña phases, sea surface temperature, time-series data, underwater temperature, upwelling inde

Physiological stress response and recovery of an important estuarine fishery species, dusky kob Argyrosomus japonicus, after a simulated catch-and-release event

Catch and release (C&R) angling is a popular pastime the world over; however, studies have found that fish can experience considerable stress during a C&R event. To determine the effect of a C&R event on angled fishes, the physiological stress response (PSR) is often assessed. However, the peak PSR only occurs after a delay and is species-specific. The dusky kob Argyrosomus japonicus is a threatened species that is heavily exploited in South African estuarine fisheries. Given its collapsed-stock status, it is critical to understand the effects of C&R angling on the PSR of this species. The aim of this study was to plot the time-course of the PSR of A. japonicus to determine when the peak PSR occurs. Time had a significant effect on blood lactate (p < 0.05) and glucose (p < 0.05) levels, with both peaking 30–40 minutes after a stressor, but time did not have a significant effect on plasma cortisol levels (p > 0.05). Blood lactate and glucose levels reached recovery by 150 minutes. The results suggest that blood sampling should be done 30–40 minutes after a stressor, and although A. japonicus is able to recover quickly from a C&R event, its delayed PSR may render it vulnerable to post-release predation. Keywords: angling, blood lactate, blood glucose, cortisol, physiology, recreational fisheries, South Afric