R. Greenfield

DNA BARCODING REVEALS MICRO-EVOLUTIONARY CHANGES AND RIVER SYSTEM-LEVEL PHYLOGEOGRAPHIC RESOLUTION OF AFRICAN SILVER CATFISH, SCHILBE INTERMEDIUS (ACTINOPTERYGII: SILURIFORMES: SCHILBEIDAE) FROM SEVEN POPULATIONS ACROSS DIFFERENT AFRICAN RIVER SYSTEMS

Background. Under the tropics, less than 40% of known fishes are identified to species-level. Further, the ongo- ing global change poses unprecedented threat to biodiversity, and several taxa are likely to go extinct even before they could be described. Traditional ecological theory suggests that species would escape extinction risk posed by global threats (e.g., climate change) only by migrating to new environments. In this study, we hypothesise that micro-evolutionary changes (evolution within species and populations) are also important mechanisms for the survival of Schilbe intermedius in Africa, a continent subjected to uneven distribution of climate severity. Materials and methods. Using the mitochondrial cytochrome c oxidase subunit I (COI) gene, known as animal DNA barcode, we tested this hypothesis by analysing the genetic diversity and phylogenetic relations between seven populations of S. intermedius across different African river systems. Results. We reveal a clear geographical patterning in genetic variations, with three clear clusters (southern Africa, eastern Africa, and western Africa). In southern Africa, the South African population is distinct from that of Namibia and Botswana. In addition, within Nigerian populations of silver catfish, two sub-clusters emerged from two isolated river systems. We suggest that the phylogeographic pattern within African silver catfish pop- ulations mirror the past effects of selection and gene flow, and that the split within Nigerian silver catfish popu- lations might be the result of micro-evolutionary adaptive responses to local selection pressures. Conclusion. We suggest that the strong genetic difference in African silver catfish among geographically isolat- ed river systems might be the result of in situ micro-evolutionary adaptive responses to changing environments, and that DNA barcode has potential beyond species delimitation.

Richards Bay Harbour: Metal exposure monitoring over the last 34 years

Richards Bay Harbour is South Africas premier bulk cargo port. It was constructed in the Mhlathuze estuary in 1976 and over the past 34 years has become South Africas most modern and largest cargo handling port. Although no official monitoring programme is in progress various studies by different groups have provided relevant data with respect to changing metal levels in brown mussel tissue (Perna perna) over the last 34 years. Eleven elements were analysed in brown mussels from the main channel in Richards Bay Harbour using ICP-MS. The results indicate that the metal concentrations in the mussel tissue remained relatively constant between 1974 and 2005. The mean metal concentrations increased significantly in 2005 possibly due to the construction of the new coal terminal and associated dredging activities. Mean metal concentrations in the 2008 sampling event were also elevated due to increased run off during an above average rainy season.

Blood lactate levels as a biomarker for angling-induced stress in tigerfish Hydrocynus vittatus from the Okavango Delta, Botswana

Although critical in catch-and-release angling, no data are available on angling-induced stress in African gamefish. Blood lactate levels were used as a biomarker for angling-induced metabolic stress in tigerfish caught by angling in the Okavango Delta, Botswana. Blood was drawn and analysed for blood lactate from 66 anaesthetised fish. The landing time, handling time, body mass and total length were recorded prior to reviving and keeping the fish in aerated water for recovery before release. A strong positive relationship (r2 = 0.607) was found between landing time and body mass, as well as significant elevations in blood lactate concentrations following rod-and-line angling, regardless of angling time. These data suggest that longer angling time significantly increases physiological stress, which may have an impact on breading success and mortality in tigerfish.

Ecological risk assessment of trace elements in sediment: A case study from Limpopo, South Africa

This study aimed to determine the ecological risk posed by metals, in sediments from the Nyl River system in Limpopo, South Africa. Metals were extracted from sediment samples by aqua regia microwave digestion and were analysed using standard ICP-OES techniques. The ecological risk indices applied to the data included Contamination Factor, Pollution Load Index, Geo-accumulation Index and Enrichment Factor. The results showed that the levels of Ni at STW and NYL in the HF period exceeded the Canadian Sediment Quality Guidelines by a factor of 1.36 and 1.83 respectively whereas NYL and MDD had 2.57 and 1.32 times the allowed limit of Ni in the LF period. During the HF period, the GC site exceeded the allowed limit of Zn by a factor of 1.04 and NYL had 1.21 times the allowed Zn in the LF period. The levels of metals are generally low near the origin of the river and increase moving downstream. The levels of metals in the Nyl River floodplain, a Ramsar accredited wetland, were high with CF scores ranging between 0.905 and 5.82, Igeo values with a range of -0.541 to 2.441 and EF scores ranging from 0.959 to 6.171. and posed a greater risk than the other sites. This indicated that the wetland is performing its ecological function by trapping and removing toxins from the water body. The Pollution Load Index determined that the Golf Course (PLI=4.586) and STW (PLI=2.617) sites were polluted only in the low flow period whereas the Nyl River floodplain (HF PLI=79.845; LF PLI=30378.768) and Moorddrift Dam (HF PLI=1.903; LF PLI=9.256) sites were polluted in high flow and low flow periods.

The usefulness of transplantation studies in monitoring of metals in the marine environment: South African experience

Due to their close proximity to the point sources of pollution, estuaries and harbours are exposed to metals. Mussels are used worldwide to monitor marine pollution due to their ability to take up contaminants and the ease of transplantation. Mussels were collected from two reference sites and transplanted in Richards Bay Harbour (2006 and 2010) and in three harbours. Transplanted and resident mussels were removed after 6 weeks exposure and metal concentrations were analysed using ICP-MS techniques. Transplanted mussels had higher metal concentrations than the resident mussels. This was attributed to regulation of metals by the resident mussels. Metal regulation was greater in mussels that are continuously submerged as opposed to those that undergo tidal influences. For monitoring it is essential that the reference population for transplantation is considered carefully as upwelling events in the pristine reference location results in significant increases in metal bioaccumulation.

Heavy metal concentrations in the water of the Nyl River system, South Africa

The Nyl River floodplain, a Ramsar site that provides habitat for a number of endangered species, is one of the jewels in the arid Limpopo province and thus its conservation and protection are vitally important. Very little work has been done on assessing its water quality and no data have been published on the metal concentrations found in this valuable system. The aim of this project was thus to provide baseline data for metal concentrations in the Nyl River floodplain system and to determine whether there were any point sources of pollution or if its metal levels were natural. Eighteen localities along the course of the Nyl River were selected as sampling sites. Water samples were collected quarterly, between August 2001 and July 2002, and analysed using ICP-MS to determine metal content. Zinc, copper, iron, selenium, cadmium, lead, aluminium, arsenic, chromium and manganese concentrations were determined. Although metal concentrations in the water were greater than target water quality range (TWQR) values for aquatic ecosystems, they remained relatively constant throughout the system and posed little or no potential threat to the system. The results suggest that the metal content originates from natural sources.

Revisiting species delimitation within the genus Oxystele using DNA barcoding approach.

Abstract The genus Oxystele, a member of the highly diverse marine gastropod superfamily Trochoidea, is endemic to southern Africa. Members of the genus include some of the most abundant molluscs on southern African shores and are important components of littoral biodiversity in rocky intertidal habitats. Species delimitation within the genus is still controversial, especially regarding the complex O. impervia / O. variegata. Here, we assessed species boundaries within the genus using DNA barcoding and phylogenetic tree reconstruction. We analysed 56 specimens using the mitochondrial gene COI. Our analysis delimits five molecular operational taxonomic units (MOTUs), and distinguishes O. impervia from O. variegata. However, we reveal important discrepancies between MOTUs and morphology-based species identification and discuss alternative hypotheses that can account for this. Finally, we indicate the need for future study that includes additional genes, and the combination of both morphology and genetic techniques (e.g. AFLP or microsatellites) to get deeper insight into species delimitation within the genus.

Bacterial levels in the Nyl River system, Limpopo province, South Africa

Because water quantity and quality are of great importance in the arid Limpopo province, the bacterial content of water in the Nyl River System and its possible origins were assessed at five sites. Quarterly surveys took place between April 2001 and July 2002 and the water was analysed for bacterial counts using standard procedures. Heterotrophic plate counts, faecal coliform counts and total coliform counts indicated that the system was stressed. The Modimolle sewage treatment works and local agricultural activities were found to be the point and diffuse sources of bacterial contamination, respectively.

A baseline study of metal contamination along the Namibian coastline for Perna perna and Choromytilus meridionalis.

The use of bivalves such as the brown mussel (Perna perna) and the black mussel (Choromytilus meridionalis) is common in the study of marine pollution and the effect of these pollutants on ecosystems and are important in both economic and ecological roles. Namibian marine ecosystems are threatened by pollution from mining, commercial fishing and population growth. The aims of this study were to determine baseline metal concentrations, spatial variation and variation between species. Metal levels in C. meridionalis from Guano Platform (GP) are the lowest of all the sites. The most polluted sites are Rocky Point (RP), Halifax Island (HIL) and between Walvis Bay and Swakopmund (WS). The bioaccumulation of metals between P. perna and C. meridionalis were not uniform for all metals. Overall the study indicates the condition of the coastline to be mostly normal, with Cd and Pb levels being of concern.

Metal accumulation in House Sparrow (Passer domesticus) from Thohoyandou, Limpopo province, South Africa

Studies on metal pollution (cadmium, cobalt, chromium, copper, manganese and nickel) in South African terrestrial environments are severely lacking. Due to being relatively unaffected by industrialisation, the Thohoyandou region may provide data on natural levels of metals for use as baseline data. The House Sparrow (Passer domesticus) was chosen as a bio-indicator of metal pollution due to its abundance, non-migratory lifestyle and close association with humans. The aims were to determine the viability of using feathers as a non-lethal bio-indicator tissue compared with muscle. Plume feathers, flight feathers and muscle tissue were analysed using ICP-OES techniques. Analyses of tissue metal concentrations identified the following trend: plume feather > flight feather > muscle tissue. Within the Thohoyandou region, Magondi, which was affected by anthropogenic activities at the time of sampling, had significantly higher concentrations (p ≤ 0.05) for each of the metals, indicating potential metal contamination from various sources. Alternatively, Makonde had the lowest metal concentrations and may be an important reference site for future comparative studies. The results showed that the House Sparrow can be used as a bio-indicator organism in South African terrestrial environments. The plume feathers indicate that they are a good non-lethal tissue for determining metal pollution levels on a temporal scale, indicating recent metal exposure.