The phylogenetic affinities of the melanistic subspecies Trachylepis sulcata nigra have never been investigated, and it was unclear if this subspecies represented a locally adapted population or a distinct species. Sequences from the nuclear marker RAG-1 (1149 bp), two novel rapidly-evolving nuclear markers KIF24 and EXPH5 (554 bp and 941 bp respectively), and the mitochondrial gene ND2 (1056 bp) were analysed from 84 individuals of T. s. sulcata and two individuals of T. s. nigra. Additionally, the range of T. s. nigra was estimated using museum records, and correlations between environmental variables and the occurrence of melanism were explored. Molecular analyses depict T. s. nigra as nested within a strongly monophyletic T. s. sulcata, suggesting this population is not genetically isolated or distinct. We therefore recommend T. s. nigra be synonymized with T. s. sulcata. The best predictor of melanism along the coastline in this population is a high number of fog days per year, a finding consistent with studies of melanism in cordylid lizards in southern Africa. Further sampling may determine gene flow levels occurring across the contact zone of melanistic and non-melanistic phenotypes and provide insight into selective forces maintaining this trait.

The degree of maxillary molar tooth-row eruption and wear were used to assign samples of the social giant mole-rat, Fukomys mechowii, from Zambia, into nine relative age classes in order to assess ontogenetic (age) variation and craniometric sexual dimorphism, with reference to body mass. Univariate and multivariate statistical analyses showed craniometric differences between age classes 1–3 and age classes 5–9, with age class 4 being intermediate between these two age class groupings. This suggests that age class 4 lies at a point on a hypothetical growth curve where growth begins to stabilize. The intermediate placement of age class 4 in multivariate space broadly coincided with body mass categorizations into juveniles (age classes 1–3; <100 g), subadults (age class 4; c. 100–150 g), and adults (age classes 5–9; >150 g). The analyses also revealed the absence of sexual dimorphism in the relatively younger age classes 1–4 but its presence in the relatively older age classes 5–9, and these results are supported by data on body mass. These results may have implications in our understanding of the population and social structures, and reproductive strategies in this little-studied giant mole-rat.

Home-range size may reflect the physiological state and energetic requirements of an individual. In the black-tailed tree rat (Thallomys nigricauda) we expected differences in the home-range size of populations in habitats of differing productivity, as measured along an aridity gradient, and between seasons. We studied the variations in home-range size of black-tailed tree rats by radiotracking in winter 2006, 2007 and summer 2007 at three study sites along an aridity gradient in southern Africa. Home ranges were estimated using 100% and 95% minimum convex polygons (MCP) and 95% and 50% fixed kernels. Home ranges varied widely, from 166 to 80 199 m² for males and from 46 to 8810 m² for females. Males had larger home ranges than females, which supports a promiscuous mating system reported for the species. Although range size was reduced in both sexes in winter, this was not significant. We found no significant difference in home-range size along the aridity gradient. It is suggested that a combination of habitat productivity, season and breeding system influences the size of home range and that this species displays phenotypic flexibility in terms of its behavioural responses to these factors.

This study examined a suite of microsatellite markers, originally developed for other parrot species, for their usefulness in providing details about the amount of genetic variation that has been retained in the endangered echo parakeet of Mauritius. Biological samples were available from previous studies and management activities. Four microsatellite markers, originally developed for the African grey parrot, were characterized for use in the echo parakeet. Given its recent population bottleneck, a relatively high level of genetic diversity has been retained in the wild population (H_O = 0.57). The genetic data are examined for their value in the conservation management of this species, both captive and wild. A number of conservation and breeding management issues are highlighted which warrant further investigation, for example in selecting captive breeding pairs and bachelor males for public display. Whilst four mircosatellite loci can only provide a limited insight, they do provide useful information relating to the remaining echo parakeet population and highlight that further genetic studies would prove invaluable to the conservation management of this species.

The composition, abundance, distribution and seasonality of larval fishes was investigated in the permanently open Kowie Estuary on the temperate southeast coast of South Africa. Larval fishes were sampled within the estuary and marina for a period of two years. Samples were collected seasonally at 14 different sampling stations along the main channel and within the artificially-channelled marina by means of boat-based plankton tows. A total of 11 128 larval fishes were collected, representing 23 families and 38 taxa. Clupeidae and Gobiidae were the dominant fish families, contributing 47.0% and 24.7%, respectively, to the total catch. Common species included Gilchristella aestuaria (Clupeidae), Omobranchus woodii (Blennidae), an unidentified blenniid, Caffrogobius gilchristi, Caffrogobius nudiceps, Glossogobius callidus, Psammogobius knysnaensis (Gobiidae) and Solea turbynei (Soleidae) with the other species contributing <1% to the total catch. Catches varied significantly with season and were highest in summer. Estuary-resident species dominated the overall catch (91%). A notable absence of postflexion larvae and early juveniles characterized the artificial channels. This was attributed to the absence of shallow, marginal water habitat, typical of a good estuarine nursery area. The steep walls of the artificial channels reduce refuge areas, increasing predation by larger piscivores.

Fleas, lice, mites and ticks were collected from 41 Rhabdomys pumilio and seven Otomys irroratus at De Hoop Nature Reserve in the Western Cape Province of South Africa. The aims of the study were firstly to quantify parasite abundance and to record the species richness on the rodents. Secondly to record the parasite species that were shared between R. pumilio and O. irroratus and thirdly to compare the parasite abundance on R. pumilio between localities of varying antelope activity. Each rodent was individually examined under a stereoscopic microscope and its parasites were removed, counted and identified to species level. The parasite species included seven flea, one louse, nine mite and 10 tick species. Three undescribed mite species were also recovered and new locality records were obtained for six flea, two lice, two mite and one tick species. Several flea, mite and tick species were shared between R. pumilio and O. irroratus. Both the mean abundance of the total ectoparasite burdens and the mean tick abundance were significantly higher on R. pumilio individuals that were trapped in habitats preferred and occupied by large antelope species compared to habitats in which antelope were absent or rarely present.

Increasing environmental temperatures may lead to better survival of organisms that are usually susceptible to low temperatures. We investigated whether the numbers of the ice rat Otomys sloggetti robertsi, whose populations are regulated by low temperatures, have increased in the recent past as a consequence of current environmental warming in the Lesotho Drakensberg. Ice rats are endemic to the southern African alpine zone, are exclusively herbivorous, have a diurnal activity profile, and live in underground burrows. We predicted that ice rat numbers would remain stable or increase since winters have become milder. We monitored ice rat numbers in three locations, separated by 70, 80 and 130 km. The results show that the population density of ice rats has increased over threefold to 352 ice rats per hectare over the past decade. Our findings suggest that higher temperatures could have improved habitat productivity and reduced thermal stress, and thus improved winter survival of ice rats.

A total of 7748 parasites, belonging to 17 metazoan species, was recorded from 45 specimens of Clarias gariepinus (Burchell, 1822) caught from the Nwanedi-Luphephe Dams, Limpopo River System, South Africa. All host specimens were parasitized by one or more metazoan parasite species. The parasite species included five monogeneans (Gyrodactylus rysavyi, Macrogyrodactylus clarii, Macrogyrodactylus congolensis, Quadriacanthus clariadis and Q. aegypticus), four digeneans (Diplostomum type 3, Tetracotyle sp. metacercaria, Acanthostomum sp. and Glossidium pedatum), two nematodes (Contracaecum larvae and Paracamallanus cyathopharynx), two cestodes (Proteocephalus glanduligerus and Tetracampos ciliotheca), two branchiurans (Chonopeltis inermis and Dolops ranarum), one copepod (Lamproglena clariae) and one unidentified leech. Eleven parasites were satellite species, with low prevalence (<33%) and mean abundance (<12.9 parasites per host). The nematode larvae (L₃) of Contracaecum sp. were the dominant species, constituting 56% of the total metazoans (100% prevalence, mean abundance and mean intensity 96.3). Infra- and component community species richness and diversity were high. The dominance of hostspecific parasite species in the sharptooth catfish confirms that its metazoan fauna has a considerable degree of specificity. This study indicates the importance of ecological determinants of richness in metazoan communities of the sharptooth catfish from dams in an oligotrophic state.

In South Africa, relatively small, but healthy populations of Opsaridium peringueyi remain in the middle reaches of the Luvuvhu, Blyde, Sabie and Pongolo Rivers. The species may be extinct in some rivers like the Shingwedzi and lower-Olifants and its status is uncertain in the Crocodile and lower Komati/Mlumati Rivers. In many cases the rivers are transformed by the combined impact of alien species, dams and weirs, water abstraction, water regulation, pollution from industrial, agricultural, mining, forestry and urban areas as well as by sedimentation. These factors have caused the species distribution to become fragmented and have made it vulnerable to possible extinction. Because of the transformed nature of river systems in South Africa, the use of older historical data for biodiversity planning and conservation assessments might increase the risk of underrating conservation status and risks.

The greater cane rat, Thryonomys swinderianus, utilizes high fibrous plant material and is an important meat source in West Africa. An insight in its digestive physiology will enhance our understanding of its feeding habits. Digestibility coefficients of the food were determined during two seasons before the animals were euthanased. The distribution and concentrations of nutrients and energy in different parts of the gastrointestinal tract were determined at the time of day when animals practised coprophagy. Trial 1 diet in the wet season consisted of 36% neutral detergent fibre (NDF), 11% protein and 49% dry matter, while the Trial 2 diet in the dry season consisted of 53% NDF, 8–9% protein and 89% dry matter. The Trial 2 animals on the poor diet increased their daily nutrient intake, possibly increased the volume of digesta and practised frequently cophrophagy, so that faecal production was reduced and digestibility coefficients were relatively high. Coprophagy increased both protein and energy intake as soft pellets in the distal colon had higher protein and energy content than the hard faeces. Energy, protein and acid-detergent fibre were retained in the caecum of Trial 1 females and the caecum and proximal colon of the Trial 2 animals 16 hours after feeding, illustrating the importance of these two regions in the fermentation process. Water was absorbed in the distal colon as dry matter content of digesta increased 53%, 4% and 56% from the proximal colon to the distal colon. Animals produced hard faeces with only 16% and 5% lower moisture content in the dry season, compared to that produced in the wet season, as water was not a limiting factor during the trials. It was concluded that an increase in daily food intake, an increase in coprophagy and the presence of a colonic separation mechanism (that retains small particles) enable the greater cane rat to utilize high fibrous plant material. These digestive strategies seem to be comparable to those observed in other hystricomorph rodents.

The African unstriped ground squirrel (Xerus rutilus) is widely dispersed across various habitats in East Africa and hence encounters a diverse suite of predators and plant communities. It is not known how different habitats and plant characteristics affect the foraging behaviour of X. rutilus. We used giving-up densities (GUDs) as a measure of foraging efficiency to explore the foraging costs of environmental heterogeneity. To determine foraging efficiency across spatial scales, we established food patches in two microhabitats (open and cover), which were nested within three habitats (koppie, edge and bushland). When foraging in a cover microhabitat, foraging efficiency decreased away from the koppie, but when in the open microhabitat, foraging efficiency was lowest near the koppie edge. Second, to determine foraging efficiency with common plant toxins, we presented the squirrels with seeds soaked in either tannic acid, oxalic acid or distilled water (control). Foraging efficiency did not differ between tannic-treated and control seeds, but oxalic-treated seeds had higher GUDs. Overall, our results suggest that X. rutilus is a remarkably efficient forager across multiple axes of environmental heterogeneity, which may have intriguing consequences for the ecological community.

A semi-quantitative inventory of spider diversity was done in the Blouberg Nature Reserve (BNR) and Western Soutpansberg Conservancy (WSC) situated in the Savanna Biome of the Limpopo Province, South Africa. Two hundred and ninety-six samples of one person-hour work each, comprised of five methods (vegetation beating, sweep netting, aerial hand collecting, ground hand collecting and leaf litter sifting) were divided between four relatively homogenous sites (plant communities) within a vegetation type of the BNR and WSC, respectively, an average of 37 per site. In addition, 25 pitfall traps were left open for a total of 20 days in each of the eight plant communities, 200 in total. We collected 1328 adult spiders representing 186 species of which 31% were singletons in the BNR vegetation type and 909 spiders in 222 species of which 41% were singletons in the WSC vegetation type. The number of species present was estimated using six estimators. The estimates varied between 233 and 307 for the BNR and 302 and 386 for the WSC. Inventory completeness was more than 70%. However, the fit to a lognormal distribution suggests that there are 370 species (750 000 individuals) and 445 (850 000 individuals) species in the universes (16 ha) sampled within the two vegetation types. Collector experience had no effect on the results of the inventory, whereas time of day had a very small yet significant effect. Seasonality only affected abundance and richness, but not assemblage composition. Sampling methods used had the biggest effect on our results. These results are used to design an optimized sampling protocol for standardized inventories in the Savanna Biome.

The amphibian Amietophrynus regularis is distributed throughout equatorial Africa, with presumed introduced populations in the Cape Verde archipelago. Portions of the 12S and 16S rRNA mitochondrial regions of 30 specimens from Kenya, Uganda, Niger, Mali, Burkina-Faso, Ghana, Guinea-Bissau and Cape Verde were used to assess genetic diversity and to identify the most probable geographic origin for the introduction of this toad on the latter archipelago. Two lineages with 1.4% genetic divergence between them were identified in western and eastern Africa. All sequences from the different Cape Verde Islands were identical to each other and to the Guinea-Bissau samples, indicating, together with other historical evidences, that an anthropogenic introduction event probably occurred, possibly from Guinea-Bissau, but further work is needed to confirm this. As previously noted, several individuals from previous genetic studies seem to have been misidentified.

African sharptooth catfish, Clarias gariepinus, is a successful aquatic invader as it has a eurytopic physiology, is highly fecund, grows quickly and has an omnivorous diet. Despite possible threats that include predation of and competition with indigenous species, habitat degradation, and the spread of diseases and parasites, there is a lack of knowledge regarding its ecology and population dynamics within invaded systems. This study presents a mark—recapture experiment to investigate its population structure, natural mortality rate, population size and density within a population inhabiting a small, 76 ha invaded water supply reservoir in the temperate Eastern Cape region, South Africa. The adult population was found to be old ( = 120 ± 29 years) and male-dominated (1.76♂:1♀ for fish < 100 cm TL and 3.77♂: 1♀ for fish > 100 cm TL) with its maximum age estimated at one year less than the age of the reservoir. Adult abundance and density (in terms of numbers and biomass) was relatively low at 1655 fish (CV = 18%), 94.32 kg/ha (CV = 18%) and 21.78 fish/ha (CV = 16%), respectively. The estimated mean natural mortality rate was high at 0.80/year (CV = 82%). The skewed length- and age-structure suggests that the adult population is dominated by the fish that were either the initial colonizers during the reservoir filling phase or were the first internally reproduced recruits. The predominance of old, large fish in the population is also probably suppressing recruitment of younger fish. Despite the population being small, the fish are mobile and feed aggressively. Manual removal using baited longlines could be a feasible removal method.

Predators are important because they influence survival rates, population density and behaviour of prey species. However, assessing the predation pressure facing a particular species is difficult when that species faces a suite of predators. We aimed to characterize the suite of avian predators that are likely to feed on the Namaqua dwarf adder, Bitis schneideri, and used field surveys to assess their relative abundance. We used literature records to map the feeding preferences of avian species, and point counts to estimate relative abundance. Finally, we produced an index of relative predatory pressure (RPP) to assess the relative importance of each avian species as predators. We counted 490 individual birds from 30 species during 39 point counts. A cluster analysis of similarity between diets produced a dendrogram that we split into three functional groups: specialist predators, generalist predators, and non-predators. Specialist predators and generalist predators made up a total of 10.6% of the entire community by abundance. Generalist predators are likely to be the most important predators of Namaqua dwarf adders. We also noted an increased abundance of anthropophylic species outside our study site and suggest that anthropogenic areas could provide regions of increased predation pressure on small vertebrates.

Bulinus nyassanus, endemic to Lake Malawi, is an intermediate host for Schistosoma haematobium and plays an important role in transmission of this parasite along some shorelines on the Nankumba Peninsula in the southern part of the lake. Density of B. nyassanus in shallow water is usually low from January to April and a major population increase takes place during May to August when water temperatures are relatively low (about 22°C) and supposedly suboptimal for B. nyassanus. This study was designed to compare performance (growth, reproduction, survival, and hatchability of egg-masses) of B. nyassanus at four constant temperatures (22, 25, 28 and 31°C). Survival and reproduction were optimal at 25°C while growth and egg development were faster at the higher temperatures. Findings are discussed in view of the population dynamics of B. nyassanus at Cape Maclear.

The ocellated lizards in the Timon lepidus/tangitanus/pater complex include the largest lacertids living in continental Europe and North Africa. Long considered a single species (T. pater), the division of the North African ocellated lizards into two species, T. pater in Tunisia and Algeria, and T. tangitanus in Morocco, is now accepted. In this study we investigated the patterns of genetic diversity in T. tangitanus and T. pater across North Africa. We analysed 12s rRNA and 16s r RNA mtDNA fragments of 26 new samples plus 19 sequences from previous studies, using parsimony, likelihood and Bayesian approaches. Our results confirm the two North African species as well-defined entities. Within T. tangitanus from Morocco, three genetically divergent lineages with geographic congruence were uncovered; one in the north, another widely spread across Central Morocco and one in the High Atlas and farther south. A high level of divergence among the Moroccan lineages suggests the split occurred just after the divergence between T. tangitanus and T. pater. Similar patterns have been found in other species, although more studies are needed to understand the biogeographical events shaping the complex diversity in this region.

The Sahara Desert was recently proposed as the agent of vicariant speciation in the North African elephant-shrew (order Macroscelidea, Elephantulus rozeti). Based on evidence from molecular dating, however, this speciation event was estimated as having occurred in the Miocene, an early date of origin for an extant species, predating the dramatic climatic fluctuations of the Pleistocene. Here, we explore the possibility of more recent connections of populations of this species across the Sahara Desert that would have facilitated faunal exchange through the Last Glacial Maximum. We used ecological niche modelling based on current climatic datasets and known occurrence points to develop models of present-day potential distributions of E. rozeti and related taxa. Given that the Miocene scenario was proposed based on a single set of evidence, we here provide a partial test based on an independent analysis of present and past potential distributions. Our results corroborate the idea of vicariance, but indicate that distributional patterns and ecological characteristics are consistent with a more recent, post-Pleistocene vicariance across an increasingly arid Sahara. We emphasize the importance of multiple sets of evidence to be brought to bear on complex biogeographical questions, and offer models of palaeoclimatic and palaeoecological distributions and independent sources of such information to complement molecular systematic studies.

A junior homonym was detected among fossil echinoid genera and the following replacement name is proposed: Ekerekeia nom. nov. for Farquharsonia Currie, 1927 (nee Collin, 1922). Accordingly, new combinations are herein proposed for the species currently included in this genus: Ekerekeia crenulata (Kier 1972) comb. nov. from Farquharsonia crenulata Kier, 1972 and Ekerekeia somaliensis (Currie, 1927) comb. nov. from Farquharsonia somaliensis Currie, 1927.

Diurnal birds generally sleep during the hours of darkness. Most male southern African sunbirds have pectoral tufts, although the function of these is not always understood. We examined nocturnal tuft display in male malachite sunbirds (Nectarinia famosa) and found that they display their pectoral tufts almost continuously throughout the night, whilst asleep. We suggest the possible function of this behaviour and suggest that these tufts might be a deterrent to predators, as they look like ‘eyes’ in the dark. A review of the use and occurrence of pectoral tufts in southern African sunbird species is also discussed. We suggest the ‘anti-predator’ hypothesis be investigated further.