Cryptic diversity in the common flap-necked chameleon Chamaeleo dilepis in South Africa

The spatial genetic structure of a species, and whether distinct genetic lineages are present, is strongly influenced by their biology and habitat requirements. Given habitat specificity and low vagility, many herpetofaunal species are reservoirs for high levels of cryptic diversity; chameleons are a case in hand. The common flap-necked chameleon Chamaeleo dilepis has a large range that spans much of sub-Saharan Africa. Within South Africa, the species is largely confined to the north-eastern and central areas of the country, and occurs from the coastal forests in southern KwaZulu-Natal westwards into Namibia. Their large range, together with anecdotal evidence that there is considerable morphological and phenotypic diversity across the range, suggests a questionable taxonomy with possible cryptic lineages. The aims of the present study were to investigate whether C. dilepis is genetically structured across parts of its South African range, and whether this species (as it currently stands) might include cryptic lineages. To this end, 72 C. dilepis individuals sampled from four localities across South Africa (Gauteng, n = 2; KwaZulu-Natal, n = 2) were sequenced for two mitochondrial markers (ND4 and 16S). The phylogenetic results suggest that C. dilepis is indeed spatially structured. In addition, the large sequence divergence values between groups strongly suggests the presence of cryptic lineages and, pending the inclusion of more data from a larger geographic range, the group may be in need of a taxonomic revision.     

Species identification,distribution and abundance of Gerreidae (Teleostei) Bleeker,1859 in the estuaries of Natal

Comparison of published meristic and taxonomic data with measurements taken from specimens collected from Natal estuaries have provided information for an identification key to the Gerres of southern Africa. Body markings were different on each species of fry (< 40 mm S.L.) as well as immatures and adults (> 40 mm S.L.). A comparison of otoliths from the different species showed that they can be used to Identify specimens from a standard length of 20 mm. Turbidity may be a factor limiting the distribution of the genus in estuaries. The known distribution of Gerres species in the estuaries of southern Africa is given. The species of Gerres which is dominant in a particular locality depends on the salinity.     

A New Freshwater Goby (Teleostei: Gobiidae) from the Pongolo Floodplain,Zululand, South Africa

A new freshwater goby, Mugilogobius pongolensis sp. n. is described and figured as a species new to southern and eastern Africa. This record extends the zoogeographcal distribution of Mugilogobius Smitt, 1899, from the Indonesian archipelago and South Australia to the Indian Ocean and the eastern coast of Africa.     

Distribution and ecology of lesser pouched rat,Beamys hindei,in Tanzanian coastal forests

The lesser pouched rat, Beamys hindei, is a small rodent that is patchily distributed in the Eastern Arc Mountains and coastal forests in East Africa. The ecology of this species and its current distribution in coastal forests is not well known. Therefore, we conducted a study in selected coastal forests to assess the current distribution of the species and to investigate the population ecology in terms of abundance fluctuations and demographic patterns. Assessments of the species distribution were conducted in 5 forests through trapping with Sherman live traps. Data on ecology were obtained from monthly capture–mark–recapture studies conducted for 5 consecutive nights per month in two 1 ha grids set in Zaraninge Forest over a 2‐year period. The results indicate the presence of B. hindei in 3 forests where it was not previously recorded. The population abundance estimates ranged from 1 to 40 animals per month, with high numbers recorded during rainy seasons. Reproduction patterns and sex ratios did not differ between months. Survival estimates were not influenced by season, and recruitment was low, with growth rate estimates of 1 animal per month. These estimates suggest a stable population of B. hindei in Zaraninge Forest. Further studies are recommended to establish the home range, diet and burrowing behavior of the species in coastal forests in East Africa.     

A new galago species for South Africa (Primates: Strepsirhini: Galagidae)

The primate fauna of South Africa has historically been viewed as comprising three diurnal cercopithecoid taxa – chacma baboons (Papio ursinus), vervet (Chlorocebus pygerythrus) and samango monkeys (Cercopithecus albogularis) – and two nocturnal lorisoid species – the thick-tailed greater galago (Otolemur crassicaudatus) and the southern lesser galago (Galago moholi). Here we report the positive identification of a third galago species within South Africa’s borders: the Mozambique dwarf galago or Grant’s galago, Galagoides granti (Thomas and Wroughton, 1907). The taxon was previously held to be restricted to Mozambique, eastern Zimbabwe, Malawi and Tanzania, but we have also observed it in the sand forest of Tembe Elephant Park and the Tshanini Community Reserve, near the Mozambique border. The species was formerly mistaken for Galago moholi, erroneously (we believe) extending the range of the latter species into northern KwaZulu-Natal. In South Africa the two small galagos are unlikely to have overlapping ranges: Galago moholi prefers dry savanna woodlands, whereas Galagoides granti is apparently confined to dry sand forest. However, both species may coexist with the larger and more widespread Otolemur crassicaudatus, an inhabitant of moist savanna, forest edge and thicket. The true South African ranges of both small galago species need to be ascertained.     

Patterns of geographic variation between mitochondrial and nuclear markers in Heaviside's (Benguela) dolphins (Cephalorhynchus heavisidii)

The Heaviside's (or Benguela) dolphin (Cephalorhynchus heavisidii) is endemic to the west coast of southern Africa. The present study investigated the population genetic structure across a large portion of the species distribution using mitochondrial control region and nuclear (microsatellite) markers. A total of 395 biopsy skin samples were analyzed; they were collected from free‐ranging Heaviside's dolphins in 7 locations along 1650 km of coast between Table Bay, South Africa and Walvis Bay, Namibia. Both genetic markers rejected the hypothesis of 1 homogenous population but revealed contrasting results in the genetic structuring of putative populations. Mitochondrial DNA suggested either 2 populations or a fine‐scale division with 6 (sub) populations, while microsatellite markers were indicative of 2 widespread populations with measurable gene flow between them. Neutrality tests and mismatch distribution of the mitochondrial sequences indicated a departure from mutation–drift equilibrium due to a population expansion at the 2 extremes of the geographic range, but not towards the middle of the distribution. These results highlight the importance of evaluating multiple genetic markers to gain reliable insights into population processes and structure.     

Phylogeography and genetic diversity of Psammophis schokari (Serpentes) in North Africa based on mitochondrial DNA sequences

The snake Psammophis schokari has a widespread distribution across North Africa, and in Morocco/Western Sahara is represented by three different morphotypes: striped, unicoloured and the Western-Sahara morph. ND4 mitochondrial DNA sequences from 28 specimens comprising 20 P. shokari, two P. aegyptius, one P. elegans, two P. sibilans, one P. condanarus and two outgroups were analysed. Within P. schokari we identified four genetic lineages (Morocco/Western Sahara, Mauritania, Algeria and Israel) with a genetic divergence ranging from 4-5%, less than that typically found between different species. Surprisingly, Moroccan/Western Sahara and Algerian lineages are the most divergent ones. This geographic substructuring may be due to severe climate changes in the Sahara desert between the Miocene and Pleistocene associated with expansion/contraction phases of this desert. Psammophis aegyptius is the sister-taxon of Psammophis schokari with a high level of genetic divergence between them (10.7%) supporting the recognition of P. aegyptius as a distinct species. The three Moroccan/Western Sahara colour morphotypes form one genetic lineage, indicating that colour pattern does not reflect a different phylogenetic history, and is probably an ecological adaptation to the local environment.     

A Temporal Study of Niche Breadth and Overlap in Two Sympatric Species of Mystacocarida (Crustacea)

Horus is an olpiid pseudoscorpion of which nine species have been described from southern Africa; a tenth, debatable species was described from the Ivory Coast. The two most widely distributed species are H. granulatus and H. obscurus, the former occurring especially in the west and the other in the east, but their distributions overlap; in two instances they have been recorded from the same site. All species have a preference for rock outcrops, which are largely disjunct, and their regular prey comprises small ant species. Fieldwork over a period of 15 years indicated a very low dispersal rate; therefore one would expect localized ‘island’ populations rather than widely dispersed species. This means that the current species delimitations which lump geographically widespread populations may be incorrect. Mitochondrial DNA of specimens from each of 20 different localities across South Africa were analysed to test the hypothesis. Five of these localities did not yield results, but 14 yielded DNA from specimens which proved to belong to Horus and a fifteenth turned out to be a misidentified pseudoscorpion unrelated to Horus. The results were unequivocal: populations from each locality or group of closely-spaced localities were genetically distinct from any other one tested, and the greater the distance between localities, the greater the genetic differences (i.e. significant isolation by distance). This means that the current species delimitations for Horus are incorrect. It will require detailed micro-anatomical study to identify new characteristics on which species delimitations can be based in future.     

Genetic monitoring of ex situ African Penguin (Spheniscus demersus) populations in South Africa

The African Penguin (Spheniscus demersus) has suffered population declines and is listed in the IUCN Red List as Endangered. The species is endemic to the coast of southern Africa, and breeding colonies are distributed on the south-western coast of Africa. Currently, African Penguins are being kept in zoo and aquarium facilities throughout South Africa. In this study, molecular genetic data based on 12 microsatellite markers from 1 119 African Penguin samples from four facilities were generated in order to determine the level of genetic variation, population structure and differentiation, and effective population size to assist in the development of an effective captive management plan. Expected heterozygosity ranged from 0.57 to 0.62, and allelic richness from 4.2 to 5.1. However, based on differences between first- and second-generation captive birds, we conclude that the ex situ population is at risk of losing genetic variability in the future and management programmes should include exchange of birds between captive facilities in order to induce gene flow and increase effective population size. Adding individuals from in situ populations should also be considered in the future in cases where these birds cannot be rehabilitated. Molecular genetic analyses of wild penguin populations should be carried out for comparison, and to ascertain to what degree ‘in situ genetic diversity’ is represented among ex situ populations. With regular resampling and analyses, the extent of the effect of processes such as genetic drift on diversity in the ex situ penguin populations will become evident.     

On the Behaviour of the Crabeater Seal Lobodon Carcinophagus (Hombron & Jacquinot)

The sharp-nosed reed frog is widespread in Africa. Although currently recognized as one species, suggestions have been made that more than one species might exist. We analysed 237 calls of 69 males from 19 localities in the western to southern parts of Africa. Calls fall into three groups, which we recognize as cryptic species. Of eight published sound spectrograms, all can be assigned to one of the three species. We recognize Hyperolius nasutus, distributed from western Africa to the Okavango Delta in Botswana; Hyperolius viridis, from the central highlands of northwestern Zambia to southern Tanzania; and Hyperolius acuticeps> which occurs from the Ivory Coast to the southeastern coast of South Africa. We assign published names to the synonymies of these three species. No call data are available for populations in the Congo basin.     

Relative population levels of citrus thrips Scirtothrips aurantii on commercial citrus and adjacent bush

Citrus thrips Scirtothrips aurantii Faure is a serious economic pest in southern Africa. It is indigenous, breeding on many wild hosts as well as on citrus. In this northern Transvaal lowveld study, bush containing known host plants of S. aurantii was not the source of early infestation of a navel orange orchard by adult citrus thrips during September and October. Early-season damage therefore resulted from the activities of citrus thrips which had overwintered in the orchard. In contrast, S. aurantii populations on wild hosts could possibly boost orchard populations later in the season and contribute to late damage on the fruit. This is because, in one of the years, adult thrips numbers were higher in the bush than in the orchard during November and December.     

Determinants of the occurrence of a native encroacher species,Pechuelloeschea leubnitziae (wild sage), in the eastern Okavango Delta,Botswana

Although indigenous to southern Africa, Pechuel-loeschea leubnitziae is considered a problematic weed as it forms dense monotypic stands in the grasslands and woodlands of the Okavango Delta, Botswana, and is associated with veld degradation and a dominance of shade-tolerant, poor-quality grass species. Generalised linear modelling was used to determine the effect of the following environmental conditions on the likelihood of occurrence of P. leubnitziae: type of land use, vegetation type, burning history, total woody species density, soil pH and soil texture. There was no difference in P. leubnitziae presence under wildlife, large livestock and small livestock land use (p = 0.227). Only vegetation type (p<0.001) and total woody species density (p<0.001) significantly affected P. leubnitziae occurrence, with the species being rare in dense mopane woodlands and most likely to occur in mixed thornveld and mixed broadleaf woodland, although this likelihood decreased with increasing total woody species density. A single burn had no effect on P. leubnitziae occurrence, but repeated burning should be investigated as a means to reduce the vigour and recoppicing success of P. leubnitziae.     

Bird habitat preferences drive hemoparasite infection in the Neotropical region

The role that the environment plays in vector-borne parasite infection is one of the central factors for understanding disease dynamics. We assessed how Neotropical bird foraging strata and habitat preferences determine infection by parasites of the genera Haemoproteus, Plasmodium, Leucocytozoon, and Trypanosoma and filarioids, and tested for phylogenetic signal in these host–parasite associations. We performed extensive searches of the scientific literature and created a database of hemoparasite surveys. We collected data on host body mass, foraging strata, habitat preference, and migratory status, and tested if host ecological traits predict each hemoparasite occurrence and prevalence using a phylogenetic Bayesian framework. Species of Plasmodium tend to infect birds from tropical forests while birds from altitudinal environments are likely to be infected by species of Leucocytozoon. The probability of a bird being infected by filarioid or Trypanosoma is higher in lowland forests. Bird species that occur in anthropic environments and dry habitats of tropical latitudes are more susceptible to infection by species of Haemoproteus. Host foraging strata is also influential and bird species that forage in the mid-high and canopy strata are more prone to infection by species of Haemoproteus and filarioids. We also identified phylogenetic signal for host–parasite associations with the probability of infection of Neotropical birds by any hemoparasite being more similar among more closely related species. We provided a useful framework to identify environments that correlate with hemoparasite infection, which is also helpful for detecting areas with potential suitability for hemoparasite infection due to land conversion and climate change.     

Feeding habits and comparative feeding rates of three southern African arboreal squirrels

Food utilization by three arboreal squirrels was studied with regard to feeding habits and efficiency, food preferences and chemical analyses of the food. Food selected in the field by the two forest subspecies the Ngoye red squirrel Paraxerus palliatus omatus and the Tonga red squirrel, P. p. tongensis are listed. Measurements of lengths of the different parts of their intestinal tracts indicate that the southern African arboreal squirrels are more insectivorous than tropical African squirrels. With regard to feeding efficiency, the tree squirrel P. cepapi cepapl, a savanna species, is relatively more adept at handling small seeds and the flesh of fruits, whereas the two forest subspecies mainly concentrate on the endosperm of large fruits. Chemical analyses of fruits and seeds indicate that the fat content is noticeably higher in fruits and endosperm from forests and that the protein content of savanna endosperm is higher than from the forest.     

Ant species richness of fynbos and forest ecosystems in the southern Cape

The ant fauna in fynbos and forest habitats in the southern Cape are compared. There is no significant difference in ant species richness between the two undisturbed habitat types, and the only two species common to both are Acantholepis capensis and Camponotus maculatus. The degree of Hakea sericea infestation in the fynbos negatively affected ant species richness. Ant species richness in the Afromontane forest decreased from the drier to the wetter sites. The aggressive alien ant species, Iridomyrmex humilis, has not invaded natural areas to any great extent.     

Importance of bird traits for seed dispersal patterns of co‐fruiting trees in a patchy forest

Habitat fragmentation is globally one of the most important drivers of change in biodiversity. Seed dispersal by birds is crucial for tree regeneration in remnant patchy forests, yet how bird traits affect seed dispersal pattern is still poorly understood. We studied the extent to which bird traits affect seed‐removal networks and whether these traits affect seed deposition and seedling recruitment for 3 co‐fruiting tree species (Taxus chinensis, Cinnamomum bodinieri and Machilus thunbergii) in a patchy forest. A total of 17, 18 and 10 bird species were recorded foraging for seeds of T. chinensis, M. thunbergii and C. bodinieri, respectively. Frequency of bird visitation increased with tail length, wing length and body length. Furthermore, bird body length, bill length, body weight and wing length were important in the strength of the seed removal network. During foraging, 6 bird species exhibited different patterns of microhabitat utilization and their perching frequency increased with bird weight and tarsus length. As a consequence, frequency of habitat use, bird length and tarsus length were important in determining the number of deposited seeds. For seedling recruitment, seedling number increased with bird tarsus length and weight, but decreased with wing length. Overall, our results showed that various bird traits not only affected seed removal, but also influenced the subsequent processes of seed deposition and seedling distribution in a patchy forest. These results thus highlight the importance of large‐bodied birds for plant recruitment and point out the need to prioritize the protection and conservation of these birds in remnant patchy forests.     

Late Pleistocene potential distribution of the North African sengi or elephant-shrew Elephantulus rozeti (Mammalia: Macroscelidea)

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.     

The rediscovery of a lost frog: Arthroleptis troglodytes Poynton, 1963

The cave squeaker Arthroleptis troglodytes Poynton, 1963 was first collected in 1961/62, and not observed again for 54 years despite several attempts to locate it. We rediscovered this species near the type locality in the Chimanimani mountain range in eastern Zimbabwe. We describe for the first time the call and colour in life, and highlight several morphological and habitat features not previously recorded for this species.     

The phyllophorid holothurians of southern Africa with the erection of a new genus

The southern African dendrochirotid holothurians of the family Phyllophoridae (sensu Pawson & Fell, 1965) are revised and a new genus Thyonina is erected to accommodate Thyone articulata Vaney, 1908, which possesses only slender spectacle-shaped rods as body wall deposits. In addition, Thyone proceracorona Cherbonnier, 1952 and T. turrisolida Cherbonnier, 1954, are declared junior subjective synonyms of T. aurea (Quoy & Gaimard, 1833); Havelockia imperfecta Cherbonnier, 1970 is transferred to the genus Thyone, and T. venusta Selenka, 1868 (synonym T. okeni Bell, 1884) is recorded for the first time from southern Africa. These changes bring the total number of phyllophorid holothurians now known from southern Africa to five genera and 11 species. All species are keyed, briefly described and/or discussed, and their local distributions mapped.     

Integrative taxonomy helps to reveal the mask of the genus Gynandropaa (Amphibia: Anura: Dicroglossidae)

Species of the genus Gynandropaa within the family Dicroglossidae are typical spiny frogs whose taxonomic status has long been in doubt. We used integrative methods, involving morphological and molecular analyses, to elucidate the phylogenetic relationships, and to determine identities and the geographic distribution of each valid species. We obtained DNA sequence data of 5 species of Gynandropaa (complete sequences of the mitochondrial NADH dehydrogenase subunit 2 [ND2] gene, and 890 bp of 12S rRNA and 16S rRNA partial sequences) from 37 localities (including the topotypes of 5 described species) and constructed Bayesian and maximum‐likelihood trees to examine the patterns of phylogeography. A total of 28 morphological variables were taken on 624 specimens. Three clades with clear geographic patterns were recognized: clade C (from south‐western Sichuan Province and central Yunnan Province), clade E (western Guizhou Province and eastern to central Yunnan Province) and clade W (western to southern Yunnan Province). Integrating morphological characteristics and distribution information, the clades W, E and C represent Gynandropaa yunnanensis, G. phrynoides and G. sichuanensis, respectively. We draw the following conclusions: (i) the taxon G. phrynoides, formerly evaluated as a junior synonym of G. yunnanensis, is revalidated herein at the rank of species; (ii) G. liui is a junior synonym of G. sichuanensis; and (iii) G. yunnanensis is a valid species while G. bourreti is probably a subspecies of G. yunnanensis, with the distribution range from Vietnam to southern Yunnan Province. This study clears up the taxonomic status of Gynandropaa and provides important information for understanding the evolution and conservation of these spiny frogs.