Humewood, South Africa
Humewood, South Africa
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Medina M.F.,University of Texas at El Paso | Bauer A.M.,Villanova University | Branch W.R.,Bayworld | Branch W.R.,Nelson Mandela Metropolitan University | And 12 more authors.
Molecular Phylogenetics and Evolution | Year: 2016

African snake-eyed skinks are relatively small lizards of the genera Panaspis and Afroablepharus. Species allocation of these genera frequently changed during the 20th century based on morphology, ecology, and biogeography. Members of these genera occur primarily in savanna habitats throughout sub-Saharan Africa and include species whose highly conserved morphology poses challenges for taxonomic studies. We sequenced two mitochondrial (16S and cyt b) and two nuclear genes (PDC and RAG1) from 76 Panaspis and Afroablepharus samples from across eastern, central, and southern Africa. Concatenated gene-tree and divergence-dating analyses were conducted to infer phylogenies and biogeographic patterns. Molecular data sets revealed several cryptic lineages, with most radiations occurring during the mid-Miocene to Pliocene. We infer that rifting processes (including the formation of the East African Rift System) and climatic oscillations contributed to the expansion and contraction of savannas, and caused cladogenesis in snake-eyed skinks. Species in Panaspis and Afroablepharus used in this study, including type species for both genera, formed a monophyletic group. As a result, the latter genus should be synonymized with the former, which has priority. Conservatively, we continue to include the West African species P. breviceps and P. togoensis within an expanded Panaspis, but note that they occur in relatively divergent clades, and their taxonomic status may change with improved taxon sampling. Divergence estimates and cryptic speciation patterns of snake-eyed skinks were consistent with previous studies of other savanna vertebrate lineages from the same areas examined in this study. © 2016 Elsevier Inc.

Tolley K.A.,South African National Biodiversity Institute | Tolley K.A.,Stellenbosch University | Tilbury C.R.,Stellenbosch University | Measey G.J.,South African National Biodiversity Institute | And 5 more authors.
Journal of Biogeography | Year: 2011

Aim East Africa is one of the most biologically diverse regions, especially in terms of endemism and species richness. Hypotheses put forward to explain this high diversity invoke a role for forest refugia through: (1) accumulation of new species due to radiation within refugial habitats, or (2) retention of older palaeoendemic species in stable refugia. We tested these alternative hypotheses using data for a diverse genus of East African forest chameleons, Kinyongia. Location East Africa. Methods We constructed a dated phylogeny for Kinyongia using one nuclear and two mitochondrial markers. We identified areas of high phylogenetic diversity (PD) and evolutionary diversity (ED), and mapped ancestral areas to ascertain whether lineage diversification could best be explained by vicariance or dispersal. Results Vicariance best explains the present biogeographic patterns, with divergence between three major Kinyongia clades (Albertine Rift, southern Eastern Arc, northern Eastern Arc) in the early Miocene/Oligocene (>20Ma). Lineage diversification within these clades pre-dates the Pliocene (>6Ma). These dates are much older than the Plio-Pleistocene climatic shifts associated with cladogenesis in other East African taxa (e.g. birds), and instead point to a scenario whereby palaeoendemics are retained in refugia, rather than more recent radiations within refugia. Estimates of PD show that diversity was highest in the Uluguru, Nguru and East Usambara Mountains and several lineages (from Mount Kenya, South Pare and the Uluguru Mountains) stand out as being evolutionarily distinct as a result of isolation in forest refugia. PD was lower than expected by chance, suggesting that the phylogenetic signal is influenced by an unusually low number of extant lineages with long branch lengths, which is probably due to the retention of palaeoendemic lineages. Main conclusions The biogeographic patterns associated with Kinyongia are the result of long evolutionary histories in isolation. The phylogeny is dominated by ancient lineages whose origins date back to the early Miocene/Oligocene as a result of continental wide forest fragmentation and contraction due to long term climatic changes in Africa. The maintenance of palaeoendemic lineages in refugia has contributed substantially to the remarkably high biodiversity of East Africa. © 2011 Blackwell Publishing Ltd.

Vidal N.,French Natural History Museum | Marin J.,French Natural History Museum | Morini M.,French Natural History Museum | Donnellan S.,South Australian Museum | And 7 more authors.
Biology Letters | Year: 2010

Worm-like snakes (scolecophidians) are small, burrowing species with reduced vision. Although largely neglected in vertebrate research, knowledge of their biogeographical history is crucial for evaluating hypotheses of snake origins. We constructed a molecular dataset for scolecophidians with detailed sampling within the largest family, Typhlopidae (blindsnakes). Our results demonstrate that scolecophidians have had a long Gondwanan history, and that their initial diversification followed a vicariant event: the separation of East and West Gondwana approximately 150 Ma. We find that the earliest blindsnake lineages, representing two new families described here, were distributed on the palaeolandmass of India + Madagascar named here as Indigascar. Their later evolution out of Indigascar involved vicariance and several oceanic dispersal events, including a westward transatlantic one, unexpected for burrowing animals. The exceptional diversification of scolecophidians in the Cenozoic was probably linked to a parallel radiation of prey (ants and termites) as well as increased isolation of populations facilitated by their fossorial habits. © 2010 The Royal Society.

Greenbaum E.,University of Texas at El Paso | Villanueva C.O.,University of Texas at El Paso | Aristote M.M.,Institute Superieur Decologie Pour La Conservation Of La Nature | Branch W.R.,Bayworld | Branch W.R.,Nelson Mandela Metropolitan University
Zoological Journal of the Linnean Society | Year: 2011

Currently, four species of the lacertid lizard genus Adolfus are known from Central and East Africa. We sequenced up to 2825 bp of two mitochondrial [16S and cytochrome b (cyt b)] and two nuclear [(c-mos (oocyte maturation factor) and RAG1 (recombination activating gene 1)] genes from 41 samples of Adolfus (representing every species), two species each of Gastropholis and Holaspis, and in separate analyses combined these data with GenBank sequences of all other Eremiadini genera and four Lacertini outgroups. Data from DNA sequences were analysed with maximum parsimony (PAUP), maximum-likelihood (RAxML) and Bayesian inference (MrBayes) criteria. Results demonstrated that Adolfus is not monophyletic: Adolfus africanus (type species), Adolfus alleni, and Adolfus jacksoni are sister taxa, whereas Adolfus vauereselli and a new species from the Itombwe Plateau of Democratic Republic of the Congo are in a separate lineage. Holaspis and Gastropholis were recovered in separate clades. Based on these molecular data, relatively substantial sequence divergence, and multiple morphological differences, we describe a new genus of lacertid for the lineage including A. vauereselli and the new Itombwe species. The recognition of this new, endemic genus underscores the conservation importance of the Albertine Rift, especially the Itombwe Plateau, a unique region that is severely threatened by unchecked deforestation, mining, and poaching. © 2011 The Linnean Society of London.

Dalhuijsen K.,University of Witwatersrand | Branch W.R.,Bayworld | Branch W.R.,Nelson Mandela Metropolitan University | Alexander G.J.,University of Witwatersrand
African Zoology | Year: 2014

We present data from gut content analyses of Varanus albigularis (savanna monitor) and V. niloticus (water monitor) in South Africa. Both species are generalist, opportunistic feeders. We did not detect any sex-based differences in the diet of V. albigularis, and there were relatively high levels of dietary overlap between the species, although there were significant differences for certain prey types. These differences match differences in habitat use between the species: the more aquatic V. niloticus consumed aquatic prey, such as amphibians and crabs, more often than did V. albigularis. Varanus albigularis included more terrestrial prey such as diplopods in its diet. Tortoises and millipedes were also prominent in the V. albigularis diet, constituting an important component of dietary intake. Few of our samples from V. albigularis had empty stomachs, suggesting that this species may occupy a lower trophic level than its Australian counterparts. Although there is a large degree of overlap in the diets of the two species, there is a trend for V. albigularis to eat more slow-moving prey. These differences result in the species foraging at different trophic levels.

Herrmann H.-W.,University of Arizona | Branch W.R.,Bayworld | Branch W.R.,Nelson Mandela Metropolitan University
Journal of Arid Environments | Year: 2013

Namibia is mostly an arid and semi-arid country with a high number of reptile and fewer amphibian species. We review the herpetological literature dealing with Namibian species over the past fifty years, and provide up-to-date amphibian and reptile accounts using a widely accepted taxonomy and nomenclature. We critically discuss species accounts, draw attention to the historical development of species inventories for the country, and indicate species endemism for Namibia and the Namib Desert. In Namibia, the lizard families Gekkonidae, Lacertidae, and Scincidae have undergone adaptive radiations and are species-rich. This also applies to the snake family Psammophiidae.Areas of herpetological research that have received most attention are systematics (with its disciplines faunistics (area inventories), taxonomy, and phylogeny), ecology, and physiology. The former is indicative of early stages of herpetological research such as area inventories and the subsequent analyzes of the collections. The latter two were largely enabled by (1) species highly adapted to life in the hyper-arid Namib Desert, and (2) by the accessibility of these species in the Namib Desert through the infrastructure provided by the Gobabeb Research and Training Center. The majority of the eco-physiological research has focused on three highly psammophilus, diurnal lizard species; Meroles anchietae, M. cuneirostris, and Gerrhosaurus skoogi, whilst diverse geckos form the basis of eco-morphological studies.The concentration of research localities around cities and the Gobabeb Research and Training Center is characteristic for opportunistic research. Geographic centers of herpetological research have been the central Namib Desert (i.e. Gobabeb), and areas around Swakopmund and Windhoek. Extensive parts of Namibia remain barely touched. Herpetological publication frequency has been approximately the same since its beginning in the early 1800's until the 1970's. The period between 1986 and 2003 experienced a remarkable increase of publication activity that has slightly subsided around 2004 and picked up again in recent years.Recent conservation related studies investigate the impact of overgrazing with land degradation and water related issues such as canals and hydroelectric dam projects on herpetological communities. In the near future the impact of mining, especially Uranium mining in the Namib Desert, and the effects of climate change with the predicted drying and warming will demand increased attention.Advances in biotechnology with ever-increasing amounts of data and decreasing cost have and will progressively enable advances in traditional disciplines like taxonomy, phylogeny, and systematics. Additionally, these technologies will increasingly empower the newer disciplines of molecular ecology and conservation biology in Namibia.Annotated, updated species checklists highlight Namibian and Namib diversity and endemicity, and also direct researchers to the numerous taxonomic problems that still confound full understanding of the region's herpetofauna. © 2012 Elsevier Ltd.

Kelly C.M.R.,Rhodes University | Branch W.R.,Bayworld | Broadley D.G.,Natural History Museum of Zimbabwe | Barker N.P.,Rhodes University | Villet M.H.,Rhodes University
Molecular Phylogenetics and Evolution | Year: 2011

The snake family Lamprophiidae Fitzinger (Serpentes: Elapoidea) is a putatively Late Eocene radiation of nocturnal snakes endemic to the African continent. It incorporates many of the most characteristic and prolific of Africa's non-venomous snake species, including the widespread type genus Lamprophis Fitzinger, 1843 (house snakes). We used approximately 2500 bases of mitochondrial and nuclear DNA sequence data from 28 (41%) of the approximately 68 recognised lamprophiid species in nine of the eleven genera to investigate phylogenetic structure in the family and to inform taxonomy at the generic level. Cytochrome b, ND4 and tRNA gene sequences (mitochondrial) and c-mos sequences (nuclear) were analysed using Maximum Likelihood, Bayesian Inference and Maximum Parsimony methods. The genus Mehelya Csiki, 1903 was paraphyletic with respect to Gonionotophis Boulenger, 1893. To address this, the concept of Gonionotophis is expanded to include all current Mehelya species. The genus Lamprophis emerged polyphyletic: the enigmatic Lamprophis swazicus was sister to Hormonotus modestus from West Africa, and not closely related to its nominal congeners. It is moved to a new monotypic genus (Inyoka gen. nov.). The remaining Lamprophis species occur in three early-diverging lineages. (1) Lamprophis virgatus and the widely distributed Lamprophis fuliginosus species complex (which also includes Lamprophis lineatus and Lamprophis olivaceus) formed a clade for which the generic name Boaedon Duméril, Bibron & Duméril, 1854 is resurrected. (2) The water snakes (Lycodonomorphus) were nested within Lamprophis (sensu lato), sister to Lamprophis inornatus. We transfer this species to the genus Lycodonomorphus Fitzinger, 1843. (3) We restrict Lamprophis (sensu strictissimo) to a small clade of four species endemic to southern Africa: the type species of Lamprophis Fitzinger, 1843 (Lamprophis aurora) plus Lamprophis fiskii, Lamprophis fuscus and Lamprophis guttatus. © 2010 Elsevier Inc.

Conradie W.,Bayworld | Conradie W.,South African Institute For Aquatic Biodiversity | Conradie C.,23 St. Tropez
Acta Herpetologica | Year: 2015

The family Heleophrynidae is restricted to Southern Africa and comprises two genera with seven species. Tadpoles are well adapted, with huge sucker mouths, to live in the fast flowing headwaters of mountain streams. The unique sucker-like mouth has numerous transverse rows of labial teeth, which are used to attach themselves to the rock surface and to scrape algae from the rocks. In this paper data on the ontogenetic increase of labial tooth rows in tadpoles of four species of ghost frog are presented. Notes on the development of tadpoles and mouthparts are also presented. © Firenze University Press.

Conradie W.,Bayworld | Branch W.R.,Bayworld | Braack H.,Abrus Environmental Consultancy | Manson M.,Golder Associates
Herpetology Notes | Year: 2010

The diet of metamorph Giant African Bullfrogs from a semi-aquatic habitat in the Karoo were recorded. All stomachs contained prey items; insects accounted for the greatest prey diversity, with Coleopterans (11 families) dominating the 29 insect families recorded. The most abundant prey items, none of which have previously been recorded in the diet, were a conchostracan "clam shrimp" (Leptestheriella cf. inermis), an aquatic snail (Physidae) and the small frog Cacosternum boettgeri. Metamorph bullfrogs had an average SUL of 39.3 mm and a mass of 5.19 g. After nine months, including a period of winter dormancy, the frogs had an average SUL of 81.4 mm and a mass of 71.38 g, equivalent to just over a doubling in SUL and a 1326% increase in mass.

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