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Mitochondrial DNA sequences (1137 bp) of the cytochrome b gene and craniodental and craniometric data were used to investigate the evolutionary relationships of six putative rodent taxa of Otomys (family Muridae: subfamily Murinae: tribe Otomyini) co-occurring in the Western Cape and Eastern Cape provinces of South Africa. Phylogenetic analysis of 20 new sequences together with craniodental and craniometric characters of 94 adult skulls reveal the existence of a unique lineage of Otomys cf. karoensis (named herein Otomys willani sp. nov.) from the Sneeuberg Centre of Floristic Endemism in the southern Drakensberg Mountain Range. Craniometric analysis distinguished O. karoensis from O. willani and identified a further four localities in the range of the latter species. We document southern range extensions of both Sloggett's ice rat, Otomys sloggetti , and the vlei rat Otomys auratus to the Sneeuberg Mountain Range, in addition to appreciable genetic divergence between Sneeuberg and southern and central Drakensberg populations of O. sloggetti. Our results demonstrate parallel patterns of cryptic speciation in two co-occurring species complexes (Otomys irroratus s.l. and O. karoensis s.l.) associated closely with the boundaries of biomes (fynbos vs. grassland biomes) and geological formations (Cape Fold Belt vs. Great Escarpment). [ABSTRACT FROM AUTHOR]

Aim: The expansion of open habitats during the mid‐Miocene has been hypothesized as a driver of allopatric speciation for many African taxa. This habitat‐dependent mode of diversification has been implicated in the shift from C3 (e.g. forest/woodland) to C4 dominated systems (i.e. open savanna, grasslands) in a number of African squamates. We examined this hypothesis using a genus of African viperid snakes (Bitis) with both open habitat and forest‐dwelling representatives. Location: Africa. Methods: A comprehensive multilocus dataset was used to generate a calibrated species tree using a multispecies coalescent model. Individual gene trees and patterns of nuclear allele sharing were used to assess species monophyly and isolation. To test the habitat‐dependent evolution hypothesis, we generated an ancestral character state reconstruction for open and closed habitats using the dated phylogeny. This was related to the timing of open habitat expansion and forest/woodland contraction in Africa. Results: The genus Bitis originated in the Oligocene, with species level diversification in the late Miocene/Pliocene. Four well‐supported clades correspond to the recognized subgenera Bitis, Keniabitis, Macrocerastes and Calechidna. Several previously unrecognized lineages potentially represent cryptic species. Main conclusions: Habitat‐dependent evolution does not appear to have been a main driver for generic level viperine diversification: the ancestral state for Bitis was open habitat and at least one clade moved into forest in the Miocene, long after forest had contracted and fragmented. Forest‐dependent species diversified only in the late Miocene, presumably as forest became further reduced in extent, fitting an allopatric model of speciation. Although our results do not favour a general pattern of habitat‐dependent diversification in Bitis, cladogenesis within the subgenus Calechidna for "arenicolous" species (Bitis caudalis complex) and "rupicolous" species (B. atropos‐cornuta complex), corresponds to the aridification of southwest Africa. This suggests there are subtleties not captured in the broad open habitat category, which are relevant for understanding the role of habitat‐dependent evolution. [ABSTRACT FROM AUTHOR]

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., (Copyright © 2010 Elsevier Inc. All rights reserved.)

This study constitutes the first evolutionary investigation of the snake family Psammophiidae--the most widespread, most clearly defined, yet perhaps the taxonomically most problematic of Africa's family-level snake lineages. Little is known of psammophiid evolutionary relationships, and the type genus Psammophis is one of the largest and taxonomically most complex of the African snake genera. Our aims were to reconstruct psammophiid phylogenetic relationships and to improve characterisation of species boundaries in problematic Psammophis species complexes. We used approximately 2500 bases of DNA sequence from the mitochondrial and nuclear genomes, and 114 terminals covering all psammophiid genera and incorporating approximately 75% of recognised species and subspecies. Phylogenetic reconstructions were conducted primarily in a Bayesian framework and we used the Wiens/Penkrot protocol to aid species delimitation. Rhamphiophis is diphyletic, with Rhamphiophis acutus emerging sister to Psammophylax. Consequently we transfer the three subspecies of Rhamphiophis acutus to the genus Psammophylax. The monotypic genus Dipsina is sister to Psammophis. The two species of Dromophis occupy divergent positions deeply nested within Psammophis, and we therefore relegate Dromophis to the synonymy of Psammophis. Our results allow division of the taxonomically problematic Psammophis 'sibilans' species complex into two monophyletic entities, provisionally named the 'phillipsii' and 'subtaeniatus' complexes. Within these two clades we found support for the status of many existing species, but not for a distinction between P.p. phillipsii and P. mossambicus. Additionally, P. cf. phillipsii occidentalis deserves species status as the sister taxon of P. brevirostris.