Museum DNA reveals a new, potentially extinct species of rinkhals (Serpentes: Elapidae: Hemachatus) from the Eastern Highlands of Zimbabwe.

Genetic information plays a pivotal role in species recognition and delimitation, but rare or extinct animals can be difficult to obtain genetic samples from. While natural history wet collections have proven invaluable in the description of novel species, the use of these historical samples in genetic studies has been greatly impeded by DNA degradation, especially because of formalin-fixation prior to preservation. Here, we use recently developed museum genomics approaches to determine the status of an isolated population of the elapid snake genus Hemachatus from Zimbabwe. We used multiple digestion phases followed by single strand sequencing library construction and hybridisation capture to obtain 12S and 16S rDNA sequences from a poorly preserved tissue sample of this population. Phylogenetic and morphological analyses in an integrated taxonomic framework demonstrate that the Zimbabwean rinkhals population represents an old and highly distinct lineage, which we describe as a new species, Hemachatus nyangensis sp. nov. Our phylogenetic dating analysis is compatible with venom spitting having evolved in response to the threat posed by early hominins, although more data are required for a robust test of this hypothesis. This description demonstrates the power of museum genomics in revealing rare or even extinct species: Hemachatus from Zimbabwe are only known from a small area of the Eastern Highlands known for high endemism. No living specimens have been seen since the 1980s, most likely due to dramatic land-use changes in the Eastern Highlands, suggesting that the species could be extinct. In view of its recognition as a highly distinct lineage, urgent action is required to determine whether any populations survive, and to safeguard remaining habitat.

Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae).

Cobras are among the most widely known venomous snakes, and yet their taxonomy remains incompletely understood, particularly in Africa. Here, we use a combination of mitochondrial and nuclear gene sequences and morphological data to diagnose species limits within the African forest cobra, Naja (Boulengerina) melanoleuca. Mitochondrial DNA sequences reveal deep divergences within this taxon. Congruent patterns of variation in mtDNA, nuclear genes and morphology support the recognition of five separate species, confirming the species status of N. subfulva and N. peroescobari, and revealing two previously unnamed West African species, which are described as new: Naja (Boulengerina) guineensis sp. nov. Broadley, Trape, Chirio, Ineich Wüster, from the Upper Guinea forest of West Africa, and Naja (Boulengerina) savannula sp. nov. Broadley, Trape, Chirio Wüster, a banded form from the savanna-forest mosaic of the Guinea and Sudanian savannas of West Africa. The discovery of cryptic diversity in this iconic group highlights our limited understanding of tropical African biodiversity, hindering our ability to conserve it effectively.

Phylogenetic and morphological investigation of the Mochlus afer-sundevallii species complex (Squamata: Scincidae) across the arid corridor of sub-Saharan Africa.

The aridification of Africa resulted in the fragmentation of forests and the expansion of an arid corridor stretching from the northeast to southwest portion of sub-Saharan Africa, but the role this corridor has had in species-level diversification of southern African vertebrates is poorly understood. The skink species Mochlus afer and M. sundevallii inhabit wide areas of the arid corridor and are therefore an ideal species pair for studying patterns of genetic and phenotypic diversity associated with this landscape. However, species boundaries between these taxa have been controversial. Using multi-locus molecular and morphological datasets, we investigate diversification patterns of the M. afer-sundevallii Species Complex across the arid corridor. Although analyses of genetic data reveals some genetic structure among geographic populations, results of phylogenetic and morphological analyses provide little support for two distinct evolutionary lineages, suggesting that populations previously referred to as M. afer and M. sundevallii represent a single species, Mochlus sundevallii. Genetic diversity is unequally distributed across the arid corridor, with observed patterns consistent with aridification-facilitated diversification southward across southern Africa. Additional geographic and population-level sampling is necessary before more conclusive inferences can be drawn about the role historical climate transitions have played in skink diversification patterns across southern Africa.

Revalidation of Pyxicephalus angusticeps Parry, 1982 (Anura: Natatanura: Pyxicephalidae), a bullfrog endemic to the lowlands of eastern Africa.

Pyxicephalus currently contains three recognized species, viz. P. adspersus, P. edulis and P. obbianus, the former two of which have a long history of confusion. Parry (1982) described P. adspersus angusticeps from Beira, Mozambique, which was synonymized with P. edulis. We re-examine the taxonomic status of Pyxicephalus taxa from Mozambique, examining the types and contrasting them to congeners throughout Africa. Morphological characters previously used to delimit species in Pyxicephalus are examined, and problems with some identified. Additional diagnostic characters and their variation in Pyxicephalus are discussed, and a revised key is provided. Confusion among species in the genus, type localities, literature and folklore led to P. adspersus angusticeps being incorrectly synonymized with P. edulis. We formally revalidate P. angusticeps, and designate a lectotype for P. edulis. The identity of voucher specimens from previous work suggests that the breeding ecology of P. angusticeps is distinct from that of P. adspersus and P. edulis, and that the advertisement call of P. angusticeps was used as part of the evidence for elevating P. edulis out of synonymy with P. adspersus. The previous confusion of P. adspersus and P. edulis does not affect the recognition of P. angusticeps. The wider implication of the previous misidentification of P. angusticeps as P. edulis is that most of the museum material labeled as P. adspersus from East Africa is P. edulis, and most of the museum material labeled as P. edulis from East Africa is P. angusticeps. This conclusion has been confirmed from East African museum material thus far examined.

Molecular systematics of the African snake family Lamprophiidae Fitzinger, 1843 (Serpentes: Elapoidea), with particular focus on the genera Lamprophis Fitzinger 1843 and Mehelya Csiki 1903.

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.

Phylogeny, biogeography and classification of the snake superfamily Elapoidea: a rapid radiation in the late Eocene.

The snake superfamily Elapoidea presents one of the most intransigent problems in systematics of the Caenophidia. Its monophyly is undisputed and several cohesive constituent lineages have been identified (including the diverse and clinically important family Elapidae), but its basal phylogenetic structure is obscure. We investigate phylogenetic relationships and spatial and temporal history of the Elapoidea using 94 caenophidian species and approximately 2300-4300 bases of DNA sequence from one nuclear and four mitochondrial genes. Phylogenetic reconstruction was conducted in a parametric framework using complex models of sequence evolution. We employed Bayesian relaxed clocks and Penalized Likelihood with rate smoothing to date the phylogeny, in conjunction with seven fossil calibration constraints. Elapoid biogeography was investigated using maximum likelihood and maximum parsimony methods. Resolution was poor for early relationships in the Elapoidea and in Elapidae and our results imply rapid basal diversification in both clades, in the late Eocene of Africa (Elapoidea) and the mid-Oligocene of the Oriental region (Elapidae). We identify the major elapoid and elapid lineages, present a phylogenetic classification system for the superfamily (excluding Elapidae), and combine our phylogenetic, temporal and biogeographic results to provide an account of elapoid evolution in light of current palaeontological data and palaeogeographic models. © The Willi Hennig Society 2009.

The snake family Psammophiidae (Reptilia: Serpentes): phylogenetics and species delimitation in the African sand snakes (Psammophis Boie, 1825) and allied genera.

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.

The phylogeny of cobras inferred from mitochondrial DNA sequences: evolution of venom spitting and the phylogeography of the African spitting cobras (Serpentes: Elapidae: Naja nigricollis complex).

We use phylogenetic analysis of 1333 bp of mitochondrial DNA sequence to investigate the phylogeny and historical biogeography of the cobra-like elapid snakes, with special reference to the evolution of spitting and the phylogeography of the African spitting cobras, a radiation widespread in open vegetational formations throughout sub-Saharan Africa. Our results suggest that spitting adaptations appear to have evolved three times in cobras, but alternative scenarios cannot be rejected. The Asiatic Naja are monophyletic and originate from a single colonization of Asia from Africa. The radiation of the African spitting Naja appears to date back to the early Miocene and many speciation events in the group predate the Pliocene expansion of grasslands and the radiation of large grazing mammals in Africa. The cladogenic events in this complex appear to have been triggered by both ecological changes and tectonic events associated with the formation and expansion of the African Rift Valley. Taxonomically, our data confirm the inclusion of Boulengerina and Paranaja within Naja, and reveal a clade of African rainforest cobras including N. melanoleuca, Paranaja multifasciata and Boulengerina that constitutes the sister clade of the African open-formation non-spitting cobras. Naja nigricollis is polyphyletic, and we therefore recognize N. nigricincta as a separate species, more closely related to N. ashei and N. mossambica than to N. nigricollis.