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 (> 20 Ma). Lineage diversification within these clades pre-dates the Pliocene (> 6 Ma). 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 conclusionsThe 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.

The phylogenetic associations among 13 currently recognized African leaf chameleon species were investigated by making use of mitochondrial and nuclear DNA sequence data (44 taxa and 4145 characters). The gene tree indicates two divergent clades within Rhampholeon; this finding is congruent with previous morphological suggestions. The first clade (I) comprises three taxa (R. kerstenii, R. brevicaudatus and R. brachyurus) and is widely distributed in lowland forest and or non-forest biomes. The second clade (II) comprises the remaining Rhampholeon species and can be subdivided into three subclades. By contrast, most taxa belonging to clade II are confined to relict montane forest biotopes. Based on geographical, morphological and molecular evidence, it is suggested that the taxonomy of Rhampholeon be revised to include two genera (Rieppeleon and Rhampholeon) and three subgenera (Rhampholeon, Bicuspis and Rhinodigitum). There is a close correlation between geographical distribution and phylogenetic relatedness among Rhampholeon taxa, indicating that vicariance and climate change were possibly the most influential factors driving speciation in the group. A relaxed Bayesian clock suggests that speciation times coincided both with the northern movement of Africa, which caused the constriction of the pan African forest, and to rifting in east Africa ca. 20 Myr ago. Subsequent speciation among taxa was probably the result of gradual desiccation of forests between 20 and 5 Myr ago.

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The taxonomic history and composition of the genus Bradypodion as construed by Klaver & Böhme (1986) and new morphological and molecular data relevant to the taxonomy of the group is reviewed. The combined evidence strongly supports a formal rearrangement of the group into three distinct genera. Bradypodion, type species Chamaeleo pumilus Daudin 1802, is retained for the southern African species. Two new genera are erected to accommodate additional well-diagnosed clades within central and east African species previously referred to Bradypodion. Species of the “fischeri complex” are assigned to Kinyongia gen. nova, whilst the endemic Mulanje chameleon is placed in the monotypic genus Nadzikambia gen. nova.

The genus Chamaeleo, currently subdivided into two sub-genera, Chamaeleo (Chamaeleo) and Chamaeleo (Trioceros) (Klaver & Böhme 1986), is reviewed from both a morphological and genetic basis and it is concluded that the two subgenera are sufficiently distinct as to warrant their formal elevation to seperate and distinct genera. Evaluation of the soft anatomy and several other characters provide sufficient basis for making this distinction. The proposed change is supported by the demonstration of monophyletic groupings (based on two mitochondrial and one nuclear gene) consistent with distinct genera.