Coalescent analyses support multiple mainland-to-island dispersals in the evolution of Malagasy Triaenops bats (Chiroptera: Hipposideridae)

Aim We investigate the directionality of mainland‐to‐island dispersals, focusing on a case study of an African‐Malagasy bat genus, Triaenops (Hipposideridae). Taxa include T. persicus from east Africa and three Triaenops species from Madagascar (T. auritus, T. furculus, and T. rufus). The evolution of this bat family considerably post‐dated the tectonic division of Madagascar from Africa, excluding vicariance as a viable hypothesis. Therefore, we consider three biogeographical scenarios to explain these species' current ranges: (A) a single dispersal from Africa to Madagascar with subsequent speciation of the Malagasy species; (B) multiple, unidirectional dispersals from Africa to Madagascar resulting in multiple, independent Malagasy lineages; or (C) early dispersal of a proto‐species from Africa to Madagascar, with later back‐dispersal of a descendant Malagasy taxon to Africa. Location East Africa, Madagascar, and the Mozambique Channel. Methods We compare the utility of phylogenetic and coalescent methodologies to address the question of directionality in a mainland‐to‐island dispersal event for recently diverged taxa. We also emphasize the application of biologically explicit demographic systems, such as the non‐equilibrium isolation‐with‐migration model. Here, these methods are applied to a four‐species haploid genetic data set, with simulation analyses being applied to validate this approach. Results Coalescent simulations favour scenario B: multiple, unidirectional dispersals from Africa to Madagascar resulting in multiple, independent Malagasy bat lineages. From coalescent dating, we estimate that the genus Triaenops was still a single taxon approximately 2.25 Ma. The most recent Africa to Madagascar dispersal occurred much more recently (c. 660 ka), and led to the formation of the extant Malagasy species, T. rufus. Main conclusions Haploid genetic data from four species of Triaenops are statistically most consistent with multiple, unidirectional dispersals from mainland Africa to Madagascar during the late Pleistocene.     

Biogeography of ‘tropical Anagallis’ (Myrsinaceae) inferred from nuclear and plastid DNA sequence data

Aim ‘Tropical Anagallis’ corresponds to one of two evolutionary lineages within the genus Anagallis L. Generally, species within this lineage have a limited distribution in (sub‐)tropical regions in Africa or Madagascar. Two species, however, are endemic to South America, and exhibit a trans‐Atlantic disjunction with the rest of the species within the lineage. To investigate this disjunct distribution, as well as other dispersal events, the distribution of extant taxa was used to hypothesize the ancestral area(s) of distribution. Location Africa, Madagascar, Europe and South America. Methods Dispersal–vicariance analysis (DIVA) was used to optimize distribution areas onto parsimony and Bayesian phylogenies based on sequence data from four chloroplast loci and the nuclear internal transcribed spacers (ITS). Results Parsimony analysis gave one most parsimonious tree while Bayesian analysis resulted in a collapsed node due to alternative placements of Anagallis nummularifolia Baker, endemic to Madagascar. Optimization of the present distribution using DIVA, and the most parsimonious tree and six alternative topologies of the Bayesian analysis, show an origin of the lineage in Europe as most likely, although one topology indicates a broader ancestral distribution area. Dispersal to Africa appears to have been a single event, while two parallel dispersal events seem to have resulted in the American as well as Madagascan distributions. Main conclusions The lineage ‘tropical Anagallis’ evolved in Europe and may have been present in the Eocene boreotropical forests, although scarcity of fossils makes assessment of age difficult. Dispersal to South America is proposed to have been via the North Atlantic land bridge, or, more likely, through transport by the North Equatorial Current. Dispersal from Europe to Africa represents a single event, while dispersal to Madagascar from mainland Africa has occurred twice.     

A new species of Schoutedenichia Jadin & Vercammen-Grandjean, 1954 from Madagascar and a re-description of S. dutoiti (Radford, 1948) from South Africa (Acariformes: Trombiculidae)

A new chigger mite species, Schoutedenichia microcebi n. sp. is described from the grey mouse lemur Microcebus murinus (J.F. Miller) from Madagascar. The new species is closely related to S. dutoiti (Radford, 1948), a species described from a single specimen collected on a rodent in South Africa. Examination of the holotype and new material on S. dutoiti from South Africa enabled us to re-describe this species and provide new data on its hosts and geographical distribution.

     

Biogeography,rarity and endemism in Cineraria (Asteraceae–Senecioneae)

The biogeography of Cineraria (Asteraceae, Senecioneae) is assessed using a chorological approach in terms of its distribution, centres of diversity and endemism. Rare species are identified and categorised according to Rabinowitz's criteria and causes for rarity in the genus are investigated. The conservation status of the species is assessed according to IUCN criteria for Red List categories and compared to levels of rarity. The main phytogeographic affinity of Cineraria is Afromontane in association with seven recognised centres of endemism in South Africa, four in tropical Africa, in Ethiopia and in Madagascar. Fifteen species are endemic and six are near‐endemic to a specific centre of endemism or mountain range. Seventy four percent of Cineraria spp. are endemic to southern Africa with the centre of diversity in the KwaZulu‐Natal Midlands, South Africa. The rarest species number 11; of these eight are endangered or vulnerable according to IUCN Red Data Criteria and three are data deficient. Causes of rarity in Cineraria are related to narrow habitat specificity, notably soil or rock type and/or altitudinal range. Paired comparisons of the 11 rarest and commonest species reveal no convincing causal links to morphological, reproductive or life history strategy attributes in Cineraria. © 2009 University of the Witwatersrand, Botanical Journal of the Linnean Society, 2009, 160 , 130–148.     

Linking seed dispersal and genetic structure of trees: a biogeographical approach

Aim Natural and human‐induced differences in frugivore assemblages can influence the seed dispersal distances of trees. An important issue in seed dispersal systems is to understand whether differences in seed dispersal distances also affect the genetic structure of mature trees. One possible approach to test for a relationship between seed dispersal and the genetic structure of mature trees is to compare the genetic structure of two closely related tree species between two biogeographical regions that differ in frugivore assemblages and seed dispersal distances. Previous studies on two Commiphora species revealed that Commiphora guillauminii in Madagascar has a much lower seed dispersal distance than Commiphora harveyi in South Africa. We tested whether the lower seed dispersal distance might have caused decreased gene flow, resulting in a stronger genetic structure in Madagascar than in South Africa. Location Madagascar and South Africa. Methods Using amplified fragment length polymorphism markers we investigated the genetic structure of 134 trees in Madagascar and 158 trees in South Africa at a local and a regional spatial scale. Results In concordance with our hypothesis, kinship analysis suggests that gene flow was restricted mostly to 3 km in Madagascar and to 30 km in South Africa. At the local spatial scale, the genetic differentiation among groups of trees within sample sites was marginally significantly higher in Madagascar (F_ST = 0.069) than in South Africa (F_ST = 0.021). However, at a regional spatial scale genetic differentiation was lower in Madagascar (F_ST = 0.053) than in South Africa (F_ST = 0.163). Main conclusions Our results show that lower seed dispersal distances of trees were linked to higher genetic differentiation of trees only at a local spatial scale. This suggests that seed dispersal affects the genetic population structure of trees at a local, but not at a regional, spatial scale.     

Out of Africa? A dated molecular phylogeny of the cicada tribe Platypleurini Schmidt (Hemiptera: Cicadidae), with a focus on African genera and the genus Platypleura Amyot & Audinet‐Serville

The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four‐gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa. The tribe appears to have diversified during the Cenozoic, beginning c. 50–32 Ma, with most extant African lineages originating in the Miocene or later, well after the breakup of the Gondwanan landmass. Biogeographical analysis suggests an African origin for the tribe and a single dispersal event founding the Asian platypleurines, although additional taxon sampling and genetic data will be needed to confirm this pattern because key nodes in the tree are still weakly supported. Two Platypleurini genera from Madagascar (Pycna Amyot & Audinet‐Serville, Yanga Distant) are found to have originated by late Miocene dispersal of a single lineage from Africa. The genus Platypleura is recovered as polyphyletic, with Platypleura signifera Walker from South Africa and many Asian/Indian species apparently requiring assignment to different genera, and a new Platypleura concept is proposed with the synonymization of Azanicada Villet syn.n. The genera Orapa Distant and Hamza Distant, currently listed within separate tribes but suspected of platypleurine affinity, are nested deeply within the Platypleurini radiation. The tribe Orapini syn.n . is here synonymized while the tribe Hamzini is pending a decision of the ICZN to preserve nomenclatorial stability.     

Identification of cryptic species of Miniopterus bats (Chiroptera: Miniopteridae) from Madagascar and the Comoros using bioacoustics overlaid on molecular genetic and morphological characters

The number of Miniopterus bat species on Madagascar and the nearby Comoros islands (Malagasy region) has risen from four to 11. These recently described cryptic taxa have been differentiated primarily based on molecular markers and associated a posteriori morphological characters that corroborate the different clades. Members of this Old World genus are notably conservative in morphology across their range. Several sites on Madagascar hold up to four small‐bodied taxa of this genus that are morphologically similar to one another, although they can be distinguished based on the tragus, an ear structure associated with echolocation. Miniopterus often emit species‐specific calls. In the present study, we analyze the bioacoustics of the 11 species of Miniopterus currently recognized from the Malagasy region, with an initial identification of the 87 recorded and collected individuals based on molecular markers and certain morphological characters. In most cases, bioacoustic parameters differentiate species and have taxonomic utility. Miniopterus griveaudi populations, which occur on three islands (Madagascar, Anjouan, and Grande Comore), showed no significant differences in peak echolocation frequencies. After running a discriminant function analysis based on five bioacoustic parameters, some mismatched assignments of Malagasy species were found, which include allopatric sister‐taxa and sympatric, phylogenetically not closely‐related species of similar body size. Because the peak echolocation frequencies of two species (Miniopterus sororculus and Miniopterus aelleni) were independent of body size, they were acoustically distinguishable from cryptic sympatric congeners. The small variation around the allometric relationship between body size and peak echolocation frequency of Malagasy Miniopterus species suggests that intraspecific communication rather than competition or prey detection may be the driver for the acoustic divergence of these two species. Our well‐defined echolocation data allow detailed ecological work to commence aiming to test predictions about the relative roles of competition, prey availability, and social communication on the evolution of echolocation in Malagasy Miniopterus species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 284–302.     

Natural colonization or introduction? Phylogeographical relationships and morphological differentiation of house geckos (Hemidactylus) from Madagascar

Several house gecko species of the genus Hemidactylus are almost cosmopolitan lizards, with distributions that have probably been shaped by natural transoceanic dispersal as well as by more recent human introductions. Here we revise the Hemidactylus populations of Madagascar and compare them genetically with populations from other sites in the Indian Ocean region. Morphological data strongly confirm the occurrence of three Hemidactylus species on Madagascar: Hemidactylus frenatus , distributed along the western coast of Madagascar; H. platycephalus , restricted to the north-west and the widespread H. mercatorius that occurs throughout the island, including coastal areas at sea level as well as big cities (Antananarivo, Fianarantsoa) at altitudes of 1200–1300 m above sea level. Analyses of partial sequences of the 16S rRNA gene in 46 Hemidactylus specimens from Madagascar, East Africa, South Asia, and the Comoro and Mascarene archipelagos demonstrated the presence of a fourth species, H. brooki, on the Mascarenes (Réunion, Rodrigues, and Mauritius) and Comoros (Moheli). The Malagasy populations of H. platycephalus were genetically uniform and differentiated from the African and Comoroan specimens studied. H. frenatus had a relatively low genetic differentiation over the whole region with no recognizable phylogeographical structure, indicating more recent colonizations or introductions. In contrast, H. mercatorius showed a strong phylogeographical structure of haplotypes, with two distinctly different lineages in Madagascar. Moreover, all Malagasy specimens differed strongly from the single African specimen included. This indicates that populations of H. mercatorius in Madagascar have a long history that predates human settlement.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 115–130.     

The fern genus Elaphoglossum section Lepidoglossa (Dryopteridaceae) in Africa,Macaronesia, the mid‐Atlantic and southern Indian Ocean Islands

Elaphoglossum section Lepidoglossa in Africa, Macaronesia (Azores and Madeira), the mid‐Atlantic Ocean Islands (St Helena, Gough and Tristan da Cunha Island groups) and the southern Indian Ocean Islands (Marion and Prince Edward Islands) is reviewed. Fifteen Elaphoglossum species from this region are ascribed to the section. A new species, Elaphoglossum rivularum , confined to the Chimanimani Mountains in eastern Zimbabwe and formerly ascribed to E. kuhnii from West Africa, is described. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 20–63.     

Population differentiation in a purported ring species,Acacia karroo (Mimosoideae)

Acacia karroo Hayne (Mimosoideae; Fabaceae) is a highly polymorphic species, ranging in height from 1 m to more than 30 m, and with enormous variation in the architecture of adults. Some populations of A. karroo with different morphologies are situated less than 20 km apart. This species has been considered to be a ring species on the basis of allozyme variation. I wished to determine whether this was supported by sapling morphology, and by chemical and physical defences to herbivory. I raised four phenotypes from the restricted area of Zululand (South Africa) in a common garden with controls, and with water and nutrient supplementation. I found that each of the four phenotypes maintained their differences in spite of nutrient and water supplementation. There was no significant genotype by environment interaction. I also found that the coastal population was significantly larger than another phenotype that grows just 12 km inland from it, suggesting that there might be local adaptation of these genotypes to particular soil types. I confirm that A. karroo maintains morphological differentiation even when there is substantial alteration of water and nutrient availability. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 748–755.     

Paraphyly of Cyrtomium (Dryopteridaceae): evidence from rbcL and trnL-F sequence data

Cyrtomium is an Asiatic genus characterized by anastomosing veins with included veinlets, and comprises about 40 species. We sequenced rbcL and trnL-F sequences of 19 species of Cyrtomium and eight species from related genera in order to elucidate a molecular phylogeny of the genus using maximum-parsimony methods. The phylogenetic trees did not agree with traditional classifications. Cyrtomium was resolved as paraphyletic, and a clade including subseries Balansana of Cyrtomium, Cyrtogonellum, Polystichum subacutidens and Cyrtomidictyum (the BCPC clade) and a second one containing Cyrtomium sensu stricto were monophyletic. The results also implied that: (1) C. uniseriale was synonymous with C. balansae; (2) C. falcatum was likely the female parent of C. devexiscapulae; and (3) based on the rbcL and trnL-F sequence data, C. nephrolepioides and C. grossum were the female parents of C. shingianum and C. chingianum, respectively, although other evidence is needed for the confirmation of this hypothesis.     

High mortality and female‐biased operational sex ratio result in low encounter rates and moderate polyandry in a spider

The taxonomy of the Old World bat genus Otomops (Chiroptera: Molossidae) has been the subject of considerable debate. The failure of classical morphological studies to provide consistent patterns regarding interspecific relationships within Otomops has limited any understanding of the evolutionary history of the genus. We used traditional and geometric morphometric approaches to establish the species limits of taxa from sub‐Saharan Africa, the Arabian Peninsula, and Madagascar. Morphometric data supported the recent recognition of three distinct Afrotropical taxa: Otomops madagascariensis from Madagascar; Otomops martiensseni s.s. from southern, eastern, central, and western Africa; and an undescribed taxon from north‐east Africa and the Arabian Peninsula. Analyses of craniodental measurements and landmark‐based data showed significant cranial size and shape divergence between the three taxa. Cranial size and shape variation within Afro‐Arabian Otomops were strongly influenced by altitude, seasonality of precipitation, and precipitation in the driest month. Based on morphometric patterns and molecular divergence estimates, we suggest that morphological evolution within Afro‐Arabian Otomops occurred in response to the fluctuating climate during the Pleistocene on the one hand, and the increasing aridity and seasonality over north‐eastern Africa on the other. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, •• , ••–••.     

Eight new species of Marasmodes (Asteraceae,Anthemideae) from South Africa

During a stay at the Kirstenbosch Research Centre in Cape Town (South Africa), several groups of Asteraceae were studied. One of these was the genus Marasmodes (tribe Anthemideae). After a careful taxonomic study of additional material, including the first species described by A. P. de Candolle, the author has concluded that eight collections should be considered as new species. These new species are described and their relationships with the most similar species of the genus are discussed. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 330–342.     

Molecular phylogenetics of Kosteletzkya (Malvaceae,Hibisceae) reveals multiple independent and successive polyploid speciation events

Kosteletzkya s.s. is a genus of 17 species (excluding the endemic species of Madagascar), found in the New World, continental Africa, Madagascar, and Southeast Asia. Recent chromosome counts revealed diploid, tetraploid, and hexaploid species. To estimate the history of the genus, we sequenced nuclear and plastid loci for nearly all Kosteletzkya spp., in the majority of cases, with multiple accessions per species. The African species form a paraphyletic grade relative to a New World clade. Polyploidy has occurred only in some African species, resulting in the relatively ancient formation of one putative autotetraploid species (K. semota), one recent allotetraploid species (K. borkouana), two relatively ancient allotetraploid species (K. begoniifolia and K. rotundalata) and one recent allohexaploid species (K. racemosa). Our inferences regarding the hypothesized parentage of the polyploids mostly corroborate previous work based on chromosome‐pairing patterns in artificial hybrids, highlighting the utility of these complementary data sources. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 421–435.     

The lace web spiders (Araneae,Phyxelididae) of Madagascar: phylogeny,biogeography and taxonomy

We briefly review the potential history of Madagascar as either a Darwinian or a Wallacean island, summarize the phylogenetic evidence regarding the biogeography of Madagascar spiders, examine the dispersal history of the Madagascar Phyxelididae, and monograph the family in Madagascar. Molecular phylogenetic analyses for 32 Malagasy phyxelidid exemplars, nine confamilial outgroup taxa, and seven other more distant outgroups are performed for three nuclear markers and one mitochondrial genetic marker (28S, 18S, H3 and COI) utilizing Bayesian, maximum‐likelihood and parsimony methods. These analyses suggest that there are 14 species of Phyxelididae that may be recognized from Madagascar, that these may be divided into three genera, and that the Malagasy phyxelidids form a monophyletic group, probably resulting from a single invasion of the island by an ancestor from Africa. Two new genera, ten new species, and two new combinations are proposed: Manampoka atsimo gen. nov., sp. nov. ; Rahavavy gen. nov. , including R. ida sp. nov. and R. fanivelona (Griswold, 1990) comb. nov. and R. malagasyana (Griswold, 1990) comb. nov. ; and Ambohima andrefana sp. nov. , A. antsinanana sp. nov. , A. avaratra sp. nov. , A. maizina sp. nov. , A. ranohira sp. nov. , A. vato sp. nov. , A. zandry sp. nov. and A. zoky sp. nov. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 728–810.     

The antiquity of Madagascar’s grasslands and the rise of C4 grassy biomes

Aim Grasslands and savannas, which make up > 75% of Madagascar’s land area, have long been viewed as anthropogenically derived after people settled on the island c. 2 ka. We investigated this hypothesis and an alternative – that the grasslands are an insular example of the post‐Miocene spread of C₄ grassy biomes world‐wide. Location Madagascar, southern Africa, East Africa. Methods We compared the number of C₄ grass genera in Madagascar with that in southern and south‐central African floras. If the grasslands are recent we would expect to find fewer species and genera in Madagascar relative to Africa and for these species and genera to have very wide distribution ranges in Madagascar. Secondly, we searched Madagascan floras for the presence of endemic plant species or genera restricted to grasslands. We also searched for evidence of a grassland specialist fauna with species endemic to Madagascar. Plant and animal species endemic to C₄ grassy biomes would not be expected if these are of recent origin. Results Madagascar has c. 88 C₄ grass genera, including six endemic genera. Excluding African genera with only one or two species, Madagascar has 86.6% of southern Africa’s and 89.4% of south‐central Africa’s grass genera. C₄ grass species make up c. 4% of the flora of both Madagascar and southern Africa and species : genus ratios are similar (4.3 and 5.1, respectively). Turnover of grasses along geographical gradients follows similar patterns to those in South Africa, with Andropogoneae dominating in mesic biomes and Chlorideae in semi‐arid grassy biomes. At least 16 monocot genera have grassland members, many of which are endemic to Madagascar. Woody species in frequently burnt savannas include both Madagascan endemics and African species. A different woody flora, mostly endemic, occurs in less frequently burnt grasslands in the central highlands, filling a similar successional niche to montane C₄ grasslands in Africa. Diverse vertebrate and invertebrate lineages have grassland specialists, including many endemic to Madagascar (e.g. termites, ants, lizards, snakes, birds and mammals). Grassland use of the extinct fauna is poorly known but carbon isotope analysis indicates that a hippo, two giant tortoises and one extinct lemur ate C₄ or CAM (crassulacean acid metabolism) plants. Main conclusions The diversity of C₄ grass lineages in Madagascar relative to that in Africa, and the presence of plant and animal species endemic to Madagascan grassy biomes, does not fit the view that these grasslands are anthropogenically derived. We suggest that grasslands invaded Madagascar after the late Miocene, part of the world‐wide expansion of C₄ grassy biomes. Madagascar provides an interesting test case for biogeographical analysis of how these novel biomes assembled, and the sources of the flora and fauna that now occupy them. A necessary part of such an analysis would be to establish the pre‐settlement extent of the C₄ grassy biomes. Carbon isotope analysis of soil organic matter would be a feasible method for doing this.     

Patterns of diversification in two species of short‐tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests

The small‐sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 527–539.     

Cryptic speciation in the southern African vlei rat Otomys irroratus complex: evidence derived from mitochondrial cyt b and niche modelling

The vlei rat Otomys irroratus has a wide distribution in southern Africa with several datasets indicating the presence of two putative species (O. irroratus and O. auratus). In the present study we use mitochrondrial cyt b data (～950 bp) from 98 specimens (including museum material) collected throughout the range of the species to determine the geographical limits of the two recognized species, and we link this to niche modelling to validate these species. Phylogenetic analysis of the DNA sequence data, using maximum parsimony, neighbour joining and Bayesian inference, retrieved two divergent statistically well‐supported clades. Clade A occurs in the Western and Eastern Cape while Clade B occurs in the Free State, KwaZulu‐Natal, Northern Cape and Mpumalanga provinces of South Africa and Zimbabwe. Mean sequence divergence between the two clades (A and B) was 7.0% and between sub‐clades comprising clade B it was 4.8%; the two clades diverged during the Pleistocene. Within Clade A the mean sequence divergence among specimens was 1.91%. Niche modelling revealed that the incipient species occupy distinct bioclimatic niches associated with seasonality of precipitation. Our data allow insightful analysis into the factors that could have led to cladogenesis within this rodent. More significantly, the new data enable us to pinpoint the Eastern Cape province as a contact zone for the divergent species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 192–206.