A conservation assessment of the freshwater crabs of southern Africa (Brachyura: Potamonautidae)

Recent taxonomic revisions of the freshwater crabs of southern Africa (Angola, Botswana, Lesotho, Mozambique, Namibia, South Africa, Swaziland, Zambia and Zimbabwe) allow accurate depictions of their diversity, distribution patterns and conservation status. The southern African region is home to nineteen species of freshwater crabs all belonging to the genus Potamonautes (family Potamonautidae). These crabs show high levels of species endemism (84%) to the southern African region and to the country of South Africa (74%). The conservation status of each species is assessed using the IUCN (2003) Red List criteria, based on detailed compilations of the majority of known specimens. The results indicate that one species should be considered vulnerable, fifteen species least concern and three species data deficient. The results have been utilized by the IUCN for Red Lists, and may prove useful when developing a conservation strategy for southern Africa’s endemic freshwater crab fauna.     

Evolutionary systematics in African gerbilline rodents of the genus Gerbilliscus: inference from mitochondrial genes

Gerbilliscus has recently been proposed as an endemic African rodent genus distinct from the Asian Tatera. A molecular phylogeny of the genus, including nine species from southern, western and eastern Africa, is presented here based on the analysis of the cytochrome b and 16S mitochondrial genes. With an adequate taxonomic sampling over a wide geographic range, we here provide a clear picture of the phylogenetic relationships between species and species groups in this genus. Three distinct clades were resolved, corresponding to major geographical subdivisions: an eastern clade that possibly diverged first, then a southern and a western clades which appeared later. We suggest two possible hypotheses concerning the dispersal of the genus across Africa, considering also the patterns of karyotypic variation. Finally, we discuss the taxonomic status of G. gambianus and the relationships between Gerbillurus and Gerbilliscus, as previous studies have suggested that the former should be included in the latter. Our data seem to support the synonymy of the two taxa and suggest that Gerbillurus and Gerbilliscus lineages diverged from a common ancestor appeared in eastern Africa.     

Phylogeny and biogeography of the genus Lycium (Solanaceae): inferences from chloroplast DNA sequences

Lycium comprises approximately 70 species and is disjunctly distributed in temperate to subtropical regions in South America, North America, southern Africa, Eurasia, and Australia. Among them, only Lycium sandwicense A. Gray sporadically occurs widely on oceanic islands in the Pacific Ocean. To investigate phylogenetic and biogeographic relationships of the genus with emphasis on L. sandwicense, the coding region of matK, the two intergenic spacers trnT (UGU)-trnL (UAA) and trnL (UAA)-trnF (GAA), and the trnL (UAA) intron of chloroplast DNA (cpDNA) were sequenced. A strict consensus tree resulting from the phylogenetic analysis indicates the following: (1) New World species comprise a potentially paraphyletic assemblage; (2) southern African, Australian, and Eurasian species together are monophyletic; (3) southern African species are a paraphyletic assemblage; and (4) L. sandwicense is in a clade with certain New World species. The estimated biogeographic events based on the cpDNA analysis indicate that (1) Lycium originated in the New World, (2) all southern African, Australian, and Eurasian species have a common ancestor from the New World, (3) Australian and Eurasian species originated once from a southern African progenitor, and (4) L. sandwicense differentiated from the New World species.     

Contrasting spatial patterns of taxonomic and functional richness offer insights into potential loss of ecosystem services

Functional and trophic perspectives on patterns of species occurrences have the potential to offer new and interesting insights into a range of spatially explicit problems in ecology and conservation. We present the function–area relationship (FAR) and explore linkages between functional and taxonomic species richness for South African birds. We first used beak morphology to classify a subset of 151 South African bird species into 18 functional groups and calculated both the species–area relationship and the FAR at quarter-degree resolution for South Africa. The relationship between functional and taxonomic richness by cell was quadratic rather than linear, with considerable scatter around the curve. We next looked at the spatial relationships between taxonomic diversity and response diversity (i.e. diversity within functional groups) using an a priori categorization of nearly all South African birds into nine functional groups. The spatial distribution of response richness also showed considerable variation in relation to taxonomic richness. Our results demonstrate a novel approach to linking taxonomic, functional and trophic patterns in space and suggest a way in which conservation planning, which has traditionally had a taxonomic focus, could formally incorporate a more functional and food-web-based approach.     

Bridging the gap: western rock skinks (Trachylepis sulcata) have a short history in South Africa

Phylogeographic patterns in wide-ranging species in southern Africa remain largely unexplored, especially in areas north of South Africa. Here, we investigate population structuring, demographic history, and the colonization pattern of the western rock skink (Trachylepis sulcata), a rock-dwelling species with a range extending from southwestern South Africa into Angola. Using 1056 bp from the mitochondrial marker ND2 and > 2.5 kb from three nuclear genes (EXPH5, KIF24, RAG-1), we constructed allele networks, generated extended Bayesian skyline plots and performed population clustering analyses. Analyses of historical demographic patterns show an overall southward range expansion from Northern Namibia into Southern Namibia and South Africa, although we find contrasting genetic breaks across these geographic regions using nuclear and mitochondrial data. We suggest that mtDNA has introgressed across a nuclear break corresponding to the Knersvlakte region of South Africa, a previously proposed biogeographic barrier for rupicolous species. This pattern of mitochondrial variation contrasts sharply to that of other South African taxa previously investigated, which all show significant mtDNA differentiation across the Knersvlakte region. Additionally, while other taxa show divergences dating to the Pliocene, T. sulcata appears to be a recent arrival in southern Africa, having crossed this barrier and colonized South Africa in the mid-Pleistocene. The complex phylogeographic history of T. sulcata corroborates the intricate patterns of genetic variation found in South African taxa and provides novel insight into historical processes affecting species distributed across Namibia.     

Phylogenetics of the southern African dwarf chameleons, Bradypodion (Squamata: Chamaeleonidae)

The taxonomic relationships within the dwarf chameleons (Bradypodion) of southern Africa have long been controversial. Although informal phenotypic groups have been suggested, the evolutionary relationships among the 15 recognised species in southern Africa have not been previously investigated. To investigate the relationships among species within this genus, fragments of two mitochondrial genes (16S ribosomal RNA and ND2) were sequenced and analysed using maximum parsimony, maximum likelihood and Bayesian inference. All analyses showed congruent topologies, revealing at least 5 well-supported clades distributed across distinct geographic regions. The mtDNA gene tree indicated that in many instances, geographic location has played a role in shaping the evolution of this group, and that the previously suggested phenotypic groupings do not adequately reflect evolutionary relationships. Furthermore, it appears that some of the currently recognised species (described on morphology) are polyphyletic for mitochondrial sequences, most notably those occurring in the isolated forest patches of north-eastern South Africa, near the Drakensberg Escarpment.     

Systematics of the olive thrush Turdus olivaceus species complex with reference to the taxonomic status of the endangered Taita thrush T. helleri

During the last 40 years, few species of African birds have undergone more taxonomic revision than the olive thrush Turdus olivaceus. This is due to disagreement on how to partition the striking phenotypic variation among allopatric populations. The current consensus is to recognise one species T. olivaceus , split into three assemblages: (1) the olivaceus group restricted to southern Africa, (2) the swynnertoni group of the Zimbabwean and southern Malawi highlands, and (3) the abyssinicus group of the montane highlands of eastern and central Africa. Mitochondrial DNA sequences from 63 individuals were analysed to investigate the phylogenetic relationships among 16 taxa (species and subspecies) in the olivaceus species complex (plus seven outgroup species), with, particular emphasis on the relationships and taxonomic status of the endangered Taita thrush ( helleri ). Phylogenetic hypotheses generated using parsimony, maximum likelihood, and Bayesian inference identified a number of discrete clades corresponding to recognised subspecies. Northern ( abyssinicus clade) and southern populations ( olivaceus + swynnertoni clade) of olive thrush differ by 9–10% in sequence divergence. Furthermore, all analytical methods suggested that helleri (Taita Hills) and roehli (Usambara and Pare Mountains) are reciprocally monophyletic with respect to mtDNA, and 2.5 to 10.5% divergent from all other forms of olive thrush. Both helleri and roehli are surrounded in adjacent highlands by populations of olive thrush that represent a more recent radiation, suggesting that helleri and roehli may be relict taxa which have been able to maintain their genetic integrity. The results of this study support previous arguments for recognizing the arid/woodland T. smithi as a species distinct from other southern African forest populations of T. olivaceus (including the swynnertoni group). Results further suggest that T. abyssinicus , T. helleri , and T. roehli be accorded species rank.     

Resolving the native provenance of invasive fireweed (Senecio madagascariensis Poir.) in the Hawaiian Islands as inferred from phylogenetic analysis

Accurate identification of weedy species is critical to the success of biological control programs seeking host-specific control agents. Phylogenetic relationships based on internal transcribed spacer region (ITS1, ITS2) DNA sequence data were used to elucidate the most likely origin and taxonomic placement of Senecio madagascariensis Poir. (fireweed; Asteraceae) in the Hawaiian archipelago. Putative S. madagascariensis populations from Madagascar, South Africa, Swaziland, and Hawaii were included in the analysis. Different phylogenetic models (maximum parsimony and maximum likelihood) were congruent in suggesting that Hawaiian fireweed is most closely related to populations from the KwaZulu-Natal region in South Africa. Phylogenetic divergence and morphological data (achene characteristics) suggest that the S. madagascariensis complex is in need of revised alpha-level taxonomy. Taxonomic identity of invasive fireweed in Hawaii is important for finding effective biological control agents as native range populations constitute different biotypic variants across a wide geographical area. Based on our phylogenetic results, research directed at biological control of Hawaiian infestations should focus on areas in the KwaZulu-Natal region in South Africa where host-specific natural enemies are most likely to be found. Our results show that phylogeographical analysis is a potential powerful and efficient tool to address questions relevant to invasion biology of plants.     

Molecular taxonomic identification of Dacus and Ceratitis species from Sub-Saharan Africa using mitochondrial haplotypes

Several different taxa within the genera Dacus and Ceratitis (Diptera: Tephritidae) are important agricultural pests in Sub-Saharan Africa. Although the status of many of these taxa as distinct species and their phylogenetic relationships is unclear, it is clear that these pests use a wide range of host plants and are highly invasive. The great potential for economic damage inflicted by these pests requires the ability to make accurate and reliable taxonomic identification of specimens. However, many limitations and uncertainties are encountered when these species are examined using traditional approaches based on morphological identification techniques. We describe here the amplification and analysis of DNA sequences from the mitochondrial cytochrome oxidase II (COII)-tRNA(lys)-tRNA(ASP) genes from individuals of various Dacus and Ceratitis species and populations from Sub-Saharan Africa. The variation detected in the DNA sequences of these individuals is used both for clarification of their taxonomic status and the analysis of phylogenetic relationships of these taxa.     

Contrasts in the large herbivore faunas of the southern continents in the late Pleistocene and the ecological implications for human origins

Aim

Africa is renowned for the current abundance and diversity of its large mammals. The aim of this study was to assess distinctions evident in the functional composition of continental large herbivore faunas during the late Pleistocene before extinctions depleted the megafauna outside Africa.

Location

The African large herbivore fauna was compared with that formerly inhabiting South America, Australia, North America, Eurasia and tropical Asia during the late Pleistocene.

Methods

Pleistocene faunas were reconstructed from the literature in terms of their relative body size composition, grazer/browser contributions and taxonomic representations, omitting forest and island species.

Results

Although the three southern continents were closely similar in the overall species richness of large herbivores that they supported during the late Pleistocene, South America had a predominance of very large herbivores, while most of Australia's mammalian herbivores were relatively small and those of Africa were intermediate. Africa had many more grazers, especially in the size range 100–1000 kg, than other continents. The South American pattern resembled that in North America and Eurasia, while Africa and Australia diverged in different ways.

Main conclusions

Neither the total extent of savannas in each continent nor the morphological features enabling bovid radiation seemed adequate on their own to explain the greater richness of macrograzers in Africa. Africa is characterized by the widespread occurrence of arid/eutrophic savannas, which are unrepresented in other continents. The prevalence of savanna is partly attributable to the high elevation of interior eastern and southern Africa, associated with relatively low rainfall, and to the comparatively high soil fertility, related to volcanic influences. This promoted an abundance and diversity of medium‐sized grazing ruminants unrivalled elsewhere. Indigenous grasses in South America and Australia are less well adapted to withstand severe grazing than the African grasses introduced to support livestock. The locally high abundance of African ungulates presented conditions that facilitated the adaptive transition by early hominins from plant‐gatherers to meat‐scavengers.     

Molecular phylogeny and novel host associations of avian chewing lice (Insecta: Phthiraptera) from South Africa

Compared with Europe and the Americas, the ectoparasites of African birds are poorly understood, despite the avian fauna being relatively well known. Notably, previous studies documenting the host associations and genetic diversity of parasitic chewing lice of southern African birds have been limited in geographic and taxonomic scope. Recent field expeditions exploring the avian diversity in South Africa facilitated an opportunity to obtain louse specimens from a taxonomically diverse host assemblage. This study is the first to investigate avian louse host associations and diversity across a large portion of South Africa encompassing several distinct habitat types, while incorporating molecular genetic data (from portions of the mitochondrial COI and nuclear EF‐1α genes) for ectoparasite phylogenetic analyses. From 1105 South African bird individuals and 170 species examined for lice, a total of 105 new louse–host associations were observed. Morphological and genetic examination of lice with these new host associations reveals a maximum of 66 louse species new to science. Results of this study support the observation that examining museum specimens is a useful way to investigate louse diversity and host associations.     

Phylogenetic position of the southern African members of the tribe Psoraleeae based on molecular and morphological data

The tribe Psoraleeae (Leguminosae subfamily Papilionoideae) comprises 185 species in nine genera that have a nearly worldwide distribution, occurring predominantly in Mediterranean regions. About 60% of the species belong to the genera, Otholobium C.H.Stirt. and Psoralea L., which have a centre of diversity in the Cape Floristic Region of South Africa. Since previous molecular studies have sampled only a few species of the tribe from this region, this study sought to determine the phylogenetic position of the southern African genera and to test whether they are monophyletic. Phylogenetic relationships were reconstructed using DNA sequence data (trnL-F, rpoB-trnC and ITS) and seven morphological characters, which diagnose the two southern African genera. The data were analysed using the parsimony method. There was strong support for the Psoraleeae as a clade, but most of the nodes within the large genera were poorly supported. The southern African species of Psoralea and Otholobium together formed a strongly supported clade. This clade was sister to the genus Hoita Rydb., but without support. However, the Psoralea species were nested within the southern African Otholobium. Additionally, some South American species that are currently recognised as Otholobium were resolved in a clade distinct from the southern African species, making Otholobium polyphyletic. Morphological characters that separate Otholobium and Psoralea are discussed. Finally, the southern African genera as currently circumscribed are not monophyletic. However, further investigations using more informative DNA loci are required to validate this observation. Furthermore, the taxonomic placement of the South American species needs to be reviewed.     

Phylogenetic relationships and phylogeography of the Killifish species of the subgenus Chromaphyosemion (Radda, 1971) in West Africa, inferred from mitochondrial DNA sequences

We have analyzed the phylogenetic relationships of 160 specimens from 88 samples representing all defined species of the African Aplocheiloid subgenus Chromaphyosemion in order to examine the monophyly of this group, the species interrelationships, and to reveal trends in chromosomal evolution and formulate hypotheses about their evolutionary history. The data set comprised 1153 total nucleotides from the mitochondrial 12S rRNA, cytochrome oxidase I, and D-loop. The molecular-based topologies were analyzed by maximum parsimony, maximum likelihood, distance method and Bayesian inference support the monophyly of the subgenus Chromaphyosemion. All populations with ambiguous taxonomic status were assigned to an already described species except A. sp. Rio Muni which corresponds to a still undescribed species. Aphyosemion alpha and A. lugens were in basal position in the different trees that indicate a possible origin of the subgenus Chromaphyosemion in the South Cameroon-North Gabon region. Furthermore, the South Cameroon region (between 2 degrees and 3 degrees of North latitude) that accommodates half of the Chromaphyosemion species is considered to have been a refuge zone during the late quaternary dry events that Africa experienced. Phylogenetic relationships among the subgenus also revealed that chromosomal evolution is complex and should be studied at the intraspecific level.     

Phylogenetic relationships, character evolution and biogeography of southern African members of Zygophyllum (Zygophyllaceae) based on three plastid regions

The plastid coding rbcL and non-coding trnLF regions of 53 of 55 southern African Zygophyllum species were sequenced and used to evaluate the phylogenetic relationships within the southern African representatives of the genus. Published sequences of the same gene regions of Australian, Asian and North African Zygophyllum species were included to assess the relationships of the species from these regions to the southern African species. The addition of Z. stapffii from Namibia, found to be conspecific with Z. orbiculatum from Angola, lead to a greatly resolved tree. The molecular results were largely congruent with a recent sectional classification of the southern African species and supported their subdivision into subgenera Agrophyllum and Zygophyllum. Reconstruction of the character evolution of capsule dehiscence, seed attachment and seed mucilage showed that these characters allowed a division of southern African species into the two subgenera but that this could not be applied to species occurring elsewhere. Other morphological characters were found to vary and unique character combinations, rather than unique characters, were found to be of systematic value in sectional delimitation. The study suggests that repeated radiations from the horn of Africa to southern Africa and Asia and back lead to the present distribution of the taxa in the subfamily Zygophylloideae. Although this study supports some of the recent taxonomic changes in the group, the unresolved relationships between the proposed genera Tetraena and Roepera and those retained as Zygophyllum species suggest that changes to the taxonomy may have been premature.     

An ecological reassessment of the southern African carnivore guild: a case study from Member 4, Sterkfontein, South Africa

The southern African late Pliocene to early Pleistocene carnivore guild was much larger than that of the present day. Understanding how this guild may have functioned is important for the reconstruction of carnivore-hominin interactions and to assess the potential for hominin scavenging in southern Africa. In modern ecosystems, the coexistence of larger carnivore species is constrained by several factors, which include high levels of interspecific competition. Here, the composition of the fossil carnivore guild is examined using Sterkfontein Member 4 (Cradle of Humankind, South Africa) as a case study. Sterkfontein Member 4 contains 10 larger carnivore taxa (body mass > 21.5 kg) and may also contain two Australopithecus species. Two possible causes of higher numbers of carnivore species in the South African fossil record are initially considered. First, that there is a bias introduced through comparing assemblages of differing sizes; second, carnivore biodiversity may have been artificially inflated due to previous taxonomic splitting of carnivore species, such as Crocuta. These possibilities are rejected and modern ecological data are used to construct a simple spatial model to determine how many carnivores could have co-existed. Although the resulting model indicates that the carnivore taxa present in Member 4 could have co-occurred, modern ecological studies indicate that it is highly unlikely that they would have co-existed simultaneously. Considering the complex depositional processes that operate in the southern African cave sites, it is proposed that the larger carnivore guild observed in the Sterkfontein Member 4 fossil assemblage is a palimpsest created by time-averaging. In light of this, we suggest that sites which have a large number of carnivore taxa should be examined for time-averaging, while those sites which have relatively few species may be a better reflection of carnivore communities.     

Out of Africa: the slow train to australasia

We used mitochondrial DNA (mtDNA) sequences to test biogeographic hypotheses for Patiriella exigua (Asterinidae), one of the world's most widespread coastal sea stars. This small intertidal species has an entirely benthic life history and yet occurs in southern temperate waters of the Atlantic, Indian, and Pacific oceans. Despite its abundance around southern Africa, southeastern Australia, and several oceanic islands, P. exigua is absent from the shores of Western Australia, New Zealand, and South America. Phylogenetic analysis of mtDNA sequences (cytochrome oxidase I, control region) indicates that South Africa houses an assemblage of P. exigua that is not monophyletic (P = 0.04), whereas Australian and Lord Howe Island specimens form an interior monophyletic group. The placement of the root in Africa and small genetic divergences between eastern African and Australian haplotypes strongly suggest Pleistocene dispersal eastward across the Indian Ocean. Dispersal was probably achieved by rafting on wood or macroalgae, which was facilitated by the West Wind Drift. Genetic data also support Pleistocene colonization of oceanic islands (Lord Howe Island, Amsterdam Island, St. Helena). Although many biogeographers have speculated about the role of long-distance rafting, this study is one of the first to provide convincing evidence. The marked phylogeographic structure evident across small geographic scales in Australia and South Africa indicates that gene flow among populations may be generally insufficient to prevent the local evolution of monophyly. We suggest that P. exigua may rely on passive mechanisms of dispersal.     

Phylogenetic placement and population structure of Indo‐Pacific bottlenose dolphins (Tursiops aduncus) off Zanzibar,Tanzania, based on mtDNA sequences

Phylogenetic placement of bottlenose dolphins from Zanzibar, East Africa and putative population differentiation between animals found off southern and northern Zanzibar were examined using variation in mtDNA control region sequences. Samples (n= 45) from animals bycaught in fishing gear and skin biopsies collected during boat surveys were compared to published sequences (n= 173) of Indo‐Pacific bottlenose dolphin, Tursiops aduncus, from southeast Australian waters, Chinese/Indonesian waters, and South African waters (which recently was proposed as a new species) and to published sequences of common bottlenose dolphin, Tursiops truncatus. Bayesian and maximum parsimony analyses indicated a close relationship between Zanzibar and South African haplotypes, which are differentiated from both Chinese/Indonesian and Australian T. aduncus haplotypes. Our results suggest that the dolphins found off Zanzibar should be classified as T. aduncus alongside the South African animals. Further, analyses of genetic differentiation showed significant separation between the T. aduncus found off northern and southern Zanzibar despite the relatively short distance (approximately 80 km) between these areas. Much less differentiation was found between southern Zanzibar and South Africa, suggesting a more recent common evolutionary history for these populations than for the northern and southern Zanzibar populations.     

Southern African skate biodiversity and distribution

The skates (Family Rajidae) have 12 genera and possibly 28 species off southern Africa (southern Angola, Namibia, South Africa and Mozambique). The geographic and bathymetric distribution and the taxonomic composition of the southern African skate fauna are analysed and the distribution mapped. The southern African skate fauna is best known off the temperate west coast of South Africa from the intertidal to approximately 1,200 meters, but poorly known below 1,200 m and sketchily known in warm-temperate and tropical parts of the area. Southern African skates of the temperate continental shelves above 100 m are not diverse and regularly include one species of the genus Dipturus, one species of Leucoraja, two species of Raja (including R. straeleni, the most abundant skate in southern African waters) and the giant skate Rostroraja alba. All of these skates are ‘shelf overlap’ species that range onto the outer shelves and uppermost slopes, and none are confined to inshore environments. Skate diversity increases on the outer shelves and upper slopes. At least half of the skate species are endemic to the southern African region; other species also occur off East or West Africa, a few extend to European waters, and records of one species, Amblyraja taaf, appear to be of strays from nearby sub-Antarctic seas. The genus Bathyraja and softnose skate group (Arhynchobatinae) are surprisingly limited (a single species) in deep-water off southern Africa (unlike other regions including the Antarctic), and almost all of southern African skates are members of the Rajinae. Amongst rajines, the tribes Amblyrajini (Amblyraja, two species, Leucoraja, two species, and Rajella, five species) Rajini (Dipturus, six species, Okamejei, one species, Raja, two species, and Rostroraja, one species), and Anacanthobatini (Anacanthobatis, two species, and Cruriraja, three species) predominate, while Gurgesiellini has a species of Neoraja and possibly two of Malacoraja.