The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura)

A biogeographical appraisal of the threatened South East Africa Montane Archipelago ecoregion

Recent biological surveys of ancient inselbergs in southern Malawi and northern Mozambique have led to the discovery and description of many species new to science, and overlapping centres of endemism across multiple taxa. Combining these endemic taxa with data on geology and climate, we propose the 'South East Africa Montane Archipelago' (SEAMA) as a distinct ecoregion of global biological importance. The ecoregion encompasses 30 granitic inselbergs reaching > 1000 m above sea level, hosting the largest (Mt Mabu) and smallest (Mt Lico) mid-elevation rainforests in southern Africa, as well as biologically unique montane grasslands. Endemic taxa include 127 plants, 45 vertebrates (amphibians, reptiles, birds, mammals) and 45 invertebrate species (butterflies, freshwater crabs), and two endemic genera of plants and reptiles. Existing dated phylogenies of endemic animal lineages suggests this endemism arose from divergence events coinciding with repeated isolation of these mountains from the pan-African forests, together with the mountains' great age and relative climatic stability. Since 2000, the SEAMA has lost 18% of its primary humid forest cover (up to 43% in some sites)-one of the highest deforestation rates in Africa. Urgently rectifying this situation, while addressing the resource needs of local communities, is a global priority for biodiversity conservation.

The status of Tomopterna pulchra Boulenger, 1896 (Anura: Pyxicephalidae)

Tomopterna pulchra (Boulenger, 1896) was described from Lake Tanganyika based on a single specimen. It was synonymised with Tomopterna tuberculosa (Boulenger, 1882) by Loveridge (1957) who noted that it did not fully agree with the description of T. tuberculosa, especially in the difference in dorsal colouration. Genetic differences show that two species are confused, although their advertisement calls and morphology are similar, except for the presence of a pale vertebral stripe mostly in eastern populations. We consider the advertisement calls, morphology, and genetic differences, and remove Tomopterna pulchra (Boulenger, 1896) from the synonymy of Tomopterna tuberculosa. Divergence dating shows that these two species separated in the mid-Miocene. Tomopterna pulchra breeds in rocky habitats, whereas T. tuberculosa breeds in sandy areas, typical of the genus. Based on genetically confirmed specimens, presently T. tuberculosa is known in the west (Angola and Namibia) while T. pulchra is only known from the east (Zambia and Tanzania). The examination of specimens for the presence or absence of a vertebral stripe infers that these species are widespread. Further work is required to determine if the two species are sympatric, and the extent of their ranges.

Rock island melody remastered: two new species in the Afroedura bogerti Loveridge, 1944 group from Angola and Namibia

Newly collected material from northern Namibia’s Otjihipa Mountains and west-central Angola allowed us to revisit the Afroedura bogerti Loveridge, 1944 group. The employment of additional gene markers, including nuclear markers, allowed us to identify two new species in the group and infer species boundaries and potential speciation events in Afroedura from southwestern Africa. The new Namibian material is recovered as a sister species to A. donveae, from which it differs mostly by the colour of the iris (copper versus black) and dorsal colouration. Material from the first elevational gradient of the escarpment in Benguela Province, Angola was found to be more closely related to A. bogerti than A. wulfhaackei. The differences between these two species are more subtle, although the new species exhibits higher mid-body scale rows (79.5 versus 74.8), different dorsal colouration and supranasal scales always in contact (versus 57% in contact).

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

Rock island melody: A revision of the Afroedura bogerti Loveridge, 1944 group, with descriptions of four new endemic species from Angola

Four new species of flat geckos in the Afroedura bogerti Loveridge, 1944 group are described from south-western and west-central Angola. The description of these new species significantly restricts the distribution range of typical A. bogerti, a morphologically very similar species, from which they differ genetically by 5.9–12% divergence for the mitochondrial 16S ribosomal RNA gene. Morphologically and genetically, Angolan Afroedura are divided into two main groups: a mostly south-western coastal group and a west-central inland/highland group. These two groups are further divisible into three and two subgroups respectively, all geographically isolated, differing by a combination of the following features: colouration, average adult size, number of mid-body scale rows, number of scale rows on dorsal and ventral surface of each tail verticil and if nostril scales are in contact or not. All five Angolan species are morphologically distinguishable and in agreement with the molecular results. An updated dichotomous key to the Afroedura transvaalica group is provided. The new discovery adds to a growing number of endemic Pro-Namib reptiles described from Angola in recent years.

Mapping Africa's Biodiversity: More of the Same Is Just Not Good Enough

Species distribution data are fundamental to the understanding of biodiversity patterns and processes. Yet, such data are strongly affected by sampling biases, mostly related to site accessibility. The understanding of these biases is therefore crucial in systematics, biogeography, and conservation. Here we present a novel approach for quantifying sampling effort and its impact on biodiversity knowledge, focusing on Africa. In contrast to previous studies assessing sampling completeness (percentage of species recorded in relation to predicted), we investigate whether the lack of knowledge of a site attracts scientists to visit these areas and collect samples of species. We then estimate the time required to sample 90% of the continent under a Weibull distributed biodiversity sampling rate and the number of sampling events required to record $ \ge $50% of the species. Using linear and spatial regression models, we show that previous sampling has been strongly influencing the resampling of areas, attracting repeated visits. This bias has existed for over two centuries, has increased in recent decades, and is most pronounced among mammals. It may take between 172 and 274 years, depending on the group, to achieve at least one sampling event per grid cell in the entire continent. Just one visit will, however, not be enough: in order to record $ \ge $50% of the current diversity, it will require at least 12 sampling events for amphibians, 13 for mammals, and 27 for birds. Our results demonstrate the importance of sampling areas that lack primary biodiversity data and the urgency with which this needs to be done. Current practice is insufficient to adequately classify and map African biodiversity; it can lead to incorrect conclusions being drawn from biogeographic analyses and can result in misleading and self-reinforcing conservation priorities. [Amphibians; birds; mammals; sampling bias; sampling gaps; Wallacean shortfall.].

Comparison of the mitochondrial phylogeographical structure of a generalist and two specialist frog species reveals contrasting patterns in the Eastern and Western Cape provinces of South Africa

In this study, we examined the phylogeographical structure of three frog species (Anhydrophryne rattrayi, Arthroleptis wageri and Cacosternum nanum) in the Eastern and Western Cape provinces of South Africa. The first two species are forest dwelling and exhibit direct development, whereas the last species is a habitat generalist, breeding in open freshwater bodies and exhibiting rapid metamorphosis. Evolutionary relationships were inferred using combined mitochondrial DNA (mtDNA) sequence data [16S rRNA and cytochrome b (Cytb)]. Divergence times were estimated for each species using the combined mtDNA dataset, and population genetic structuring was inferred using haplotype networks and analysis of molecular variance using the rapidly evolving Cytb locus. The two forest-dwelling species (Anhydrophryne rattrayi and Arthroleptis wageri) each revealed two statistically well-supported clades and were characterized by marked genetic differentiation and the general absence of shared maternal haplotypes, indicating no maternal gene flow between conspecific populations; a result corroborated by moderate values of pairwise genetic distance. In contrast, for the generalist species C. nanum, two shallow clades were observed and several haplotypes were shared between localities, indicating moderate maternal gene flow. Diversification in the two forest-dwelling species occurred during the Plio-Pleistocene climatic oscillations and was associated with increased xeric conditions, whereas in C. nanum a recent, Holocene divergence was inferred. Ancient climatic factors thought to be causal in the divergences within each of the three species are discussed. The marked mtDNA differentiation in the two forest specialist species suggests the presence of distinct management units that should be considered in future conservation management decisions.

The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world's largest frogs

The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr , tRNAPro , tRNAPhe , tRNAVal , tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).