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The geographically widespread species Afrixalus laevis (Anura: Hyperoliidae) currently has a disjunct distribution in western Central Africa (Cameroon, Equatorial Guinea, Gabon, and possibly adjacent countries) and the area in and near the Albertine Rift in eastern Democratic Republic of the Congo and neighboring countries. At least two herpetologists have previously suggested that these disjunct populations represent distinct species, and herein, we utilize an integrative taxonomic approach with molecular and morphological data to reconcile the taxonomy of these spiny reed frogs. We sequenced 1554 base pairs of the 16S and RAG1 genes from 34 samples of A. laevis and one sample of A. orophilus (sympatric with eastern populations of A. laevis), and combined these data with previously sequenced GenBank Afrixalus samples via the bioinformatics toolkit SuperCRUNCH. Phylogenetic trees, dated phylogenetic analyses, and species-delimitation analyses were generated with RAxML, BEAST, and BPP, respectively. Eleven mensural characters were taken from multiple specimens of A. laevis and A. orophilus, and compared with paired t-tests and analyses of covariance. These combined results suggested populations of A. laevis in western Central Africa (Cameroon and Bioko Island, Equatorial Guinea) represent one species, whereas populations from the Albertine Rift and nearby forests represent two undescribed taxa that are sister to A. dorsimaculatus. The two new species (A. lacustris sp. nov. and A. phantasma sp. nov.) are distinguished by our phylogenetic and species-delimitation analyses, significant differences in several mensural characters, qualitative morphological differences, and by their non-overlapping elevational distribution.

Crocodiles play important roles in many ecosystems, but their populations worldwide are threatened by human exploitation and habitat destruction. We studied ontogenetic changes in habitat use and seasonal activity patterns in a population of Nile crocodiles (Crocodylus niloticus) inhabiting the Lake Albert Delta Wetland System, a Ramsar Site of international importance in Murchison Falls National Park of western Uganda. A total of 186 crocodile observations were made from monthly surveys of five transects during October 2017 to September 2018. Crocodiles exhibited a marginally bi-modal seasonal pattern, with the fewest observations from July to August and October to November, and the highest observations from January to February and April to May. Crocodiles were most frequently encountered along the north shore of the delta, especially on riverbanks with woody vegetation, followed by Cyperus papyrus-Vossia dominated habitats, while crocodiles were infrequently observed on islands and muddy banks. Habitat niche breadth was narrowest in hatchlings and widest in sub-adults, with juveniles and large adults exhibiting intermediate values. Overlap in habitat resource use across size classes was generally high, with the lowest overlap between hatchlings and juveniles, and the highest between large and sub-adult crocodiles. Our study on Nile crocodiles in the Lake Albert delta provides insights into habitat partitioning among different demographic segments of this population that can be utilized to improve its management in one of Africa’s Great Lakes by spatially and temporally focusing conservation efforts on the most used habitats and seasonal aggregations, respectively.

1. The area of the Murchison Falls-Albert Delta is among the most important for conservation in East Africa dueto the high species richness, and the presence of several endemic species of conservation concern.2. Here, we report a study on the diversity patterns and community structure of the herpetofauna of this area.3. Field studies were conducted in the Albert Nile Delta Ramsar site between 1st October 2017 and 9th September2018. The data collection relied on Visual Encounter Surveys (VES), pitfall trapping, and dip netting. Descriptive statistics, i.e. species numbers in each transect were used as a measure of the present biodiversity, whereasChao1 and Chao species estimator algorithms were used to predict the potential number of species found ineach site/habitat.4. A total of 898 individuals representing 25 reptile species belonging to four orders, 15 families, and 20 generawere recorded during the 12 months of surveys.5. The data shows some non-random spatial and temporal patterns whereby there is a cyclic reptilian diversitypeaking during the December-March and again towards June-August-September which are peaks of the dryseason.6. The most frequently encountered species were Varanus niloticus, Crocodylus niloticus, Agama agama, Trachylepis maculilabris, and Lygodactylus guttularis, which accounted for almost 90% of all recorded individuals.7. A total of 27 amphibian species, belonging to nine families and 10 genera were recorded during the periodof the survey. The diversity and abundance graphs would indicate amphibians having bimodal peaks (September-December, and March-May). The diversity seemed to dip during the dry season months – which is theopposite case for reptiles.

Uganda is one of the most species rich countries in Africa because of the presence of several major biomes. However, it is also a country that has lost much of its natural habitat to agriculture. Uganda is a country that has been better surveyed for its biodiversity than many African countries, but despite this, there has not been a comprehensive analysis of the critical sites that contribute to biodiversity conservation at a global, as well as at a national level. We here present such an assessment using mammals, birds, reptiles, amphibians, and plants as surrogate taxa. We identified 36 terrestrial sites that are of sufficient global importance to qualify as Key Biodiversity Areas (KBAs), using the Global Standard for the Identification of KBAs, which complement an additional nine freshwater sites. National red listing of species and ecosystems was used to identify sites of national importance for conservation. We employ a conservation planning approach using Marxan to identify the minimum set of sites needed to conserve all the globally and nationally threatened species and nationally threatened habitats in Uganda. The findings show that most of the remaining natural habitat in Uganda is important for the conservation of globally and nationally threatened species and threatened habitat. Large areas of irreplaceable habitat occur outside protected areas, although more extensive surveys of these areas would likely reduce the area that is irreplaceable.

The African river frog genus Amietia is found near rivers and other lentic water sources throughout central, eastern, and southern Africa. Because the genus includes multiple morphologically conservative species, taxonomic studies of river frogs have been relatively limited. We sampled 79 individuals of Amietia from multiple localities in and near the Albertine Rift (AR) of Burundi, Democratic Republic of the Congo, and Uganda. We utilized single-gene (16S) and concatenated (12S, 16S, cyt b and RAG1) gene-tree analyses and coalescent species-tree analyses to construct phylogenetic trees. Two divergence dating approaches were used in BEAST, including secondary calibration points with 12S, 16S, cyt b and RAG1, and a molecular clock with the 12S, 16S, and cyt b genes. All analyses recovered Amietia as monophyletic with strong support, and revealed several well-supported cryptic lineages, which is consistent with other recent phylogeography studies of AR amphibians. Dating estimates were similar, and Amietia diversification is coincident with global cooling and aridification events in the Miocene and Pliocene, respectively. Our results suggest additional taxonomic work is needed to describe multiple new species of AR Amietia, some of which have limited geographic distributions that are likely to be of conservation concern.

We studied the effects of forest management on amphibian communities in the Budongo Central Forest Reserve, Uganda. We sampled amphibians from May to August of 2012 in four compartments with different logging and arboricide-treatment histories. We used pitfall traps with drift fences combined with visual encounter surveys to sample amphibians from 36 plots in four 1-km long transects along the Sonso River. From 126 encounters across plots, we recorded 25 frog species belonging to six families and eight genera. Arthroleptidae was the most diverse family represented by 10 species within two genera. Arthroleptis had the highest number of species (six), Ptychadena the second most (five), followed by Leptopelis (four) and Sclerophrys (four). Species composition differed across transects. The unlogged study site possessed the highest species richness, diversity, and evenness, and had the greatest frequency of species encounters. The most heavily logged site had the lowest species diversity and fewest amount of species encounters. This site also had the most dissimilar species composition among sites and was significantly different in species richness compared to the unlogged site. The two moderately logged sites had the second and third most species, and had the most similar species composition to each other. Our study provides data on the amphibian species of a protected site in the Albertine Rift, part of the Eastern Afromontane biodiversity hotspot, and results suggest that the forest management regimes in Budongo have exerted an influence over the amphibian communities after more than 50 years of forest recovery.

Members of the snake subfamily Aparallactinae occur in various habitats throughout sub-Saharan Africa. The monophyly of aparallactine snakes is well established, but relationships within the subfamily are poorly known. We sampled 158 individuals from six of eight aparallactine genera in sub-Saharan Africa. We employed concatenated gene-tree analyses, divergence dating approaches, and ancestral-area reconstructions to infer phylogenies and biogeographic patterns with a multi-locus data set consisting of three mitochondrial (16S, cyt b, and ND4) and two nuclear genes (c-mos and RAG1). As a result, we uncover several cryptic lineages and elevate a lineage of Polemon to full species status. Diversification occurred predominantly during the Miocene, with a few speciation events occurring subsequently in the Pliocene and Pleistocene. Biogeographic analyses suggested that the Zambezian biogeographic region, comprising grasslands and woodlands, facilitated radiations, vicariance, and dispersal for many aparallactines. Moreover, the geographic distributions of many forest species were fragmented during xeric and cooler conditions, which likely led to diversification events. Biogeographic patterns of aparallactine snakes are consistent with previous studies of other sub-Saharan herpetofauna.

Several biogeographic barriers in the Central African highlands have reduced gene flow among populations of many terrestrial species in predictable ways. Yet, a comprehensive understanding of mechanisms underlying species divergence in the Afrotropics can be obscured by unrecognized levels of cryptic diversity, particularly in widespread species. We implemented a multilocus phylogeographic approach to examine diversity within the widely distributed Central African pygmy chameleon, Rhampholeon boulengeri. Gene-tree analyses coupled with a comparative coalescent-based species delimitation framework revealed R. boulengeri as a complex of at least six genetically distinct species. The spatiotemporal speciation patterns for these cryptic species conform to general biogeographic hypotheses supporting vicariance as the main factor behind patterns of divergence in the Albertine Rift, a biodiversity hotspot in Central Africa. However, we found that parapatric species and sister species inhabited adjacent habitats, but were found in largely non-overlapping elevational ranges in the Albertine Rift, suggesting that differentiation in elevation was also an important mode of divergence. The phylogeographic patterns recovered for the genus-level phylogeny provide additional evidence for speciation by isolation in forest refugia, and dating estimates indicated that the Miocene was a significant period for this diversification. Our results highlight the importance of investigating cryptic diversity in widespread species to improve understanding of diversification patterns in environmentally diverse regions such as the montane Afrotropics.

The food habits of a freshwater pelomedusid turtle (Pelomedusa subrufa) were studied by fecal analysis and stomach flushing in 2 study areas in Nigeria. Males and females were predominantly carnivorous; they fed mainly on fish, tadpoles, and aquatic invertebrates but also on terrestrial vertebrates. Sexes overlapped highly in dietary habits during both wet and dry season. Body size clearly affected diet composition of turtles but did so only during the dry season (with smaller individuals feeding primarily on invertebrates and small vertebrates, and larger individuals on homeotherm vertebrates). There was a strong effect of season on diet composition, and turtles responded to increasing dryness with a shift from a diet based on aquatic organisms during the wet season to a diet based on terrestrial organisms, including small vertebrates, during the dry season.

Broad-scale ecological correlates affecting species richness and abundance patterns of amphibians were studied in 37 sampling sites from 15 independent protected areas in the Albertine Rift, East Africa. Amphibians were caught by a combination of sampling techniques, including time-constrained visual searching, pitfalls with drift fences, dip-netting, and opportunistic observations. In total, 73 species of amphibians were recorded, some of them occurring only once in the samples and some more than 1,000 times. Once relative field effort at each study site was taken into account, multivariate regression analyses showed that amphibian species richness was positively influenced by percent canopy cover and altitude. On the other hand, population abundance was influenced by a combination of three different variables: positively by percent canopy cover and rainfall, and negatively by human activities. The rainforest proved to play a very important role in the ecological distribution of species, with about 63% of the species being in one way or the other linked to it either as forest specialists, inhabitants of forest ecotones, or inhabitants of both forests and forest ecotones. These results have wide conservation implications. Indeed, as the mature rainforest habitat (especially at mid altitude-highland) proved to be the key habitat for the amphibian communities of the Albertine Rift, it should be a priority to recommend an accurate management and conservation of mature forests in local and regional protection programs.

Community structure was studied across six different habitat types in an amphibian assemblage constituted by 24 species belonging to five families, from Lake Nabugabo, Uganda. We employed a suite of different statistical methods, including univariate, multivariate, and Monte Carlo procedures to investigate the randomness/nonrandomness and the seasonal effects (wet versus dry season) of the community assembly. We calculated for each species in each habitat type an index of relative abundance by using a time constrained counting technique, with 48 1-h counts for each habitat type. Co-occurrence was analysed by C score with 30 000 simulations; resource partitioning patterns by RA2 and RA3 algorithms with 30 000 simulations; and apparent dissimilarity among species in terms of habitat use by UPGMA dendrograms. After pooling data from wet and dry seasons, it resulted that the amphibian community was non-randomly assembled according to C-score analyses, but both RA2 and RA3 were unable to uncover any competitive structure for the dataset. Seasonal effects were evident, and although C score analyses confirmed a nonrandom structure for the community under study (particularly in wet season), RA3 showed that species with high relative abundance tended to significantly concentrate in one habitat type (swamp forest) rather than to partition the habitat resource. UPGMA dendrograms grouped the species differently in dry versus wet seasons. Overall, the comparative evidence of 1) non-random community structure according to C-score analysis, and 2) absence of resource partitioning according to niche overlap null models analysis, suggests that community organization in Lake Nabugabo amphibians is generated by habitat affinities rather than by interspecific competition.

The Albertine Rift is one of the most important regions for conservation in Africa. It contains more vertebrate species than any other region on the continent and contains more endemic species of vertebrate than any other region on mainland Africa. This paper compiles all currently known species distribution information for plants, endemic butterfly species and four vertebrate taxa from the Albertine Rift. The literature on fish species richness and endemism is also reviewed to assess the importance of the larger lakes in the Rift for conservation. We use data from 38 protected and unprotected areas to prioritise sites within the Albertine Rift for conservation based upon their numbers of endemic and globally threatened species. Virunga and Kahuzi Biega National Parks and Itombwe Massif in Democratic Republic of Congo, Bwindi Impenetrable and Kibale National Parks in Uganda, and Nyungwe National Park in Rwanda rank highest in terms of numbers of both endemic and globally threatened species. Six conservation landscapes are described that include most of these sites and it is argued that a focus on these landscapes may be a more holistic method to ensure the safety of the priority areas of the Albertine Rift.

Batrachochytrium dendrobatidis (Bd), the cause of chytridiomycosis, is a pathogenic fungus that is found worldwide and is a major contributor to amphibian declines and extinctions. We report results of a comprehensive effort to assess the distribution and threat of Bd in one of the Earth's most important biodiversity hotspots, the Albertine Rift in central Africa. In herpetological surveys conducted between 2010 and 2014, 1018 skin swabs from 17 amphibian genera in 39 sites across the Albertine Rift were tested for Bd by PCR. Overall, 19.5% of amphibians tested positive from all sites combined. Skin tissue samples from 163 amphibians were examined histologically; of these two had superficial epidermal intracorneal fungal colonization and lesions consistent with the disease chytridiomycosis. One amphibian was found dead during the surveys, and all others encountered appeared healthy. We found no evidence for Bd-induced mortality events, a finding consistent with other studies. To gain a historical perspective about Bd in the Albertine Rift, skin swabs from 232 museum-archived amphibians collected as voucher specimens from 1925-1994 were tested for Bd. Of these, one sample was positive; an Itombwe River frog (Phrynobatrachus asper) collected in 1950 in the Itombwe highlands. This finding represents the earliest record of Bd in the Democratic Republic of Congo. We modeled the distribution of Bd in the Albertine Rift using MaxEnt software, and trained our model for improved predictability. Our model predicts that Bd is currently widespread across the Albertine Rift, with moderate habitat suitability extending into the lowlands. Under climatic modeling scenarios our model predicts that optimal habitat suitability of Bd will decrease causing a major range contraction of the fungus by 2080. Our baseline data and modeling predictions are important for comparative studies, especially if significant changes in amphibian health status or climactic conditions are encountered in the future.

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