Small mammal community structure in West Africa: a meta‐analysis using null models

Peer‐reviewed studies on the community structure of small mammals (Rodentia and Soricomorpha) from the Gulf of Guinea region of West Africa were reviewed. To detect nonrandom patterns in the various assemblages under study, the original datasets were re‐analysed using null models [two independent randomization algorithms (RA) for niche overlap] and Monte Carlo simulations. The total species richness in the countries considered in this review was 45 species for soricomorphs and 101 for rodents, and the studies reviewed here reported data for 53.3% of these soricomorph species and for 76.2% of these rodent species. Nonrandom habitat niche partitioning was rarely observed in both rodents and soricomorphs. Instead, aggregated use of habitat resources was frequently detected in both groups. Forest habitat was generally selected as aggregating resource type by small mammal assemblages. Thus, contrary to expectations, our review revealed little evidence for interspecific competition along the habitat niche axis in West African small mammals. However, it is possible that the aggregated use of the forest resource by small mammal species may be apparent, but that the various species partitioned space at a lower scale, for instance selecting different microhabitats. Interspecific competition appeared to be stronger in altered habitats, as predicted by previous studies on other forest organisms in West Africa.     

Nonrandom co-occurrence patterns of rainforest chameleons

Null‐model analysis of co‐occurrence patterns is a powerful tool to identify ‘structure’ in community ecology data sets. We evaluated the community structure of chameleons in rainforest regions of Nigeria and Cameroon using available data in the literature, including peer‐reviewed articles and unpublished environmental reports to industries. We performed Monte Carlo simulations (5000 iterations, using the sequential swap algorithm) under several model assumptions to derive co‐occurrence patterns among species. Food and spatial (habitat) segregation patterns in both lowland rainforest and montane forest were investigated. We subjected four indices of co‐occurrence patterns (C‐ratio, number of checkerboard species pairs, number of species combinations, and V‐score) to randomization procedures. Overall, the chameleon communities do not show random organization, but instead exhibit precise deterministic patterns. In lowland rainforest, chameleon communities are assembled deterministically along the food niche resource axis, but not along the habitat niche resource axis. The opposite holds for chameleon communities in montane rainforest. We predict that these patterns can be generalized to other regions of tropical Africa, thus helping to determine the general structure of chameleon communities in tropical African forests.     

Do lizard communities partition the trophic niche? A worldwide meta‐analysis using null models

Lizards have been widely used as model organisms in community ecology over the past 30 years. I have reviewed more than 50 studies from the literature on the community ecology of lizards worldwide, with a focus on studies from 1990–2007. I determined if there is support for the hypotheses that many lizard communities 1) are non‐randomly organized along the trophic niche dimension, and 2) partition the available food resource to minimize interspecific competition. I used data on number of prey items and percentage of prey volume, to calculate dietary overlap among species. I compared true datasets to randomly generate new datasets produced by 3×10⁴ Monte Carlo permutations using two algorithms (RA2 and RA3). The great majority (more than 80%) of the communities were randomly organized along the trophic niche dimension using RA2 or RA3; the frequency of occurrence of detecting a non‐random structure in lizard community dietary studies did not differ significantly between datasets based on either number of prey items or prey volume. Thus, lizard communities usually do not partition the trophic niche axis. Concerning the number of prey items, logistic regression models showed that the presence of a structure in the dataset did not depend on number of species, method employed to obtain dietary data, matrix size, or location (continent), but instead significantly depended on whether a community was tropical. Concerning prey volume, presence of a structure in the dataset also did not depend on number of species, method employed to obtain dietary data, and tropical vs non‐tropical origin, but was marginally dependent on continent (South America was favoured for identifying a structure in the dataset) and matrix size. In general, a structure in the dataset was more often uncovered by using RA2 than RA3. Overall, I conclude that 1) lizard communities are unlikely to partition available food resources, and 2) as the method for identifying dietary items does not allow for accurate prey identification (at least at the genus level), there is a risk of obtaining false null results about community structure. This is because structure along the trophic niche axis is genuinely rare in lizards and also because inappropriate methods may erroneously lead to this conclusion. Therefore, conclusions from studies utilizing stomach dissection as a source of diet data (still common in the literature) should be cautiously considered for ethical reasons and because it is difficult to find any difference between stomach‐dissection and fecal‐pellet data when assessing the presence of a structure in datasets. My data also showed there are minor differences in the probability of detecting a structure in datasets using prey item number or prey volume data for lizards. The biases, both statistical and biological, associated with this meta‐analysis are discussed.     

The Southern African orchid flora: composition, sources and endemism

Aim The Southern African orchid flora is taxonomically well known, but the biogeographical and diversity patterns have not yet been analysed. In particular, we want to establish whether (a) it is, like the Southern African flora in general, more diverse than would be expected from its latitude and area; (b) it is an African flora, or whether it contains palaeoendemic relicts of a Gondwanan orchid flora; (c) the diversity and endemism in the orchid flora is concentrated in particular biomes and habitat types; and (d) the patterns of endemism in the flora can be accounted for by current environmental parameters, or whether we need to invoke historical explanations. Location Southern Africa. Methods We used the recent floristic account of the Southern African orchids, in conjunction with a data base of over 14,642 herbarium records, to assign the species and subspecies of Southern African orchids to biomes, habitats, and clades. We explored the relationship between the number and endemism of entities (species, subspecies and varieties) and the biomes and habitats. We compared the richness of this flora with that of 31 other regions from all continents and latitudes, to establish whether the Southern African orchid flora is richer or poorer than expected. We assigned the Southern African orchid species to 16 monophyletic clades and mapped the global distribution of these clades to establish the continental affinities of the flora. Main conclusions The Southern African orchid flora is not any more diverse than could be expected from its latitude or area, while the two tropical African floras included were less diverse than expected. Latitude is an excellent predictor of regional orchid species richness; this might indicate that available habitat is more important for orchid diversity than gross area available, since latitude is probably correlated with the extent of suitable habitat. The Southern African orchid flora is clearly an African flora, since all clades are also found in tropical Africa, while many of them are absent from the Americas or Asia. Conversely, while most African orchid clades are also found in Southern Africa, both the Americas and Asia contain many clades absent from Africa. The distribution of orchid entities among the biomes in Southern Africa is very uneven, with two of the seven biomes totally devoid of orchids. Habitats and biomes that have no equivalent in tropical Africa are high in endemism, and habitats and biomes which are also well developed in tropical Africa are low in endemism. Endemism appears largely explained in terms of modern habitats. However, two patterns (the high endemism in the Succulent Karoo and the lack of endemism in the southern Cape among epiphytic orchids) may also be explained in terms of Quaternary climatic changes.     

Phylogeographic Reconstruction of African Yellow Fever Virus Isolates Indicates Recent Simultaneous Dispersal into East and West Africa

Yellow fever virus (YFV) is a mosquito-borne flavivirus that is a major public health problem in tropical areas of Africa and South America. There have been detailed studies on YFV ecology in West Africa and South America, but current understanding of YFV circulation on the African continent is incomplete. This inadequacy is especially notable for East and Central Africa, for which the unpredictability of human outbreaks is compounded by limitations in both historical and present surveillance efforts. Sparse availability of nucleotide sequence data makes it difficult to investigate the dispersal of YFV in these regions of the continent. To remedy this, we constructed Bayesian phylogenetic and geographic analyses utilizing 49 partial genomic sequences to infer the structure of YFV divergence across the known range of the virus on the African continent. Relaxed clock analysis demonstrated evidence for simultaneous divergence of YFV into east and west lineages, a finding that differs from previous hypotheses of YFV dispersal from reservoirs located on edges of the endemic range. Using discrete and continuous geographic diffusion models, we provide detailed structure of YFV lineage diversity. Significant transition links between extant East and West African lineages are presented, implying connection between areas of known sylvatic cycling. The results of demographic modeling reinforce the existence of a stably maintained population of YFV with spillover events into human populations occurring periodically. Geographically distinct foci of circulation are reconstructed, which have significant implications for studies of YFV ecology and emergence of human disease. We propose further incorporation of Bayesian phylogeography into formal GIS analyses to augment studies of arboviral disease.     

Tropical China Plant Diversity,Ecology and Conservation – a Glimpse at the Current State

Tropical and subtropical ecosystems, especially those found on limestone substrates, are among the most diverse terrestrial habitats in China. However, little is known about patterns of plant diversity, ecology and conservation status within these ecosystems. In this special issue we present five reviews and/or in-depth studies of these tropical Chinese plants and ecosystems that capture current research efforts in tropical China plant ecology.     

The spatial and temporal distributions of arthropods in forest canopies: uniting disparate patterns with hypotheses for specialisation

Arguably the majority of species on Earth utilise tropical rainforest canopies, and much progress has been made in describing arboreal assemblages, especially for arthropods. The most commonly described patterns for tropical rainforest insect communities are host specificity, spatial specialisation (predominantly vertical stratification), and temporal changes in abundance (seasonality and circadian rhythms). Here I review the recurrent results with respect to each of these patterns and discuss the evolutionary selective forces that have generated them in an attempt to unite these patterns in a holistic evolutionary framework. I propose that species can be quantified along a generalist–specialist scale not only with respect to host specificity, but also other spatial and temporal distribution patterns, where specialisation is a function of the extent of activity across space and time for particular species. When all of these distribution patterns are viewed through the paradigm of specialisation, hypotheses that have been proposed to explain the evolution of host specificity can also be applied to explain the generation and maintenance of other spatial and temporal distribution patterns. The main driver for most spatial and temporal distribution patterns is resource availability. Generally, the distribution of insects follows that of the resources they exploit, which are spatially stratified and vary temporally in availability. Physiological adaptations are primarily important for host specificity, where nutritional and chemical variation among host plants in particular, but also certain prey species and fungi, influence host range. Physiological tolerances of abiotic conditions are also important for explaining the spatial and temporal distributions of some insect species, especially in drier forest environments where desiccation is an ever‐present threat. However, it is likely that for most species in moist tropical rainforests, abiotic conditions are valuable indicators of resource availability, rather than physiologically limiting factors. Overall, each distribution pattern is influenced by the same evolutionary forces, but at differing intensities. Consequently, each pattern is linked and not mutually exclusive of the other distribution patterns. Most studies have examined each of these patterns in isolation. Future work should focus on examining the evolutionary drivers of these patterns in concert. Only then can the relative strength of resource availability and distribution, host defensive phenotypes, and biotic and abiotic interactions on insect distribution patterns be determined.     

Tree Species Composition Predicts Epiphytic Lichen Communities in an African Montane Rain Forest

The ecology of many tropical rain forest organisms, not the least in Africa, remains poorly understood. Here, we present a detailed ecological study of epiphytic lichens in the equatorial montane rain forest of Bwindi National Park (331 km²), Uganda. We evaluated all major lichen growth forms, including selected groups of crustose lichens. In 14 transects at elevations of 1290 m to 2500 m, we sampled 276 trees belonging to 60 species. We recorded all lichen species on each tree trunk between ground level and 2 m above the ground, yielding 191 lichen species in 67 genera, with a mean of 4.7 species per tree. We used non‐metric multi‐dimensional scaling to separate epiphytic lichen assemblages according to tree species composition and elevation. Structural equation modeling indicated that elevation influenced tree species composition and that tree species composition largely determined lichen species composition. Thus, elevation acted indirectly on the lichen assemblages. Further studies examining factors such as bark properties and lichen colonization ecology may clarify what determines the association between tree species and lichen assemblages. The link between lichen assemblages and large‐scale elevation patterns, as well as disturbance and regrowth histories, warrants further study. An analysis of lichen species composition on individual tree species that occur over large elevation ranges would distinguish the effect of tree species on lichen assemblages from the effect of elevation and thus climate. Our study highlights the limited extent of our knowledge of tropical epiphytic lichens.     

Taxonomy and diversity of Afroalpine Chironomidae (Insecta: Diptera) on Mount Kenya and the Rwenzori Mountains, East Africa

Aim Anthropogenic climate change is expected to result in the complete loss of glaciers from the high mountains of tropical Africa, with profound impacts on the hydrology and ecology of unique tropical cold‐water lakes located downstream from them. This study examines the biodiversity of Chironomidae (Insecta: Diptera) communities in these scarce Afroalpine lake systems, in order to determine their uniqueness in relation to lowland African lakes and alpine lakes in temperate regions, and to evaluate the potential of Afroalpine Chironomidae as biological indicators to monitor future changes in the ecological integrity of their habitat. Location Mount Kenya (Kenya) and Rwenzori Mountains (Uganda). Methods The species composition of Afroalpine chironomid communities was assessed using recent larval death assemblages extracted from the surface sediments of 11 high‐mountain lakes between 2900 and 4575 m. Results were compared with similar faunal data from 68 East African lakes at low and middle elevation (750–2760 m), and with literature records of Chironomidae species distribution in sub‐Saharan Africa, the Palaearctic region and elsewhere. All recovered taxa were fully described and illustrated. Results The 11‐lake analysis yielded 1744 subfossil chironomid larvae belonging to 16 distinct taxa of full‐grown larvae, and three taxa of less differentiated juveniles. Eleven of these 16 are not known to occur in African lakes at lower elevation, and eight taxa (or 50% of total species richness) appear restricted to the specific habitat of cold lakes above 3900 m, where night‐time freezing is frequent year‐round. The faunal transition zone coincides broadly with the Ericaceous zone of terrestrial vegetation (c. 3000–4000 m). Snowline depression during the Quaternary ice ages must have facilitated dispersion of cold‐stenothermous species among the high mountains of equatorial East Africa, but less so from or to the Palaearctic region via the Ethiopian highlands. Main conclusions Chironomid communities in glacier‐fed lakes on Africa's highest mountains are highly distinct from those of lowland African lakes, and potentially unique on a continental scale. By virtue of excellent preservation and their spatial and temporal integration of local community dynamics, chironomid larval death assemblages extracted from surface sediments are powerful biological indicators for monitoring the hydrological and ecological changes associated with the current retreat and loss of Africa's glaciers.     

Phylogenetic structure of mammal assemblages at large geographical scales: linking phylogenetic community ecology with macroecology

Phylogenetic community ecology seeks to explain the processes involved in the formation of species assemblages by analysing their phylogenetic structure, and to date has focused primarily on local-scale communities. Macroecology, on the other hand, is concerned with the structure of assemblages at large geographical scales, but has remained largely non-phylogenetic. Analysing the phylogenetic structure of large-scale assemblages provides a link between these two research programmes. In this paper, I ask whether we should expect large-scale assemblages to show significant phylogenetic structure, by outlining some of the ecological and macroevolutionary processes that may play a role in assemblage formation. As a case study, I then explore the phylogenetic structure of carnivore assemblages within the terrestrial ecoregions of Africa. Many assemblages at these scales are indeed phylogenetically non-random (either clustered or overdispersed). One interpretation of the observed patterns of phylogenetic structure is that many clades underwent rapid biome-filling radiations, followed by diversification slowdown and competitive sorting as niche space became saturated.     

Species richness and composition of amphibians and reptiles in a fragmented forest landscape in northeastern Bolivia

We quantified patterns of species richness and species composition of frogs and reptiles (lizards and snakes) among three habitats (continuous forest, forest islands, and a seasonally flooded savannah) and between forest island size and isolation classes in a floristic transition zone in northeastern Santa Cruz Department, Bolivia. Species richness was similar across macrohabitats, as was faunal composition of forested habitats, although savannah harbored a distinct herpetofauna. On forest islands, richness and composition of forest frogs was largely related to isolation, whereas reptiles were affected by both isolation and habitat. The observation that isolation rather than area was the primary driver of distribution patterns on forest islands stands in contrast to many studies, and may be a function of (1) the greater range in forest island isolation values compared to area or (2) the long history of isolation in this landscape.     

A hotspot revisited – a biogeographical analysis of West African amphibians

Aim The study was aimed at testing whether West Africa can be regarded as a distinct biogeographic region based on amphibian assemblages. If so, we asked what were the relationships of these assemblages with those in Central Africa, and whether West African amphibian distributions showed biogeographic substructure. We further investigated what events or processes may explain the observed patterns. Location Sub‐Saharan Africa. Methods  Presence–absence data of amphibian assemblages derived from field surveys and the literature were statistically analysed using three different multivariate techniques (consensus clustering, Monmonier analysis and nonmetric multidimensional scaling) to emphasize consistent results. Results We showed that West Africa has unique amphibian assemblages, which could be clearly demarcated from Central African assemblages, particularly by the geographic barrier of the Cross River. Further biogeographic subdivisions were detected to the west of this barrier. Habitat, mainly forest, was the best factor explaining our observed pattern. Overall, intra‐regional similarity (e.g. within West Africa) was higher than intra‐habitat similarity (e.g. within forest) across regions. Main conclusions Our results are compared with previous works and interpreted in the light of the known evolutionary history of West and Central Africa. The observed pattern may be explained by postulated differences in river continuity through time, with West African rivers serving as more or less constant barriers in contrast to those in Central Africa. Our results demonstrate the uniqueness of West African amphibian assemblages, highlighting the need for their conservation as many are under acute anthropogenic pressure.     

TROPICS ACCELERATE THE EVOLUTION OF HYBRID MALE STERILITY IN DROSOPHILA

Understanding the evolutionary mechanisms that facilitate speciation and explain global patterns of species diversity has remained a challenge for decades. The most general pattern of species biodiversity is the latitudinal gradient, whereby species richness increases toward the tropics. Although such a global pattern probably has a multitude of causes, recent attention has focused on the hypothesis that speciation and the evolution of reproductive isolation occur faster in the tropics. Here, I tested this prediction using a dataset on premating and postzygotic isolation between recently diverged Drosophila species. Results showed that while the evolution of premating isolation was not greater between tropical Drosophila relative to nontropical species, postzygotic isolation evolved faster in the tropics. In particular, hybrid male sterility was much greater among tropical Drosophila compared to nontropical species pairs of similar genetic age. Several testable explanations for the novel pattern are discussed, including greater role for sterility‐inducing bacterial endosymbionts in the tropics and more intense sperm–sperm competition or sperm–egg sexual conflict in the tropics. The results imply that processes of speciation in the tropics may evolve at different rates or may even be somewhat different from those at higher latitudes.     

Testing metabolic ecology theory for allometric scaling of tree size, growth and mortality in tropical forests

The theory of metabolic ecology predicts specific relationships among tree stem diameter, biomass, height, growth and mortality. As demographic rates are important to estimates of carbon fluxes in forests, this theory might offer important insights into the global carbon budget, and deserves careful assessment. We assembled data from 10 old-growth tropical forests encompassing censuses of 367 ha and > 1.7 million trees to test the theory's predictions. We also developed a set of alternative predictions that retained some assumptions of metabolic ecology while also considering how availability of a key limiting resource, light, changes with tree size. Our results show that there are no universal scaling relationships of growth or mortality with size among trees in tropical forests. Observed patterns were consistent with our alternative model in the one site where we had the data necessary to evaluate it, and were inconsistent with the predictions of metabolic ecology in all forests.     

Resource partitioning and interspecific competition in snakes: the search for general geographical and guild patterns

The role of interspecific competition as a key factor in the ecology of natural communities where species exploit limited resources is well established, and the study of competition dynamics in snake communities has received much attention in recent years. Twenty years ago, an acclaimed review ( Toft 1985 ) suggested that snakes were atypical among vertebrates because sympatric species usually partition the food niche. Here, I review the articles published in the last two decades with the aim of finding any general geographical or guild patterns and assessing if Toft's main conclusion is still supported by new evidence. Where appropriate, I use Monte Carlo simulations to establish whether observed patterns of niche overlap are real, or if they have occurred by chance. My study shows clear congruence in the patterns of coexistence exhibited by snake communities in different regions of the world, i.e.: (1) cold regions of the northern hemisphere (high latitudes and altitudes) exhibit low species richness and a very low, or even absent, potential for interspecific competition; (2) aquatic snakes that form communities in temperate regions generally partition the food type available and exhibit a broad similarity in habitat use with subtle differences in microhabitat use; (3) terrestrial snake communities in temperate regions are very variable in terms of their coexistence dynamics and show no evidence of generalised patterns; (4) sympatric viperids in Europe, North America and, most interestingly, tropical Asia partition the available habitat but not the prey resource; (5) competition is much stronger in tropical snake communities, and the intensity of this process fluctuates throughout the year being most intense during periods of low food availability; (6) in general, tropical snakes partition the food resource (prey type and/or prey size), but when this resource is not partitioned competitive exclusion can occur. Prey resource availability is a fundamental variable for all snake communities; this is clearly documented by studies on terrestrial snakes in Australia where, due to a relative scarcity of prey availability in the field, sympatry among species is much rarer than in other continents. I conclude that, although there are several notable exceptions, Toft's main conclusion is still supported by empirical evidence. However, I disagree with Toft's conclusion that most snakes are food specialists, and I contend that interspecific competition is important in structuring many (if not most) of the snake communities around the world.     

Neutral theory and community ecology

I review the mathematical and biological aspects of Hubbell's (2001) neutral theory of species abundance for ecological communities, and clarify its historical connections with closely related approaches in population genetics. A selective overview of the empirical evidence for and against this theory is provided, with a special emphasis on tropical plant communities. The neutral theory predicts many of the basic patterns of biodiversity, confirming its heuristic power. The strict assumption of equivalence that defines neutrality, equivalence among individuals, finds little empirical support in general. However, a weaker assumption holds for stable communities, the equivalence of average fitness among species. One reason for the surprising success of the neutral theory is that all the theories of species coexistence satisfying the fitness equivalence assumption, including many theories of niche differentiation, generate exactly the same patterns as the neutral theory. Hubbell's neutral theory represents an important synthesis and a much needed demonstration of the pivotal role of intraspecific variability in ecology. Further improvements should lead to an explicit linking to niche‐based processes. This research programme will depend crucially on forthcoming theoretical and empirical achievements.     

Palaeobotanical studies from tropical Africa: relevance to the evolution of forest, woodland and savannah biomes

Fossil plants provide data on climate, community composition and structure, all of which are relevant to the definition and recognition of biomes. Macrofossils reflect local vegetation, whereas pollen assemblages sample a larger area. The earliest solid evidence for angiosperm tropical rainforest in Africa is based primarily on Late Eocene to Late Oligocene (ca. 39-26 Myr ago) pollen assemblages from Cameroon, which are rich in forest families. Plant macrofossil assemblages from elsewhere in interior Africa for this time interval are rare, but new work at Chilga in the northwestern Ethiopian Highlands documents forest communities at 28 Myr ago. Initial results indicate botanical affinities with lowland West African forest. The earliest known woodland community in tropical Africa is dated at 46 Myr ago in northern Tanzania, as documented by leaves and fruits from lake deposits. The community around the lake was dominated by caesalpinioid legumes, but included Acacia, for which this, to my knowledge, is the earliest record. This community is structurally similar to modern miombo, although it is different at the generic level. The grass-dominated savannah biome began to expand in the Middle Miocene (16 Myr ago), and became widespread in the Late Miocene (ca. 8 Myr ago), as documented by pollen and carbon isotopes from both West and East Africa.     

Exploring the pteridophyte flora of the Eastern Afromontane biodiversity hotspot

In this review, we explore our current understanding of the fern and lycophyte diversity occurring in the Eastern Afromontane Biodiversity Hotspot (EABH). The review explores the species diversity of this region in the context of the Afromadagascan pteridophyte diversity based on an exhaustive species list assembled in the synopsis of Afromadagascan pteridophytes published by Roux in 2009. The list was updated by incorporating recent progress in our understanding of the taxonomy and phylogeny of these plants. Evidence for a distinct pteridophyte flora occurring in the East African mountain region was discovered using ordination and clustering analyses. This EABH floras shares links to other Afromadagascan pteridophyte floras such as the one in the tropical lowland forests of central and western Africa. These floras share the dominance of species that preferably occur in humid climates whereas other African pteridophyte floras tend to contain a higher proportion of xeric adapted ferns. The phylogenetic composition of the EABH pteridophyte flora was assessed by comparing global versus local proportion of orders, families, and genera. This analysis revealed distinct patterns that are partly caused by the radiation of Blotiella and Triplophyllum besides selective colonization of species pre-adapted to Afromadagascan climates. In situ speciation in the East African tropical mountains may have contributed to the global diversity of widespread genera such as Asplenium and Pteris. In summary, this is the first comprehensive attempt to assess the pteridophyte diversity of the East African mountains providing the framework for future studies on their conservation, ecology, and evolution.