A framework for delineating biogeographical regions based on species distributions

Aim Biogeographical regionalizations, such as zoogeographical regions, floristic kingdoms or ecoregions, represent categorizations central to many basic and applied questions in biogeography, ecology, evolution and conservation. Traditionally established by experts based on qualitative evidence, the lack of transparency and quantitative support has set constraints on their utility. The recent availability of global species range maps, novel multivariate techniques and enhanced computational power now enable a quantitative scrutiny and extension of biogeographical regionalizations that will facilitate new and more rigorous uses. In this paper we develop and illustrate a methodological roadmap for species‐level biogeographical regionalizations at the global scale and apply it to mammals. Location Global. Methods We explore the relative usefulness of ordination and clustering methods and validation techniques. The performance of nine different clustering algorithms is tested at different taxonomic levels. The grain of regionalization (i.e. the number of clusters) will usually be driven by the purpose of the study, but we present several approaches that provide guidance. Results Non‐metric multidimensional scaling offers a valuable first step in identifying and illustrating biogeographical transition zones. For the clustering of regions, the nine different hierarchical clustering methods varied greatly in utility, with UPGMA (unweighted pair‐group method using arithmetic averages) agglomerative hierarchical clustering having consistently the best performance. The UPGMA approach allows a tree‐like phenetic representation of the relative distances of regions and can be applied at different levels of taxonomic resolution. We find that the new quantitative biogeographical regions exhibit both striking similarities to and differences from the classic primary geographical divisions of the world’s biota. Specifically, our results provide evidence that the Sahara, northern Africa, the Arabian Peninsula and parts of the Middle East should be regarded as part of the Afrotropics. Further, the position of the New Guinean continental shelf, Lydekker’s Line, is supported as an appropriate border to separate the Oriental and Australian regions. Main conclusions We propose that this sort of new, quantitative delineation and relationship assessment across taxonomic and geographical grains is likely to offer opportunities for more rigorous inference in historical and ecological biogeography and conservation.     

The world's biogeographical regions: cluster analyses based on bat distributions

Aim Both floral kingdoms and faunal regions have so far been intuitively defined. This study was conducted to compare these with an analytical regionalization based on cluster analyses in a fairly homogeneous, globally distributed group of organisms: the bats (order Chiroptera). This comparison was used to discuss the possibilities of employing clustering techniques in global biogeography. Location The study considered bat distributions world‐wide. Methods Analyses were conducted both for presence/absence of genera and species, and for the number of species in each genus. Clusters distinguished at selected dissimilarity values were mapped. Results A set of c. 10 regional clusters recurred in the analyses, broadly corresponding not only to the world's accepted faunal regions and subregions, but also to the floral kingdoms and subkingdoms. Main conclusions This study is an analytical confirmation of the fact that similar global distribution patterns are to be found in different groups of organisms. Cluster analyses can be used to refine global regionalization schemes, and, with the accumulation of such data for different taxa and ecologically defined groups, shared patterns can be used to draft one common global biogeographical regionalization. At the same time, differences between the regionalization schemes derived for different groups can be used to partial out the role of dispersal abilities, body size, evolutionary age, etc., in determining global distribution patterns.     

Water for small‐scale biogas digesters in sub‐Saharan Africa

Biogas could provide a more sustainable energy source than wood fuels for rural households in sub‐Saharan African. However, functioning of biogas digesters can be limited in areas of low water availability. The water required is approximately 50 dm³ day^?1 for each cow and 10 dm³ day^?1 for each pig providing manure to the digester, or 25 (±6) dm³ day^?1 for each person in the household, using a digester volume of 1.3 (±0.3) m³ capita^?1. Here, we consider the potential of domestic water recycling, rainwater harvesting, and aquaculture to supply the water needed for digestion in different countries of sub‐Saharan Africa. Domestic water recycling was found to be important in every country but was usually insufficient to meet the requirements of the digester, with households in 72% of countries need to collect additional water. Rooftop rainwater harvesting also has an important role, iron roofs being more effective than thatched roofs at collecting water. However, even with an iron roof, the size of roof commonly found in sub‐Saharan Africa (15 to 40 m²) is too small to collect sufficient water, requiring an extra area (in m²) for each person of (R/100) (where R is the rainfall in mm). If there is a local market for fish, stocking a pond with tilapia, fed on plankton growing on bioslurry from the digester, could provide an important source of additional income and hold the water required by the digester. In areas where rainfall is low and seasonal, the fishpond might be stocked only in the rainy season, allowing the pond to be covered during the dry period to reduce evaporation. If evaporative losses (E in mm) exceed rainfall, an extra catchment area is needed to maintain the water level in the pond, equivalent to approximately (1.5 × ((E?R)/R)) m² for each person in the household.     

Fire in sub‐Saharan Africa: The fuel,cure and connectivity hypothesis

Aim

Past analyses of satellite‐based fire activity in tropical savannas support the intermediate fire–productivity hypothesis (IFP), which posits a close correlation with estimates of total net primary productivity in drier savannas and declines towards the extremes. However, these analyses ignore the distinct roles played by herbaceous and woody vegetation in fire ignition and spread. We hypothesize that, as herbaceous vegetation provides the primary fuel, fire activity in African savannas is asymptotically correlated with herbaceous production. Conversely, woody production affects fires indirectly through effects on herbaceous production and its connectivity. In contrast to the IFP, we propose the fuel, cure and connectivity (FCC) conceptual model for tropical fire activity. The FCC model makes explicit the distinct role of herbaceous and woody fuels, avoiding the confounding interpretation of the role of total production, while providing opportunities to quantify fuel curability, effects of trees on herbaceous fuel growth and connectivity, and human management.

Location

Sub‐Saharan Africa (SSA).

Time period

2003–2015.

Major taxa studied

Woody and herbaceous vegetation.

Methods

We used boosted regression tree analysis to test competing models explaining fire activity: (a) aggregate fuel loads; and (b) partitioned woody and herbaceous fuel loads; both derived from MODIS leaf area index.

Results

Herbaceous fuel load was consistently most influential, providing more explanatory power than overall biomass in fire activity. Fuel curability rated second, then human population density (HPD), and woody biomass was least important. We observed an asymptotic relationship between herbaceous fuel load and fire activity consistent with the FCC model; trees promote fires at low densites but suppress fires at higher densities; fires were rare in wetter regions, emphasizing the need for fuel to cure; and fires were concentrated in areas of low human population, underscoring the crucial role of land management.

Conclusions

The proposed FCC framework provides a more nuanced understanding of fire activity in tropical ecosystems, where herbaceous biomass is the key determinant of fire activity.     

Analysis of climate signals in the crop yield record of sub‐Saharan Africa

Food security and agriculture productivity assessments in sub‐Saharan Africa (SSA) require a better understanding of how climate and other drivers influence regional crop yields. In this paper, our objective was to identify the climate signal in the realized yields of maize, sorghum, and groundnut in SSA. We explored the relation between crop yields and scale‐compatible climate data for the 1962–2014 period using Random Forest, a diagnostic machine learning technique. We found that improved agricultural technology and country fixed effects are three times more important than climate variables for explaining changes in crop yields in SSA. We also found that increasing temperatures reduced yields for all three crops in the temperature range observed in SSA, while precipitation increased yields up to a level roughly matching crop evapotranspiration. Crop yields exhibited both linear and nonlinear responses to temperature and precipitation, respectively. For maize, technology steadily increased yields by about 1% (13 kg/ha) per year while increasing temperatures decreased yields by 0.8% (10 kg/ha) per °C. This study demonstrates that although we should expect increases in future crop yields due to improving technology, the potential yields could be progressively reduced due to warmer and drier climates.     

Climate anomalies affect annual survival rates of swifts wintering in sub‐Saharan Africa

Several species of migratory swifts breed in the Western Palearctic, but they differ in reproductive traits and nonbreeding areas explored in Africa. We examined survival and recapture probabilities of two species of swifts by capture–mark–recapture data collected in northern Italy (Pallid Swift Apus pallidus in Carmagnola, Turin, and Common Swift Apus apus in Guiglia, Modena) in the breeding season (May–July). Apparent survival rates were relatively high (>71%), comparable to other studies of European swifts, but showed marked annual variations. We used geolocators to establish the exact wintering areas of birds breeding in our study colonies. Common Swifts explored the Sahel zone during migration and spent the winter in SE Africa, while the Pallid Swifts remained in the Sahel zone for a longer time, shifting locations southeast down to Cameroun and Nigeria later in winter. These movements followed the seasonal rains from north to south (October to December). In both species, we found large yearly differences in survival probabilities related to different climatic indices. In the Pallid Swift, wintering in Western Africa, the Sahel rainfall index best explained survival, with driest seasons associated with reduced survival. In the Common Swift, wintering in SE Africa, the El Niño–Southern Oscillation (ENSO) cycle performed significantly better than Sahel rainfall or North Atlantic Oscillation (NAO). Extreme events and precipitation anomalies in Eastern Africa during La Niña events resulted in reduced survival probabilities in Common Swifts. Our study shows that the two species of swifts have similar average annual survival, but their survival varies between years and is strongly affected by different climatic drivers associated with their respective wintering areas. This finding could suggest important ecological diversification that should be taken into account when comparing survival and area use of similar species that migrate between temperate breeding areas and tropical wintering areas.     

Integrating phylogenetic and taxonomic evidence illuminates complex biogeographic patterns along Huxley’s modification of Wallace’s Line

Aim Nearly 150 years ago, T. H. Huxley modified Wallace’s Line, including the island of Palawan as a component of the Asian biogeographic realm and separating it from the oceanic Philippines. Although Huxley recognized some characteristics of a transition between the regions, Palawan has since been regarded primarily as a peripheral component of the Sunda Shelf. However, several recent phylogenetic studies of Southeast Asian lineages document populations on Palawan to be closely related to taxa from the oceanic Philippines, apparently contradicting the biogeographic association of Palawan with the Sunda Shelf. In the light of recent evidence, we evaluate taxonomic and phylogenetic data in an attempt to identify the origin(s) of Palawan’s terrestrial vertebrate fauna. Location The Sunda Shelf and the Philippines. Methods We review distributional and phylogenetic data for populations of terrestrial vertebrates from Palawan. Using taxonomic data, we compare the number of Palawan taxa (species and genera) shared with the Sunda Shelf and oceanic Philippines. Among widespread lineages, we use phylogenetic data to identify the number of Palawan taxa with sister relationships to populations or species from the Sunda Shelf or oceanic Philippines. Results Although many terrestrial vertebrate taxa are shared between Palawan and the Sunda Shelf, an increasing number of species and populations are now recognized as close relatives of lineages from the oceanic Philippines. Among the 39 putative lineages included in molecular phylogenetic studies with sampling from the Sunda Shelf, Palawan and the oceanic Philippines, 17 of them reveal sister relationships between lineages from Palawan and the oceanic Philippines. Main conclusions Rather than a simple nested subset of Sunda Shelf populations, Palawan is best viewed as having played multiple biogeographic roles, including a young and old extension of the Sunda Shelf, a springboard to diversification in the oceanic Philippines, and a biogeographic component of the Philippine archipelago. Palawan has a long, complex geological history, which may explain this variation in pattern. Huxley originally noted transitional elements in Palawan’s fauna; we therefore suggest that his modification of Wallace’s Line should be recognized as a filter zone, reflecting both his original intent and available taxonomic and molecular evidence.     

Age–area scaling of extinction debt within isolated terrestrial vertebrate assemblages

A new model of delayed species loss (extinction debt) within isolated communities is applied to a large data set of terrestrial vertebrate assemblages (n = 188) occupying habitat fragments or islands varying greatly in size and age. The model encapsulates previous approaches based on diversity‐dependent (DD) extinction rates while allowing for a more flexible treatment of temporal dynamics. Three important results emerge. First, species loss rate slows down with the age of the isolate, a strong and general pattern largely unnoticed so far. Secondly, while being good candidates in the light of previous works, DD models fail to account for this pattern, a result that necessitates a search for other mechanisms. Thirdly, a simple diversity‐independent model based on area (converted into population size) and age explains 97% of the variability in species loss rate and appears to be a promising predictive tool to handle extinction debt following habitat loss.     

Land‐use change outweighs projected effects of changing rainfall on tree cover in sub‐Saharan Africa

Global change will likely affect savanna and forest structure and distributions, with implications for diversity within both biomes. Few studies have examined the impacts of both expected precipitation and land use changes on vegetation structure in the future, despite their likely severity. Here, we modeled tree cover in sub‐Saharan Africa, as a proxy for vegetation structure and land cover change, using climatic, edaphic, and anthropic data (R² = 0.97). Projected tree cover for the year 2070, simulated using scenarios that include climate and land use projections, generally decreased, both in forest and savanna, although the directionality of changes varied locally. The main driver of tree cover changes was land use change; the effects of precipitation change were minor by comparison. Interestingly, carbon emissions mitigation via increasing biofuels production resulted in decreases in tree cover, more severe than scenarios with more intense precipitation change, especially within savannas. Evaluation of tree cover change against protected area extent at the WWF Ecoregion scale suggested areas of high biodiversity and ecosystem services concern. Those forests most vulnerable to large decreases in tree cover were also highly protected, potentially buffering the effects of global change. Meanwhile, savannas, especially where they immediately bordered forests (e.g. West and Central Africa), were characterized by a dearth of protected areas, making them highly vulnerable. Savanna must become an explicit policy priority in the face of climate and land use change if conservation and livelihoods are to remain viable into the next century.     

Hierarchical partitioning of ant diversity: implications for conservation of biogeographical diversity in arid and semi‐arid areas

Aim The scale of observation is important in detecting the spatial variation of biological assemblages, which should be taken into consideration for an appropriate plan of biogeographical conservation. We investigated whether (1) World Wildlife Fund’s ecoregion units are the appropriate scale for conserving ant diversity in Iran, (2) each ecoregion represents a distinct ant community composition and (3) patterns of diversity partitioning differ among four ecoregions. Location Iran, a sampling transect along four arid and semi‐arid ecoregions. Methods We applied hierarchical partitioning to data collected from a nested sampling design including four hierarchical levels: ‘local’, ‘landscape’, ‘ecoregional’ and ‘whole‐region’. Observed alpha and beta diversity components were compared with values of null distributions. Hierarchical cluster analysis was applied to evaluate similarity of ant species composition among ecoregions. Results Partitioning of whole‐region species richness showed that 85% of the species richness was generated by beta diversity among ecoregions and landscapes. The highest value of diversity was generated by beta diversity among ecoregions. Unlike whole‐region partitioning, separate partitioning within each ecoregion revealed that beta component among localities contributed to species richness of each ecoregion. Ecoregions showed different patterns of diversity partitioning. The alpha component contributed largely to the total diversity of two ecoregions, but for two other ecoregions, beta component contributed more than alpha component. Cluster analysis identified four discrete ant species compositions; however, it split landscapes of one ecoregion into two distinct groups. Main conclusions Whole‐region diversity partitioning indicates that ecoregions represent the appropriate scale for conserving ant diversity and that each ecoregion has a distinct ant fauna. However, different conservation strategies should be considered for different ecoregions owing to the differing scales of variation within them. Boundaries of ecoregions remain a subject for further studies. The influence of climate change on ecoregional boundaries should be considered and should be predicted with respect to future conservation maps.     

Phytoplankton assemblages and community structure in tropical temporary freshwater ponds in sub‐Saharan Africa1

Anthropogenic and climatic factors are important determinants of algal distribution in aquatic systems. This study aimed to identify temporary pond‐groups of phytoplankton assemblages and to establish the interactions between environmental variables and phytoplankton structure. Phytoplankton samples were collected and preserved with 5% formalin; water samples for chemical analysis were taken in August and September 2007, 2008, and 2009 in 86 ponds randomly selected in the Sahelian sector and the Sudanian sector (protected and unprotected areas) of Burkina Faso. Plankton species were examined using light microscopy and identified using standard methods. A Fuchs‐Rosenthal chamber was used for algal cell counting. NMDS ordination, indicator species analysis and canonical analysis were performed using Pc‐Ord and CANOCO. Kruskal–Wallis and Mann–Whitney U‐tests using the software Statistica were performed to compare parameters between pond‐groups. Three pond‐groups were identified: the Sahelian pond‐group, dominated by Lyngbya martensiana and Pseudanabaena constricta; the protected area pond‐group, dominated by Euglena caudata and Trachelomonas raciborskii; and the unprotected area pond‐group, dominated by Closterium venus and Euglena proxima. At P < 0.05, species composition and abundance in algal groups were mostly associated with nitrate, pH, dissolved oxygen, and conductivity. The Sahelian and the Sudanian sectors were different in pH, water transparency, and species richness. Univariate and multivariate analyses illustrate that variations in the physicochemical properties of water and algal structure followed climatic and anthropogenic gradients. The classification of ponds into algal associations demonstrated that algal assemblages may be used as reliable indicators of habitat conditions.     

Hotspots of climate change impacts in sub‐Saharan Africa and implications for adaptation and development

Development efforts for poverty reduction and food security in sub‐Saharan Africa will have to consider future climate change impacts. Large uncertainties in climate change impact assessments do not necessarily complicate, but can inform development strategies. The design of development strategies will need to consider the likelihood, strength, and interaction of climate change impacts across biosphere properties. We here explore the spread of climate change impact projections and develop a composite impact measure to identify hotspots of climate change impacts, addressing likelihood and strength of impacts. Overlapping impacts in different biosphere properties (e.g. flooding, yields) will not only claim additional capacity to respond, but will also narrow the options to respond and develop. Regions with severest projected climate change impacts often coincide with regions of high population density and poverty rates. Science and policy need to propose ways of preparing these areas for development under climate change impacts.     

Considerations for stakeholder engagement and COVID‐19 related clinical trials’ conduct in sub‐Saharan Africa

The aim of this study is to determine how stakeholder engagement can be adapted for the conduct of COVID‐19‐related clinical trials in sub‐Saharan Africa. Nine essential stakeholder engagement practices were reviewed: formative research; stakeholder engagement plan; communications and issues management plan; protocol development; informed consent process; standard of prevention for vaccine research and standard of care for treatment research; policies on trial‐related physical, psychological, financial, and/or social harms; trial accrual, follow‐up, exit trial closure and results dissemination; and post‐trial access to trial products or procedures. The norms, values, and practices of collectivist societies in Sub‐Saharan Africa and the low research literacy pose challenges to the conduct of clinical trials. Civil‐society organizations, members of community advisory boards and ethics committees, young persons, COVID‐19 survivors, researchers, government, and the private sector are assets for the implementation and translation of COVID‐19 related clinical trials. Adapting ethics guidelines to the socio‐cultural context of the region can facilitate achieving the aim of stakeholder engagement.     

Geographical gradients of species richness: a test of the water‐energy conjecture of Hawkins et al. (2003) using European data for five taxa

Aims We present an analysis of grid‐based species‐richness data for European plants, mammals, birds, amphibians and reptiles, designed to test the proposition of Hawkins et al. (2003a ) that the single best factor describing richness variation switches from the water regime to the energy regime in the mid‐latitudes and that the ‘breakpoint’ is related to the physiological character of the taxa. We go on to develop subregional models showing the extent to which regional model fits vary as a function of the extent of the study system, and compare the relative performance of ‘water’, ‘energy’ and ‘water–energy’ models of richness for southern, northern and pan‐European models. Location Western Europe. Methods We use atlas data comprising species range data for 187 species of mammals, 445 species of breeding birds, 58 amphibians, 91 reptiles and 2362 plant species, inserted into a c. 50 × 50 km grid cell system. We used 11 modelled climate variables, averaged for the period 1961–90. Statistical analyses were carried out using generalized additive models (GAMs), with splines simplified to a maximum of four degrees of freedom, and we tested for spatial autocorrelation using Moran's I values obtained at 10 different distance intervals. We selected favoured models on the grounds of deviance explained combined with a simple parsimony criterion, such that we selected either: (1) the best two‐variable energy, water or water–energy model, or (2) a four‐variable water–energy model, where the latter improved on the best two‐variable model by a minimum of 5% deviance explained. Results Threshold energy values, at which richness shows a transition from an increasing to a decreasing function of annual solar radiation, were identified for all taxa apart from reptiles. We found conditional support for the switch from dominance of water variables (southern models) to energy variables (northern models). Our favoured models switched between ‘water’ and ‘energy’ for mammals, and between ‘energy’ and ‘water–energy’ for birds, depending on whether we used data of pan‐European extent, southern or northern subsets. Deviance explained in our favoured models varied from 15% (birds, southern Europe) to 72% (amphibians, northern Europe), i.e. ranging from very poor to good fits with the data. Comparison with previous work indicates that our models are generally consistent with (if sometimes weaker than) previous findings. Main conclusions Our models are incomplete representations of factors influencing macro‐scale richness patterns across Europe, taking no explicit account of, for example, topographic variation, human influences or long‐term climatic variation. However, with the exception of birds, for which only the northern model attains over one‐third deviance explained, the models show that climate can account for meaningful proportions of the deviance. We find general support for considering water and energy regimes together in modelling species richness, and for the proposition that water is more limiting in southern Europe and energy in the north. Our analyses demonstrate the sensitivity of model outcomes to the geographical location and extent of the study system, illustrating that simple curve‐fitting exercises like these, particularly if based on regions with the complex history and geography characteristic of Europe, are unlikely to provide the basis for global, predictive models. However, such exercises may be of value in detecting which aspects of water and energy regimes may be of most importance in refining independently generated global models for regional application.     

Conservation biogeography in North-east India: hierarchical analysis of cross-taxon distributional congruence

Distributional similarity (congruence) between phylogenetically independent taxonomic groups has important biogeographical as well as conservation implications. When multiple groups show congruence, one or two of them can be used as surrogates of diversity in others; thus, simplifying some of the challenges of area prioritization for conservation action. Here we test for congruence in complementarity between amphibians, reptiles and birds across seven tropical rainforest sites in the Eastern Himalaya and Indo-Burma global biodiversity hotspots. The results show that while frogs and lizards are strongly congruent with each other, birds as a whole do not show congruence with either of them. However, certain bird subgroups delineated on the basis of broad ecological niche and life history attributes are significantly congruent with both frogs and lizards. Multiple Mantel regression between environmental variable and species distribution dissimilarity matrices indicate that along with differential response to between-site ecological differences, inherent life-history characteristics shared by certain groups contributes to observed patterns of congruence. Our analyses indicate that examining biologically distinct subsets of larger groups can improve the resolution of congruence analyses. This approach can refine area-prioritization initiatives by revealing fine-scale discordances between otherwise concordant groups, and vice versa. Given that monetary resources do not always allow inclusion of multiple groups in biodiversity inventorying efforts, performing such analyses also makes economic sense because it can provide better resolution even with single-group data. In the context of conservation in North-east India, the results highlight the biogeographical complexity of the region, and also point at future priorities for biodiversity inventorying and conservation prioritization, both in terms of areas as well as taxonomic groups.