Separating the effects of number of individuals sampled and competition on species diversity: an experimental and analytic approach

1 Species richness typically increases with the number of individuals sampled, although many ecological processes that influence species richness are also well known to depend on density of individuals. We separated the effects of density on species richness that are due to sampling, from those due to density-dependent ecological processes such as competition or predation, by manipulating the density of an entire community.
2 A seed bank from a community of desert annual plants that occur on semi-stabilized sand dunes in Israel was collected from the field and sown in an experimental garden at a range of densities from 1/16 to eight times the natural density. The species pool observed in the lowest density plots was used as the null community, which was repeatedly sampled to calculate the species richness (and other diversity indices) in higher density plots that would be expected from sampling considerations alone. The significance of deviations of observed diversity from this expected diversity was then evaluated.
3 Both observed and expected number of species increased substantially with the experimental increase in density. However, observed species richness, the Shannon–Wiener diversity index and Simpson's diversity index were often significantly lower than that expected based on sampling considerations. The magnitude of the deviation from expected increased significantly with increasing density for richness and the Shannon–Wiener index. This provides some of the first direct experimental evidence from diverse natural assemblages that increasing competition among all the individuals in a community can lead to competitive exclusion.     

Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity.     

Global patterns of diversity among the specialist birds of riverine landscapes

1. Despite the growing view that biodiversity provides a unifying theme in river ecology, global perspectives on richness in riverine landscapes are limited. As a result, there is little theory or quantitative data on features that might have influenced global patterns in riverine richness, nor are there clear indications of which riverine landscapes are important to conservation at the global scale. As conspicuous elements of the vertebrate fauna of riverine landscapes, we mapped the global distributions of all of the world's specialist riverine birds and assessed their richness in relation to latitude, altitude, primary productivity and geomorphological complexity (surface configuration). 2. Specialist riverine birds, typical of high‐energy riverine landscapes and dependent wholly or partly on production from river ecosystems, occur in 16 families. They are represented by an estimated 60 species divided equally between the passerines and non‐passerines. Major radiation has occurred among different families on different continents, indicating that birds have evolved several times into the niches provided by riverine landscapes. 3. Continental richness varies from four species in Europe to 28 in Asia, with richness on the latter continent disproportionately larger than would be expected from a random distribution with respect to land area. Richness is greatest in mountainous regions at latitudes of 20–40°N in the riverine landscapes of the Himalayan mountains, where 13 species overlap in range. 4. Family, genus and species richness in specialist riverine birds all increase significantly with productivity and surface configuration (i.e. relief). However, family richness was the best single predictor of the numbers of species or genera. In keeping with the effect of surface configuration, river‐bird richness peaks globally at 1300–1400 m altitude, and most species occur typically on small, fast rivers where they feed predominantly on invertebrates. Increased lengths of such streams in areas of high relief and rainfall might have been responsible for species–area effects. 5. We propose the hypothesis that the diversity in channel forms and habitats in riverine landscapes, in addition to high temperature and primary productivity, have been prerequisites to the development of global patterns in the richness of specialist riverine organisms. We advocate tests of this hypothesis in other taxonomic groups. We draw attention, however, to the challenges of categorically defining riverine organisms in such tests because (i) rivers grade into many other habitat types across several different ecotones and (ii) `terrestrialisation' processes in riverine landscapes means that they offer habitat for organisms whose evolutionary origins are not exclusively riverine.     

On the relationship between plant species diversity and genetic diversity of Plantago lanceolata (Plantaginaceae) within and between grassland communities

Aims and Methods The relationship between genetic diversity and species diversity and the underlying mechanisms are of both fundamental and applied interest. We used amplified fragment length polymorphism (AFLP) and vegetation records to investigate the association between genetic diversity of Plantago lanceolata and plant species diversity using 15 grassland communities in central Germany. We used correlation and partial correlation analyses to examine whether relationships between genetic and species diversity were direct or mediated by environmental differences between habitats.Important findings Both within- and between-population genetic diversity of P. lanceolata were significantly positively correlated with plant species diversity within and between sites. Simple and partial correlations revealed that the positive correlations indirectly resulted from the effects of abiotic habitat characteristics on plant species diversity and, via abundance, on genetic diversity of P. lanceolata. Thus, they did not reflect a direct causal relationship between plant species diversity and genetic diversity of P. lanceolata, as would have been expected based on the hypothesis of a positive relationship between plant species diversity and niche diversity.     

The mid-domain effect cannot explain the diversity gradient of Nearctic birds

A recent explanation for diversity gradients proposes a ‘null model’ based on how species ranges are constrained by the geometry of bounded domains. We conduct a test of this hypothesis by comparing patterns predicted by two two‐dimensional geometric models against observed diversity patterns for terrestrially feeding Nearctic birds. Consistent with previous tests in two‐dimensional space, we find empirical support for the hypothesis to be very weak. We also point out a fundamental conceptual flaw in the hypothesis with respect to the key assumption that ranges can exist independently of the environment in which they are embedded that undermines its theoretical basis as well. We conclude that the mid‐domain effect has little empirical support and no theoretical support for its existence, and recommend that it be eliminated as a potential explanation for diversity gradients.     

Spatial and environmental determinants of vascular plant species richness distribution in the Iberian Peninsula and Balearic Islands

Using an exhaustive data compilation, Iberian vascular plant species richness in 50 times 50 UTM grid cells was regressed against 24 explanatory variables (spatial, geographical, topographical, geological, climatic, land use and environmental diversity variables) using Generalized Linear Models and partial regression analysis in order to ascertain the relative contribution of primary, heterogeneous and spatially structured variables. The species richness variation accounted for by these variables is reasonably high (65% of total deviance). Little less than half of this variation is accounted for spatially structured variables. A purely spatial component of variation is hardly significant. The most significant variables are those related to altitude, and particularly maximum altitude, whose cubic response reflects the occurrence of the maximum number of species at the highest altitudes. This result highlighted the importance of Iberian mountains as hotspots of diversity and the relevance of large and small scale historical factors in contemporary plant distribution patterns. Climatic or energy-related variables contributed little, whereas geological (calcareous and acid rocks) and, to a lesser extent, environmental heterogeneity variables (land use diversity and altitude range) seem to be more important.     

Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak

Understanding how specific environmental factors shape gene flow while disentangling their importance relative to the effects of geographical isolation is a major question in evolutionary biology and a specific goal of landscape genetics. Here, we combine information from nuclear microsatellite markers and ecological niche modelling to study the association between climate and spatial genetic structure and variability in Engelmann oak (Quercus engelmannii), a wind-pollinated species with high potential for gene flow. We first test whether genetic diversity is associated with climatic niche suitability and stability since the Last Glacial Maximum (LGM). Second, we use causal modelling to analyse the potential influence of climatic factors (current and LGM niche suitability) and altitude in the observed patterns of genetic structure. We found that genetic diversity is negatively associated with local climatic stability since the LGM, which may be due to higher immigration rates in unstable patches during favourable climatic periods and/or temporally varying selection. Analyses of spatial genetic structure revealed the presence of three main genetic clusters, a pattern that is mainly driven by two highly differentiated populations located in the northern edge of the species distribution range. After controlling for geographic distance, causal modelling analyses showed that genetic relatedness decreases with the environmental divergence among sampling sites estimated as altitude and current and LGM niche suitability. Natural selection against nonlocal genotypes and/or asynchrony in reproductive phenology may explain this pattern. Overall, this study suggests that local environmental conditions can shape patterns of genetic structure and variability even in species with high potential for gene flow and relatively small distribution ranges.     

Scaling down distribution maps from atlas data: a test of different approaches with virtual species

Aim Conservation managers are increasingly looking for modelled projections of species distributions to inform management strategies; however, the coarse resolution of available data usually compromises their helpfulness. The aim of this paper is to delineate and test different approaches for converting coarse‐grain occurrence data into high‐resolution predictions, and to clarify the conceptual circumstances affecting the accuracy of downscaled models. Location We used environmental data from a real landscape, southern Africa, and simulated species distributions within this landscape. Methods We built 10 virtual species at a resolution of 5 arcmin, and for each species we simulated atlas range maps at four decreasing resolutions (15, 30, 60, 120 arcmin). We tested the ability of three downscaling strategies to produce high‐resolution predictions using two modelling techniques: generalized linear models and generalized boosted models. We calibrated reference models with high‐resolution data and we compared the relative reduction of predictive performance in the downscaled models by using a null model approach. We also estimated the applicability of downscaling procedures to different situations by using distribution data for Mediterranean reptiles. Results All reference models achieved high performance measures. For all strategies, we observed a reduction of predictive performance proportional to the degree of downscaling. The differences in evaluation indices between reference models and downscaled projections obtained from atlases at 15 and 30 arcmin were never statistically significant. The accuracy of projections scaled down from 60 arcmin largely depended on the combination of approach and algorithm adopted. Projections scaled down from 120 arcmin gave misleading results in all cases. Main conclusions Moderate levels of downscaling allow for reasonably accurate results, regardless of the technique used. The most general effect of scaling down coarse‐grain data is the reduction of model specificity. The models can successfully delineate a species’ environmental association up until a 12‐fold downscaling, although with an increasing approximation that causes the overestimation of true distributions. We suggest appropriate procedures to mitigate the commission error introduced by downscaling at intermediate levels (approximately 12‐fold). Reductions of grain size > 12‐fold are discouraged.     

Orchids of the West Indies: predictability of diversity and endemism

Aim We examined phytogeographical patterns of West Indian orchids, and related island area and maximum elevation with orchid species richness and endemism. We expected strong species–area relationships, but that these would differ between low and montane island groups. In so far as maximum island elevation is a surrogate for habitat diversity, we anticipated a strong relationship with maximum elevation and both species richness and endemism for montane islands. Location The West Indies. Methods Our data included 49 islands and 728 species. Islands were classified as either montane (≥ 300 m elevation) or low (< 300 m). Linear and multivariate regression analyses were run to detect relationships between either area or maximum island elevation and species richness or the number of island endemic species. Results For all 49 islands, the species–area relationship was strong, producing a z‐value of 0.47 (slope of the regression line) and explaining 46% of the variation. For 18 relatively homogeneous, low islands we found a non‐significant slope of z = −0.01 that explained only 0.1% of the variation. The 31 montane islands had a highly significant species–area relationship, with z = 0.49 and accounting for 65% of the variation. Species numbers were also strongly related to maximum island elevation. For all islands < 750 km², we found a small‐island effect, which reduced the species–area relationship to a non‐significant z = 0.16, with only 5% of the variation explained by the model. Species–area relationships for montane islands of at least 750 km² were strong and significant, but maximum elevation was the best predictor of species richness and accounted for 79% of the variation. The frequency of single‐island endemics was high (42%) but nearly all occurred on just nine montane islands (300 species). The taxonomic distribution of endemics was also skewed, suggesting that seed dispersability, while remarkable in some taxa, is very limited in others. Montane island endemics showed strong species–area and species–elevation relationships. Main conclusions Area and elevation are good predictors of orchid species diversity and endemism in the West Indies, but these associations are driven by the extraordinarily strong relationships of large, montane islands. The species richness of low islands showed no significant relationship with either variable. A small‐island effect exists, but the montane islands had a significant relationship between species diversity and maximum elevation. Thus, patterns of Caribbean orchid diversity are dependent on an interplay between area and topographic diversity.     

Estimating and conserving patterns of invertebrate diversity: a test case of New Zealand land snails

Aim Using New Zealand land snails as a case study, we evaluated recent spatial modelling approaches for the analysis of diversity in species‐rich invertebrate groups. Applications and prospects for improved conservation assessment were investigated. Location New Zealand. Methods The study used a spatially extensive and taxonomically comprehensive, plot‐based dataset on community structure in New Zealand land snails. Generalized regression analysis and spatial prediction (GRASP) was used to model and predict species richness as a function of environmental variables (including aspects of climate, soils and vegetation). Generalized dissimilarity modelling (GDM) was used to model turnover in species composition in relation to environmental and geographical distances, and to assess community similarity and the representativeness of the reserve network. Results Observed land snail richness in 20 × 20 m plots ranged from 1 to 74 (mean 17.5). The GRASP model explained a modest 27% of the variation in richness. The GDM model explained 57% of the variation in species turnover and indicated approximately equal amounts related to environmental (Cody’s beta diversity) and geographical distance (Cody’s gamma diversity). Temperature and moisture were the most important environmental variables. Results indicate that snail distributions are not only sorted by environment but are also strongly influenced by historical effects consistent with those expected of poorly dispersing taxa that have persisted in refugia during past climatic change. The GDM model enabled spatial classifications of snail communities, highlighting diverse communities in heterogeneous regions, such as the South Island mountains, and also enabled continuous depictions of community similarity and adequacy of New Zealand’s protected natural areas network. Main conclusions The GRASP and GDM analyses allowed us to model and depict spatial patterns of diversity in land snail communities involving 845 species, and produce community classifications and estimates of community similarity. These tools advance conservation assessment in species‐rich groups, but require further conceptual and methodological development.     

Global diversity of island floras from a macroecological perspective

Islands harbour a significant portion of all plant species worldwide. Their biota are often characterized by narrow distributions and are particularly susceptible to biological invasions and climate change. To date, the global richness pattern of islands is only poorly documented and factors causing differences in species numbers remain controversial. Here, we present the first global analysis of 488 island and 970 mainland floras. We test the relationship between island characteristics (area, isolation, topography, climate and geology) and species richness using traditional and spatial models. Area is the strongest determinant of island species numbers ( R ² = 0.66) but a weaker predictor for mainlands ( R ² = 0.25). Multivariate analyses reveal that all investigated variables significantly contribute to insular species richness with area being the strongest followed by isolation, temperature and precipitation with about equally strong effects. Elevation and island geology show relatively weak yet significant effects. Together these variables account for 85% of the global variation in species richness.     

The mid‐domain effect matters: simulation analyses of range‐size distribution data from Mount Kinabalu,Borneo

Aim In simulation exercises, mid‐domain peaks in species richness arise as a result of the random placement of modelled species ranges within simulated geometric constraints. This has been called the mid‐domain effect (MDE). Where close correspondence is found between such simulations and empirical data, it is not possible to reject the hypothesis that empirical species richness patterns result from the MDE rather than being the outcome (wholly or largely) of other factors. To separate the influence of the MDE from other factors we therefore need to evaluate variables other than species richness. The distribution of range sizes gives different predictions between models including the MDE or not. Here, we produce predictions for species richness and distribution of range sizes from one model without the MDE and from two MDE models: a classical MDE model encompassing only species with their entire range within the domain (range‐restricted MDE), and a model encompassing all species with the theoretical midpoint within the domain (midpoint‐restricted MDE). These predictions are compared with observations from the elevational pattern of range‐size distributions and species richness of vascular plants. Location Mount Kinabalu, Borneo. Methods The data set analysed comprises more than 28,000 plant specimens with information on elevation. Species ranges are simulated with various assumptions for the three models, and the species simulated are subsequently subjected to a sampling that simulates the actual collection of species on Mount Kinabalu. The resulting pattern of species richness and species range‐size distributions are compared with the observed pattern. Results The comparison of simulated and observed patterns indicates that an underlying monotonically decreasing trend in species richness with elevation is essential to explain fully the observed pattern of richness and range size. When the underlying trend is accounted for, the MDE model that restricts the distributions of theoretical midpoints performs better than both the classical MDE model and the model that does not incorporate geometric constraints. Main conclusions Of the three models evaluated here, the midpoint‐restricted MDE model is found to be the best for explaining species richness and species range‐size distributions on Mount Kinabalu.     

Climate change and the future restructuring of Neotropical anuran biodiversity

Climate change is likely to impact multiple dimensions of biodiversity. Species range shifts are expected and may drive changes in the composition of species assemblages. In some regions, changes in climate may precipitate the loss of geographically restricted, niche specialists and facilitate their replacement by more widespread, niche generalists, leading to decreases in β-diversity and biotic homogenization. However, in other regions climate change may drive local extinctions and range contraction, leading to increases in β-diversity and biotic heterogenization. Regional topography should be a strong determinant of such changes as mountainous areas often are home to many geographically restricted species, whereas lowlands and plains are more often inhabited by widespread generalists. Climate warming, therefore, may simultaneously bring about opposite trends in β-diversity in mountainous highlands versus relatively flat lowlands. To test this hypothesis, we used species distribution modelling to map the present-day distributions of 2669 Neotropical anuran species, and then generated projections of their future distributions assuming future climate change scenarios. Using traditional metrics of β-diversity, we mapped shifts in biotic homogenization across the entire Neotropical region. We used generalized additive models to then evaluate how changes in β-diversity were associated with shifts in species richness, phylogenetic diversity and one measure of ecological generalism. Consistent with our hypothesis, we find increasing biotic homogenization in most highlands, associated with increased numbers of generalists and, to a lesser extent, losses of specialists, leading to an overall increase in alpha diversity, but lower mean phylogenetic diversity. In the lowlands, biotic heterogenization was more common, and primarily driven by local extinctions of generalists, leading to lower α-diversity, but higher mean phylogenetic diversity. Our results suggest that impacts of climate change on β-diversity are likely to vary regionally, but will generally lead to lower diversity, with increases in β-diversity offset by decreases in α-diversity.     

The performance of range maps and species distribution models representing the geographic variation of species richness at different resolutions

Aim The method used to generate hypotheses about species distributions, in addition to spatial scale, may affect the biodiversity patterns that are then observed. We compared the performance of range maps and MaxEnt species distribution models at different spatial resolutions by examining the degree of similarity between predicted species richness and composition against observed values from well‐surveyed cells (WSCs). Location Mexico. Methods We estimated amphibian richness distributions at five spatial resolutions (from 0.083° to 2°) by overlaying 370 individual range maps or MaxEnt predictions, comparing the similarity of the spatial patterns and correlating predicted values with the observed values for WSCs. Additionally, we looked at species composition and assessed commission and omission errors associated with each method. Results MaxEnt predictions reveal greater geographic differences in richness between species rich and species poor regions than the range maps did at the five resolutions assessed. Correlations between species richness values estimated by either of the two procedures and the observed values from the WSCs increased with decreasing resolution. The slopes of the regressions between the predicted and observed values indicate that MaxEnt overpredicts observed species richness at all of the resolutions used, while range maps underpredict them, except at the finest resolution. Prediction errors did not vary significantly between methods at any resolution and tended to decrease with decreasing resolution. The accuracy of both procedures was clearly different when commission and omission errors were examined separately. Main conclusions Despite the congruent increase in the geographic richness patterns obtained from both procedures as resolution decreases, the maps created with these methods cannot be used interchangeably because of notable differences in the species compositions they report.     

The distribution of cultivated species of Porophyllum (Asteraceae) and their wild relatives under climate change

The geographic distribution of plant species is already being affected by climate change. Cropping patterns of edible plant species and their wild relatives will also be affected, making it important to predict possible changes to their distributions in the future. Currently, species distribution models are valuable tools that allow the estimation of species’ potential distributions, in the recent past as well as during other time spans for which climate data have been obtained. With the aim of evaluating how species distributions respond to current and future climate changes, in this work species distribution models were generated for two cultivated species of the Porophyllum genus (Asteraceae), known commonly as ‘pápalos' or ‘pápaloquelites', as well as their Mexican wild relatives, at five points in time (21,000 years ago, present, 2020, 2050, and 2080). Using a database of 1442 entries for 16 species of Porophyllum and 19 environmental variables, species distribution models were constructed for each time period using the Maxent modelling algorithm; those constructed for the future used a severe climate change scenario. The results demonstrate contrasting effects between the two cultivated species; for P. linaria, the future scenario suggests a decrease in distribution area, while for P. macrocephalum distribution is predicted to increase. Similar trends are observed in their wild relatives, where 11 species will tend to decrease in distribution area, while three are predicted to increase. It is concluded that the most important agricultural areas where the cultivated species are grown will not be greatly affected, while the areas inhabited by the wild species will. However, while the results suggest that climate change will affect the distribution of the cultivated species in contrasting ways, evaluations at finer scales are recommended to clarify the impact within cultivation zones.