Point process models,the dimensions of biodiversity and the importance of small-scale biotic interactions

Aims Recent mechanistic explanations for community assembly focus on the debates surrounding niche-based deterministic and dispersal-based stochastic models. This body of work has emphasized the importance of both habitat filtering and dispersal limitation, and many of these works have utilized the assumption of species spatial independence to simplify the complexity of the spatial modeling in natural communities when given dispersal limitation and/or habitat filtering. One potential drawback of this simplification is that it does not consider species interactions and how they may influence the spatial distribution of species, phylogenetic and functional diversity. Here, we assess the validity of the assumption of species spatial independence using data from a subtropical forest plot in southeastern China.Methods We use the four most commonly employed spatial statistical models—the homogeneous Poisson process representing pure random effect, the heterogeneous Poisson process for the effect of habitat heterogeneity, the homogenous Thomas process for sole dispersal limitation and the heterogeneous Thomas process for joint effect of habitat heterogeneity and dispersal limitation—to investigate the contribution of different mechanisms in shaping the species, phylogenetic and functional structures of communities.Important findings Our evidence from species, phylogenetic and functional diversity demonstrates that the habitat filtering and/or dispersal-based models perform well and the assumption of species spatial independence is relatively valid at larger scales (50×50 m). Conversely, at local scales (10×10 and 20×20 m), the models often fail to predict the species, phylogenetic and functional diversity, suggesting that the assumption of species spatial independence is invalid and that biotic interactions are increasingly important at these spatial scales.     

江西省自然保护区发展布局空缺分析

通过专家咨询、数量标准化、主观赋权等方法,对江西省96个县(市、区)的高等动植物种类、珍稀物种种类、天然林面积和蓄积、天然湿地面积、已建自然保护区面积等进行评分,计算96个县(市、区)的物种多样性、天然林资源、天然湿地等自然资源的综合评分值和自然保护区建设的空缺评分值,并借助GIS技术分析了江西省自然保护区空间布局特点及存在的主要问题,研究提出了自然保护区空间规划布局建议,为江西省自然保护区中远期发展规划提供科学依据。     

Between geometry and biology: the problem of universality of the species-area relationship

The species-area relationship (SAR) is considered to be one of a few generalities in ecology, yet a universal model of its shape and slope has remained elusive. Recently, Harte et al. argued that the slope of the SAR for a given area is driven by a single parameter, the ratio between total number of individuals and number of species (i.e., the mean population size across species at a given scale). We provide a geometric interpretation of this dependence. At the same time, however, we show that this dependence cannot be universal across taxa: if it holds for a taxon composed from two subsets of species and also for one of its subsets, it cannot simultaneously hold for the other subset. Using three data sets, we show that the slope of the SAR considerably varies around the prediction. We estimate the limits of this variation by using geometric considerations, providing a theory based on species spatial turnover at different scales. We argue that the SAR cannot be strictly universal, but its slope at each particular scale varies within the constraints given by species' spatial turnover at finer spatial scales, and this variation is biologically informative.     

The scale of analysis determines the spatial pattern of woody species diversity in the Mediterranean environment

We examine the spatial pattern of woody species diversity at different scales, in two sites of Mt. Holomontas in northern Greece, which falls within the transitional zone between temperate forests and Mediterranean-type ecosystems. We investigate how diversity is distributed in space and whether the perceived pattern changes with the scale of observation. We use two different metrics of diversity: species richness and species turnover. Our main finding is that the spatial pattern of diversity changes with the scale of observation or analysis. For a given scale, the pattern of species richness (alpha diversity) is negatively correlated with the pattern of species turnover (beta diversity). Species-rich areas have more species in common with their neighbors than species-poor areas. The between-scale disparity of the spatial pattern of diversity may be a general feature of ecological systems. For this to be validated, studies with different groups of species in different biomes and in different biogeographical areas are required; our study contributes to this direction providing evidence that this holds true for woody species in Mediterranean communities. Finally, we discuss how these findings might affect important issues in theoretical and applied ecology, such as identifying the environmental factors driving biodiversity.     

Phylogenetic autocorrelation and evolutionary interpretation of the higher-taxon approach for biodiversity analyses.

Although in most recent broad-scale analyses, diversity is measured by counting the number of species in a given area or spatial unity (species richness), a 'top-down' approach has been used sometimes, counting higher-taxon (genera, family) instead of species with some advantages. However, this higher-taxon approach is quite empirical and the cut-off level is usually arbitrarily defined. In this work, we show that the higher-taxon approach could be theoretically linked with models of phenotypic diversification by means of phylogenetic autocorrelation analysis in such a way that the taxonomic (or phylogenetic) rank to be used could not be necessarily arbitrary. This rank expresses past time in which taxa became independent for a given phenotypic trait or for the evolution of average phenotypes across different traits. We illustrated the approach by evaluating phylogenetic patches for 23 morphological, ecological and behavioural characters in New World terrestrial Carnivora. The higher-taxon counts at 18.8 mya (S(L)) defined by phylogenetic correlograms are highly correlated with species richness (r = 0.899; P < 0.001 with ca. 13 degrees of freedom by taking spatial autocorrelation into account). However, S(L) in North America is usually larger than in South America. Thus, although there are more species in South and Central America, the fast recent diversification that occurred in this region generated species that are "redundant" in relation to lineages that were present at 18.8 my. BP. Therefore, the number of lineages can be comparatively used as a measure of evolutionary diversity under a given model of phenotypic divergence among lower taxonomic units.     

Spatial grain and the causes of regional diversity gradients in ants

Gradients of species richness (S; the number of species of a given taxon in a given area and time) are ubiquitous. A key goal in ecology is to understand whether and how the many processes that generate these gradients act at different spatial scales. Here we evaluate six hypotheses for diversity gradients with 49 New World ant communities, from tundra to rain forest. We contrast their performance at three spatial grains from S(plot), the average number of ant species nesting in a m2 plot, through Fisher's alpha, an index that treats our 30 1-m2 plots as subsamples of a locality's diversity. At the smallest grain, S(plot), was tightly correlated (r2 = 0.99) with colony abundance in a fashion indistinguishable from the packing of randomly selected individuals into a fixed space. As spatial grain increased, the coaction of two factors linked to high net rates of diversification--warm temperatures and large areas of uniform climate--accounted for 75% of the variation in Fisher's alpha. However, the mechanisms underlying these correlations (i.e., precisely how temperature and area shape the balance of speciation to extinction) remain elusive.     

Distribution of specialist and generalist species along spatial gradients of habitat disturbance and fragmentation

In this paper, we tested whether the spatial distribution of a given species in more or less fragmented and disturbed landscapes depends on the species habitat specialization. We studied 891 spatial replicates from the French Breeding Bird Survey (FBBS) monitored at least two years during 2001–2005, and two independent landscape databases measuring respectively landscape fragmentation and recent landscape disturbance on each FBBS replicate. We used a continuous habitat specialization index for the 105 most common bird species monitored by the FBBS. We further modelled the spatial variation in abundance of each species according to fragmentation and disturbance across FBBS replicates, accounting for habitat differences and spatial trends. We then tested whether more or less specialized species responded to landscape fragmentation and disturbance. We found that the more specialist a species, the more negative its spatial response to landscape fragmentation and disturbance. Although there was a very high variation around these tendencies indicating that there are many other drivers of species distribution, our results suggest that measuring specialization may be helpful in predicting which species are likely to thrive in human degraded landscapes. We also emphasize the need to consider both positive and negative species responses when assessing consequences of habitat change in communities.     

Analytical evidence for scale-invariance in the shape of species abundance distributions

The distribution of species abundances within an ecological community provides a window into ecological processes and has important applications in conservation biology as an indicator of disturbance. Previous work indicates that species abundance distributions might be independent of the scales at which they are measured which has implications for data interpretation. Here we formulate an analytically tractable model for the species abundance distribution at different scales and discuss the biological relevance of its assumptions. Our model shows that as scale increases, the shape of the species abundance distribution converges to a particular shape given uniquely by the Jaccard index of spatial species turnover and by a parameter for the spatial correlation of abundances. Our model indicates that the shape of the species abundance distribution is taxon specific but does not depend on sample area, provided this area is large. We conclude that the species abundance distribution may indeed serve as an indicator of disturbances affecting species spatial turnover and that the assumption of conservation of energy in ecosystems, which is part of the Maximum Entropy approach, should be re-evaluated.     

Bird diversity patterns in Neotropical temperate farmlands: The role of environmental factors and trophic groups in the spring and autumn

Productivity, habitat heterogeneity and environmental similarity are of the most widely accepted hypotheses to explain spatial patterns of species richness and species composition similarity. Environmental factors may exhibit seasonal changes affecting species distributions. We explored possible changes in spatial patterns of bird species richness and species composition similarity. Feeding habits are likely to have a major influence in bird–environment associations and, given that food availability shows seasonal changes in temperate climates, we expect those associations to differ by trophic group (insectivores or granivores). We surveyed birds and estimated environmental variables along line‐transects covering an E‐W gradient of annual precipitation in the Pampas of Argentina during the autumn and the spring. We examined responses of bird species richness to spatial changes in habitat productivity and heterogeneity using regression analyses, and explored potential differences between seasons of those responses. Furthermore, we used Mantel tests to examine the relationship between species composition similarity and both the environmental similarity between sites and the geographic distance between sites, also assessing differences between seasons in those relationships. Richness of insectivorous birds was directly related to primary productivity in both seasons, whereas richness of seed‐eaters showed a positive association with habitat heterogeneity during the spring. Species composition similarity between assemblages was correlated with both productivity similarity and geographic proximity during the autumn and the spring, except for insectivore assemblages. Diversity within main trophic groups seemed to reflect differences in their spatial patterns as a response to changes between seasons in the spatial patterns of food resources. Our findings suggest that considering different seasons and functional groups in the analyses of diversity spatial pattern could contribute to better understand the determinants of biological diversity in temperate climates.     

Evaluating the reliability of species distribution models with an indirect measure of bird reproductive performance

Measures of fitness such as reproductive performance are considered reliable indicators of habitat quality for a species. Such measures are, however, only available in a restricted number of sites, which prevents them from being used to quantify habitat quality across landscapes or regions. Alternatively, species presence records can be used along with environmental variables to build models that predict the distribution of species across larger spatial extents. Model predictions are often used for management purposes as they are assumed to describe the quality of the habitats to support a species. Yet, given that species are often present both in optimal and suboptimal areas, the use of data collected during the breeding season to build these models may potentially result in misleading predictions of habitat quality for the reproduction of the species, with potentially significant conservation consequences. In this study we analysed the relationship between fitness parameters informing on habitat quality for reproduction and predictions of species distribution models at multiple spatial scales using two independent sets of data. For 19 passerine bird species, we compared an indirect measure of reproductive performance (ratio of juveniles‐to‐adults) – obtained from Constant Effort Sites (CES) mist‐netting data in Catalonia – with the predictions of models based on bird presence records collected during the Catalan Breeding Bird Atlas (CBBA). A positive relationship between the predictions derived from species distribution models and the reproductive performance of the species was found for almost half of the species at one or more spatial scales. This result suggests that species distribution models may help to predict habitat quality for some species over some extents. However, caution is needed as this is not consistent for all species at all scales. Further work based on species‐ and scale‐specific approaches is now required to understand in which situations species distribution models provide predictions that are in line with reproductive performance.     

Influence of edaphic factors on the spatial structure of inland halophytic communities: a case study in China

Abstract. In order to understand the influence of edaphic factors on the spatial structure of inland halophytic plant communities, a 2.6 km² study site, located on the lower fringe of the alluvial fan of the Hutubi River, in an arid region of China, was sampled and mapped. 105 patches were found to be homogeneous in species composition. Plant species and their coverage were recorded in each patch. 45 patches were randomly selected for the measurement of edaphic variables. A map with quadrat locations and boundaries of patches was digitized into a GIS and related to the vegetation and edaphic data matrices. CCA was used to evaluate the relative importance of edaphic factors in explaining the variation of the species assemblages and to identify the ecological preferences of species. The spatial structure of the communities and the main edaphic factors were analyzed using correlograms, Mantel correlograms and clustering under constraint of spatial contiguity. Gradient analysis showed that there are two distinct vegetation gradients in the study area, one of which is determined mainly by soil moisture (determined by depth to the water table), and the other by soil salinity (determined by electrical conductivity and hydrolytic alkalinity of the first soil layer). However, spatial analyses showed that at the sampling scale the halophytic communities in the study area are structured along one main spatial gradient determined by the water table level. Similar spatial autocorrelation structures between the factors related to the first soil layer and the communities, given our sampling scale, could not be detected. Our results suggest that the relative importance of the effects of different edaphic factors on the spatial structure of halophytic communities is scale-dependent. The partitioning of species variation indicates that in addition to edaphic factors, other factors, such as biotic interactions, may play an important role in structuring these communities.     

Phylogeny contributes more than site characteristics and traits to the spatial distribution pattern of tropical tree populations

Dispersal mechanism, species height, sexual system, and wood density are potential drivers of the spatial distribution pattern of tropical tree populations. These traits are usually conserved among closely related species, thus populations of these species should have more similar spatial distribution patterns than populations of phylogenetically distant species. Additionally, variation in the abiotic and biotic environment might result in distinct spatial distribution patterns of local populations of the same species. We employed variation partitioning to determine the degree to which traits, shared evolutionary history, site characteristics, and their joint effects govern the degree of overdispersion or aggregation of tree populations at different spatial scales within fourteen 1‐ha plots of the Atlantic Rainforest in southeastern Brazil. We quantified the degree of overdispersion or aggregation with a new standardized index err(r) based on standardized effect sizes of the pair correlation function. Variation in err(r) was mostly explained by phylogenetic relationships among species (70–95%, depending on spatial scale), indicating that traits not included in our analysis are important drivers of the spatial distribution pattern. Site characteristics explained a smaller part of the variation, indicating context‐dependence. Finally, the traits studied here provided the smallest explanation of the variation, suggesting a minor role of seed dispersal. Residual variation in err(r) ranged from 5–29%, indicating that stochasticity and/or variables not included in the models (e.g. direct measures of post‐dispersal processes) also influence the spatial distribution pattern of the populations. Our results suggest that many ecological processes act in concert at the study site and that their importance changes with spatial scale. Additionally, the relative importance of these processes differs from that previously described for other tropical forests. Determining why a given ecological process is more important in some tropical tree communities than in others are promising venues for further research.     

The impact of spatial structure on the accuracy of contour maps of small data sets

Spatial analysis of insect counts provides important information about how insect species respond to the heterogeneity of a given sampling space. Contour mapping is widely used to visualize spatial pest distribution patterns in anthropogenic environments, and in this study we outlined recommendations regarding semivariogram analysis of small data sets (N < 50). Second, we examined how contour maps based upon linear kriging were affected by the spatial structure of the given data set, as error estimation of contour maps appears to have received little attention in the entomological domain. We used weekly trap catches of the warehouse beetle, Trogoderma variabile, and the accuracy assessment was based upon data sets that had either a random spatial structure or were characterized by asymptotic spatial dependence. Asymptotic spatial dependence (typically described with a semivariogram analysis) means that trap catches at locations close to each other are more similar than trap catches at locations further apart. Trap catches were poorly predicted for data sets with a random spatial structure, while there was a significant correlation between observed and predicted trap catches for the spatially rearranged data sets. Therefore, for data sets with a random spatial structure we recommend visualization of the insect counts as scale-sized dots rather than as contour maps.     

Native communities determine the identity of exotic invaders even at scales at which communities are unsaturated

Aim To determine why some communities are more invasible than others and how this depends on spatial scale. Our previous work in serpentine ecosystems showed that native and exotic diversity are negatively correlated at small scales, but became positively correlated at larger scales. We hypothesized that this pattern was the result of classic niche partitioning at small scales where the environment is homogeneous, and a shift to the dominance of coexistence mechanisms that depend on spatial heterogeneity in the environment at large scales. Location Serpentine ecosystem, Northern California. Methods We test the above hypotheses using the phylogenetic relatedness of natives and exotics. We hypothesized that (1) at small scales, native and exotic species should be more distantly related than expected from a random assemblage model because with biotic resistance, successful invaders should have niches that are different from those of the natives present and (2) at large scales, native and exotic species should not be more distantly related than expected. Result We find strong support for the first hypothesis providing further evidence of biotic resistance at small scales. However, at large scales, native and exotic species were also more distantly related than expected. Importantly, however, natives and exotics were more distantly related at small scales than they were at large scales, suggesting that in the transition from small to large scales, biotic resistance is relaxed but still present. Communities at large scales were not saturated in the sense that more species could enter the community, increasing species richness. However, species did not invade indiscriminately. Exotic species closely related to species already established the community were excluded. Main conclusions Native communities determine the identity of exotic invaders even at large spatial scales where communities are unsaturated. These results hold promise for predicting which species will invade a community given the species present.     

Coexisting small mammals display contrasting strategies for tolerating instability in arable habitat

Small mammal species are abundant and common throughout Europe and often utilise areas that are subject to agricultural land use. Arable farmland is an example of a frequently disturbed habitat, and this study questioned how such disturbance affected the two most common species in the region; one a habitat generalist and one a habitat specialist. We confirmed the prediction that wood mice (Apodemus sylvaticus, a habitat generalist) would make use of a variety of habitats and that bank voles (Myodes glareolus, a habitat specialist) would make greater use of the more stable portions of the study site. We surveyed the study site intensively in order to test whether there was continuity in the spatial arrangement of individuals of both species, given the strategy employed. The spatial arrangement of wood mice varied with season but remained stable for bank voles. We found no association, positive or negative, between the spatial distributions of the two species, suggesting that spatial competitive exclusion did not occur. This work provides further insight into how these small mammal species are affected by agricultural disturbance and predictions can be made about how the species will respond under CAP Reform greening practices.     

Measuring Spider Richness: Effects of Different Sampling Methods and Spatial and Temporal Scales

Assessing the richness of invertebrate taxa to aid conservation and management requires a better understanding of the potential sources of error. Patterns of richness for heathland spiders at the species and family levels were compared across three sampling methods, four spatial scales, and monthly intervals (for 16 months). A total of 33 families and 130 species was collected: pitfall traps collected 94% of species, sweep net, 25%, and visual search, 41%. The sampling methods produced variable results. Pitfall trap and sweep net techniques identified significant, yet contrasting spatial differences in the number of families and species at one spatial scale. Pitfall trap data reflected strong temporal variation that influenced spatial patterns in richness (across one spatial scale for families and two for species). The use of broader temporal scales introduced a potential failure to detect significant differences in the richness of ground active spiders, and this risk varied spatially. The sweep net is not recommended for this habitat, although a method that targets the foliage is required for a more complete faunal assessment. Visual searches detected no significant patterns in richness, yet given its potential and increasing use for rapid biodiversity surveys, ways to improve sampling efficiency are suggested.     

Autoregressive modelling of species richness in the Brazilian Cerrado.

Spatial autocorrelation is the lack of independence between pairs of observations at given distances within a geographical space, a phenomenon commonly found in ecological data. Taking into account spatial autocorrelation when evaluating problems in geographical ecology, including gradients in species richness, is important to describe both the spatial structure in data and to correct the bias in Type I errors of standard statistical analyses. However, to effectively solve these problems it is necessary to establish the best way to incorporate the spatial structure to be used in the models. In this paper, we applied autoregressive models based on different types of connections and distances between 181 cells covering the Cerrado region of Central Brazil to study the spatial variation in mammal and bird species richness across the biome. Spatial structure was stronger for birds than for mammals, with R(2) values ranging from 0.77 to 0.94 for mammals and from 0.77 to 0.97 for birds, for models based on different definitions of spatial structures. According to the Akaike Information Criterion (AIC), the best autoregressive model was obtained by using the rook connection. In general, these results furnish guidelines for future modelling of species richness patterns in relation to environmental predictors and other variables expressing human occupation in the biome.     

Modeling the Circulation of a Disease Between Two Host Populations on non Coincident Spatial Domains

We derive a reaction–diffusion system modeling the spatial propagation of a disease with kinetics occurring on distinct spatial domains. This corresponds to the actual invasion of a disease from a species living in a given spatial domain toward a second species living in a different spatial domain. We study the global existence of solutions and discuss the long time behavior of solutions. Then we consider a special case, based on a model of brain worm infection from white-tailed deer to moose populations, for which we discuss the invasion success/failure process and disprove a conjecture stated in an earlier work.     

Covariances among join-count spatial autocorrelation measures

Spatial distributions of biological variables are often well-characterized with pairwise measures of spatial autocorrelation. In this article, the probability theory for products and covariances of join-count spatial autocorrelation measures are developed for spatial distributions of multiple nominal (e.g. species or genotypes) types. This more fully describes the joint distributions of pairwise measures in spatial distributions of multiple (i.e. more than two) types. An example is given on how the covariances can be used for finding standard errors of weighted averages of join-counts in spatial autocorrelation analysis of more than two types, as is typical for genetic data for multiallelic loci.     

Spatio‐temporal scaling of biodiversity and the species–time relationship in a stream fish assemblage

1. The increase of species richness with the area of the habitat sampled, that is the species–area relationship, and its temporal analogue, the species–time relationship (STR), are among the few general laws in ecology with strong conservation implications. However, these two scale‐dependent phenomena have rarely been considered together in biodiversity assessment, especially in freshwater systems. 2. We examined how the spatial scale of sampling influences STRs for a Central‐European stream fish assemblage (second‐order Bernecei stream, Hungary) using field survey data in two simulation‐based experiments. 3. In experiment one, we examined how increasing the number of channel units, such as riffles and pools (13 altogether), and the number of field surveys involved in the analyses (12 sampling occasions during 3 years), influence species richness. Complete nested curves were constructed to quantify how many species one observes in the community on average for a given number of sampling occasions at a given spatial scale. 4. In experiment two, we examined STRs for the Bernecei fish assemblage from a landscape perspective. Here, we evaluated a 10‐year reach level data set (2000–09) for the Bernecei stream and its recipient watercourse (third‐order Kemence stream) to complement results on experiment one and to explore the mechanisms behind the observed patterns in more detail. 5. Experiment one indicated the strong influence of the spatial scale of sampling on the accumulation of species richness, although time clearly had an additional effect. The simulation methodology advocated here helped to estimate the number of species in a diverse combination of spatial and temporal scale and, therefore, to determine how different scale combinations influence sampling sufficiency. 6. Experiment two revealed differences in STRs between the upstream (Bernecei) and downstream (Kemence) sites, with steeper curves for the downstream site. Equations of STR curves were within the range observed in other studies, predominantly from terrestrial systems. Assemblage composition data suggested that extinction–colonisation dynamics of rare, non‐resident (i.e. satellite) species influenced patterns in STRs. 7. Our results highlight that the determination of species richness can benefit from the joint consideration of spatial and temporal scales in biodiversity inventory surveys. Additionally, we reveal how our randomisation‐based methodology may help to quantify the scale dependency of diversity components (α, β, γ) in both space and time, which have critical importance in the applied context.