Estimating species richness and accumulation by modeling species occurrence and detectability

A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.     

The invasion paradox: reconciling pattern and process in species invasions

The invasion paradox describes the co-occurrence of independent lines of support for both a negative and a positive relationship between native biodiversity and the invasions of exotic species. The paradox leaves the implications of native-exotic species richness relationships open to debate: Are rich native communities more or less susceptible to invasion by exotic species? We reviewed the considerable observational, experimental, and theoretical evidence describing the paradox and sought generalizations concerning where and why the paradox occurs, its implications for community ecology and assembly processes, and its relevance for restoration, management, and policy associated with species invasions. The crux of the paradox concerns positive associations between native and exotic species richness at broad spatial scales, and negative associations at fine scales, especially in experiments in which diversity was directly manipulated. We identified eight processes that can generate either negative or positive native-exotic richness relationships, but none can generate both. As all eight processes have been shown to be important in some systems, a simple general theory of the paradox, and thus of the relationship between diversity and invasibility, is probably unrealistic. Nonetheless, we outline several key issues that help resolve the paradox, discuss the difficult juxtaposition of experimental and observational data (which often ask subtly different questions), and identify important themes for additional study. We conclude that natively rich ecosystems are likely to be hotspots for exotic species, but that reduction of local species richness can further accelerate the invasion of these and other vulnerable habitats.     

Spatial heterogeneity influences native and nonnative plant species richness

Spatial heterogeneity may have differential effects on the distribution of native and nonnative plant species richness. We examined the effects of spatial heterogeneity on native and nonnative plant species richness distributions in the central part of Rocky Mountain National Park, Colorado, USA. Spatial heterogeneity around vegetation plots was characterized using landscape metrics, environmental/topographic variables (slope, aspect, elevation, and distance from stream or river), and soil variables (nitrogen, clay, and sand). The landscape metrics represented five components of landscape heterogeneity and were measured at four spatial extents (within varying radii of 120, 240, 480, and 960 m) using the FRAGSTATS landscape pattern analysis program. Akaike's Information Criterion adjusted for small sample size (AICc) was used to select the best models from a set of multiple linear regression models developed for native and nonnative plant species richness at four spatial extents and three levels of ecological hierarchy (i.e., landscape, land cover, and community). Both native and nonnative plant species richness were positively correlated with edge density, Simpson's diversity index and interspersion/juxtaposition index, and were negatively correlated with mean patch size. The amount of variation explained at four spatial extents and three hierarchical levels ranged from 30% to 70%. At the landscape level, the best models explained 43% of the variation in native plant species richness and 70% of the variation in nonnative plant species richness (240-m extent). In general, the amount of variation explained was always higher for nonnative plant species richness, and the inclusion of landscape metrics always significantly improved the models. The best models explained 66% of the variation in nonnative plant species richness for both the conifer land cover type and lodgepole pine community. The relative influence of the components of spatial heterogeneity differed for native and nonnative plant species richness and varied with the spatial extent of analysis and levels of ecological hierarchy. The study offers an approach to quantify spatial heterogeneity to improve models of plant biodiversity. The results demonstrate that ecologists must recognize the importance of spatial heterogeneity in managing native and nonnative plant species.     

Quadratic diversity: Its maximization can reduce the richness of species

In recent decades numerous diversity indices have been introduced. Among them the quadratic entropy index Q expresses the mean difference between two individuals chosen from the community at random. Differing from diversity indices habitually employed, Q does not satisfy a property postulated earlier for those measures. Namely, the uniform distribution of species does not necessarily yield the maximal index value. Q is based on the difference matrix of species. For a given matrix one can seek for the vector yielding the maximum quadratic entropy. This task leads to a quadratic programming problem. Using the appropriate program of a program package, we determined the maximum vector for a genetic difference matrix of crane species, as published in the literature. We discovered that some components (frequencies) in the maximum vector are equal to zero. That is, by maximizing the quadratic diversity some species can be eliminated. We discuss briefly the possible implications of this observation. Moreover, even if all elements in the maximum vector are positive, the elements can differ.     

Running to stand still: temperature effects on species richness, species turnover, and functional community dynamics

The information on temperature-mediated changes in biodiversity in local assemblages is scarce and mainly addresses the change in species richness. However, warming may have more consistent effects on species turnover than on the number of species. Moreover, very few studies extended the analysis of changes in biodiversity and species composition to questions of associated ecosystem functions such as primary production. Here, we synthesize 4 case studies employing microalgal microcosms within the Aquashift priority program to ask (1) do warming-related shifts in species richness correspond to changes in the rate of biomass production, (2) do similar relationships prevail for evenness, and (3) do warming-related shifts in species turnover stabilize or destabilize biomass production? Two of the four cases are previously unpublished, and for a third case, the link between diversity and functional consequences of temperature was not analyzed before. We found accelerated loss of species with warming in all cases. Biomass production was lower with lower species richness in most cases but increased with lower evenness. Most importantly, the relation between functional and compositional stability was different between cases: More rapid extinction resulted in more variable biomass in 2 cases conducted with a limited species pool, indicating that compositional destabilization relates to functional variability. By contrast, the only experiment with a large species pool (30 species) allowed previously rare species to become dominant in the community and showed more stable biomass at high turnover, indicating that compensatory dynamics (turnover) can promote functional stability. These 4 independent experiments highlight the need to consider both compositional and functional consequences of altered temperature regimes.     

Recruitment limitation constrains local species richness and productivity in dry grassland

Species coexistence and local-scale species richness are limited by the availability of seeds and microsites for germination and establishment. We conducted a seed addition experiment in seminatural grassland at three sites in southern Switzerland and repeated the experiment in two successive years to evaluate various circumstances under which seed limitation and establishment success affect community functioning. A collection of 144,000 seeds of 22 meadow species including grasses and forbs of local provenance was gathered, and seeds were individually sown in a density that resembled natural seed rain. The three communities were seed limited. Three years after sowing, single species varied in emergence (0-50%), survival (0-69%), and establishment rates (0-27%). One annual and 13 perennial species reached reproductive stage. Low establishment at one site and reduced growth at another site indicated stronger microsite limitation compared to the third site. Recruitment was influenced by differences in abiotic environmental conditions between sites (water availability, soil minerals) and by within-site differences in biotic interaction (competition). At the least water-limited site, sowing resulted in an increase in phytomass due to establishment of short-lived perennials in the second and third years after sowing. This increase persisted over the following two years due to establishment of longer-lived perennials. After sowing in a wetter year with higher phytomass, however, productivity did not increase, because higher intensity of competition in an early phase of establishment resulted in less vigorous plants later on. Due to the generally favorable weather conditions during this study, sowing year had a small effect on numbers of established individuals over all species. Recruitment limitation can thus constrain local-scale species richness and productivity, either by a lack of seeds or by reduced seedling growth, likely due to competition from the established vegetation.     

A unified model of avian species richness on islands and continents

How many species in a given taxon should be found in a delimited area in a specified place in the world? Some recent literature suggests that the answer to this question depends strongly on the geographical, evolutionary, and ecological context. For example, current theory suggests that species accumulate as a function of area differently on continents and islands. Species richness-climate relationships have been examined separately on continents and on islands. This study tests the hypotheses that (1) the functional relationship between richness and climate is the same on continents and islands; (2) the species-area slope depends on distance-based isolation; (3) species-area relationships differ among land bridge islands, oceanic islands, and continents; (4) richness differs among biogeographic regions independently of climate and isolation. We related bird species numbers in a worldwide sample of 240 continental parcels and 346 islands to several environmental variables. We found that breeding bird richness varies similarly on islands and on continents as a function of mean annual temperature, an area x precipitation interaction, and the distance separating insular samples from the nearest continent (R2 = 0.86). Most studies to date have postulated that the slope of the species-area relationship depends upon isolation. In contrast, we found no such interaction. A richness-environment relationship derived using Old World sites accurately predicts patterns of richness in the New World and vice versa (R2 = 0.85). Our results suggest that most of the global variation in richness is not strongly context-specific; rather, it reflects a small number of general environmental constraints operating on both continents and islands.     

On the relationship between regional and local species richness: a test of saturation theory

What are the local community consequences of changes in regional species richness and composition? To answer this question we followed the assembly of microarthropod communities in defaunated areas of moss, embedded in a larger moss "region." Regions were created by combining moss from spatially distinct sites, resulting in regional species pools that differed in both microarthropod richness and composition, but not area. Regional effects were less important than seasonality for local richness. Initial differences in regional richness had no direct effect on local species richness at any time along a successional gradient of 0.5-16 months. The structure of the regional pool affected both local richness and local composition, but these effects were seasonally dependent. Local species richness differed substantially between dates along the successional gradient and continued to increase 16 months after assembly began. To the best of our knowledge, this is the first critical test of saturation theory that experimentally manipulates regional richness. Further, our results failed to support the most important mechanisms proposed to explain the local richness-regional richness relationship. The results demonstrate that complicated interactions between assembly time, seasonality, and regional species pools contribute to structuring local species richness and composition in this community.     

Modifying native and exotic species richness correlations: the influence of fire and seed addition.

An important goal in restoration is to increase the richness of native species while reducing exotic species. However, native species richness is often positively correlated with exotic species richness. In a grassland-savanna system in Michigan (USA), we show that management that focuses on changing the nature of the exotic-native richness relationship can be used to restore native communities. Native and exotic species richnesses were positively correlated, likely due to a shared coupling with aboveground live biomass (a surrogate for productivity). The addition of native seed shifted the exotic-native richness relationship from a linear positive to a monotonic relationship: in areas of intermediate levels of exotic species richness, seed addition increased native diversity without an associated effect on exotic diversity, but in areas of high or low exotic richness, it did not affect native species richness. Prescribed burning broke the correlation between native and exotic richness with no consistent effect on the richness of either group. However, when burning was combined with native-seed addition, the relationship between native and exotic richness was maintained and was shifted upwards, enhancing native recruitment. Although aboveground productivity was strongly related to species richness across the landscape, changes in productivity did not drive these shifts.     

Combining geodiversity with climate and topography to account for threatened species richness

Understanding threatened species diversity is important for long‐term conservation planning. Geodiversity—the diversity of Earth surface materials, forms, and processes—may be a useful biodiversity surrogate for conservation and have conservation value itself. Geodiversity and species richness relationships have been demonstrated; establishing whether geodiversity relates to threatened species’ diversity and distribution pattern is a logical next step for conservation. We used 4 geodiversity variables (rock‐type and soil‐type richness, geomorphological diversity, and hydrological feature diversity) and 4 climatic and topographic variables to model threatened species diversity across 31 of Finland's national parks. We also analyzed rarity‐weighted richness (a measure of site complementarity) of threatened vascular plants, fungi, bryophytes, and all species combined. Our 1‐km² resolution data set included 271 threatened species from 16 major taxa. We modeled threatened species richness (raw and rarity weighted) with boosted regression trees. Climatic variables, especially the annual temperature sum above 5 °C, dominated our models, which is consistent with the critical role of temperature in this boreal environment. Geodiversity added significant explanatory power. High geodiversity values were consistently associated with high threatened species richness across taxa. The combined effect of geodiversity variables was even more pronounced in the rarity‐weighted richness analyses (except for fungi) than in those for species richness. Geodiversity measures correlated most strongly with species richness (raw and rarity weighted) of threatened vascular plants and bryophytes and were weakest for molluscs, lichens, and mammals. Although simple measures of topography improve biodiversity modeling, our results suggest that geodiversity data relating to geology, landforms, and hydrology are also worth including. This reinforces recent arguments that conserving nature's stage is an important principle in conservation.     

Maximum species richness at intermediate frequencies of disturbance: consistency among levels of productivity

Development of a mechanistic understanding and predictions of patterns of biodiversity is a central theme in ecology. One of the most influential theories, the intermediate disturbance hypothesis (IDH), predicts maximum diversity at intermediate levels of disturbance frequency. The dynamic equilibrium model (DEM), an extension of the IDH, predicts that the level of productivity determines at what frequency of disturbance maximum diversity occurs. To test, and contrast, the predictions of these two models, a field experiment on marine hard-substratum assemblages was conducted with seven levels of disturbance frequency and three levels of nutrient availability. Consistent with the IDH, maximum diversity, measured as species richness, was observed at an intermediate frequency of disturbance. Despite documented effects on productivity, the relationship between disturbance and diversity was not altered by the nutrient treatments. Thus, in this system the DEM did not improve the understanding of patterns of diversity compared to the IDH. Furthermore, it is suggested that careful consideration of measurements and practical definitions of productivity in natural assemblages is necessary for a rigorous test of the DEM.     

The influence of productivity on the species richness of plants: a critical assessment

Despite much scrutiny the relationship between productivity and species richness remains controversial, and there is little agreement about causal processes. We present the results of a survey of 159 productivity-plant species richness (P-PSR) relationships from 131 published studies. We critically assessed each study with respect to experimental design and for the appropriateness of the surrogates used for productivity. We were able to accept only 60 of the reported relationships as robust tests of the P-PSR relationship and a further 18 as robust tests of the biomass species richness relationship. Previous analyses have found that unimodal P-PSR relationships predominate. In contrast, we found that, in studies that used data of continental to global extent, all P-PSR relationships were positive regardless of grain, that almost all were also positive in data sets of regional extent, and that unimodal relationships were not dominant even in studies of fine grain or small spatial extent. Our results differ substantially from previous meta-analyses because previous studies have included a large number of studies that do not meet basic experimental design criteria for objectively testing P-PSR relationships. These results have important implications for theory that attempts to explain species richness patterns. We critically review four dominant theories in light of our results and develop new falsifiable predictions of relationship from these theories at both small and large spatial scales.     

The age of island-like habitats impacts habitat specialist species richness

While the effects of contemporaneous local environment on species richness have been repeatedly documented, much less is known about historical effects, especially over large temporal scales. Using fen sites in the Western Carpathian Mountains with known radiocarbon-dated ages spanning Late Glacial to modern times (16 975-270 cal years before 2008), we have compiled richness data from the same plots for three groups of taxa with contrasting dispersal modes: (1) vascular plants, which have macroscopic propagules possessing variable, but rather low, dispersal abilities; (2) bryophytes, which have microscopic propagules that are readily transported long distances by air; and (3) terrestrial and freshwater mollusks, which have macroscopic individuals with slow active migration rates, but which also often possess high passive dispersal abilities. Using path analysis we tested the relationships between species richness and habitat age, area, isolation, and altitude for these groups. When only matrix-derived taxa were considered, no significant positive relation was noted between species richness and habitat size or age. When only calcareous-fen specialists were considered, however, habitat age was found to significantly affect vascular plant richness and, marginally, also bryophyte richness, whereas mollusk richness was significantly affected by habitat area. These results suggest that in inland insular systems only habitat specialist (i.e., interpatch disperser and/or relict species) richness is influenced by habitat age and/or area, with habitat age becoming more important as species dispersal ability decreases.     

Aquatic plant community invasibility and scale-dependent patterns in native and invasive species richness

Invasive species richness often is negatively correlated with native species richness at the small spatial scale of sampling plots, but positively correlated in larger areas. The pattern at small scales has been interpreted as evidence that native plants can competitively exclude invasive species. Large-scale patterns have been understood to result from environmental heterogeneity, among other causes. We investigated species richness patterns among submerged and floating-leaved aquatic plants (87 native species and eight invasives) in 103 temperate lakes in Connecticut (northeastern USA) and found neither a consistently negative relationship at small (3-m2) scales, nor a positive relationship at large scales. Native species richness at sampling locations was uncorrelated with invasive species richness in 37 of the 60 lakes where invasive plants occurred; richness was negatively correlated in 16 lakes and positively correlated in seven. No correlation between native and invasive species richness was found at larger spatial scales (whole lakes and counties). Increases in richness with area were uncorrelated with abiotic heterogeneity. Logistic regression showed that the probability of occurrence of five invasive species increased in sampling locations (3 m2, n = 2980 samples) where native plants occurred, indicating that native plant species richness provided no resistance against invasion. However, the probability of three invasive species' occurrence declined as native plant density increased, indicating that density, if not species richness, provided some resistance with these species. Density had no effect on occurrence of three other invasive species. Based on these results, native species may resist invasion at small spatial scales only in communities where density is high (i.e., in communities where competition among individuals contributes to community structure). Most hydrophyte communities, however, appear to be maintained in a nonequilibrial condition by stress and/or disturbance. Therefore, most aquatic plant communities in temperate lakes are likely to be vulnerable to invasion.     

Generalised Additive Models and Random Forest Approach as effective methods for predictive species density and functional species richness

Environmental and Ecological Statistics - Species distribution modelling (SDM) is a family of statistical methods where species occurrence/density/richness are combined with environmental...     

Relationships between species richness, evenness, and abundance in a southwestern savanna

Species richness and evenness are components of biological diversity that may or may not be correlated with one another and with patterns of species abundance. We compared these attributes among flowering plants, grasshoppers, butterflies, lizards, summer birds, winter birds, and rodents across 48 plots in the grasslands and mesquite-oak savannas of southeastern Arizona. Species richness and evenness were uncorrelated or weakly negatively correlated for each taxonomic group, supporting the conclusion that richness alone is an incomplete measure of diversity. In each case, richness was positively correlated with one or more measures of abundance. By contrast, evenness usually was negatively correlated with the abundance variables, reflecting the fact that plots with high evenness generally were those where all species present were about equally uncommon. Therefore richness, but not evenness, usually was a positive predictor of places of conservation value, if these are defined as places where species of interest are especially abundant. Species diversity was more positively correlated with evenness than with richness among grasshoppers and flowering plants, in contrast to the other taxonomic groups, and the positive correlations between richness and abundance were comparatively weak for grasshoppers and plants as well. Both of these differences can be attributed to the fact that assemblages of plants and grasshoppers were numerically dominated by small subsets of common species (grasses and certain spur-throated grasshoppers) whose abundances differed greatly among plots in ways unrelated to species richness of the groups as a whole.     

Interactive effects of disturbance and dispersal directionality on species richness and composition in metacommunities

Dispersal among ecological communities is usually assumed to be random in direction, or to vary in distance or frequency among species. However, a variety of natural systems and types of organisms may experience dispersal that is biased by directional currents or by gravity on hillslopes. We developed a general model for competing species in metacommunities to evaluate the role of directionally biased dispersal on species diversity, abundance, and traits. In parallel, we tested the role of directionally biased dispersal on communities in a microcosm experiment with protists and rotifers. Both the model and experiment independently demonstrated that diversity in local communities was reduced by directionally biased dispersal, especially dispersal that was biased away from disturbed patches. Abundance of species (and composition) in local communities was a product of disturbance intensity but not dispersal directionality. High disturbance selected for species with high intrinsic growth rates and low competitive abilities. Overall, our conclusions about the key role of dispersal directionality in (meta)communities seem robust and general, since they were supported both by the model, which was set in a general framework and not parameterized to fit to a specific system, and by a specific experimental test with microcosms.