Scale dependence in plant biodiversity

Bottom-up global biodiversity metrics needed for businesses to assess and manage their impact

Ensuring that companies can assess and manage their impacts on biodiversity will be crucial to solving the current biodiversity crisis, and regulatory and public pressure to disclose these impacts is increasing. Top-down intactness metrics (e.g., Mean Species Abundance) can be valuable for generating high-level or first-tier assessments of impact risk but do not provide sufficient precision or guidance for companies, regulators, or third-party assessors. New metrics based on bottom-up assessments of biodiversity (e.g., the Species Threat Abatement and Restoration metric) can accommodate spatial variation of biodiversity and provide more specific guidance for actions to avoid, reduce, remediate, and compensate for impacts and to identify positive opportunities.

Floristic Richness in a Mediterranean Hotspot: A Journey across Italy

Species richness is a fundamental property of biodiversity patterns and is properly expressed by the species-area relationship (SAR), namely the increase in the number of species with the area. Here, we studied and explored the species-area relationship with respect to vascular plant species in Italy and compared vascular plant richness among Italian administrative regions. Concerning the entire vascular flora (native and alien), the best-performing formula is the Arrhenius' Power function: S = c Az. The constants of this function are c = 241.2 and z = 0.281. The best-performing formula concerning just native (c = 245.2 and z = 0.263) and alien (c = 10.1 and z = 0.404) richness is the Power function as well. The floristically richest Italian regions considering the entire flora are Liguria, Friuli Venezia Giulia, and Trentino-Alto Adige, which are also the regions that are richest in alien flora unfortunately. Regions of particular naturalistic interest are Abruzzo, Valle d'Aosta, and Molise, because only these three regions exhibit native floristic richness that is higher than expected, and this is coupled with an alien floristic richness that is lower than expected. On the contrary, four regions (Lombardia, Veneto, Toscana, and Emilia-Romagna) show potentially severe conservation problems due to biological invasions since they experience native floristic richness that is lower than expected, with an alien floristic richness that is higher than expected. This study offers for the first time the 'c' and 'z' constants specifically calibrated at the national level for Italian vascular flora. The availability of such constants allows the calculation of the number of expected species for a given area to be investigated, providing a robust starting hypothesis for floristic studies.

Scale dependence of urban green space cooling efficiency: A case study in Beijing metropolitan area

Urban Green Space (UGS), providing environmental, social and economic benefits simultaneously, has been regarded as a cost-effective Nature-based Solution (NbS) to combat the effects of urban heat island (UHI). Under the dual pressure of increasing demand for limited land resources and mitigating UHI, how to scientifically and effectively use the limited space to obtain the maximum cooling efficiency (scaling of cooling intensity and UGS size) is an important component of strategic urban green planning. However, the scale dependence of UGS cooling effect has not yet been sufficiently quantified, particularly with respect to involving small and medium size UGS. Here, we explored the size-dependent UGS cooling efficiency in Beijing using 10,003 UGS patches extracted from high-resolution remote sensing images. We found that 5922 UGS (59.20 %) exhibited a "cooling island effect", the cooling service of UGS could reduce land surface temperature by 0.06 ± 0.05 °C to 3.81 ± 1.01 °C, and the cooling intensity enhanced nonlinearly with increasing size and closely related to the complexity of UGS shape and vegetation quality. We further showed that the cooling efficiency of small, medium and large UGS was -0.004 ± 0.03 (n = 2201), 0.79 ± 0.01 (n = 3570), 0.19 ± 0.03 (n = 151), respectively, suggesting that strategic urban greening to combat urban heat should target on increasing medium-sized UGS and managing the layout of green space. These findings emphasize the significance of considering and further exploring the scale dependence of UGS cooling effect in mitigating urban heat.

The contribution of plant life and growth forms to global gradients of vascular plant diversity

Plant life and growth forms (shortened to 'plant forms') represent key functional strategies of plants in relation to their environment and provide important insights into the ecological constraints acting on the distribution of biodiversity. Despite their functional importance, how the spectra of plant forms contribute to global gradients of plant diversity is unresolved. Using a novel dataset comprising > 295 000 species, we quantify the contribution of different plant forms to global gradients of vascular plant diversity. Furthermore, we establish how plant form distributions in different biogeographical regions are associated with contemporary and paleoclimate conditions, environmental heterogeneity and phylogeny. We find a major shift in representation of woody perennials in tropical latitudes to herb-dominated floras in temperate and boreal regions, following a sharp latitudinal gradient in plant form diversity from the tropics to the poles. We also find significant functional differences between regions, mirroring life and growth form responses to environmental conditions, which is mostly explained by contemporary climate (18-87%), and phylogeny (6-62%), with paleoclimate and heterogeneity playing a lesser role (< 23%). This research highlights variation in the importance of different plant forms to diversity gradients world-wide, shedding light on the ecological and evolutionary pressures constraining plant-trait distributions.

On the shape and origins of the freshwater species-area relationship

The species-area relationship (SAR) has over a 150-year-long history in ecology, but how its shape and origins vary across scales and organisms remains incompletely understood. This is the first subcontinental freshwater study to examine both these properties of the SAR in a spatially explicit way across major organismal groups (diatoms, insects, and fish) that differ in body size and dispersal capacity. First, to describe the SAR shape, we evaluated the fit of three commonly used models, logarithmic, power, and Michaelis-Menten. Second, we proposed a hierarchical framework to explain the variability in the SAR shape, captured by the parameters of the SAR model. According to this framework, scale and species group were the top predictors of the SAR shape, climatic factors (heterogeneity and median conditions) represented the second predictor level, and metacommunity properties (intraspecific spatial aggregation, γ-diversity, and species abundance distribution) the third predictor level. We calculated the SAR as a sample-based rarefaction curve using 60 streams within landscape windows (scales) in the United States, ranging from 160,000 to 6,760,000 km² . First, we found that all models provided good fits (R²  ≥ 0.93), but the frequency of the best-fitting model was strongly dependent on organism, scale, and metacommunity properties. The Michaelis-Menten model was most common in fish, at the largest scales, and at the highest levels of intraspecific spatial aggregation. The power model was most frequent in diatoms and insects, at smaller scales, and in metacommunities with the lowest evenness. The logarithmic model fit best exclusively at the smallest scales and in species-poor metacommunities, primarily fish. Second, we tested our framework with the parameters of the most broadly used SAR model, the log-log form of the power model, using a structural equation model. This model supported our framework and revealed that the SAR slope was best predicted by scale- and organism-dependent metacommunity properties, particularly spatial aggregation, whereas the intercept responded most strongly to species group and γ-diversity. Future research should investigate from the perspective of our framework how shifts in metacommunity properties due to climate change may alter the SAR.

Does Ungulate Herbivory Translate into Diversity of Woody Plants? A Long-Term Study in a Montane Forest Ecosystem in Austria

Different species-specific traits of woody plant species, feeding preferences of herbivores together with resulting effects on plant competition are expected to translate into different plant community structures and expressions of biodiversity. We studied the diversity of woody plant species (trees and shrubs) and structural diversity of forest trees, using a 30-year and an 18-year dataset of ungulate exclosure-control plot pairs in a mixed alpine forest community in Austria. We surveyed the tallest individuals per tree species and plot and analyzed the collective of top-height individuals per plot pair. Incidence data for exclosure and control plots were aggregated. Comparing species diversity and diversity of height classes on the plots throughout time, we calculated diversity profiles based on Hill numbers. Diversity of top height individuals and structural diversity, expressed by height classes, were two diversity aspects that differed between exclosures and control plots. Other diversity estimates of woody plant species showed huge variation without significant differences between plots. Height growth was significantly suppressed by ungulate herbivory. Effects of ungulate herbivores in forest ecosystems are highly complex and context-dependent and thus not reducible to simple top-down forces. Long-term surveys provide data that reflect “ultimate” effects of herbivory interacting with other drivers of community dynamics.

Urban biotic homogenization: Approaches and knowledge gaps

Urbanization is restructuring ecosystems at an unprecedented pace, with complex and profound consequences for life on Earth. One of the hypothesized trajectories of urban ecosystems and species communities is biotic homogenization, possibly leading to very similar species assemblages in cities across the globe. Urbanization can, however, also have the opposite effect: biotic diversification, with cities, at least at the local scale, becoming biologically more diverse, mainly as a consequence of high species introduction rates and habitat diversification. Applying the hierarchy-of-hypotheses approach, we systematically map and structure the comprehensive body of literature on the urban biotic homogenization (UBH) hypothesis, comprising 225 individual studies (i.e., tests of the hypothesis) retrieved from 145 publications. The UBH hypothesis is studied at multiple levels with a multitude of approaches and underlying assumptions. We show that UBH is generally used with two very different connotations: about half of the studies investigated a potential increase in community similarity across cities, whereas the other half investigated biotic homogenization within cities, the latter being supported more frequently. We also found strong research biases: (1) a taxonomic bias towards birds and plants, (2) a bias towards small and medium distances (<5000 km) in comparisons across cities, (3) a dominance of studies substituting space for time versus true temporal studies, (4) a strong focus on terrestrial versus aquatic systems, (5) more extraurban (including periurban) areas than natural or rural ecosystems for comparison to urban systems, (6) a bias towards taxonomic versus functional, phylogenetic, and temporal homogenization, and (7) more studies undertaken in Europe and North America than in other continents. The overall level of empirical support for the UBH hypothesis was mixed, with 55% of the studies reporting supporting evidence. Results significantly differed when a natural/nature reserve, an extraurban, or rural/agricultural area served as reference to infer biotic homogenization, with homogenization being detected least frequently when urban systems were compared to agricultural, i.e., other anthropogenically influenced, study sites. We provide an evidence map and a bibliographic network and identify key references on UBH with the goal to enhance accessibility and orientation for future research on this topic.

Complex ecological and socioeconomic impacts on medicinal plant diversity

Medicinal plant diversity (MPD) is an important component of plant diversity. Over-collection based on medicinal and economic value has the potential to damage the stability of the regional ecosystem. It is important to understand the current distribution of MPD and the factors influencing it. However, it is still unclear whether environmental and socioeconomic conditions have an impact on their distribution. We selected the Inner Mongolia as a representative study area which covers a wide area, accounting for 12.29% of China’s national land area and 0.79% of the world’s land area. At the same time, the region is a long-standing traditional medicinal area for Mongolians in China. Therefore, the region is significantly influenced by changes in environmental factors and socio-economic factors. We used 9-years field survey of the distribution of medicinal plants in Inner Mongolia for assessing the distribution of MPD as influenced by environmental and socioeconomic activities by combining spatial analyses, species distribution models, and generalized additive models. The results from the spatial analysis show that the western region of Inner Mongolia is the main cold spot area of the MPD, and the central-eastern and northeastern regions of Inner Mongolia are the main hot spot areas of the MPD. At the same time, the distribution of cold spots and hot spots of MPD is more obvious at large spatial scales, and with the refinement of spatial scales, the cold spots in scattered areas are gradually revealed, which is indicative for the conservation and development of MPD at different spatial scales. Under the future climate change of shared socioeconomic pathways (SSP), areas with high habitat suitability for medicinal plants remain mainly dominated by the Yellow River, Yin Mountains, and Greater Khingan Range. Notably, the SSP245 development pathway remains the most significant concern in either long- or short-term development. The nonlinear relationship between the driving factors of MPD at different spatial scales shows that temperature, precipitation and socioeconomic development do have complex effects on MPD. The presence of a certain temperature, altitude, and precipitation range has an optimal facilitation effect on MPD, rather than a single facilitation effect. This complex nonlinear correlation provides a reference for further studies on plant diversity and sustainable development and management. In this study, the spatial distribution of medicinal plant resources and the extent to which they are driven by ecological and socioeconomic factors were analyzed through a macroscopic approach. This provides a reference for larger-scale studies on the environmental and socioeconomic influences on the distribution of plant resources.

Global patterns of vascular plant alpha diversity

Global patterns of regional (gamma) plant diversity are relatively well known, but whether these patterns hold for local communities, and the dependence on spatial grain, remain controversial. Using data on 170,272 georeferenced local plant assemblages, we created global maps of alpha diversity (local species richness) for vascular plants at three different spatial grains, for forests and non-forests. We show that alpha diversity is consistently high across grains in some regions (for example, Andean-Amazonian foothills), but regional 'scaling anomalies' (deviations from the positive correlation) exist elsewhere, particularly in Eurasian temperate forests with disproportionally higher fine-grained richness and many African tropical forests with disproportionally higher coarse-grained richness. The influence of different climatic, topographic and biogeographical variables on alpha diversity also varies across grains. Our multi-grain maps return a nuanced understanding of vascular plant biodiversity patterns that complements classic maps of biodiversity hotspots and will improve predictions of global change effects on biodiversity.

Relationship between diversity and stability of a karst plant community

The relationships among species diversity, functional diversity, functional redundancy, and community stability are central to community and ecosystem ecology. In this paper, a "space substitution for time" approach is used to study the plant communities at different stages of the natural recovery process of degraded karst vegetation on the karst plateau of Guizhou. These restoration stages include the herbaceous stage, herbaceous and shrub transition stage, shrub stage, tree and shrub transition stage, and tree stage. We calculated the functional diversity and functional redundancy of the community based on functional characteristics and mediated the relationship between functional diversity, functional redundancy, and stability of the plant community through changes in functional diversity and functional redundancy. This study aims to reveal the mechanisms of changes in species diversity and community stability and thus further reveals the intrinsic reasons for maintaining the stability of karst plant communities. The most important results include the following: (1) Species diversity, functional redundancy, and stability gradually increased with restoration, and there were significant differences among the different stages; functional diversity increased at first and then decreased, and reached the highest level at the tree and shrub transition stage; (2) Plant height and specific leaf area were functional traits that influenced the diversity and stability of the plant community, with plant height being positively correlated with plant community diversity and stability, and specific leaf area being negatively correlated with plant community diversity and stability; (3) During the community's recovery, functional diversity and functional redundancy interacted to maintain stability. In the early and late stages of recovery, the effect of functional redundancy on stability was greater than that of functional diversity, but it was the opposite in the middle stages; (4) The tree and shrub transition stage is the likely point at which the functional diversity of plant communities in karst areas reaches saturation, and the growth rate of functional redundancy after functional diversity saturation is greater than that before saturation. Overall, community stability increased with species diversity; habitat heterogeneity increased functional diversity in the early stages of recovery; and habitat homogeneity increased functional redundancy.

Assessing the Impact of Soil on Species Diversity Estimation Based on UAV Imaging Spectroscopy in a Natural Alpine Steppe

Grassland species diversity monitoring is essential to grassland resource protection and utilization. “Spectral variation hypothesis” (SVH) provides a remote sensing method for monitoring grassland species diversity at pixel scale by calculating spectral heterogeneity. However, the pixel spectrum is easily affected by soil and other background factors in natural grassland. Unmanned aerial vehicle (UAV)-based imaging spectroscopy provides the possibility of soil information removal by virtue of its high spatial and spectral resolution. In this study, UAV-imaging spectroscopy data with a spatial resolution of 0.2 m obtained in two sites of typical alpine steppe within the Sanjiangyuan National Nature Reserve were used to analyze the relationships between four spectral diversity metrics (coefficient of variation based on NDVI (CVNDVI), coefficient of variation based on multiple bands (CVMulti), minimum convex hull volume (CHV) and minimum convex hull area (CHA)) and two species diversity indices (species richness and the Shannon–Wiener index). Meanwhile, two soil removal methods (based on NDVI threshold and the linear spectral unmixing model) were used to investigate the impact of soil on species diversity estimation. The results showed that the Shannon–Wiener index had a better response to spectral diversity than species richness, and CVMulti showed the best correlation with the Shannon–Wiener index between the four spectral diversity metrics after removing soil information using the linear spectral unmixing model. It indicated that the estimation ability of spectral diversity to species diversity was significantly improved after removing the soil information. Our findings demonstrated the applicability of the spectral variation hypothesis in natural grassland, and illustrated the impact of soil on species diversity estimation.

Small-scale drivers on plant and ant diversity in a grassland habitat through a multifaceted approach

Semi-natural grasslands are characterized by high biodiversity and require multifaceted approaches to monitor their biodiversity. Moreover, grasslands comprise a multitude of microhabitats, making the scale of investigation of fundamental importance. Despite their wide distribution, grasslands are highly threatened and are considered of high conservation priority by Directive no. 92/43/EEC. Here, we investigate the effects of small-scale ecological differences between two ecosites present within the EU habitat of Community Interest of semi-natural dry grasslands on calcareous substrates (6210 according to Dir. 92/43/EEC) occurring on a Mediterranean mountain. We measured taxonomic and functional diversity of plant and ant communities, evaluating the differences among the two ecosites, how these differences are influenced by the environment and whether vegetation affects composition of the ant community. Our results show that taxonomic and functional diversity of plant and ant communities are influenced by the environment. While vegetation has no effect on ant communities, we found plant and ant community composition differed across the two ecosites, filtering ant and plant species according to their functional traits, even at a small spatial scale. Our findings imply that small-scale monitoring is needed to effectively conserve priority habitats, especially for those that comprise multiple microhabitats.

Biodiversity at the global scale: the synthesis continues

Traditionally, the generation and use of biodiversity data and their associated specimen objects have been primarily the purview of individuals and small research groups. While deposition of data and specimens in herbaria and other repositories has long been the norm, throughout most of their history, these resources have been accessible only to a small community of specialists. Through recent concerted efforts, primarily at the level of national and international governmental agencies over the last two decades, the pace of biodiversity data accumulation has accelerated, and a wider array of biodiversity scientists has gained access to this massive accumulation of resources, applying them to an ever-widening compass of research pursuits. We review how these new resources and increasing access to them are affecting the landscape of biodiversity research in plants today, focusing on new applications across evolution, ecology, and other fields that have been enabled specifically by the availability of these data and the global scope that was previously beyond the reach of individual investigators. We give an overview of recent advances organized along three lines: broad-scale analyses of distributional data and spatial information, phylogenetic research circumscribing large clades with comprehensive taxon sampling, and data sets derived from improved accessibility of biodiversity literature. We also review synergies between large data resources and more traditional data collection paradigms, describe shortfalls and how to overcome them, and reflect on the future of plant biodiversity analyses in light of increasing linkages between data types and scientists in our field.

Scale gaps in landscape phenology: challenges and opportunities

Phenology, or the timing of life history events, can be heterogeneous across biological communities and landscapes and can vary across a wide variety of spatiotemporal scales. Here, we synthesize information from landscape phenology studies across different scales of measurement around a set of core concepts. We highlight why phenology is scale dependent and identify gaps in the spatiotemporal scales of phenological observations and inferences. We discuss the consequences of these gaps and describe opportunities to address the inherent sensitivities of phenological metrics to measurement scale. Although most studies we review and discuss are focused on plants, our work provides a broadly relevant overview of the role of observation scale in landscape phenology and a general approach for measuring and reporting scale dependence.

Spatial scaling of plant and bird diversity from 50 to 10,000 ha in a lowland tropical rainforest

While there are numerous studies of diversity patterns both within local communities and at regional scales, the intermediate scale of tens to thousands of km² is often neglected. Here we present detailed local data on plant communities (using 20 × 20 m plots) and bird communities (using point counts) for a 50 ha ForestGEO plot in lowland rainforest at Wanang, Papua New Guinea. We compare these local diversity patterns with those documented in the surrounding 10,000 ha of lowland rainforest. Woody plant species richness was lower within 50 ha (88% of 10,000 ha richness), even when both were surveyed with identical sampling effort. In contrast, bird communities exhibited identical species accumulation patterns at both spatial scales. Similarity in species composition (Chao-Jaccard) remained constant while similarity in dominance structure (Bray–Curtis) decreased with increased distance between samples across the range from < 1 to 13.8 km for both plant and bird communities. The similarity decay was more rapid in plants, but in both cases was slow. The results indicate low to zero beta-diversity at the spatial scale represented here, particularly for birds but also for woody plants. A 50 ha plot provided a highly accurate representation of broader-scale diversity and community composition within 10,000 ha for birds, and a relatively good representation for woody plants. This suggests potential for wider generalization of data from ForestGEO plots which are almost always locally unreplicated, at least for those in lowland tropical forest.

Grazing affects vegetation diversity and heterogeneity in California vernal pools

Disturbance often increases local-scale (α) diversity by suppressing dominant competitors. However, widespread disturbances may also reduce biotic heterogeneity (β diversity) by making the identities and abundances of species more similar among patches. Landscape-scale (γ) diversity may also decline if disturbance-sensitive species are lost. California's vernal pool plant communities are species rich, in part because of two scales of β diversity: (1) within pools, as species composition changes with depth (referred to here as vertical β diversity), and (2) between pools, in response to dispersal limitation and variation in pool attributes (referred to here as horizontal β diversity). We asked how grazing by livestock, a common management practice, affects vernal pool plant diversity at multiple hierarchical spatial scales. In terms of abundance-weighted diversity, grazing increased α both within local pool habitat zones and at the whole-pool scale, as well as γ at the pasture scale without influencing horizontal or vertical β diversity. In terms of species richness, increases in α diversity within habitat zones and within whole pools led to small decreases in horizontal β diversity as species occupancy increased. This had a dampened effect on species richness at the γ (pasture) scale without any loss of disturbance-sensitive species. We conclude that grazing increases species richness and evenness (α) by reducing competitive dominance, without large disruptions to the critical spatial heterogeneity (β) that generates high landscape-level diversity (γ).

Selective extinctions resulting from random habitat destruction lead to under-estimates of local and regional biodiversity loss in a manipulative field experiment

Land-use change is a significant cause of anthropogenic extinctions, which are likely to continue and accelerate as habitat conversion proceeds in most biomes. One way to understand the effects of habitat loss on biodiversity is through improved tools for predicting the number and identity of species losses in response to habitat loss. There are relatively few methods for predicting extinctions and even fewer opportunities for rigorously assessing the quality of these predictions. In this paper, we address these issues by applying a new method based on rarefaction to predict species losses after random, but aggregated, habitat loss. We compare predictions from three rarefaction models, individual-based, sample-based, and spatially clustered, to those derived from a commonly used extinction estimation method, the species-area relationship (SAR). We apply each method to a mesocosm experiment, in which we aim to predict species richness and extinctions of arthropods immediately following 50% habitat loss. While each model produced strikingly accurate predictions of species richness immediately after the habitat loss disturbance, each model significantly underestimated the number of extinctions occurring at both the local (within-mesocosm) and regional (treatment-wide) scales. Despite the stochastic nature of our small-scale, short-term, and randomly applied habitat loss experiment, we found surprisingly clear evidence for extinction selectivity, for example, when abundant species with low extinction probabilities were extirpated following habitat loss. The important role played by selective extinction even in this contrived experimental system suggests that ecologically driven, trait-based extinctions play an equally important role to stochastic extinction, even when the disturbance itself has no clear selectivity. As a result, neutrally stochastic null models such as the SAR and rarefaction are likely to underestimate extinctions caused by habitat loss. Nevertheless, given the difficulty of predicting extinctions, null models provide useful benchmarks for conservation planning by providing minimum estimates and probabilities of species extinctions.

Combining botanical collections and ecological data to better describe plant community diversity

In this age of rapid biodiversity loss, we must continue to refine our approaches to describing variation in life on Earth. Combining knowledge and research tools from multiple disciplines is one way to better describe complex natural systems. Understanding plant community diversity requires documenting both pattern and process. We must first know which species exist, and where (i.e., taxonomic and biogeographic patterns), before we can determine why they exist there (i.e., ecological and evolutionary processes). Floristic botanists often use collections-based approaches to elucidate biodiversity patterns, while plant ecologists use hypothesis-driven statistical approaches to describe underlying processes. Because of these different disciplinary histories and research goals, floristic botanists and plant ecologists often remain siloed in their work. Here, using a case study from an urban greenway in Colorado, USA, we illustrate that the collections-based, opportunistic sampling of floristic botanists is highly complementary to the transect- or plot-based sampling of plant ecologists. We found that floristic sampling captured a community species pool four times larger than that captured using ecological transects, with rarefaction and non-parametric species estimation indicating that it would be prohibitive to capture the "true" community species pool if constrained to sampling within transects. We further illustrate that the discrepancy in species pool size between approaches led to a different interpretation of the greenway's ecological condition in some cases (e.g., transects missed uncommon cultivated species escaping from nearby gardens) but not others (e.g., plant species distributions among functional groups were similar between species pools). Finally, we show that while using transects to estimate plant relative abundances necessarily trades off with a fuller assessment of the species pool, it is an indispensable indicator of ecosystem health, as evidenced by three non-native grasses contributing to 50% of plant cover along the highly modified urban greenway. We suggest that actively fostering collaborations between floristic botanists and ecologists can create new insights into the maintenance of species diversity at the community scale.

Different Predictors Shape the Diversity Patterns of Epiphytic and Non-epiphytic Liverworts in Montane Forests of Uganda

We studied the influence of regional and local variables on the liverwort diversity within natural forest vegetation of Uganda to contribute to our understanding of the mechanisms and processes determining species richness. To this end, we compared the species richness distribution patterns of epiphytic and non-epiphytic liverworts (Marchantiophytina) in 24 plots in the forests of four Ugandan national parks. We recorded a total of 119 species and subspecies from 18 families, including 16 new species records for the country. We used generalized linear models (GLMs) and the relative variable importance of regional and local climatic and environmental variables to assess their respective impact on the species diversity. We found that the richness patterns of total and epiphytic richness were largely driven by regional climatic factors related to temperature and water-availability. In contrast, species diversity of non-epiphytic and rare species was additionally strongly determined by local-scale microhabitat factors such as height of forest canopy and slope inclination, reflecting the availability of suitable microhabitats. We conclude that macroclimatic variables perform well in predicting epiphytic liverwort richness, whereas the adequate prediction of non-epiphytic richness requires site-specific variables. Also, we propose that richness of epiphytic liverworts will be impacted more directly by climate change than richness of non-epiphytic and rare species.

Análise fractal do padrão espacial de plantas em pastagem

RESUMO Avaliou-se o uso da análise fractal como ferramenta na determinação de padrões na escala de pastejo em pastagens naturais submetidas a diferentes manejos. Os tratamentos testados em Santa Maria foram: pastejo com queima, pastejo sem queima, exclusão com queima, exclusão sem queima. Em Bagé, os tratamentos avaliados foram: pastagem natural e pastagem natural com introdução de azevém, trevo-branco e cornichão. A caracterização da composição florística da pastagem foi realizada pelo método Botanal. A diversidade da pastagem foi calculada pelos índices de Shannon (H’) e equitabilidade. A informação da dimensão fractal foi calculada pela regressão entre H’(ε) e o logaritmo natural de ε, sendo a inclinação da linha a informação da dimensão fractal. Os índices de Shannon e equitabilidade demonstraram dependência em relação à área amostral, onde a maior diversidade florística e a homogeneidade da frequência de distribuição de plantas entre espécies foram observadas no intervalo amostral de 0,87 e 1,03m2. A dimensão fractal pode ser uma ferramenta na determinação de padrões na comunidade vegetal na escala reduzida de pastejo. A limitação do emprego dessa técnica para escalas reduzidas é a necessidade de um número maior de repetições.

Temperature-Dominated Driving Mechanisms of the Plant Diversity in Temperate Forests, Northeast China

Climate, topography, and tree structure have different effects on plant diversity that vary with spatial scale. In this study, we assessed the contribution of these drivers and how they affect the vascular plant richness of different functional groups in a temperate forest ecosystem in Northeast China. We investigated about 0.986 million plants from 3160 sites to quantify the impact of annual mean temperature, sunshine duration, annual precipitation, standard deviation of diameter at breast height, and forest type on richness of vascular plants (total species, tree, treelet, shrub, and herb, separately) using the gradient boosting model. The results show that annual mean temperature had the strongest impact on plant richness. The tree richness peaked at intermediate annual mean temperature and sunshine duration and increased with annual precipitation. The Shannon diversity index and Simpson dominance index increased with annual precipitation and standard deviation of diameter at breast height, decreased with sunshine duration, and peaked at intermediate annual mean temperature and forest type. The total richness and understory richness increased with annual mean temperature and standard deviation of diameter at breast height and peaked at intermediate sunshine duration and annual precipitation. A comprehensive mechanism was found to regulate the plant diversity in forest ecosystems. The relationship between tree richness and annual mean temperature with latitudinal effect could be affected by the differences in number and size of tree individuals, indicating that plant diversity varies with the utilization of energy. The force driving plant richness varied with the functional group due to the different environmental resource requirements and the life history strategies of plants layers.

Integrating Computational Methods to Investigate the Macroecology of Microbiomes

Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as “everything is everywhere, but the environment selects”) as well as applied ecological problems, such as those posed by human induced global environmental changes.

Forest Climax Phenomenon: An Invariance of Scale

We can think of forests as multiscale multispecies networks, constantly evolving toward a climax or potential natural community—the successional process-pattern of natural regeneration that exhibits sensitivity to initial conditions. This is why I look into forest succession in light of the Red Queen hypothesis and focus on the key aspects of ecological self-organisation: dynamical criticality, evolvability and intransitivity. The idea of the review is that forest climax should be associated with habitat dynamics driven by a large continuum of ecologically equivalent time scales, so that the same ecological conclusions could be drawn statistically from any scale. A synthesis of the literature is undertaken in order to (1) present the framework for assessing habitat dynamics and (2) present the types of successional trajectories based on tree regeneration mode in forest gaps. In general, there are four types of successional trajectories within the process-pattern of forest regeneration that exhibits sensitivity to initial conditions: advance reproduction specialists, advance reproduction generalists, early reproduction generalists and early reproduction specialists. A successional trajectory is an expression of a fractal connectivity among certain patterns of natural regeneration in the multiscale multispecies networks of landscape habitats. Theoretically, the organically derived measures of pattern diversity, integrity and complexity, determined by the rates of recruitment, growth and mortality of forest tree species, are the means to test the efficacy of specific interventions to avert the disturbance-related decline in forest regeneration. That is of relevance to the emerging field of biocomplexity research.

Optimizing future biodiversity sampling by citizen scientists

We are currently in the midst of Earth's sixth extinction event, and measuring biodiversity trends in space and time is essential for prioritizing limited resources for conservation. At the same time, the scope of the necessary biodiversity monitoring is overwhelming funding for professional scientific monitoring. In response, scientists are increasingly using citizen science data to monitor biodiversity. But citizen science data are ‘noisy’, with redundancies and gaps arising from unstructured human behaviours in space and time. We ask whether the information content of these data can be maximized for the express purpose of trend estimation. We develop and execute a novel framework which assigns every citizen science sampling event a marginal value, derived from the importance of an observation to our understanding of overall population trends. We then make this framework predictive, estimating the expected marginal value of future biodiversity observations. We find that past observations are useful in forecasting where high-value observations will occur in the future. Interestingly, we find high value in both ‘hotspots’, which are frequently sampled locations, and ‘coldspots’, which are areas far from recent sampling, suggesting that an optimal sampling regime balances ‘hotspot’ sampling with a spread across the landscape.

Improving big citizen science data: Moving beyond haphazard sampling

Citizen science is mainstream: millions of people contribute data to a growing array of citizen science projects annually, forming massive datasets that will drive research for years to come. Many citizen science projects implement a “leaderboard” framework, ranking the contributions based on number of records or species, encouraging further participation. But is every data point equally “valuable?” Citizen scientists collect data with distinct spatial and temporal biases, leading to unfortunate gaps and redundancies, which create statistical and informational problems for downstream analyses. Up to this point, the haphazard structure of the data has been seen as an unfortunate but unchangeable aspect of citizen science data. However, we argue here that this issue can actually be addressed: we provide a very simple, tractable framework that could be adapted by broadscale citizen science projects to allow citizen scientists to optimize the marginal value of their efforts, increasing the overall collective knowledge.

Citizen scientists collect data with distinct spatial and temporal biases, leading to unfortunate gaps and redundancies, and creating statistical and informational problems for downstream analyses. This Essay argues that by using a tractable framework which incentivizes looking, rather than finding, this issue can actually be addressed.

The influence of spatial sampling scales on ant-plant interaction network architecture

Despite great interest in metrics to quantify the structure of ecological networks, the effects of sampling and scale remain poorly understood. In fact, one of the most challenging issues in ecology is how to define suitable scales (i.e., temporal or spatial) to accurately describe and understand ecological systems. Here, we sampled a series of ant-plant interaction networks in the southern Brazilian Amazon rainforest in order to determine whether the spatial sampling scale, from local to regional, affects our understanding of the structure of these networks. To this end, we recorded ant-plant interactions in adjacent 25 × 30 m subplots (local sampling scale) nested within twelve 250 × 30 m plots (regional sampling scale). Moreover, we combined adjacent or random subplots and plots in order to increase the spatial sampling scales at the local and regional levels. We then calculated commonly used binary and quantitative network-level metrics for both sampling scales (i.e., number of species and interactions, nestedness, specialization and modularity), all of which encompass a wide array of structural patterns in interaction networks. We observed increasing species and interactions across sampling scales, and while most network descriptors remained relatively constant at the local level, there was more variation at the regional scale. Among all metrics, specialization was most constant across different spatial sampling scales. Furthermore, we observed that adjacent assembly did not generate more variation in network descriptor values compared to random assembly. This finding indicates that the spatially aggregated distribution of species/individuals and abiotic conditions does not affect the organization of these interacting assemblages. Our results have a direct impact on our empirical and theoretical understanding of the ecological dynamics of species interactions by demonstrating that small spatial sampling scales should suffice to record some patterns commonly found in ant-plant interaction networks in a highly diverse tropical rainforest.

Trade-offs in the provisioning and stability of ecosystem services in agroecosystems

Changes in land use generate trade-offs in the delivery of ecosystem services in agricultural landscapes. However, we know little about how the stability of ecosystem services responds to landscape composition, and what ecological mechanisms underlie these trade-offs. Here, we develop a model to investigate the dynamics of three ecosystem services in intensively managed agroecosystems, i.e., pollination-independent crop yield, crop pollination, and biodiversity. Our model reveals trade-offs and synergies imposed by landscape composition that affect not only the magnitude but also the stability of ecosystem service delivery. Trade-offs involving crop pollination are strongly affected by the degree to which crops depend on pollination and by their relative requirement for pollinator densities. We show conditions for crop production to increase with biodiversity and decreasing crop area, reconciling farmers' profitability and biodiversity conservation. Our results further suggest that, for pollination-dependent crops, management strategies that focus on maximizing yield will often overlook its stability. Given that agriculture has become more pollination-dependent over time, it is essential to understand the mechanisms driving these trade-offs to ensure food security.

Intensive land-use drives regional-scale homogenization of plant communities

Intensive anthropogenic land-use causes habitat loss and landscape homogenization, which leads to the decrease of biodiversity and ecosystem degradation. Therefore, it is important to study the influence of landscape heterogeneity on biodiversity. In this study, vegetation surveys conducted at 53 sites in the Tabu River basin, located at the agro-pastoral ecotone of Inner Mongolia of China, revealed 146 species. Species diversity was evaluated at three scales: species richness within patches (alpha diversity), between patches (beta diversity) and at the landscape scale (gamma diversity). We analyzed landscape heterogeneity (LH_total) and its driving factors including environmental variables (LHDF_env-var, such as precipitation and altitude), environmental heterogeneity (LHDF_env-het) and human activities (LHDF_hum). We used structural equation modeling (SEM) to evaluate the response of species richness to landscape heterogeneity at three scales and determined the relative contribution of driving factors in explaining species diversity at these scales. The results of the study are summarized as follows: 1) Alpha diversity was the dominant component of gamma diversity in the Tabu River basin in Inner Mongolia. 2) There is no significant correlation (P = 0.512) between alpha diversity and LH_total; with the increase of LH_total beta and gamma diversities showed hump-shaped relationships. 3) LHDF_env-het was the primary factor in maintaining alpha diversity, with heterogeneity of mean annual precipitation (MAP), temperature (MAT) and altitude (ALT) acting as three largest contributors. LHDF_hum primarily contributed to the maintenance of beta diversity. 4) LHDF_hum was the primary contributor to gamma diversity, and human activity exceeded threshold values for positive effects. Based on our findings we suggest liming agricultural use along the river to prevent reductions in species diversity.

Improving extinction projections across scales and habitats using the countryside species-area relationship

The species-area relationship (SAR) has been often used to project species extinctions as a consequence of habitat loss. However, recent studies have suggested that the SAR may overestimate species extinctions, at least in the short-term. We argue that the main reason for this overestimation is that the classic SAR ignores the persistence of species in human-modified habitats. We use data collected worldwide to analyse what is the fraction of bird and plant species that remain in different human-modified habitats at the local scale after full habitat conversion. We observe that both taxa have consistent responses to the different land-use types, with strongest reductions in species richness in cropland across the globe, and in pasture in the tropics. We show that the results from these studies cannot be linearly scaled from plots to large regions, as this again overestimates the impacts of land-use change on biodiversity. The countryside SAR provides a unifying framework to incorporate both the effect of species persistence in the landscape matrix and the non-linear response of the proportion of species extinctions to sampling area, generating more realistic projections of biodiversity loss.

The underlying processes of a soil mite metacommunity on a small scale

Metacommunity theory provides an understanding of how ecological processes regulate local community assemblies. However, few field studies have evaluated the underlying mechanisms of a metacommunity on a small scale through revealing the relative roles of spatial and environmental filtering in structuring local community composition. Based on a spatially explicit sampling design in 2012 and 2013, this study aims to evaluate the underlying processes of a soil mite metacommunity on a small spatial scale (50 m) in a temperate deciduous forest located at the Maoershan Ecosystem Research Station, Northeast China. Moran's eigenvector maps (MEMs) were used to model independent spatial variables. The relative importance of spatial (including trend variables, i.e., geographical coordinates, and broad- and fine-scale spatial variables) and environmental factors in driving the soil mite metacommunity was determined by variation partitioning. Mantel and partial Mantel tests and a redundancy analysis (RDA) were also used to identify the relative contributions of spatial and environmental variables. The results of variation partitioning suggested that the relatively large and significant variance was a result of spatial variables (including broad- and fine-scale spatial variables and trend), indicating the importance of dispersal limitation and autocorrelation processes. The significant contribution of environmental variables was detected in 2012 based on a partial Mantel test, and soil moisture and soil organic matter were especially important for the soil mite metacommunity composition in both years. The study suggested that the soil mite metacommunity was primarily regulated by dispersal limitation due to broad-scale and neutral biotic processes at a fine-scale and that environmental filtering might be of subordinate importance. In conclusion, a combination of metacommunity perspectives between neutral and species sorting theories was suggested to be important in the observed structure of the soil mite metacommunity at the studied small scale.

Species-area relationships and additive partitioning of diversity of native and nonnative herpetofauna of the West Indies

To evaluate the regional biogeographical patterns of West Indian native and nonnative herpetofauna, we derived and updated data on the presence/absence of all herpetofauna in this region from the recently published reviews. We divided the records into 24 taxonomic groups and classified each species as native or nonnative at each locality. For each taxonomic group and in aggregate, we then assessed the following: (1) multiple species-area relationship (SAR) models; (2) C- and Z-values, typically interpreted to represent insularity or dispersal ability; and (3) the average diversity of islands, among-island heterogeneity, γ-diversity, and the contribution of area effect toward explaining among-island heterogeneity using additive diversity partitioning approach. We found the following: (1) SARs were best modeled using the Cumulative Weibull and Lomolino relationships; (2) the Cumulative Weibull and Lomolino regressions displayed both convex and sigmoid curves; and (3) the Cumulative Weibull regressions were more conservative than Lomolino at displaying sigmoid curves within the range of island size studied. The Z-value of all herpetofauna was overestimated by Darlington (Zoogeography: The geographic distribution of animals, John Wiley, New York, 1957), and Z-values were ranked: (1) native > nonnative; (2) reptiles > amphibians; (3) snake > lizard > frog > turtle > crocodilian; and (4) increased from lower- to higher-level taxonomic groups. Additive diversity partitioning showed that area had a weaker effect on explaining the among-island heterogeneity for nonnative species than for native species. Our findings imply that the flexibility of Cumulative Weibull and Lomolino has been underappreciated in the literature. Z-value is an average of different slopes from different scales and could be artificially overestimated due to oversampling islands of intermediate to large size. Lower extinction rate, higher colonization, and more in situ speciation could contribute to high richness of native species on large islands, enlarging area effect on explaining the between-island heterogeneity for native species, whereas economic isolation on large islands could decrease the predicted richness, lowering the area effect for nonnative species. For most of the small islands less affected by human activities, extinction and dispersal limitation are the primary processes producing low species richness pattern, which decreases the overall average diversity with a large among-island heterogeneity corresponding to the high value of this region as a biodiversity hotspot.

Altitudinal patterns of plant diversity on the Jade Dragon Snow Mountain, southwestern China

Background

Understanding altitudinal patterns of biological diversity and their underlying mechanisms is critically important for biodiversity conservation in mountainous regions. The contribution of area to plant diversity patterns is widely acknowledged and may mask the effects of other determinant factors. In this context, it is important to examine altitudinal patterns of corrected taxon richness by eliminating the area effect. Here we adopt two methods to correct observed taxon richness: a power-law relationship between richness and area, hereafter “method 1”; and richness counted in equal-area altitudinal bands, hereafter “method 2”. We compare these two methods on the Jade Dragon Snow Mountain, which is the nearest large-scale altitudinal gradient to the Equator in the Northern Hemisphere.

Results

We find that seed plant species richness, genus richness, family richness, and species richness of trees, shrubs, herbs and Groups I–III (species with elevational range size <150, between 150 and 500, and >500 m, respectively) display distinct hump-shaped patterns along the equal-elevation altitudinal gradient. The corrected taxon richness based on method 2 (TRcor₂) also shows hump-shaped patterns for all plant groups, while the one based on method 1 (TRcor₁) does not. As for the abiotic factors influencing the patterns, mean annual temperature, mean annual precipitation, and mid-domain effect explain a larger part of the variation in TRcor₂ than in TRcor₁.

Conclusions

In conclusion, for biodiversity patterns on the Jade Dragon Snow Mountain, method 2 preserves the significant influences of abiotic factors to the greatest degree while eliminating the area effect. Our results thus reveal that although the classical method 1 has earned more attention and approval in previous research, method 2 can perform better under certain circumstances. We not only confirm the essential contribution of method 1 in community ecology, but also highlight the significant role of method 2 in eliminating the area effect, and call for more application of method 2 in further macroecological studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s40064-016-3052-1) contains supplementary material, which is available to authorized users.

Disentangling vegetation diversity from climate-energy and habitat heterogeneity for explaining animal geographic patterns

Broad-scale animal diversity patterns have been traditionally explained by hypotheses focused on climate-energy and habitat heterogeneity, without considering the direct influence of vegetation structure and composition. However, integrating these factors when considering plant-animal correlates still poses a major challenge because plant communities are controlled by abiotic factors that may, at the same time, influence animal distributions. By testing whether the number and variation of plant community types in Europe explain country-level diversity in six animal groups, we propose a conceptual framework in which vegetation diversity represents a bridge between abiotic factors and animal diversity. We show that vegetation diversity explains variation in animal richness not accounted for by altitudinal range or potential evapotranspiration, being the best predictor for butterflies, beetles, and amphibians. Moreover, the dissimilarity of plant community types explains the highest proportion of variation in animal assemblages across the studied regions, an effect that outperforms the effect of climate and their shared contribution with pure spatial variation. Our results at the country level suggest that vegetation diversity, as estimated from broad-scale classifications of plant communities, may contribute to our understanding of animal richness and may be disentangled, at least to a degree, from climate-energy and abiotic habitat heterogeneity.

Water level effect on herbaceous plant assemblages at an artificial reservoir-Lago Azul State Park, Southern Brazil

This study presents the effect of water level variation on the assemblages of herbaceous species in Mourão I Reservoir, Lago Azul State Park, Southern Brazil. The structure and distribution of populations was examined in February (dry period) and April (rainy period), 2011, in two transects. These transects started at the forest edge towards the center of the lake. The end of the transect coincided with the end of the plants within the lake. On every two meters along of the transects we sampled a wooden square of 0.25 m(2) for species biomass analysis.The macrophyte stand was composed entirely of emergent species. Considering the periods, most species were less frequent in the rainy period (April), but Ipomea ramosissima (Poir.) Choisy, Commelina nudiflora L., Eleocharis acuntagula (Roxb.) Schult. and Verbena litorales (Kunth.) had their frequency increased during this period, probably due to their resistance. The influence of flood as measured by the NMDS point out that both before and after the flood, there are plots with distinct compositions and biomass. The water level variation affects the dynamics of plant composition and structure in marginal areas of the Reservoir.

Future habitat loss and extinctions driven by land-use change in biodiversity hotspots under four scenarios of climate-change mitigation

Numerous species have been pushed into extinction as an increasing portion of Earth's land surface has been appropriated for human enterprise. In the future, global biodiversity will be affected by both climate change and land-use change, the latter of which is currently the primary driver of species extinctions. How societies address climate change will critically affect biodiversity because climate-change mitigation policies will reduce direct climate-change impacts; however, these policies will influence land-use decisions, which could have negative impacts on habitat for a substantial number of species. We assessed the potential impact future climate policy could have on the loss of habitable area in biodiversity hotspots due to associated land-use changes. We estimated past extinctions from historical land-use changes (1500-2005) based on the global gridded land-use data used for the Intergovernmental Panel on Climate Change Fifth Assessment Report and habitat extent and species data for each hotspot. We then estimated potential extinctions due to future land-use changes under alternative climate-change scenarios (2005-2100). Future land-use changes are projected to reduce natural vegetative cover by 26-58% in the hotspots. As a consequence, the number of additional species extinctions, relative to those already incurred between 1500 and 2005, due to land-use change by 2100 across all hotspots ranged from about 220 to 21000 (0.2% to 16%), depending on the climate-change mitigation scenario and biological factors such as the slope of the species-area relationship and the contribution of wood harvest to extinctions. These estimates of potential future extinctions were driven by land-use change only and likely would have been higher if the direct effects of climate change had been considered. Future extinctions could potentially be reduced by incorporating habitat preservation into scenario development to reduce projected future land-use changes in hotspots or by lessening the impact of future land-use activities on biodiversity within hotspots.