SPCIS: Standardized Plant Community with Introduced Status database.

The movement of plant species across the globe exposes native communities to new species introductions. While introductions are pervasive, two aspects of variability underlie patterns and processes of biological invasions at macroecological scales. First, only a portion of introduced species become invaders capable of substantially impacting ecosystems. Second, species that do become invasive at one location may not be invasive in others; impacts depend on invader abundance and recipient species and conditions. Accounting for these phenomena is essential to accurately understand the patterns of plant invasion and explain the idiosyncratic results reflected in the literature on biological invasions. The lack of community-level richness and the abundance of data spanning broad scales and environmental conditions have until now hindered our understanding of invasions at a macroecological scale. To address this limitation, we leveraged quantitative surveys of plant communities in the USA and integrated and harmonized nine datasets into the Standardized Plant Community with Introduced Status (SPCIS) database. The database contains 14,056 unique taxa identified within 83,391 sampling units, of which 52.6% have at least one introduced species. The SPCIS database includes comparable information on plant species occurrence, abundance, and native status across the 50 U.S. States and Puerto Rico. SPCIS can be used to answer macro-scale questions about native plant communities and interactions with invasive plants. There are no copyright restrictions on the data, and we ask the users of this dataset to cite this paper, the respective paper(s) corresponding to the dataset sampling design (all references are provided in Data S1: Metadata S1: Class II-B-2), and the references described in Data S1: Metadata S1: Class III-B-4 as applicable to the dataset being utilized.

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.

The adaptive challenge of extreme conditions shapes evolutionary diversity of plant assemblages at continental scales.

The tropical conservatism hypothesis (TCH) posits that the latitudinal gradient in biological diversity arises because most extant clades of animals and plants originated when tropical environments were more widespread and because the colonization of colder and more seasonal temperate environments is limited by the phylogenetically conserved environmental tolerances of these tropical clades. Recent studies have claimed support of the TCH, indicating that temperate plant diversity stems from a few more recently derived lineages that are nested within tropical clades, with the colonization of the temperate zone being associated with key adaptations to survive colder temperatures and regular freezing. Drought, however, is an additional physiological stress that could shape diversity gradients. Here, we evaluate patterns of evolutionary diversity in plant assemblages spanning the full extent of climatic gradients in North and South America. We find that in both hemispheres, extratropical dry biomes house the lowest evolutionary diversity, while tropical moist forests and many temperate mixed forests harbor the highest. Together, our results support a more nuanced view of the TCH, with environments that are radically different from the ancestral niche of angiosperms having limited, phylogenetically clustered diversity relative to environments that show lower levels of deviation from this niche. Thus, we argue that ongoing expansion of arid environments is likely to entail higher loss of evolutionary diversity not just in the wet tropics but in many extratropical moist regions as well.

Tree canopy cover constrains the fertility-diversity relationship in plant communities of the southeastern United States.

The goal of elucidating the primary mechanisms constraining the assembly and distribution of biodiversity remains among the central unresolved challenges facing the field of ecology. Simulation studies and experimental manipulations have focused on how patterns in community assembly result from bivariate relationships along productivity or environmental gradients. However, the joint influence of multiple resource gradients on the distribution of species richness in natural communities remains understudied. Using data from a large network of multiscale vegetation plots across forests and woodlands of the southeastern United States, we find significant evidence for the scale-dependent, joint constraints of forest structure and soil resources on the distribution of vascular plant species richness. In addition to their significant partial effects on species richness, understory light levels and soil fertility positively interact, suggesting a trade-off between the two limiting resources with species richness peaking both in high-light, low-fertility conditions as well as low-light, high-fertility settings. This finding provides a novel perspective on the biodiversity-productivity relationship that suggests a transition in limiting resources from soil nutrients to light availability when enhanced productivity results in reduced light resources for subordinate individuals. Results likewise have meaningful implications for our understanding of scale-dependent community assembly processes as size-asymmetric competition replaces environmental filtering as the primary assembly mechanism structuring temperate forest communities along an increasing soil fertility gradient.

Similar factors underlie tree abundance in forests in native and alien ranges.

AIM: Alien plant species can cause severe ecological and economic problems, and therefore attract a lot of research interest in biogeography and related fields. To identify potential future invasive species, we need to better understand the mechanisms underlying the abundances of invasive tree species in their new ranges, and whether these mechanisms differ between their native and alien ranges. Here, we test two hypotheses: that greater relative abundance is promoted by (a) functional difference from locally co-occurring trees, and (b) higher values than locally co-occurring trees for traits linked to competitive ability. LOCATION: Global. TIME PERIOD: Recent. MAJOR TAXA STUDIED: Trees. METHODS: We combined three global plant databases: sPlot vegetation-plot database, TRY plant trait database and Global Naturalized Alien Flora (GloNAF) database. We used a hierarchical Bayesian linear regression model to assess the factors associated with variation in local abundance, and how these relationships vary between native and alien ranges and depend on species' traits. RESULTS: In both ranges, species reach highest abundance if they are functionally similar to co-occurring species, yet are taller and have higher seed mass and wood density than co-occurring species. MAIN CONCLUSIONS: Our results suggest that light limitation leads to strong environmental and biotic filtering, and that it is advantageous to be taller and have denser wood. The striking similarities in abundance between native and alien ranges imply that information from tree species' native ranges can be used to predict in which habitats introduced species may become dominant.

Succession, regression and loss: does evidence of saltwater exposure explain recent changes in the tree communities of North Carolina's Coastal Plain?

BACKGROUND AND AIMS: Coastal plant communities globally are highly vulnerable to future sea-level rise and storm damage, but the extent to which these habitats are affected by the various environmental perturbations associated with chronic salinization remains unclear. In this study, we examine the relationship between North Carolina wetland tree community composition and basal area change and indicators of salinization such as soil salt ion content and elevation. METHODS: We surveyed 34 forest plots in forested, freshwater wetlands across the Albemarle-Pamlico Peninsula. A subset of our study sites had been sampled during the previous decade as part of the Carolina Vegetation Survey, enabling us to investigate the environmental effects on current community structure, and community change over time. KEY RESULTS: Multi-variate (ordination) analysis and linear regression models of tree community composition revealed that elevation and soil salt content were correlated with changes in total site tree basal area. Shifts in tree community composition were, however, only weakly correlated with indicators of salinization, specifically elevation, soil sulphate and sodium, but not chloride. While the majority of plots experienced gains in basal area over the past decade, consistent with secondary succession, sites with high soil salt content or low elevation experienced basal area (biomass) loss during the same period. CONCLUSIONS: The key factors associated with chronic saltwater intrusion (soil ion content) likely explain recent changes in tree biomass, and potential shifts in community composition in low-elevation sites along the North Carolina coast. Not only is it probable that other coastal forest ecosystems worldwide will experience similar stressors and shifts in community biomass and structure as sea levels rise, but the ability of these habitats to deliver key ecosystem services like carbon sequestration and flood defence will be compromised as a result.

The commonness of rarity: Global and future distribution of rarity across land plants.

A key feature of life's diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth's plant biodiversity that are rare. A large fraction, ~36.5% of Earth's ~435,000 plant species, are exceedingly rare. Sampling biases and prominent models, such as neutral theory and the k-niche model, cannot account for the observed prevalence of rarity. Our results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth's plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species. Estimates of global species abundance distributions have important implications for risk assessments and conservation planning in this era of rapid global change.

Global trait-environment relationships of plant communities.

Plant functional traits directly affect ecosystem functions. At the species level, trait combinations depend on trade-offs representing different ecological strategies, but at the community level trait combinations are expected to be decoupled from these trade-offs because different strategies can facilitate co-existence within communities. A key question is to what extent community-level trait composition is globally filtered and how well it is related to global versus local environmental drivers. Here, we perform a global, plot-level analysis of trait-environment relationships, using a database with more than 1.1 million vegetation plots and 26,632 plant species with trait information. Although we found a strong filtering of 17 functional traits, similar climate and soil conditions support communities differing greatly in mean trait values. The two main community trait axes that capture half of the global trait variation (plant stature and resource acquisitiveness) reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale. Similarly, within-plot trait variation does not vary systematically with macro-environment. Our results indicate that, at fine spatial grain, macro-environmental drivers are much less important for functional trait composition than has been assumed from floristic analyses restricted to co-occurrence in large grid cells. Instead, trait combinations seem to be predominantly filtered by local-scale factors such as disturbance, fine-scale soil conditions, niche partitioning and biotic interactions.

The native-exotic species richness relationship varies with spatial grain of measurement and environmental conditions.

Biological invasions can have dramatic impacts on communities and biodiversity, and are critical considerations in conservation and management decisions. We present a novel analysis to determine how exotic species success varies with community richness and scale of measurement. Using 5,022 plots representing natural vegetation of the Carolinas, we calculated native and exotic species richness of all vascular plants at five grain sizes. To avoid spatial pseudoreplication, we randomly selected unique subplots from each larger plot, re-selecting 100 times to develop an empirical distribution of the native-exotic richness relationship (NERR). Because observed NERRs vary with spatial scale, we developed separate scale-specific null-model distributions to compare to the empirical data. For each spatial scale, we compared the empirical distribution of 100 slopes to the null distribution containing 99 permutations of species origin per empirical slope. We also analyzed the dataset according to broad assignments corresponding to environmental conditions, using the formation type assigned to each community. The plots followed across most scales the general trend that exotic richness increases with native richness. At the smallest scale, however, the NERR was negative. The slope of the NERR is significantly higher than the null model at the largest observed scale and significantly lower than the null model at the smallest two observed scales. The NERR for most formations follows the general pattern with scale for the entire dataset. Warm temperate forests expressed essentially 0 slope at the largest spatial grain, decreasing to a negative relationship at 1 m2 and smaller. Temperate freshwater marshes and wet meadows and shrublands expressed a positive relationship at all spatial grains, demonstrating that unique environmental and biogeographic conditions differentially affect exotic species. Further, these results indicate that exotic species are unevenly distributed across natural communities and that community assembly processes vary with scale.

Limited sampling hampers "big data" estimation of species richness in a tropical biodiversity hotspot.

Macro-scale species richness studies often use museum specimens as their main source of information. However, such datasets are often strongly biased due to variation in sampling effort in space and time. These biases may strongly affect diversity estimates and may, thereby, obstruct solid inference on the underlying diversity drivers, as well as mislead conservation prioritization. In recent years, this has resulted in an increased focus on developing methods to correct for sampling bias. In this study, we use sample-size-correcting methods to examine patterns of tropical plant diversity in Ecuador, one of the most species-rich and climatically heterogeneous biodiversity hotspots. Species richness estimates were calculated based on 205,735 georeferenced specimens of 15,788 species using the Margalef diversity index, the Chao estimator, the second-order Jackknife and Bootstrapping resampling methods, and Hill numbers and rarefaction. Species richness was heavily correlated with sampling effort, and only rarefaction was able to remove this effect, and we recommend this method for estimation of species richness with "big data" collections.

Intercontinental comparison of habitat levels of invasion between temperate North America and Europe.

Several studies have demonstrated that floras of the New World contain larger proportions of alien species than those of the Old World; however, the differences in fine-scale invasion patterns are poorly known. We compared the levels of invasion in analogous habitats of two environmentally similar regions in temperate North America and Europe (the Carolinas and the Czech Republic), using comprehensive vegetation-plot databases. Native and alien vascular plant species were identified within 4165 vegetation plots assigned to 12 habitats occurring in both areas. The level of invasion was calculated for each habitat (1) as the proportion of aliens recorded cumulatively across multiple plots (habitat scale) and (2) as the mean proportion of aliens per plot (plot scale), both separately for all alien species and for the subgroup of aliens originating in one region and invading the other. The proportions of species native on one continent and invading the other were also calculated for each habitat to compare the alien species exchange between continents. Habitat levels of invasion showed remarkably similar patterns on the two continents. There were significant positive relationships for the levels of invasion, both for all alien species (habitat-scale R2 = 0.907; plot-scale R2 = 0.676) and for those that originated on the opposite continent (habitat-scale R2 = 0.624; plot-scale R2 = 0.708). In both regions, the most and the least invaded habitats were the same, but on average, North American habitats showed higher habitat-scale levels of invasion than their European counterparts. At the same time, a larger proportion of alien species was provided by European habitats for invasion to North America than vice versa. The consistent intercontinental pattern of habitat levels of invasion suggests that these levels are driven by similar mechanisms in distant regions. Habitat conditions are likely to have stronger effect on the level of invasion than the identity of alien species, as shown by similar levels of invasion in analogous habitats despite different geographical origins of alien species. The higher flux of alien species from Europe to North America is consistent with a generally higher level of invasion of North American habitats.

Functional trait space and the latitudinal diversity gradient.

The processes causing the latitudinal gradient in species richness remain elusive. Ecological theories for the origin of biodiversity gradients, such as competitive exclusion, neutral dynamics, and environmental filtering, make predictions for how functional diversity should vary at the alpha (within local assemblages), beta (among assemblages), and gamma (regional pool) scales. We test these predictions by quantifying hypervolumes constructed from functional traits representing major axes of plant strategy variation (specific leaf area, plant height, and seed mass) in tree assemblages spanning the temperate and tropical New World. Alpha-scale trait volume decreases with absolute latitude and is often lower than sampling expectation, consistent with environmental filtering theory. Beta-scale overlap decays with geographic distance fastest in the temperate zone, again consistent with environmental filtering theory. In contrast, gamma-scale trait space shows a hump-shaped relationship with absolute latitude, consistent with no theory. Furthermore, the overall temperate trait hypervolume was larger than the overall tropical hypervolume, indicating that the temperate zone permits a wider range of trait combinations or that niche packing is stronger in the tropical zone. Although there are limitations in the data, our analyses suggest that multiple processes have shaped trait diversity in trees, reflecting no consistent support for any one theory.

Habitat area and climate stability determine geographical variation in plant species range sizes.

Despite being a fundamental aspect of biodiversity, little is known about what controls species range sizes. This is especially the case for hyperdiverse organisms such as plants. We use the largest botanical data set assembled to date to quantify geographical variation in range size for ~ 85 000 plant species across the New World. We assess prominent hypothesised range-size controls, finding that plant range sizes are codetermined by habitat area and long- and short-term climate stability. Strong short- and long-term climate instability in large parts of North America, including past glaciations, are associated with broad-ranged species. In contrast, small habitat areas and a stable climate characterise areas with high concentrations of small-ranged species in the Andes, Central America and the Brazilian Atlantic Rainforest region. The joint roles of area and climate stability strengthen concerns over the potential effects of future climate change and habitat loss on biodiversity.

The taxonomic name resolution service: an online tool for automated standardization of plant names.

BACKGROUND: The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this 'names problem' has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. RESULTS: The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. CONCLUSIONS: We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.

Integration of local and regional species-area relationships from space-time species accumulation.

A long-standing observation in community ecology is that the scaling of species richness, as exemplified by species-area curves, differs on local and regional scales. This decoupling of scales may be largely due to sampling processes (the increasing constraint imposed by sampling fewer individuals at fine scales), as distinct from ecological processes, such as environmental heterogeneity, that operate across scales. Removal of the sampling constraint from fine-scale richness estimates should yield species-area curves that behave like those of the regions in which they are embedded, but an effective method for this removal has not been available. We suggest an approach that incorporates the manner in which small areas accumulate species over time as a way to remove the signature of sampling processes from fine-scale species-area curves. We report for three species-rich grasslands from two continents how local plant species richness is distributed through time at multiple, nested spatial scales, and we ask whether sampling-corrected curves reflect the spatial scaling of richness of each larger floristic province. Our analysis suggests that fine-scale values of richness are highly constrained by sampling processes, but once these constraints are removed, the spatial scaling of species richness is consistent from the scale of individuals to that of an entire province.