changeRangeR: An R package for reproducible biodiversity change metrics from species distribution estimates

Conservation planning and decision-making rely on evaluations of biodiversity status and threats that are based upon species' distribution estimates. However, gaps exist regarding automated tools to delineate species' current ranges from distribution estimates and use those estimates to calculate both species- and community-level biodiversity metrics. Here, we introduce changeRangeR, an R package that facilitates workflows to reproducibly transform estimates of species' distributions into metrics relevant for conservation. For example, by combining predictions from species distribution models (SDMs) with other maps of environmental data (e.g., suitable forest cover), researchers can characterize the proportion of a species' range that is under protection, metrics used under the IUCN Criteria A and B guidelines (Area of Occupancy and Extent of Occurrence), and other more general metrics such as taxonomic and phylogenetic diversity and endemism. Further, changeRangeR facilitates temporal comparisons among biodiversity metrics to inform efforts toward complementarity and consideration of future scenarios in conservation decisions. changeRangeR also provides tools to determine the effects of modeling decisions through sensitivity tests. Transparent and repeatable workflows for calculating biodiversity change metrics from SDMs such as those provided by changeRangeR are essential to inform conservation decision-making efforts and represent key extensions for SDM methodology and associated metadata documentation.journal articl

wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions

Released 4 years ago, the Wallace EcoMod application (R package wallace) provided an open-source and interactive platform for modeling species niches and distributions that served as a reproducible toolbox and educational resource. wallace harnesses R package tools documented in the literature and makes them available via a graphical user interface that runs analyses and returns code to document and reproduce them. Since its release, feedback from users and partners helped identify key areas for advancement, leading to the development of wallace 2. Following the vision of growth by community expansion, the core development team engaged with collaborators and undertook a major restructuring of the application to enable: simplified addition of custom modules to expand methodological options, analyses for multiple species in the same session, improved metadata features, new database connections, and saving/loading sessions. wallace 2 features nine new modules and added functionalities that facilitate data acquisition from climate-simulation, botanical and paleontological databases; custom data inputs; model metadata tracking; and citations for R packages used (to promote documentation and give credit to developers). Three of these modules compose a new component for environmental space analyses (e.g., niche overlap). This expansion was paired with outreach to the biogeography and biodiversity communities, including international presentations and workshops that take advantage of the software's extensive guidance text. Additionally, the advances extend accessibility with a cloud-computing implementation and include a suite of comprehensive unit tests. The features in wallace 2 greatly improve its expandability, breadth of analyses, and reproducibility options, including the use of emerging metadata standards. The new architecture serves as an example for other modular software, especially those developed using the rapidly proliferating R package shiny, by showcasing straightforward module ingestion and unit testing. Importantly, wallace 2 sets the stage for future expansions, including those enabling biodiversity estimation and threat assessments for conservation.journal articl

ENM2020 : A FREE ONLINE COURSE AND SET OF RESOURCES ON MODELING SPECIES NICHES AND DISTRIBUTIONS

The field of distributional ecology has seen considerable recent attention, particularly surrounding the theory, protocols, and tools for Ecological Niche Modeling (ENM) or Species Distribution Modeling (SDM). Such analyses have grown steadily over the past two decades-including a maturation of relevant theory and key concepts-but methodological consensus has yet to be reached. In response, and following an online course taught in Spanish in 2018, we designed a comprehensive English-language course covering much of the underlying theory and methods currently applied in this broad field. Here, we summarize that course, ENM2020, and provide links by which resources produced for it can be accessed into the future. ENM2020 lasted 43 weeks, with presentations from 52 instructors, who engaged with >2500 participants globally through >14,000 hours of viewing and >90,000 views of instructional video and question-and-answer sessions. Each major topic was introduced by an "Overview" talk, followed by more detailed lectures on subtopics. The hierarchical and modular format of the course permits updates, corrections, or alternative viewpoints, and generally facilitates revision and reuse, including the use of only the Overview lectures for introductory courses. All course materials are free and openly accessible (CC-BY license) to ensure these resources remain available to all interested in distributional ecology.Peer reviewe

Biological invasions: a field synopsis, systematic review, and database of the literature

Species introductions of anthropogenic origins are a major aspect of rapid ecological change globally. Research on biological invasions has generated a large literature on many different aspects of this phenomenon. Here, we describe and categorize some aspects of this literature, to better understand what has been studied and what we know, mapping well-studied areas and important gaps. To do so, we employ the techniques of systematic reviewing widely adopted in other scientific disciplines, to further the use of approaches in reviewing the literature that are as scientific, repeatable, and transparent as those employed in a primary study. We identified 2398 relevant studies in a field synopsis of the biological invasions literature. A majority of these studies (58%) were concerned with hypotheses for causes of biological invasions, while studies on impacts of invasions were the next most common (32% of the publications). We examined 1537 papers in greater detail in a systematic review. Superior competitive abilities of invaders, environmental disturbance, and invaded community species richness were the most common hypotheses examined. Most studies examined only a single hypothesis. Almost half of the papers were field observational studies. Studies of terrestrial invasions dominate the literature, with most of these concerning plant invasions. The focus of the literature overall is uneven, with important gaps in areas of theoretical and practical importance

Data from: Divergent trait and environment relationships among parallel radiations in Pelargonium (Geraniaceae): a role for evolutionary legacy?

Functional traits in closely related lineages are expected to vary similarly along common environmental gradients due to shared evolutionary and biogeographic history, or legacy effects, and due to biophysical tradeoffs in construction. We test these predictions in Pelargonium, a relatively recent evolutionary radiation. Bayesian phylogenetic mixed effects models assessed, at the subclade level, associations between plant height, leaf area, leaf nitrogen content and leaf mass per area (LMA), and five environmental variables capturing temperature and rainfall gradients across the Greater Cape Floristic Region of South Africa. Trait-trait integration was assessed via pairwise-correlations within subclades. Of 20 trait-environment associations, 17 differed among subclades. Signs of regression coefficients diverged for height, leaf area and leaf nitrogen content, but not for LMA. Subclades also differed in trait-trait relationships and these differences were modulated by rainfall seasonality. Leave-one-out cross-validation revealed that whether trait variation was better predicted by environmental predictors or trait-trait integration depended on the clade and trait in question. Legacy signals in trait-environment and trait-trait relationships were apparently lost during the earliest diversification of Pelargonium, but then retained during subsequent subclade evolution. Overall, we demonstrate that global-scale patterns are poor predictors of patterns of trait variation at finer geographic and taxonomic scales

Data from: Assessing the joint behavior of species traits as filtered by environment

Understanding and predicting how species traits are shaped by prevailing environmental conditions is an important yet challenging task in ecology. Functional trait based approaches can replace potentially idiosyncratic species-specific response models in learning about community behavior across environmental gradients. Customarily, models for traits given environment consider only trait means to predict species and functional diversity, as intra-taxon variability in traits is often thought to be negligible. A growing body of literature indicates that intra-taxon trait variability is substantial and critical in structuring plant communities and assessing ecosystem function. We propose flexible joint trait distribution models given environment and across species that incorporate intra-taxon variability as well as inter-site/plot variability. Using a Bayesian framework, our joint trait distribution models allow for mixed continuous, binary, and ordinal trait variables and incorporate dependence among traits enabling both joint and conditional trait prediction at unobserved sites. The models can be used to inform about the well-known fourth-corner problem, which attempts to interpret trait-by-environment matrices. We demonstrate the utility of our methodology through joint predictive trait distributions for individual species as well as joint community-weighted trait distributions for environments while incorporating intra-taxon trait variability. Explicit details on the probabilistic interpretations of the random trait-by-environment matrices obtained arising under our model are also provided to address the fourth-corner problem. Finally, our joint trait distribution model is applied to simulated and real vegetation data collected from the Greater Cape Floristic Region of South Africa. The proposed methodology places a fully model-based foundation on explaining intra-taxon trait variation given environment. It extends the utility and interpretability of commonly applied techniques for investigating community-weighted traits and illuminates randomness in the fourth-corner problem

individualXtraitsXenv

Trait values and environmental conditions at sample collection locations for individual plants. All values are untransformed

plotXspecies_coverXenv

Percent cover values for Protea, Pelargonium, Erica, and Restio in vegetation plots. Environmental conditions at plot locations are included. All values are untransformed

Data from: Processes of community assembly in an environmentally heterogeneous, high biodiversity region

Despite decades of study, the relative importance of niche-based versus neutral processes in community assembly remains largely ambiguous. Recent work suggests niche-based processes are more easily detectable at coarser spatial scales, while neutrality dominates at finer scales. Analyses of functional traits with multi-year multi-site biodiversity inventories may provide deeper insights into assembly processes and the effects of spatial scale. We examined associations between community composition, species functional traits, and environmental conditions for plant communities in the Kouga-Baviaanskloof region, an area within South Africa's Cape Floristic Region (CFR) containing high α and β diversity. This region contains strong climatic gradients and topographic heterogeneity, and is comprised of distinct vegetation classes with varying fire histories, making it an ideal location to assess the role of niche-based environmental filtering on community composition by examining how traits vary with environment. We combined functional trait measurements for over 300 species with observations from vegetation surveys carried out in 1991/1992 and repeated in 2011/2012. We applied redundancy analysis, quantile regression, and null model tests to examine trends in species turnover and functional traits along environmental gradients in space and through time. Functional trait values were weakly associated with most spatial environmental gradients and only showed trends with respect to vegetation class and time since fire. However, survey plots showed greater compositional and functional stability through time than expected based on null models. Taken together, we found clear evidence for functional distinctions between vegetation classes, suggesting strong environmental filtering at this scale, most likely driven by fire dynamics. In contrast, there was little evidence of filtering effects along environmental gradients within vegetation classes, suggesting that assembly processes are largely neutral at this scale, likely the result of very high functional redundancy among species in the regional species pool