Summary1. New analytical tools applied to long-term data demonstrate that ecological communities are highly dynamic over time. We developed an R package, library("codyn"), to help ecologists easily implement these metrics and gain broader insights into ecological community dynamics. 2. library("codyn") provides temporal diversity indices and community stability metrics. All functions are designed to be easily implemented over multiple replicates. 3. Temporal diversity indices include species turnover, mean rank shifts and rate of community change over time. Community stability metrics calculate overall stability and patterns of species covariance and synchrony over time, and include a null-modelling method to test significance. 4. Finally, library("codyn") contains vignettes that describe methods and reproduce figures from published papers to help users contextualize and apply functions to their own data.

Determining how ecological communities will respond to global environmental change remains a challenging research problem. Recent meta-analyses concluded that most communities are undergoing compositional change despite no net change in local species richness. We explored how species richness and composition of co-occurring plant, grasshopper, breeding bird and small mammal communities in arid and mesic grasslands changed in response to increasing aridity and fire frequency. In the arid system, grassland and shrubland plant and breeding bird communities were undergoing directional change, whereas grasshopper and small mammal communities were stable. In the mesic system, all communities were undergoing directional change regardless of fire frequency. Despite directional change in composition in some communities, species richness of all communities did not change because compositional change resulted more from reordering of species abundances than turnover in species composition. Thus, species reordering, not changes in richness, explains long-term dynamics in these grass and shrub dominated communities.

Heterogeneity is increasingly recognized as a foundational characteristic of ecological systems. Under global change, understanding temporal community heterogeneity is necessary for predicting the stability of ecosystem functions and services. Indeed, spatial heterogeneity is commonly used in alternative stable state theory as a predictor of temporal heterogeneity and therefore an early indicator of regime shifts. To evaluate whether spatial heterogeneity in species composition is predictive of temporal heterogeneity in ecological communities, we analyzed 68 community data sets spanning freshwater and terrestrial systems where measures of species abundance were replicated over space and time. Of the 68 data sets, 55 (81%) had a weak to strongly positive relationship between spatial and temporal heterogeneity, while in the remaining communities the relationship was weak to strongly negative (19%). Based on a mixed model analysis, we found a significant but weak overall positive relationship between spatial and temporal heterogeneity across all data sets combined, and within aquatic and terrestrial data sets separately. In addition, lifespan and successional stage were negatively and positively related to temporal heterogeneity, respectively. We conclude that spatial heterogeneity may be a predictor of temporal heterogeneity in ecological communities, and that this relationship may be a general property of many terrestrial and aquatic communities.

Detecting and understanding disturbance is a challenge in ecology that has grown more critical with global environmental change and the emergence of research on social–ecological systems. We identify three areas of research need: developing a flexible framework that incorporates feedback loops between social and ecological systems, anticipating whether a disturbance will change vulnerability to other environmental drivers, and incorporating changes in system sensitivity to disturbance in the face of global changes in environmental drivers. In the present article, we review how discoveries from the US Long Term Ecological Research (LTER) Network have influenced theoretical paradigms in disturbance ecology, and we refine a framework for describing social–ecological disturbance that addresses these three challenges. By operationalizing this framework for seven LTER sites spanning distinct biomes, we show how disturbance can maintain or alter ecosystem state, drive spatial patterns at landscape scales, influence social–ecological interactions, and cause divergent outcomes depending on other environmental changes.

Aim Seasonally dry tropical forest (SDTF) of the Caribbean Islands (primarily West Indies) is floristically distinct from Neotropical SDTF in Central and South America. We evaluate whether tree species composition was associated with climatic gradients or geographical distance. Turnover (dissimilarity) in species composition of different islands or among more distant sites would suggest communities structured by speciation and dispersal limitations. A nested pattern would be consistent with a steep resource gradient. Correlation of species composition with climatic variation would suggest communities structured by broad‐scale environmental filtering. Location The West Indies (The Bahamas, Cuba, Hispaniola, Jamaica, Puerto Rico, US Virgin Islands, Guadeloupe, Martinique, St. Lucia), Providencia (Colombia), south Florida (USA) and Florida Keys (USA). Taxon Seed plants—woody taxa (primarily trees). Methods We compiled 572 plots from 23 surveys conducted between 1969 and 2016. Hierarchical clustering of species in plots, and indicator species analysis for the resulting groups of sites, identified geographical patterns of turnover in species composition. Nonparametric analysis of variance, applied to principal components of bioclimatic variables, determined the degree of covariation in climate with location. Nestedness versus turnover in species composition was evaluated using beta diversity partitioning. Generalized dissimilarity modelling partitioned the effect of climate versus geographical distance on species composition. Results Despite a set of commonly occurring species, SDTF tree community composition was distinct among islands and was characterized by spatial turnover on climatic gradients that covaried with geographical gradients. Greater Antillean islands were characterized by endemic indicator species. Northern subtropical areas supported distinct, rather than nested, SDTF communities in spite of low levels of endemism. Main conclusions The SDTF species composition was correlated with climatic variation. SDTF on large Greater Antillean islands (Hispaniola, Jamaica and Cuba) was characterized by endemic species, consistent with their geological history and the biogeography of plant lineages. These results suggest that both environmental filtering and speciation shape Caribbean SDTF tree communities.