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This article is a Commentary on Cosme et al., 215: 113–125.

A large array of species distribution model (SDM) approaches has been developed for explaining and predicting the occurrences of individual species or species assemblages. Given the wealth of existing models, it is unclear which models perform best for interpolation or extrapolation of existing data sets, particularly when one is concerned with species assemblages. We compared the predictive performance of 33 variants of 15 widely applied and recently emerged SDMs in the context of multispecies data, including both joint SDMs that model multiple species together, and stacked SDMs that model each species individually combining the predictions afterward. We offer a comprehensive evaluation of these SDM approaches by examining their performance in predicting withheld empirical validation data of different sizes representing five different taxonomic groups, and for prediction tasks related to both interpolation and extrapolation. We measure predictive performance by 12 measures of accuracy, discrimination power, calibration, and precision of predictions, for the biological levels of species occurrence, species richness, and community composition. Our results show large variation among the models in their predictive performance, especially for communities comprising many species that are rare. The results do not reveal any major trade‐offs among measures of model performance; the same models performed generally well in terms of accuracy, discrimination, and calibration, and for the biological levels of individual species, species richness, and community composition. In contrast, the models that gave the most precise predictions were not well calibrated, suggesting that poorly performing models can make overconfident predictions. However, none of the models performed well for all prediction tasks. As a general strategy, we therefore propose that researchers fit a small set of models showing complementary performance, and then apply a cross‐validation procedure involving separate data to establish which of these models performs best for the goal of the study.

Species assemble into communities through ecological and evolutionary processes. Phylogenetic niche conservatism—the tendency of species to retain ancestral ecological distributions—is thought to influence which species from a regional species pool can persist in a particular environment. We analyzed data for seed plants in China to test hypotheses about the distribution of species within regional floras. Of 16 environmental variables, actual evapotranspiration, minimum temperature of the coldest month, and annual precipitation most strongly influenced regional species richness, phylogenetic dispersion, and phylogenetic diversity for both gymnosperms (cone-bearing plants) and angiosperms (flowering plants). For most evolutionary clades at, and above, the family level, the relationships between metrics of phylogenetic dispersion (i.e., average phylogenetic distance among species), or phylogenetic diversity, and the 3 environmental variables were consistent with the tropical niche conservatism hypothesis, which predicts closer phylogenetic relatedness and reduced phylogenetic diversity with increasing environmental stress. The slopes of the relationships between phylogenetic relatedness and the 3 environmental drivers identified in this analysis were steeper for primarily tropical clades, implying greater niche conservatism, than for primarily temperate clades. These observations suggest that the distributions of seed plants across large-scale environmental gradients in China are constrained by conserved adaptations to the physical environment, i.e., phylogenetic niche conservatism.

Darwin proposed two seemingly contradictory hypotheses regarding factors influencing the outcome of biological invasions. He initially posited that nonnative species closely related to native species would be more likely to successfully establish, because they might share adaptations to the local environment (preadaptation hypothesis). However, based on observations that the majority of naturalized plant species in the United States belonged to nonnative genera, he concluded that the lack of competitive exclusion would facilitate the establishment of alien invaders phylogenetically distinct from the native flora (competition-relatedness hypothesis). To date, no consensus has been reached regarding these opposing hypotheses. Here, following Darwin, we use the flora of the United States to examine patterns of taxonomic and phylogenetic relatedness between native and nonnative taxa across thousands of nested locations ranging in size and extent, from local to regional scales. We find that the probability of observing the signature of environmental filtering over that of competition increases with spatial scale. Further, native and nonnative species tended to be less related in warm, humid environments. Our work provides an empirical assessment of the role of observation scale and climate in biological invasions and demonstrates that Darwin’s two opposing hypotheses need not be mutually exclusive.

Questions: How do fine scale community assembly processes (e.g., environmental filtering, symmetric competition, hierarchical competition, facilitation) vary along a natural stress gradient on coastal sand dunes? How does local environmental heterogeneity affect these processes? Location: Mediterranean coastal sand dunes, central Italy (Montalto Marina, Lazio region). Methods: We quantified spatial (co-occurrence) and functional patterns (degree of divergence in the traits of co-occurring species) at a fine scale (0.5 m × 0.5 m subplots) in herbaceous communities (2 m × 2 m plots) of coastal habitats along the sea–inland vegetation zonation. We then studied how the fine-scale co-occurrence patterns (aggregation vs segregation) varied across habitats of the zonation. Finally, we fitted linear models assessing the relationship of the fine-scale functional patterns (convergence vs divergence) with (1) the average environmental conditions along the sea–inland environmental stress gradient, and (2) the environmental heterogeneity within plots. Results: Spatial and functional patterns conveyed complementary information. Within-community spatial segregation was more common further from the sea, which suggests the dominance of competitive processes in the least stressed communities. Fine-scale convergence or divergence depended, for all functional traits, on the average environmental conditions of the community along the gradient, suggesting an effect of environmental stress on the prevailing assembly processes. However, it also depended on the environmental heterogeneity within the community, suggesting that micro-abiotic filtering might play a more important role than previously anticipated in determining fine-scale community assembly. Conclusions: Our results suggest that contrasting assembly processes act simultaneously on community assembly along environmental gradients, both as a function of average environmental conditions and of local heterogeneity. Future studies assessing community assembly should therefore avoid neglecting the role of micro-abiotic filtering in shaping functional patterns. Moreover, only by integrating multiple sources of information (trait patterns, spatial patterns and environmental variation) were we able to disentangle fine-scale community assembly processes and reinforce our interpretation of community patterns.

Island disharmony refers to the biased representation of higher taxa on islands compared to their mainland source regions and represents a central concept in island biology. Here, we develop a generalizable framework for approximating these source regions and conduct the first global assessment of island disharmony and its underlying drivers. We compiled vascular plant species lists for 178 oceanic islands and 735 mainland regions. Using mainland data only, we modelled species turnover as a function of environmental and geographic distance and predicted the proportion of shared species between each island and mainland region. We then quantified the over‐ or under‐representation of families on individual islands (representational disharmony) by contrasting the observed number of species against a null model of random colonization from the mainland source pool, and analysed the effects of six family‐level functional traits on the resulting measure. Furthermore, we aggregated the values of representational disharmony per island to characterize overall taxonomic bias of a given flora (compositional disharmony), and analysed this second measure as a function of four island biogeographical variables. Our results indicate considerable variation in representational disharmony both within and among plant families. Examples of generally over‐represented families include Urticaceae, Convolvulaceae and almost all pteridophyte families. Other families such as Asteraceae and Orchidaceae were generally under‐represented, with local peaks of over‐representation in known radiation hotspots. Abiotic pollination and a lack of dispersal specialization were most strongly associated with an insular over‐representation of families, whereas other family‐level traits showed minor effects. With respect to compositional disharmony, large, high‐elevation islands tended to have the most disharmonic floras. Our results provide important insights into the taxon‐ and island‐specific drivers of disharmony. The proposed framework allows overcoming the limitations of previous approaches and provides a quantitative basis for incorporating functional and phylogenetic approaches into future studies of island disharmony.

Patterns in community composition are scale-dependent and generally difficult to distinguish. Therefore, quantifying the main assembly processes in various systems and across different datasets has remained challenging. Building on the PER-SIMPER method, we propose a new metric, the dispersal-niche continuum index (DNCI), which estimates whether dispersal or niche processes dominate community assembly and facilitates the comparisons of processes among datasets. The DNCI was tested for robustness using simulations and applied to observational datasets comprising organismal groups with different trophic level and dispersal potential. Based on the robustness tests, the DNCI discriminated the respective contribution of niche and dispersal processes in pairwise comparisons of site groups with less than 40% and 30% differences in their taxa and site numbers, respectively. In the observational datasets, the DNCI suggested that dispersal rather than niche assembly was the dominant assembly process which, however, varied in intensity among organismal groups and study contexts, including spatial scale and ecosystem types. The proposed DNCI measures the relative strength of community assembly processes in a way that is simple, easily quantifiable and comparable across datasets. We discuss the strengths and weaknesses of the DNCI and provide perspectives for future research.

Aim We present the first global analysis of elevational gradients in functional and phylogenetic diversity of birds and test for signals of deterministic processes (i.e., environmental filtering and limiting similarity) in community assembly. Further, we examine for latitudinal effects in the strength of these processes. Location Forty‐six elevational gradients across the globe. Time period Current (between 1924 and 2016). Major taxa Birds. Methods We systematically selected, compiled and analysed published data on bird diversity along elevational gradients. For each gradient, we calculated functional and phylogenetic diversity across elevations and described the main patterns for each diversity metric. Then, we calculated standardized effect sizes (SES) of each metric and used these SES values to (a) test the signals of deterministic processes shaping assemblages across elevations and (b) to compare changes in within‐mountain diversity, among mountains located at different latitudes. Results Birds displayed eight different patterns of functional and phylogenetic diversity across elevations, but no global pattern of increase or decrease was found. There is, however, a consistent global pattern of phylogenetic clustering, with mountain species being more closely related to each other at any given elevation. Latitude had a significant effect on within‐mountain changes in functional and phylogenetic diversity across elevations, with more negative slopes (stronger decline in diversity metrics with increasing elevation) in tropical mountains. Main conclusions Our findings challenge the idea that the decline of functional and phylogenetic diversity with elevation is a general pattern, emphasizing the uniqueness of each mountain system. In spite of this great variability, we found a latitudinal effect in the patterns of within‐mountain functional and phylogenetic dispersion of birds after controlling for effects of species richness. Environmental filtering, thus, may act differently in tropical and temperate mountains, and calls for more comparative studies on the mechanisms driving community assembly at different latitudes.

A central issue of community ecology is finding rules that explain the composition and abundance of coexisting species. Nowadays two main processes, environmental filtering and limiting similarity, are thought to play the main roles in structuring communities. Their relative importance under different environmental conditions, however, is still not properly clarified. We studied the strength and the effect of environmental filtering (causing convergence) and limiting similarity (causing divergence) in 137 sample plots along an extremely long environmental gradient ranging from open sand grasslands to highly productive marshes, using a trait‐based approach. The main environmental gradient (i.e. productivity) was characterized by the Normalized Difference Vegetation Index, an indicator of above‐ground live biomass. Cover of the plant species was estimated visually. Values of 11 plant traits were collected from field measurements and data bases. Mean and dispersion of the trait values of the plots were quantified by community‐weighted means and Rao's quadratic entropy. Trait convergence and divergence were tested by randomization tests, followed by the study of changes in effect size along the productivity gradient by fitting generalized additive mixed models (GAMM). For vegetative traits we found mainly convergence, indicating the filtering effect of environmental constraints, while traits related to regeneration showed divergence. The strength of convergence in vegetative traits generally decreased as productivity grew, indicating that while under harsh conditions environmental constraints strongly limit the possible trait values, under more benign conditions various water and nutrient use strategies are adaptable. At high productivity, the strength of divergence in regenerative traits decreased. Since the larger diversity of vegetative traits found here reduces competition, the importance of diverse reproductive strategy is probably lower. Synthesis. Our results partly support the stress‐dominance hypothesis, but reveal that assembly rules are more complex. The relative importance of environmental filtering and limiting similarity depends on the trait and on the environmental conditions of the habitat. Traits related to resource use are generally limited by environmental filtering, and this restriction is weakening as conditions become more favourable, while traits related to regeneration are constrained by limiting similarity and are more diverse under harsh conditions.

Many species assemblages represent a nonrandom subset of a larger species pool. When an assemblage tends to contain close evolutionary relatives or species with similar functional traits, it can be described as phylogenetically or functionally clustered. Clustering is often interpreted as evidence for filtering by some combination of environmental and biotic factors. At sufficiently large spatial extents, however, biogeographic barriers can also lead to strong clustering. Here, we suggest that the breakdown of biogeographic barriers associated with human introductions of exotic species can be used as an unintentional experiment to assess their importance in driving phylogenetic and functional structure. An important role of biogeographic barriers would be revealed by a breakdown in clustering, particularly phylogenetic clustering, following species introductions. On the other hand, a role of filtering can be supported by similar patterns of clustering in the native and exotic assemblages along environmental gradients. We test these predictions using the grasses of California, a diverse group including many introduced species. Native grass assemblages in the state are highly clustered with respect to the global grass species pool, both phylogenetically and functionally. Within the state, variation in the strength of clustering is well explained by climatic variables, suggesting an important role for environmental‐biotic filtering. Further, subregions within the state with highly clustered native assemblages also contain highly clustered exotic assemblages. Contrary to expectation, though, the introduction of exotic species led to even more strongly clustered assemblages. We conclude that biogeographic barriers have generally not excluded the major grass lineages (e.g., tribes) from the state and likely act only on finer taxonomic scales (for example, excluding particular genera). Our approach should prove broadly applicable and contribute to improved understanding of broad‐scale patterns of assemblage structure.