Modeling mammal response to fire based on species’ traits

Fire has shaped ecological communities worldwide for millennia, but impacts of fire on individual species are often poorly understood. We performed a meta-analysis to predict which traits, habitat, or study variables and fire characteristics affect how mammal species respond to fire. We modeled effect sizes of measures of population abundance or occupancy as a function of various combinations of these traits and variables with phylogenetic least squares regression. Nine of 115 modeled species (7.83%) returned statistically significant effect sizes, suggesting most mammals are resilient to fire. The top-ranked model predicted a negative impact of fire on species with lower reproductive rates, regardless of fire type (estimate = –0.68), a positive impact of burrowing in prescribed fires (estimate = 1.46) but not wildfires, and a positive impact of average fire return interval for wildfires (estimate = 0.93) but not prescribed fires. If a species’ International Union for Conservation of Nature Red List assessment includes fire as a known or possible threat, the species was predicted to respond negatively to wildfire relative to prescribed fire (estimate = –2.84). These findings provide evidence of experts’ abilities to predict whether fire is a threat to a mammal species and the ability of managers to meet the needs of fire-threatened species through prescribed fire. Where empirical data are lacking, our methods provide a basis for predicting mammal responses to fire and thus can guide conservation actions or interventions in species or communities.     

Trait similarity patterns within grass and grasshopper communities: multitrophic community assembly at work

Trait-based community assembly theory suggests that trait variation among co-occurring species is shaped by two main processes: abiotic filtering, important in stressful environments and promoting similarity, and competition, more important in productive environments and promoting dissimilarity. Previous studies have indeed found trait similarity to decline along productivity gradients. However, these studies have always been done on single trophic levels. Here, we investigated how interactions between trophic levels affect trait similarity patterns along environmental gradients. We propose three hypotheses for the main drivers of trait similarity patterns of plants and herbivores along environmental gradients: (1) environmental control of both, (2) bottom-up control of herbivore trait variation, and (3) top-down control of grass trait variation. To test this, we collected data on the community composition and trait variation of grasses (41 species) and grasshoppers (53 species) in 50 plots in a South African savanna. Structural equation models were used to investigate how the range and spacing of within-community functional trait values of both grasses and their insect herbivores (grasshoppers; Acrididae) respond to (1) rainfall and fire frequency gradients and (2) the trait similarity patterns of the other trophic level. The analyses revealed that traits of co-occurring grasses became more similar toward lower rainfall and higher fire frequency (environmental control), while showing little evidence for top-down control. Grasshopper trait range patterns, on the other hand, were mostly directly driven by vegetation structure and grass trait range patterns (bottom-up control), while environmental factors had mostly indirect effects via plant traits. Our study shows the potential to expand trait-based community assembly theory to include trophic interactions.     

Seed arrival and ecological filters interact to assemble high-diversity plant communities

Two prominent mechanisms proposed to structure biodiversity are niche-based ecological filtering and chance arrival of propagules from the species pool. Seed arrival is hypothesized to play a particularly strong role in high-diversity plant communities with large potential species pools and many rare species, but few studies have explored how seed arrival and local ecological filters interactively assemble species-rich communities in space and time. We experimentally manipulated seed arrival and multiple ecological filters in high-diversity, herbaceous-dominated groundcover communities in longleaf pine savannas, which contain the highest small-scale species richness in North America (up to > 40 species/m2). We tested three hypotheses: (1) local communities constitute relatively open-membership assemblages, in which increased seed arrival from the species pool strongly increases species richness; (2) ecological filters imposed by local fire intensity and soil moisture influence recruitment and richness of immigrating species; and (3) ecological filters increase similarity in the composition of immigrating species. In a two-year factorial field experiment, we manipulated local fire intensity by increasing pre-fire fuel loads, soil moisture using rain shelters and irrigation, and seed arrival by adding seeds from the local species pool. Seed arrival increased species richness regardless of fire intensity and soil moisture but interacted with both ecological filters to influence community assembly. High-intensity fire decreased richness of resident species, suggesting an important abiotic filter. In contrast, high-intensity fire increased recruitment and richness of immigrating species, presumably by decreasing effects of other ecological filters (competition and resource limitation) in postfire environments. Drought decreased recruitment and richness of immigrating species, whereas wet soil conditions increased recruitment but decreased or had little effect on richness. Moreover, some ecological filters (wet soil conditions and, to a lesser extent, high-intensity fire) increased similarity in the composition of immigrating species, illustrating conditions that influence deterministic community assembly in species-rich communities. Our experiment provides insights into how dispersal-assembly mechanisms may interact with niche-assembly mechanisms in space (spatial variation in disturbance) and time (temporal variation in resource availability) to structure high-diversity communities and can help guide conservation of threatened longleaf pine ecosystems in the face of habitat fragmentation and environmental change.     

A trait-based test for habitat filtering: convex hull volume

Community assembly theory suggests that two processes affect the distribution of trait values within communities: competition and habitat filtering. Within a local community, competition leads to ecological differentiation of coexisting species, while habitat filtering reduces the spread of trait values, reflecting shared ecological tolerances. Many statistical tests for the effects of competition exist in the literature, but measures of habitat filtering are less well-developed. Here, we present convex hull volume, a construct from computational geometry, which provides an n-dimensional measure of the volume of trait space occupied by species in a community. Combined with ecological null models, this measure offers a useful test for habitat filtering. We use convex hull volume and a null model to analyze California woody-plant trait and community data. Our results show that observed plant communities occupy less trait space than expected from random assembly, a result consistent with habitat filtering.     

Trait space of rare plants in a fire‐dependent ecosystem

The causes of species rarity are of critical concern because of the high extinction risk associated with rarity. Studies examining individual rare species have limited generality, whereas trait‐based approaches offer a means to identify functional causes of rarity that can be applied to communities with disparate species pools. Differences in functional traits between rare and common species may be indicative of the functional causes of species rarity and may therefore be useful in crafting species conservation strategies. However, there is a conspicuous lack of studies comparing the functional traits of rare species and co‐occurring common species. We measured 18 important functional traits for 19 rare and 134 common understory plant species from North Carolina's Sandhills region and compared their trait distributions to determine whether there are significant functional differences that may explain species rarity. Flowering, fire, and tissue‐chemistry traits differed significantly between rare and common, co‐occurring species. Differences in specific traits suggest that fire suppression has driven rarity in this system and that changes to the timing and severity of prescribed fire may improve conservation success. Our method provides a useful tool to prioritize conservation efforts in other systems based on the likelihood that rare species are functionally capable of persisting.     

Species phylogenetic relatedness, priority effects, and ecosystem functioning

Species immigration history can structure ecological communities through priority effects, which are often mediated by competition. As competition tends to be stronger between species with more similar niches, we hypothesize that species phylogenetic relatedness, under niche conservatism, may be a reasonable surrogate of niche similarity between species, and thus influence the strength of priority effects. We tested this hypothesis using a laboratory microcosm experiment in which we established bacterial species pools with different levels of phylogenetic relatedness and manipulated the immigration history of species from each pool into microcosms. Our results showed that strong priority effects, and hence multiple community states, only emerged for the species pool with the greatest phylogenetic relatedness. Community assembly also resulted in a significant positive relationship between bacterial phylogenetic diversity and ecosystem functions. Interestingly, these results emerged despite a lack of phylogenetic conservatism for most of the bacterial functional traits considered. Our results highlight the utility of phylogenetic information for understanding the structure and functioning of ecological communities, even when phylogenetically conserved functional traits are not identified or measured.     

Disturbance and resource availability act differently on the same suite of plant traits: revisiting assembly hypotheses

Understanding the mechanisms of trait selection at the scale of plant communities is a crucial step toward predicting community assembly. Although it is commonly assumed that disturbance and resource availability constrain separate suites of traits, representing the regenerative and established phases, respectively, a quantification and test of this accepted hypothesis is still lacking due to limitations of traditional statistical techniques. In this paper we quantify, using structural equation modeling (SEM), the relative contributions of disturbance and resource availability to the selection of suites of traits at the community scale. Our model specifies and reflects previously obtained ecological insights, taking disturbance and nutrient availability as central drivers affecting leaf, allometric, seed, and phenology traits in 156 (semi-) natural plant communities throughout The Netherlands. The common hypothesis positing that disturbance and resource availability each affect a set of mutually independent traits was not consistent with the data. Instead, our final model shows that most traits are strongly affected by both drivers. In addition, trait-trait constraints are more important in community assembly than environmental drivers in half of the cases. Both aspects of trait selection are crucial for correctly predicting ecosystem processes and community assembly, and they provide new insights into hitherto underappreciated ecological interactions.     

Succession and Disturbance in Sandhills Vegetation: Constructing Models for Managing Biological Diversity

Abstract: The Centennial Sandhills of southwest Montana support a mosaic of shrub-dominated vegetation in various stages of succession. The persistence of rare plants and plant communities depends on the presence of both early and late seral vegetation. Disturbances by fire, grazing, and burrowing are important processes opposing plant succession and influencing vegetation dynamics. We sampled vegetation in wind erosion (blowout), deposition, and stabilized sites on upper and lower slopes. Canonical correspondence analysis was employed to describe vegetation changes that occur during succession as soil organic matter and plant canopy cover increase and bare soil decreases. We used information on the effects of fire, ungulate grazing, and pocket gopher (  Thomomys talpoides ) burrowing, and our empirically derived successional sequence, to develop a model of sandhills vegetation dynamics operating at local and regional scales. The model suggests that fire followed by intense ungulate grazing may be the only way to restore early seral vegetation to areas of low topographic relief. In areas of high topographic relief, restoring presettlement fire frequency should be adequate to maintain pocket gopher habitat and thus a high proportion of early seral vegetation. These hypotheses should be tested through a process of adaptive management aimed at sustaining a mosaic of early and late seral vegetation capable of supporting the full spectrum of native species.     

What enables coexistence in plant communities? Weak versus strong species traits and the role of local processes

Explaining the coexistence of species that basically depend on the same resources has been a brainteaser for generations of ecologists. Different mechanisms have been proposed to facilitate coexistence in plant communities, where space is an important resource. Using a stochastic cellular automaton simulation model we analyze - separately and in combination - the influence of different species traits and processes which alter local competition on the coexistence of plant species over a fixed time horizon. We show that different species traits operate on different time scales in competition. We therefore suggest the concept of weak versus strong traits according to short- or long-term exclusion of species differing in these traits. As a consequence, highly non-linear trade-offs between weak and strong traits can result in communities. Furthermore, we found that trade-offs based on physiological species traits such as plant lifetime, dispersal range and plant growth, did not support broad and long-term coexistence—further processes such as density-dependent mortality and light-dependent colonization were necessary. This suggests that coexistence in plant communities requires (stabilizing) local processes to support the (equalizing) trade-offs in species traits.     

Simulating the effects of frequent fire on southern California coastal shrublands.

Fire disturbance is a primary agent of change in the mediterranean-climate chaparral shrublands of southern California, USA. However, fire frequency has been steadily increasing in coastal regions due to ignitions at the growing wildland-urban interface. Although chaparral is resilient to a range of fire frequencies, successively short intervals between fires can threaten the persistence of some species, and the effects may differ according to plant functional type. California shrublands support high levels of biological diversity, including many endangered and endemic species. Therefore, it is important to understand the long-term effects of altered fire regimes on these communities. A spatially explicit simulation model of landscape disturbance and succession (LANDIS) was used to predict the effects of frequent fire on the distribution of dominant plant functional types in a study area administered by the National Park Service. Shrubs dependent on fire-cued seed germination were most sensitive to frequent fire and lost substantial cover to other functional types, including drought-deciduous subshrubs that typify coastal sage scrub and nonnative annual grasses. Shrubs that resprout were favored by higher fire frequencies and gained in extent under these treatments. Due to this potential for vegetation change, caution is advised against the widespread use of prescribed fire in the region.     

Linking fruit traits to variation in predispersal vertebrate seed predation, insect seed predation, and pathogen attack

The importance of vertebrates, invertebrates, and pathogens for plant communities has long been recognized, but their absolute and relative importance in early recruitment of multiple coexisting tropical plant species has not been quantified. Further, little is known about the relationship of fruit traits to seed mortality due to natural enemies in tropical plants. To investigate the influences of vertebrates, invertebrates, and pathogens on reproduction of seven canopy plant species varying in fruit traits, we quantified reductions in fruit development and seed germination due to vertebrates, invertebrates, and fungal pathogens through experimental removal of these enemies using canopy exclosures, insecticide, and fungicide, respectively. We also measured morphological fruit traits hypothesized to mediate interactions of plants with natural enemies of seeds. Vertebrates, invertebrates, and fungi differentially affected predispersal seed mortality depending on the plant species. Fruit morphology explained some variation among species; species with larger fruit and less physical protection surrounding seeds exhibited greater negative effects of fungi on fruit development and germination and experienced reduced seed survival integrated over fruit development and germination in response to vertebrates. Within species, variation in seed size also contributed to variation in natural enemy effects on seed viability. Further, seedling growth was higher for seeds that developed in vertebrate exclosures for Anacardium excelsum and under the fungicide treatment for Castilla elastica, suggesting that predispersal effects of natural enemies may carry through to the seedling stage. This is the first experimental test of the relative effects of vertebrates, invertebrates, and pathogens on seed survival in the canopy. This study motivates further investigation to determine the generality of our results for plant communities. If there is strong variation in natural enemy attack among species related to differences in fruit morphology, then quantification of fruit traits will aid in predicting the outcomes of interactions between plants and their natural enemies. This is particularly important in tropical forests, where high species diversity makes it logistically impossible to study every plant life history stage of every species.     

Are trade-offs in plant resprouting manifested in community seed banks?

Trade-offs in allocation to resprouting vs. seedling regeneration in plants are predicted to occur along fire disturbance gradients. Increased resprouting ability should be generally favored in plant communities with a high probability of crown fire return. Hence, communities dominated by resprouters are predicted to have smaller seed banks than those dominated by species killed by fire. We tested whether there were trait shifts in resprouting ability among growth forms (short-lived herbaceous vs. ground-dwelling perennials vs. shrubs) and among communities (rocky outcrop vs. sclerophyll forest) with contrasting probabilities of crown fire return. Resprouting was more common in ground-dwelling perennials and in the sclerophyll forest community with a high probability of crown fire. Soil seed banks were sampled in rocky outcrop and sclerophyll forest communities in recently burned (18 months) and long-since-burned (12 years) locations at interspersed replicated sites. Collected seed banks were treated with orthogonal treatments of fire stimuli or no stimuli, and seedling emergence was measured in controlled conditions. Seed bank composition reflected the pattern of extant vegetation, with resprouting species being more common in the community with a higher probability of crown fire. Overall, however, resprouting species were poorly represented in the seed bank compared to those species killed by fire. Predicted shifts in allocation to seed production were strongly manifested in community seed banks across the disturbance gradient. Fewer species, seedlings, and seedlings per adult emerged from seed banks in the sclerophyll forest. This suggests that the dominance of resprouting species influences recruitment at the community scale. Community patterns in the seed bank also reflected predicted trade-offs with plant size and growth rate. Short-lived species that are killed by fire dominated the seed bank on rocky outcrops, while longer-lived resprouting species were found in low abundance. Life history trade-offs in persistence and regeneration strongly contribute to coexistence patterns between and within communities with contrasting probabilities of fire return.     

A comparison of taxon co-occurrence patterns for macro- and microorganisms

We examine co-occurrence patterns of microorganisms to evaluate community assembly "rules". We use methods previously applied to macroorganisms, both to evaluate their applicability to microorganisms and to allow comparison of co-occurrence patterns observed in microorganisms to those found in macroorganisms. We use a null model analysis of 124 incidence matrices from microbial communities, including bacteria, archaea, fungi, and algae, and we compare these results to previously published findings from a meta-analysis of almost 100 macroorganism data sets. We show that assemblages of microorganisms demonstrate nonrandom patterns of co-occurrence that are broadly similar to those found in assemblages of macroorganisms. These results suggest that some taxon co-occurrence patterns may be general characteristics of communities of organisms from all domains of life. We also find that co-occurrence in microbial communities does not vary among taxonomic groups or habitat types. However, we find that the degree of co-occurrence does vary among studies that use different methods to survey microbial communities. Finally, we discuss the potential effects of the undersampling of microbial communities on our results, as well as processes that may contribute to nonrandom patterns of co-occurrence in both macrobial and microbial communities such as competition, habitat filtering, historical effects, and neutral processes.     

Differential responses of vertebrate and invertebrate herbivores to traits of New Zealand subalpine shrubs

Plant traits are influenced by herbivore diet selection, but little is known about how traits are affected by different types of herbivores. We related eight traits of 27 subalpine shrub species in South Island, New Zealand, to damage of these shrubs by introduced red deer (Cervus elaphus) and native invertebrate herbivores using phylogenetically explicit modeling. Deer preferentially consumed species that grew quickly, were low in foliar tannins, or had high leaf area per unit mass. However, these traits did not trade off against each other; rather, they could be related to different multivariate defense strategies. Although the proportion of leaves damaged by leaf-chewing invertebrates also increased with stem growth, invertebrates did not damage the same fast growing species as those preferred by deer. Other traits may also be important in determining herbivore preferences, as suggested by the high proportion of variation in herbivory explained by phylogeny. Last, we found that the composition of invertebrate herbivore communities was more similar among closely related shrubs, and consequently, the range of invertebrate-plant associations may change if introduced deer shift plant composition toward slow-growing species. Overall, our results demonstrate the importance of herbivore type and coevolved interactions for the adaptive significance of plant traits.     

Trajectories of change in sagebrush steppe vegetation communities in relation to multiple wildfires

Repeated perturbations, both biotic and abiotic, can lead to fundamental changes in the nature of ecosystems, including changes in state. Sagebrush steppe communities provide important habitat for wildlife and grazing for livestock. Fire is an integral part of these systems, but there is concern that increased ignition frequencies and invasive species are fundamentally altering them. Despite these issues, the majority of studies of fire effects in systems dominated by Artemisia tridentata wyomingensis have focused on the effects of single burns. The Arid Lands Ecology Reserve (ALE), in south-central Washington (U.S.A.), was one of the largest contiguous areas of sagebrush steppe habitat in the state until large wildfires burned the majority of it in 2000 and 2007. We analyzed data from permanent vegetation transects established in 1996 and resampled in 2002 and 2009. Our objective was to describe how the fires, and subsequent postfire restoration efforts, affected communities' successional pathways. Plant communities differed in response to repeated fire and restoration; these differences could largely be ascribed to the functional traits of the dominant species. Low-elevation communities, previously dominated by obligate seeders, moved furthest from their initial composition and were dominated by weedy, early-successional species in 2009. Higher-elevation sites with resprouting shrubs, native bunchgrasses, and few invasive species were generally more resilient to the effects of repeated disturbances. Shrub cover has been almost entirely removed from ALE, although there was some recovery where communities were dominated by resprouters. Bromus tectorum dominance was reduced by herbicide application in areas where it was previously abundant, but it increased significantly in untreated areas. Several resprouting species, notably Phlox longifolia and Poa secunda, expanded remarkably following competitive release from shrub canopies and/or abundant B. tectorum. Our results suggest that community dynamics can be understood through a state and transition model with two axes (shrub/grass and native/invasive abundance), although such models also need to account for differences in plant functional traits and disturbance regimes. We use our results to develop a conceptual model that will be validated with further research.     

Quantifying the importance of local niche-based and stochastic processes to tropical tree community assembly

Although niche-based and stochastic processes, including dispersal limitation and demographic stochasticity, can each contribute to community assembly, it is difficult to quantify the relative importance of each process in natural vegetation. Here, we extend Shipley's maxent model (Community Assembly by Trait Selection, CATS) for the prediction of relative abundances to incorporate both trait-based filtering and dispersal limitation from the larger landscape and develop a statistical decomposition of the proportions of the total information content of relative abundances in local communities that are attributable to trait-based filtering, dispersal limitation, and demographic stochasticity. We apply the method to tree communities in a mature, species-rich, tropical forest in French Guiana at 1-, 0.25- and 0.04-ha scales. Trait data consisted of species' means of 17 functional traits measured over both the entire meta-community and separately in each of nine 1-ha plots. Trait means calculated separately for each site always gave better predictions. There was clear evidence of trait-based filtering at all spatial scales. Trait-based filtering was the most important process at the 1-ha scale (34%), whereas demographic stochasticity was the most important at smaller scales (37-53%). Dispersal limitation from the meta-community was less important and approximately constant across scales (-9%), and there was also an unresolved association between site-specific traits and meta-community relative abundances. Our method allows one to quantify the relative importance of local niche-based and meta-community processes and demographic stochasticity during community assembly across spatial and temporal scales.     

Interactive effects of disturbance and dispersal directionality on species richness and composition in metacommunities

Dispersal among ecological communities is usually assumed to be random in direction, or to vary in distance or frequency among species. However, a variety of natural systems and types of organisms may experience dispersal that is biased by directional currents or by gravity on hillslopes. We developed a general model for competing species in metacommunities to evaluate the role of directionally biased dispersal on species diversity, abundance, and traits. In parallel, we tested the role of directionally biased dispersal on communities in a microcosm experiment with protists and rotifers. Both the model and experiment independently demonstrated that diversity in local communities was reduced by directionally biased dispersal, especially dispersal that was biased away from disturbed patches. Abundance of species (and composition) in local communities was a product of disturbance intensity but not dispersal directionality. High disturbance selected for species with high intrinsic growth rates and low competitive abilities. Overall, our conclusions about the key role of dispersal directionality in (meta)communities seem robust and general, since they were supported both by the model, which was set in a general framework and not parameterized to fit to a specific system, and by a specific experimental test with microcosms.     

Conservation Threats Due to Human-Caused Increases in Fire Frequency in Mediterranean-Climate Ecosystems

Periodic wildfire is an important natural process in Mediterranean-climate ecosystems, but increasing fire recurrence threatens the fragile ecology of these regions. Because most fires are human-caused, we investigated how human population patterns affect fire frequency. Prior research in California suggests the relationship between population density and fire frequency is not linear. There are few human ignitions in areas with low population density, so fire frequency is low. As population density increases, human ignitions and fire frequency also increase, but beyond a density threshold, the relationship becomes negative as fuels become sparser and fire suppression resources are concentrated. We tested whether this hypothesis also applies to the other Mediterranean-climate ecosystems of the world. We used global satellite databases of population, fire activity, and land cover to evaluate the spatial relationship between humans and fire in the world's five Mediterranean-climate ecosystems. Both the mean and median population densities were consistently and substantially higher in areas with than without fire, but fire again peaked at intermediate population densities, which suggests that the spatial relationship is complex and nonlinear. Some land-cover types burned more frequently than expected, but no systematic differences were observed across the five regions. The consistent association between higher population densities and fire suggests that regardless of differences between land-cover types, natural fire regimes, or overall population, the presence of people in Mediterranean-climate regions strongly affects the frequency of fires; thus, population growth in areas now sparsely settled presents a conservation concern. Considering the sensitivity of plant species to repeated burning and the global conservation significance of Mediterranean-climate ecosystems, conservation planning needs to consider the human influence on fire frequency. Fine-scale spatial analysis of relationships between people and fire may help identify areas where increases in fire frequency will threaten ecologically valuable areas.     

Small-scale grassland assembly patterns differ above and below the soil surface

The existence of deterministic assembly rules for plant communities remains an important and unresolved topic in ecology. Most studies examining community assembly have sampled aboveground species diversity and composition. However, plants also coexist belowground, and many coexistence theories invoke belowground competition as an explanation for aboveground patterns. We used next-generation sequencing that enables the identification of roots and rhizomes from mixed-species samples to measure coexisting species at small scales in temperate grasslands. We used comparable data from above (conventional methods) and below (molecular techniques) the soil surface (0.1 x 0.1 x 0.1 m volume). To detect evidence for nonrandom patterns in the direction of biotic or abiotic assembly processes, we used three assembly rules tests (richness variance, guild proportionality, and species co-occurrence indices) as well as pairwise association tests. We found support for biotic assembly rules aboveground, with lower variance in species richness than expected and more negative species associations. Belowground plant communities were structured more by abiotic processes, with greater variability in richness and guild proportionality than expected. Belowground assembly is largely driven by abiotic processes, with little evidence for competition-driven assembly, and this has implications for plant coexistence theories that are based on competition for soil resources.     

A new method for broad-scale modeling and projection of plant assemblages under climatic,biotic, and environmental cofiltering

There is increasing interestin broad-scale analysis, modeling, and prediction of the distribution and composition of plant species assemblages under climatic, environmental, and biotic change, particularly for conservation purposes. We devised a method to reliably predict the impact of climate change on large assemblages of plant communities, while also considering competing biotic and environmental factors. To this purpose, we first used multilabel algorithms in order to convert the task of explaining a large assemblage of plant communities into a classification framework able to capture with high cross-validated accuracy the pattern of species distributions under a composite set of biotic and abiotic factors. We applied our model to a large set of plant communities in the Swiss Alps. Our model explained presences and absences of 175 plant species in 608 plots with >87% cross-validated accuracy, predicted decreases in α, β, and γ diversity by 2040 under both moderate and extreme climate scenarios, and identified likely advantaged and disadvantaged plant species under climate change. Multilabel variable selection revealed the overriding importance of topography, soils, and temperature extremes (rather than averages) in determining the distribution of plant species in the study area and their response to climate change. Our method addressed a number of challenging research problems, such as scaling to large numbers of species, considering species relationships and rarity, and addressing an overwhelming proportion of absences in presence–absence matrices. By handling hundreds to thousands of plants and plots simultaneously over large areas, our method can inform broad-scale conservation of plant species under climate change because it allows species that require urgent conservation action (assisted migration, seed conservation, and ex situ conservation) to be detected and prioritized. Our method also increases the practicality of assisted colonization of plant species by helping to prevent ill-advised introduction of plant species with limited future survival probability.