Network motifs involving both competition and facilitation predict biodiversity in alpine plant communities.

Biological diversity depends on multiple, cooccurring ecological interactions. However, most studies focus on one interaction type at a time, leaving community ecologists unsure of how positive and negative associations among species combine to influence biodiversity patterns. Using surveys of plant populations in alpine communities worldwide, we explore patterns of positive and negative associations among triads of species (modules) and their relationship to local biodiversity. Three modules, each incorporating both positive and negative associations, were overrepresented, thus acting as "network motifs." Furthermore, the overrepresentation of these network motifs is positively linked to species diversity globally. A theoretical model illustrates that these network motifs, based on competition between facilitated species or facilitation between inferior competitors, increase local persistence. Our findings suggest that the interplay of competition and facilitation is crucial for maintaining biodiversity.

Consumer pressure and supplemental pollination mediate shrub facilitation of a native annual desert plant.

Shrubs are important factors in the assembly of desert plant and animal communities. By providing shelter and resources to other plants and animals, shrubs can change plant-animal interactions including those with consumers and pollinators. Here, we test the hypothesis that shrubs facilitate the reproduction of other desert plants by influencing pollination and compensation for consumer pressure. We used the known benefactor Larrea tridentata as our focal shrub species and the flowering annual Malacothrix glabrata as a potential protege in the Mojave Desert. We tested the effects of facilitation (shrub microsite), consumer pressure (both artificial folivory and florivory), and pollination (ambient or supplemented) on flower and seed production of the annual M. glabrata. We found that floral production and seed mass were similar between microsites but that pollen was limited under shrubs in the absence of any other manipulation. Plants under shrubs produced more flowers and seeds than in the open when folivory and florivory treatments were applied. Malacothrix glabrata experienced a cost to association with L. tridentata in terms of pollen limitation but plants were better able to compensate for consumer pressure under shrubs through increased flower and seed production when damaged. Therefore, association with shrubs involves a reproductive trade-off between costs to pollination and benefits to compensation for consumer pressure.

Net plant interactions are highly variable and weakly dependent on climate at the global scale.

Although plant-plant interactions (i.e. competition and facilitation) have long been recognised as key drivers of plant community composition and dynamics, their global patterns and relationships with climate have remained unclear. Here, we assembled a global database of 10,502 pairs of empirical data from the literature to address the patterns of and climatic effects on the net outcome of plant interactions in natural communities. We found that plant interactions varied among plant performance indicators, interaction types and biomes, yet competition occurred more frequently than facilitation in plant communities worldwide. Unexpectedly, plant interactions showed weak latitudinal pattern and were weakly related to climate. Our study provides a global comprehensive overview of plant interactions, highlighting competition as a fundamental mechanism structuring plant communities worldwide. We suggest that further investigations should focus more on local factors (e.g. microclimate, soil and disturbance) than on macroclimate to identify key environmental determinants of interactions in plant communities.

The Hierarchy-of-Hypotheses Approach: A Synthesis Method for Enhancing Theory Development in Ecology and Evolution.

In the current era of Big Data, existing synthesis tools such as formal meta-analyses are critical means to handle the deluge of information. However, there is a need for complementary tools that help to (a) organize evidence, (b) organize theory, and (c) closely connect evidence to theory. We present the hierarchy-of-hypotheses (HoH) approach to address these issues. In an HoH, hypotheses are conceptually and visually structured in a hierarchically nested way where the lower branches can be directly connected to empirical results. Used for organizing evidence, this tool allows researchers to conceptually connect empirical results derived through diverse approaches and to reveal under which circumstances hypotheses are applicable. Used for organizing theory, it allows researchers to uncover mechanistic components of hypotheses and previously neglected conceptual connections. In the present article, we offer guidance on how to build an HoH, provide examples from population and evolutionary biology and propose terminological clarifications.

Ten simple rules for writing statistical book reviews.

Statistical books can provide deep insights into statistics and software. There are, however, many resources available to the practitioner. Book reviews have the capacity to function as a critical mechanism for the learner to assess the merits of engaging in part, in full, or at all with a book. The "ten simple rules" format, pioneered in computational biology, was applied here to writing effective book reviews for statistics because of the wide breadth of offerings in this domain, including topical introductions, computational solutions, and theory. Learning by doing is a popular paradigm in statistics and computation, but there is still a niche for books in the pedagogy of self-taught and instruction-based learning. Primarily, these rules ensure that book reviews function as a form of short syntheses to inform and guide readers in deciding to use a specific book relative to other options for resolving statistical challenges.

Facilitation with a grain of salt: reduced pollinator visitation is an indirect cost of association with the foundation species creosote bush (Larrea tridentata).

PREMISE: In arid ecosystems, shrub facilitation is a critical process driving plant community structure and assembly, often resulting in increased densities of annual plants beneath shrub canopies. Pollinator-mediated interactions can have fitness consequences for both plant interactors but are largely unexplored as an indirect consequence of direct shrub-annual facilitation. METHODS: We tested the capacity of the geographically widespread creosote bush (Larrea tridentata) to influence pollinator visitation to its annual understory during its phenological shift into spring flowering. We used small video cameras to record pollinator visitation and foraging behavior on potted transplants of a representative flowering annual. We concurrently evaluated L. tridentata's positive role as a foundation plant in this system by measuring the associated plant and arthropod communities and deploying data loggers to measure understory microclimates. RESULTS: Pollinator visitation to the flowering annual desert dandelion, Malacothrix glabrata, was lower when beneath the canopy of L. tridentata, and further declined throughout the study site as L. tridentata entered full bloom. We confirmed the role of L. tridentata as a foundation species in this system through its concurrent, positive effects on annual plant cover (a proxy for biomass), the abundance and richness of the understory arthropod community and its ability to create stable microclimates. CONCLUSIONS: Direct and indirect shrub effects on other species function simultaneously to shift net outcomes even within predominantly net positive facilitation complexes.

Facilitation costs and benefits function simultaneously on stress gradients for animals.

Understanding the variation in species interactions along environmental stress gradients is crucial for making robust ecological predictions about community responses to changing environmental conditions. The facilitation-competition framework has provided a strong basis for predictions (e.g. the stress-gradient hypothesis, SGH), yet the mechanisms behind patterns in animal interactions on stress gradients are poorly explored in particular for mobile animals. Here, we proposed a conceptual framework modelling changes in facilitation costs and benefits along stress gradients and experimentally tested this framework by measuring fitness outcomes of benefactor-beneficiary interactions across resource quality levels. Three arthropod consumer models from a broad array of environmental conditions were used including aquatic detritivores, potato moths and rainforest carrion beetles. We detected a shift to more positive interactions at increasing levels of stress thereby supporting the application of the SGH to mobile animals. While most benefactors paid no significant cost of facilitation, an increase in potato moth beneficiary's growth at high resource stress triggered costs for benefactors. This study is the first to experimentally show that both costs and benefits function simultaneously on stress gradients for animals. The proposed conceptual framework could guide future studies examining species interaction outcomes for both animals and plants in an increasingly stressed world.

The effect of consumer pressure and abiotic stress on positive plant interactions are mediated by extreme climatic events.

Environmental extremes resulting from a changing climate can have profound implications for plant interactions in desert communities. Positive interactions can buffer plant communities from abiotic stress and consumer pressure caused by climatic extremes, but limited research has explored this empirically. We tested the hypothesis that the mechanism of shrub facilitation on an annual plant community can change with precipitation extremes in deserts. During years of extreme drought and above-average rainfall in a desert, we measured plant interactions and biomass while manipulating a soil moisture gradient and reducing consumer pressure. Shrubs facilitated the annual plant community at all levels of soil moisture through reductions in microclimatic stress in both years and herbivore protection in the wet year only. Shrub facilitation and the high rainfall year contributed to the dominance of a competitive annual species in the plant community. Precipitation patterns in deserts determine the magnitude and type of facilitation mechanisms. Moreover, shrub facilitation mediates the interspecific competition within the associated annual community between years with different rainfall amounts. Examining multiple drivers during extreme climate events is a challenging area of research, but it is a necessary consideration given forecasts predicting that these events will increase in frequency and magnitude.

Ambient changes exceed treatment effects on plant species abundance in global change experiments.

The responses of species to environmental changes will determine future community composition and ecosystem function. Many syntheses of global change experiments examine the magnitude of treatment effect sizes, but we lack an understanding of how plant responses to treatments compare to ongoing changes in the unmanipulated (ambient or background) system. We used a database of long-term global change studies manipulating CO2 , nutrients, water, and temperature to answer three questions: (a) How do changes in plant species abundance in ambient plots relate to those in treated plots? (b) How does the magnitude of ambient change in species-level abundance over time relate to responsiveness to global change treatments? (c) Does the direction of species-level responses to global change treatments differ from the direction of ambient change? We estimated temporal trends in plant abundance for 791 plant species in ambient and treated plots across 16 long-term global change experiments yielding 2,116 experiment-species-treatment combinations. Surprisingly, for most species (57%) the magnitude of ambient change was greater than the magnitude of treatment effects. However, the direction of ambient change, whether a species was increasing or decreasing in abundance under ambient conditions, had no bearing on the direction of treatment effects. Although ambient communities are inherently dynamic, there is now widespread evidence that anthropogenic drivers are directionally altering plant communities in many ecosystems. Thus, global change treatment effects must be interpreted in the context of plant species trajectories that are likely driven by ongoing environmental changes.

Competition does not come at the expense of colonization in seed morphs with increased size and dispersal.

PREMISE OF THE STUDY: Seed-level trade-offs of heterocarpic species remain poorly understood. We propose that seedlings emerging from seeds with a permanent pappus (dispersing seeds) are stronger competitors than those emerging from seeds without a pappus (nondispersing seeds) because dispersing seeds are larger and germinate faster than nondispersing seeds in Centaurea solstitialis. METHODS: We conducted a competition experiment with both seed morphs, in which we recorded emergence rate and proportion, estimated seed dispersal by wind (anemochory) and by mammals (exozoochory), and measured size and abundance of seed morphs. KEY RESULTS: We found that seedlings from pappus seeds had greater competitive abilities than those from non-pappus seeds. Similarly, pappus seedlings emerged at much faster rates and larger proportions than non-pappus seedlings. Pappus seeds were larger, were more numerous, and displayed improved exozoochory compared to non-pappus seeds. Anemochory was poor for both seed morphs. CONCLUSIONS: We found support for our hypothesis, raising in turn the possibility that competition and colonization are positively associated in seed morphs of heterocarpic species with enhanced exozoochory of larger seeds. These findings are not consistent with those from heterocarpic species with enhanced anemochory of smaller seeds or slower-germinating seeds. Our results additionally suggest that pappus and non-pappus seeds of C. solstitialis display a task-division strategy in which pappus morphs colonize and preempt unoccupied sites through improved dispersal and fast and large emergence of seedlings with increased competitive abilities, whereas non-pappus morphs promote site persistence through delayed germination and dormancy. This strategy may contribute to the success of C. solstitialis in highly variable environments.

The effects of foundation species on community assembly: a global study on alpine cushion plant communities.

Foundation species can change plant community structure by modulating important ecological processes such as community assembly, yet this topic is poorly understood. In alpine systems, cushion plants commonly act as foundation species by ameliorating local conditions. Here, we analyze diversity patterns of species' assembly within cushions and in adjacent surrounding open substrates (83 sites across five continents) calculating floristic dissimilarity between replicate plots, and using linear models to analyze relationships between microhabitats and species diversity. Floristic dissimilarity did not change across biogeographic regions, but was consistently lower in the cushions than in the open microhabitat. Cushion plants appear to enable recruitment of many relatively stress-intolerant species that otherwise would not establish in these communities, yet the niche space constructed by cushion plants supports a more homogeneous composition of species than the niche space beyond the cushion's influence. As a result, cushion plants support higher α-diversity and a larger species pool, but harbor assemblies with lower ß-diversity than open microhabitats. We conclude that habitats with and without dominant foundation species can strongly differ in the processes that drive species recruitment, and thus the relationship between local and regional species diversity.

Facilitative plant interactions and climate simultaneously drive alpine plant diversity.

Interactions among species determine local-scale diversity, but local interactions are thought to have minor effects at larger scales. However, quantitative comparisons of the importance of biotic interactions relative to other drivers are rarely made at larger scales. Using a data set spanning 78 sites and five continents, we assessed the relative importance of biotic interactions and climate in determining plant diversity in alpine ecosystems dominated by nurse-plant cushion species. Climate variables related with water balance showed the highest correlation with richness at the global scale. Strikingly, although the effect of cushion species on diversity was lower than that of climate, its contribution was still substantial. In particular, cushion species enhanced species richness more in systems with inherently impoverished local diversity. Nurse species appear to act as a 'safety net' sustaining diversity under harsh conditions, demonstrating that climate and species interactions should be integrated when predicting future biodiversity effects of climate change.

The context dependence of beneficiary feedback effects on benefactors in plant facilitation.

Facilitative effects of some species on others are a major driver of biodiversity. These positive effects of a benefactor on its beneficiary can result in negative feedback effects of the beneficiary on the benefactor and reduced fitness of the benefactor. However, in contrast to the wealth of studies on facilitative effects in different environments, we know little about whether the feedback effects show predictable patterns of context dependence. We reanalyzed a global data set on alpine cushion plants, previously used to assess their positive effects on biodiversity and the nature of the beneficiary feedback effects, to specifically assess the context dependence of how small- and large-scale drivers alter the feedback effects of cushion-associated (beneficiary) species on their cushion benefactors using structural equation modelling. The effect of beneficiaries on cushions became negative when beneficiary diversity increased and facilitation was more intense. Local-scale biotic and climatic conditions mediated these community-scale processes, having indirect effects on the feedback effect. High-productivity sites demonstrated weaker negative feedback effects of beneficiaries on the benefactor. Our results indicate a limited impact of the beneficiary feedback effects on benefactor cushions, but strong context dependence. This context dependence may help to explain the ecological and evolutionary persistence of this widespread facilitative system.

A global analysis of bidirectional interactions in alpine plant communities shows facilitators experiencing strong reciprocal fitness costs.

Facilitative interactions are defined as positive effects of one species on another, but bidirectional feedbacks may be positive, neutral, or negative. Understanding the bidirectional nature of these interactions is a fundamental prerequisite for the assessment of the potential evolutionary consequences of facilitation. In a global study combining observational and experimental approaches, we quantified the impact of the cover and richness of species associated with alpine cushion plants on reproductive traits of the benefactor cushions. We found a decline in cushion seed production with increasing cover of cushion-associated species, indicating that being a benefactor came at an overall cost. The effect of cushion-associated species was negative for flower density and seed set of cushions, but not for fruit set and seed quality. Richness of cushion-associated species had positive effects on seed density and modulated the effects of their abundance on flower density and fruit set, indicating that the costs and benefits of harboring associated species depend on the composition of the plant assemblage. Our study demonstrates 'parasitic' interactions among plants over a wide range of species and environments in alpine systems, and we consider their implications for the possible selective effects of interactions between benefactor and beneficiary species.

The microclimatic effects of the native shrub Ephedra californica (Mormon tea) in California drylands.

Introduction: The impacts of climate change can be profound in many ecosystems worldwide, including drylands such as arid and semi-arid scrublands and grasslands. Foundation plants such as shrubs can provide microclimatic refuges for a variety of taxa. These shrubs can directly influence micro6 environmental measures, and indirectly increase the local environmental heterogeneity as a result. We examined the hypothesis that, in comparison to an open gap, foundation shrubs improve the microclimate beneath their canopy and that microclimate is in turn a significant predictor of annual vegetation. The following predictions were made: 1) mean air temperature (NSAT), ground temperature (SGT), and vapour pressure deficit (VPD) will be significantly lower under the shrubs than in the open microsites; 2) shrub canopy size predicts microclimate; 3) site-level aridity estimates and percent shrub cover influence annual plant abundance and richness; and 4) the site13 level mean of NSAT and VPD predict annual plant abundance and richness. Methods: Our study took place in Southwestern California, U.S.A. We used a handheld device with a probe to measure microclimatic variables such as near-surface air temperature (NSAT), near-surface relative humidity (NSRH), and surface ground temperature (SGT) at the shrub species Ephedra californica and in the open gap, across six sites in California, United States. Air temperature and RH were then used to calculate VPD. The mean number of vascular plant species across each site was also recorded. Results & discussion: Only SGT was significantly reduced under shrub canopies. Canopy volume was not a significant predictor of all three microclimatic variables, demonstrating that even small, low-stature shrubs can have facilitative effects. Furthermore, total shrub cover and aridity at sites significantly predicted mean plant richness and abundance. There were significantly more plants associated with shrubs and there were significantly more species associated with the open. Mean air temperature and VPD at the site-level significantly predicted vegetation abundance and richness, though microsite-level differences were only significant for richness. Foundation shrubs are a focal point of resiliency in dryland ecosystems. Understanding their impact on microclimate can inform us of better management, conservation, and restoration frameworks.

Native shrub densities predict burrow co-occurrence patterns in Central California Drylands.

Ecological resource availability is crucial for the persistence and survival of local desert animal communities. Dryland resources such as shrubs and burrows positively benefit animal species by mitigating harsh abiotic factors and providing habitat. Understanding the role of native shrubs, many of which serve as foundation species within desert regions, as well as the function of underground burrows as resources, provides insights into habitat utilization. In this study, we seek to better understand the co-occurrence of these two resources as a first step in quantifying key patterns locally and regionally in drylands. We tested whether the presence of burrows increased with the density of foundational shrubs near the burrows at two scales-within a 5 m radius of every burrow recorded and at the site level-defined as discrete ecological areas. We performed fieldwork across 31 sites within the arid and semiarid regions of Central California. We used a combination of burrow field surveys and satellite imagery to document both vertebrate animal burrow frequencies and shrub densities. Additionally, the accuracy of the shrub data was verified through ground truthing. Both fine-scale and site-level shrub densities positively predicted the relative likelihood of burrows and the frequency of burrows, respectively. The existence of two highly utilized dryland resources and the relationship between them signal that areas abundant in both resources will likely better support resident animal species. This finding underscores the significance of incorporating both shrub density and burrow frequency in studies of habitat interconnectivity and quality. The co-occurrence patterns of these resources will support novel habitat management and conservation strategies designed around both conservation and restoration efforts.

Shrub density effects on the presence of an endangered lizard of the Carrizo Plain National Monument, California.

Positive associations between animals and foundational shrub species are frequent in desert ecosystems for shelter, resources, refuge, and other key ecological processes. Herein, we tested the impact of the density of the shrub species Ephedra californica on the presence and habitat use of the federally endangered lizard species, Gambelia sila. To do this, we used a 3-year radio telemetry dataset and satellite-based counts of shrub density across sites at the Carrizo Plain National Monument in San Luis Obispo County, CA. The effect of shrub density on lizard presence was contrasted with previous shrub cover analyses to determine whether measures of shrub density were superior to shrub cover in predicting lizard presence. Increasing shrub density increased lizard presence. As shrub density increased, lizards were located more frequently "above ground" versus "below ground" in burrows. Male lizards had significantly larger home ranges than females, but both sexes were similarly associated with increasing shrub densities. Shrub density and shrub cover models did not significantly differ in their prediction of lizard presence. These findings suggest that both habitat measures are effective analogs and that ecologically, both cover and the density of foundation shrub species are key factors for some desert lizards.

Trait evolution during a rapid global weed invasion despite little genetic differentiation.

Invasive species often possess a great capacity to adapt to novel environments in the form of spatial trait variation, as a result of varying selection regimes, genetic drift, or plasticity. We explored the geographic differentiation in several phenotypic traits related to plant growth, reproduction, and defense in the highly invasive Centaurea solstitialis by measuring neutral genetic differentiation (F ST), and comparing it with phenotypic differentiation (P ST), in a common garden experiment in individuals originating from regions representing the species distribution across five continents. Native plants were more fecund than non-native plants, but the latter displayed considerably larger seed mass. We found indication of divergent selection for these two reproductive traits but little overall genetic differentiation between native and non-native ranges. The native versus invasive P ST-F ST comparisons demonstrated that, in several invasive regions, seed mass had increased proportionally more than the genetic differentiation. Traits displayed different associations with climate variables in different regions. Both capitula numbers and seed mass were associated with winter temperature and precipitation and summer aridity in some regions. Overall, our study suggests that rapid evolution has accompanied invasive success of C. solstitialis and provides new insights into traits and their genetic bases that can contribute to fitness advantages in non-native populations.

Reproducibility in ecology and evolution: Minimum standards for data and code.

We call for journals to commit to requiring open data be archived in a format that will be simple and clear for readers to understand and use. If applied consistently, these requirements will allow contributors to be acknowledged for their work through citation of open data, and facilitate scientific progress.