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.

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.

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.

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 early bird gets the return: The benefits of publishing your data sooner.

The benefits of publishing your data sooner versus later in Ecology and Evolution.

Determinants of community compositional change are equally affected by global change.

Global change is impacting plant community composition, but the mechanisms underlying these changes are unclear. Using a dataset of 58 global change experiments, we tested the five fundamental mechanisms of community change: changes in evenness and richness, reordering, species gains and losses. We found 71% of communities were impacted by global change treatments, and 88% of communities that were exposed to two or more global change drivers were impacted. Further, all mechanisms of change were equally likely to be affected by global change treatments-species losses and changes in richness were just as common as species gains and reordering. We also found no evidence of a progression of community changes, for example, reordering and changes in evenness did not precede species gains and losses. We demonstrate that all processes underlying plant community composition changes are equally affected by treatments and often occur simultaneously, necessitating a wholistic approach to quantifying community changes.

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.

Online but not remote: Adapting field-based ecology laboratories for online learning.

Teaching ecology effectively and experientially has become more challenging for at least two reasons today. Most experiences of our students are urban, and we now face the near immediate and continuing need to deliver courses (either partially or wholly) online because of COVID-19. Therefore, providing a learning experience that connects students to their environment within an ecological framework remains crucial and perhaps therapeutic to mental health. Here, we describe how prior to the pandemic we adapted our field-based laboratories to include data collection, analysis, and interpretation, along with the development of a citizen-science approach for online delivery. This design is simple to implement, does not require extensive work, and maintains the veracity of original learning outcomes. Collaboration online following field data collection in ecology courses within the context of cities offers further options to adapt to student experience levels, resource availability, and accessibility, as well as bringing instructors and students together to build an open well-curated data set that can be used in ecology courses where no laboratories are available. Finally, it promotes an open collaboration among ecology instructors that can drive lasting conversations about ecology curriculum.

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.

Shrubs as magnets for pollination: A test of facilitation and reciprocity in a shrub-annual facilitation system.

The magnet species hypothesis proposes that flowering plants that are attractive to pollinators can increase the relative pollination rates of neighbouring plants by acting as 'magnets.' Here, we test the hypothesis that insect-pollinated shrub species Larrea tridentata and wind-pollinated shrub species Ambrosia dumosa act as magnets for the pollinator visitation of understory annual plant species in an arid ecosystem. As an extension to the magnet species hypothesis, we propose the double magnet species hypothesis in which we further test for reciprocity by the floral island created in the understory of the benefactor shrubs as an additional pollinator magnet for the shrub itself. We used an annual plant placed near each shrub and the open to measure the effect of shrubs on annuals. The double magnet species hypothesis was tested using L. tridentata with and without surrounding annuals. We measured pollinator visitation and visit duration using video and in-situ observation techniques to test whether shrubs increase pollinator visitation to understory annual plants, if insect-pollinated shrubs act as better pollinator magnets than wind-pollinated shrubs (to determine the effects of the floral resource itself), and whether shrubs with annuals in their understory have higher pollinator visitation rates relative to shrubs without annuals. We found that insect-pollinated shrubs increased the visitation rate and duration of visits by pollinators to their understory plants and that wind-pollinated shrubs decreased the duration of visits of some insect visitors, but these relationships varied between years. While the presence of annuals did not change the visitation rate of all possible pollinators to L. tridentata flowers, they did decrease the visitation duration of specifically bees, indicating a negative reciprocal effect of the understory on pollination. Thus, the concentrated floral resources of flowers on insect-pollinated shrubs can act as a magnet that attract pollinators but that in turn provide a cost to pollination of the shrub. However, while wind-pollinated shrubs may provide other benefits, they may provide a cost to the pollination of their understory. These findings support the magnet species hypothesis as an additional mechanism of facilitation by insect-pollinated shrubs to other plant species within arid ecosystems.

A meta-analysis contrasting active versus passive restoration practices in dryland agricultural ecosystems.

Restoration of agricultural drylands globally, here farmlands and grazing lands, is a priority for ecosystem function and biodiversity preservation. Natural areas in drylands are recognized as biodiversity hotspots and face continued human impacts. Global water shortages are driving increased agricultural land retirement providing the opportunity to reclaim some of these lands for natural habitat. We used meta-analysis to contrast different classes of dryland restoration practices. All interventions were categorized as active and passive for the analyses of efficacy in dryland agricultural ecosystems. We evaluated the impact of 19 specific restoration practices from 42 studies on soil, plant, animal, and general habitat targets across 16 countries, for a total of 1,427 independent observations. Passive vegetation restoration and grazing exclusion led to net positive restoration outcomes. Passive restoration practices were more variable and less effective than active restoration practices. Furthermore, passive soil restoration led to net negative restoration outcomes. Active restoration practices consistently led to positive outcomes for soil, plant, and habitat targets. Water supplementation was the most effective restoration practice. These findings suggest that active interventions are necessary and critical in most instances for dryland agricultural ecosystems likely because of severe anthropogenic pressures and concurrent environmental stressors-both past and present.

A contrast of meta and metafor packages for meta-analyses in R.

There is extensive choice in R to support meta-analyses.Two packages in this ecosystem include meta and metafor and provide an excellent opportunity to apply a structured checklist previously developed for contrasts between R packages relevant to challenges in ecology and evolution.Meta is a direct, intuitive choice for rapid implementation of general meta-analytical statistics. Metafor is a comprehensive package best suited for relatively more complex models.Both packages provide estimates of heterogeneity, excellent visualization tools, and functions to explore publication bias.The package metafor has a steeper learning curve but greater rewards. Reference to the learning curve and capacities of the statistical software Stata provided a benchmark outside the R ecosystem and confirmed the consistency in statistics.The usefulness of meta-analyses is not just in the synthesis of the research but in the process of doing the scientific synthesis. Reporting of contrasts and checks for robust statistics is an important contribution to more transparent and reproducible scientific syntheses.

How the ecology and evolution of the COVID-19 pandemic changed learning.

The coronavirus disease 2019 (COVID-19) pandemic introduced an abrupt change in human behavior globally. Here, we discuss unique insights the pandemic has provided into the eco-evolutionary role of pathogens in ecosystems and present data that indicates the pandemic may have fundamentally changed our learning choices. COVID-19 has indirectly affected many organisms and processes by changing the behavior of humans to avoid being infected. The pandemic also changed our learning behavior by affecting the relative importance of information and forcing teaching and learning into a framework that accommodates human behavioral measures to avoid disease transmission. Not only are these indirect effects on the environment occurring through a unique mechanistic pathway in ecology, the pandemic along with its effects on us provides a profound example of the role risk can play in the transmission of information between the at risk. Ultimately, these changes in our learning behavior led to this special issue "Taking learning online in Ecology and Evolution." The special issue was a call to the community to take learning in new directions, including online and distributed experiences. The topics examined include a significant component of DIY ecology and evolution that is experiential but done individually, opportunities to use online tools and apps to be more inclusive, student-focused strategies for teaching online, how to reinvent conferences, strategies to retain experiential learning safely, emerging forms of teaching such as citizen science, apps and podcasting, and ideas on how to accommodate ever changing constraints in the college classroom, to name a few. The collective consensus in our fields is that these times are challenging but we can continue to improve and innovate on existing developments, and more broadly and importantly, this situation may provide an opportunity to reset some of the existing practices that fail to promote an effective and inclusive learning environment.

Online conferences for better learning.

Conferences provide an invaluable set of opportunities for professional development. Online, virtual, and distributed conferences do not necessarily mean less opportunity for growth and innovation in science but varied and novel options for communicating the scientific process. Open science and many existing tools are in place in the practice of contemporary ecology and evolution to provide latitude for a much broader scope of sharing and thus learning from conferences. A brief overview of the science supporting online conferences and a highlight of some of the open science concepts in ecology and evolution are provided here to enable better learning through better planning for online conferences.

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.

A systematic review of the direct and indirect effects of herbivory on plant reproduction mediated by pollination.

BACKGROUND: Plant reproduction is influenced by the net outcome of plant-herbivore and plant-pollinator interactions. While both herbivore impacts and pollinator impacts on plant reproduction have been widely studied, few studies examine them in concert. METHODOLOGY: Here, we review the contemporary literature that examines the net outcomes of herbivory and pollination on plant reproduction and the impacts of herbivores on pollination through damage to shared host plants using systematic review tools. The direct or indirect effects of herbivores on floral tissue and reported mechanisms were compiled including the taxonomic breadth of herbivores, plants and pollinators. RESULTS: A total of 4,304 studies were examined producing 59 relevant studies for synthesis that reported both pollinator and herbivore measures. A total of 49% of studies examined the impact of direct damage to floral tissue through partial florivory while 36% of studies also examined the impact of vegetative damage on pollination through folivory, root herbivory, and stem damage. Only three studies examined the effects of both direct and indirect damage to pollination outcomes within the same study. CONCLUSIONS: It is not unreasonable to assume that plants often sustain simultaneous forms of damage to different tissues and that the net effects can be assessed through differences in reproductive output. Further research that controls for other relative drivers of reproductive output but examines more than one pathway of damage simultaneously will inform our understanding of the mechanistic relevance of herbivore impacts on pollination and also highlight interactions between herbivores and pollinators through plants. It is clear that herbivory can impact plant fitness through pollination; however, the relative importance of direct and indirect damage to floral tissue on plant reproduction is still largely unknown.

Shrub and vegetation cover predict resource selection use by an endangered species of desert lizard.

Globally, no species is exempt from the constraints associated with limited available habitat or resources, and endangered species in particular warrant critical examination. In most cases, these species are restricted to limited locations, and the relative likelihood of resource use within the space they can access is important. Using Gambelia sila, one of the first vertebrate species listed as endangered, we used resource selection function analysis of telemetry and remotely sensed data to identity key drivers of selected versus available locations for this species in Carrizo Plain National Monument, USA. We examined the probability of selection given different resource types. Increasing shrub cover, lower and relatively more flat sites, increasing normalized difference vegetation index, and solar radiation all significantly predicted likelihood of observed selection within the area sampled. Imagery data were also validated with fine-scale field data showing that large-scale contrasts of selection relative to available location patterns for animal species are a useful lens for potential habitat. Key environmental infrastructure such as foundation plant species including shrubs or local differences in the physical attributes were relevant to this endangered species.

A checklist for choosing between R packages in ecology and evolution.

The open source and free programming language R is a phenomenal mechanism to address a multiplicity of challenges in ecology and evolution. It is also a complex ecosystem because of the diversity of solutions available to the analyst.Packages for R enhance and specialize the capacity to explore both niche data/experiments and more common needs. However, the paradox of choice or how we select between many seemingly similar options can be overwhelming and lead to different potential outcomes.There is extensive choice in ecology and evolution between packages for both fundamental statistics and for more specialized domain-level analyses.Here, we provide a checklist to inform these decisions based on the principles of resilience, need, and integration with scientific workflows for evidence.It is important to explore choices in any analytical coding environment-not just R-for solutions to challenges in ecology and evolution, and document this process because it advances reproducible science, promotes a deeper understand of the scientific evidence, and ensures that the outcomes are correct, representative, and robust.