Showing papers in "Ecology in 2019"

The Global Naturalized Alien Flora (GloNAF) database

Abstract: This dataset provides the Global Naturalized Alien Flora (GloNAF) database, version 1.2. GloNAF represents a data compendium on the occurrence and identity of naturalized alien vascular plant taxa across geographic regions (e.g. countries, states, provinces, districts, islands) around the globe. The dataset includes 13,939 taxa and covers 1,029 regions (including 381 islands). The dataset is based on 210 data sources. For each taxon-by-region combination, we provide information on whether the taxon is considered to be naturalized in the specific region (i.e. has established self-sustaining populations in the wild). Non-native taxa are marked as "alien", when it is not clear whether they are naturalized. To facilitate alignment with other plant databases, we provide for each taxon the name as given in the original data source and the standardized taxon and family names used by The Plant List Version 1.1 (http://www.theplantlist.org/). We provide an ESRI shapefile including polygons for each region and information on whether it is an island or a mainland region, the country and the Taxonomic Databases Working Group (TDWG) regions it is part of (TDWG levels 1-4). We also provide several variables that can be used to filter the data according to quality and completeness of alien taxon lists, which vary among the combinations of regions and data sources. A previous version of the GloNAF dataset (version 1.1) has already been used in several studies on, for example, historical spatial flows of taxa between continents and geographical patterns and determinants of naturalization across different taxonomic groups. We intend the updated and expanded GloNAF version presented here to be a global resource useful for studying plant invasions and changes in biodiversity from regional to global scales. We release these data into the public domain under a Creative Commons Zero license waiver (https://creativecommons.org/share-your-work/public-domain/cc0/). When you use the data in your publication, we request that you cite this data paper. If GloNAF is a major part of the data analyzed in your study, you should consider inviting the GloNAF core team (see Metadata S1: Originators in the Overall project description) as collaborators. If you plan to use the GloNAF dataset, we encourage you to contact the GloNAF core team to check whether there have been recent updates of the dataset, and whether similar analyses are already ongoing.

A theory of pulse dynamics and disturbance in ecology.

Abstract: We propose four postulates as the minimum set of logical propositions necessary for a theory of pulse dynamics and disturbance in ecosystems: (1) resource dynamics characterizes the magnitude, rate, and duration of resource change caused by pulse events, including the continuing changes in resources that are the result of abiotic and biotic processes; (2) energy flux characterizes the energy flow that controls the variation in the rates of resource assimilation across ecosystems; (3) patch dynamics characterizes the distribution of resource patches over space and time, and the resulting patterns of biotic diversity, ecosystem structure, and cross-scale feedbacks of pulses processes; and (4) biotic trait diversity characterizes the evolutionary responses to pulse dynamics and, in turn, the way trait diversity affects ecosystem dynamics during and after pulse events. We apply the four postulates to an important class of pulse events, biomass-altering disturbances, and derive seven generalizations that predict disturbance magnitude, resource trajectory, rate of resource change, disturbance probability, biotic trait diversification at evolutionary scales, biotic diversity at ecological scales, and functional resilience. Ultimately, theory must define the variable combinations that result in dynamic stability, comprising resistance, recovery, and adaptation.

The bioelements, the elementome, and the biogeochemical niche.

Abstract: Every living creature on Earth is made of atoms of the various bioelements that are harnessed in the construction of molecules, tissues, organisms, and communities, as we know them. Organisms need these bioelements in specific quantities and proportions to survive and grow. Distinct species have different functions and life strategies, and have therefore developed distinct structures and adopted a certain combination of metabolic and physiological processes. Each species is thus also expected to have different requirements for each bioelement. We therefore propose that a "biogeochemical niche" can be associated with the classical ecological niche of each species. We show from field data examples that a biogeochemical niche is characterized by a particular elementome defined as the content of all (or at least most) bioelements. The differences in elementome among species are a function of taxonomy and phylogenetic distance, sympatry (the bioelemental compositions should differ more among coexisting than among non-coexisting species to avoid competitive pressure), and homeostasis with a continuum between high homeostasis/low plasticity and low homeostasis/high plasticity. This proposed biogeochemical niche hypothesis has the advantage relative to other associated theoretical niche hypotheses that it can be easily characterized by actual quantification of a measurable trait: the elementome of a given organism or a community, being potentially applicable across taxa and habitats. The changes in bioelemental availability can determine genotypic selection and therefore have a feedback on ecosystem function and organization, and, at the end, become another driving factor of the evolution of life and the environment.

A practical guide for combining data to model species distributions

Abstract: Understanding and accurately modeling species distributions lies at the heart of many problems in ecology, evolution, and conservation. Multiple sources of data are increasingly available for modeling species distributions, such as data from citizen science programs, atlases, museums, and planned surveys. Yet reliably combining data sources can be challenging because data sources can vary considerably in their design, gradients covered, and potential sampling biases. We review, synthesize, and illustrate recent developments in combining multiple sources of data for species distribution modeling. We identify five ways in which multiple sources of data are typically combined for modeling species distributions. These approaches vary in their ability to accommodate sampling design, bias, and uncertainty when quantifying environmental relationships in species distribution models. Many of the challenges for combining data are solved through the prudent use of integrated species distribution models: models that simultaneously combine different data sources on species locations to quantify environmental relationships for explaining species distribution. We illustrate these approaches using planned survey data on 24 species of birds coupled with opportunistically collected eBird data in the southeastern United States. This example illustrates some of the benefits of data integration, such as increased precision in environmental relationships, greater predictive accuracy, and accounting for sample bias. Yet it also illustrates challenges of combining data sources with vastly different sampling methodologies and amounts of data. We provide one solution to this challenge through the use of weighted joint likelihoods. Weighted joint likelihoods provide a means to emphasize data sources based on different criteria (e.g., sample size), and we find that weighting improves predictions for all species considered. We conclude by providing practical guidance on combining multiple sources of data for modeling species distributions.

Movement responses to environment: fast inference of variation among southern elephant seals with a mixed effects model

Abstract: Like many species, movement patterns of southern elephant seals (Mirounga leonina) are being influenced by long‐term environmental change. These seals migrate up to 4,000 km from their breeding colonies, foraging for months in a variety of Southern Ocean habitats. Understanding how movement patterns vary with environmental features and how these relationships differ among individuals employing different foraging strategies can provide insight into foraging performance at a population level. We apply new fast‐estimation tools to fit mixed effects within a random walk movement model, rapidly inferring among‐individual variability in southern elephant seal environment–movement relationships. We found that seals making foraging trips to the sea ice on or near the Antarctic continental shelf consistently reduced speed and directionality (move persistence) with increasing sea‐ice coverage but had variable responses to chlorophyll a concentration, whereas seals foraging in the open ocean reduced move persistence in regions where circumpolar deep water shoaled. Given future climate scenarios, open‐ocean foragers may encounter more productive habitat but sea‐ice foragers may see reduced habitat availability. Our approach is scalable to large telemetry data sets and allows flexible combinations of mixed effects to be evaluated via model selection, thereby illuminating the ecological context of animal movements that underlie habitat usage.

ATLANTIC BIRD TRAITS: a data set of bird morphological traits from the Atlantic forests of South America

Abstract: Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820-2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities.

High rates of primary production in structurally complex forests

Abstract: Structure-function relationships are central to many ecological paradigms. Chief among these is the linkage of net primary production (NPP) with species diversity and canopy structure. Using the National Ecological Observatory Network (NEON) as a subcontinental-scale research platform, we examined how temperate-forest NPP relates to several measures of site-level canopy structure and tree species diversity. Novel multidimensional canopy traits describing structural complexity, most notably canopy rugosity, were more strongly related to site NPP than were species diversity measures and other commonly characterized canopy structural features. The amount of variation in site-level NPP explained by canopy rugosity alone was 83%, which was substantially greater than that explained individually by vegetation area index (31%) or Shannon's index of species diversity (30%). Forests that were more structurally complex, had higher vegetation-area indices, or were more diverse absorbed more light and used light more efficiently to power biomass production, but these relationships were most strongly tied to structural complexity. Implications for ecosystem modeling and management are wide ranging, suggesting structural complexity traits are broad, mechanistically robust indicators of NPP that, in application, could improve the prediction and management of temperate forest carbon sequestration.

Spatial scale modulates the inference of metacommunity assembly processes.

Abstract: The abundance and distribution of species across the landscape depend on the interaction between local, spatial, and stochastic processes. However, empirical syntheses relating these processes to spatiotemporal patterns of structure in metacommunities remain elusive. One important reason for this lack of synthesis is that the relative importance of the core assembly processes (dispersal, selection, and drift) critically depends on the spatial grain and extent over which communities are studied. To illustrate this, we simulated different aspects of community assembly on heterogeneous landscapes, including the strength of response to environmental heterogeneity (inherent to niche theory) vs. dispersal and stochastic drift (inherent to neutral theory). We show that increasing spatial extent leads to increasing importance of niche selection, whereas increasing spatial grain leads to decreasing importance of niche selection. The strength of these scaling effects depended on environment configuration, dispersal capacity, and niche breadth. By mapping the variation observed from the scaling effects in simulations, we could recreate the entire range of variation observed within and among empirical studies. This means that variation in the relative importance of assembly processes among empirical studies is largely scale dependent and cannot be directly compared. The scaling coefficient of the relative contribution of assembly processes, however, can be interpreted as a scale-integrative estimate to compare assembly processes across different regions and ecosystems. This emphasizes the necessity to consider spatial scaling as an explicit component of studies intended to infer the importance of community assembly processes.

Correlation of native and exotic species richness: a global meta-analysis finds no invasion paradox across scales.

Abstract: Support for the "biotic resistance hypothesis," that species-rich communities are more successful at resisting invasion by exotic species than are species-poor communities, has long been debated. It has been argued that native-exotic richness relationships (NERR) are negative at small spatial scales and positive at large scales, but evidence for the role of spatial scale on NERR has been contradictory. However, no formal quantitative synthesis has previously examined whether NERR is scale-dependent across multiple studies, and previous studies on NERR have not distinguished spatial grain and extent, which may drive very different ecological processes. We used a global systematic review and hierarchical mixed-effects meta-analysis to provide a comprehensive quantitative assessment of the patterns of NERR over a range of spatial grain sizes and spatial extents, based on 204 individual cases of observational (non-experimental) NERRs from 101 publications. We show that NERR was indeed highly scale dependent across studies and increased with the log of grain size. However, mean NERR was not negative at any grain size, although there was high heterogeneity at small grain sizes. We found no clear patterns of NERR across different spatial extents, suggesting that extent plays a less important role in determining NERR than does grain, although there was a complex interaction between extent and grain size. Almost all studies on NERR were conducted in North America, western Europe, and a few other regions, with little information on tropical or Arctic regions. We did find that NERR increased northward in temperate regions and also varied with longitude. We discuss possible explanations for the patterns we found, and caution that our results do not show that invasive species are benign or have no negative consequences for biodiversity preservation. This study represents the first global quantitative analysis of scale-based NERR, and casts doubt on the existence of an "invasion paradox" of negative NERR at small scales and positive correlations at large scales in non-experimental studies.

Enhanced activity of soil nutrient-releasing enzymes after plant invasion: a meta-analysis.

Abstract: Plant invasion can significantly alter soil nutrient cycling of ecosystems. How these changes are linked to soil enzyme activities is still unknown, however, even though these are proximate agents of organic matter decomposition and nutrient release. We performed a meta-analysis of 60 case studies examining responses of 10 unique soil enzymes to plant invasion, and tested whether invaded soils differed in their enzyme activities from uninvaded soils. We also examined whether increases in soil nutrient-releasing enzyme activity were paralleled by enhanced soil nutrient availability after plant invasion. Overall, we found that plant invasion had significant impacts on the activities of seven types of soil enzymes. Plant invasion had inconsistent impacts on C-decomposing enzymes, but invaded sites had significantly higher activities of soil enzymes related to N- and P-release than noninvaded sites. Increases in nutrient-releasing enzyme activity after plant invasion ranged from +23% to +69%, which potentially results in a linear increase of soil nutrient availability in response to enhanced enzyme activities. Invaded soils also had higher nutrient stocks and soil microbial biomass than uninvaded soils. Our results suggest that enhanced activity of soil nutrient-releasing enzymes after plant invasion may accelerate nutrient cycling, potentially creating a nutrient-rich soil environment that benefits invaders and promotes their persistence, as invasive plants often appear to be more resource-demanding and competitive than native species.

Narrow pollen diets are associated with declining Midwestern bumble bee species

Abstract: Many species of bumble bee (Bombus) have declined in range and abundance across Europe, the Americas, and Asia, whereas other species have persisted and remain common and widespread. One explanation as to why some species have declined, based primarily on studies of the European bumble bee fauna, is that declining species have relatively narrow pollen-foraging niches and are less able to use alternative host plants in the absence of their preferred hosts. Though extensively explored in Europe, this hypothesis has not been investigated in North America, in part due to incomplete information on the foraging niche of many species. We selected 12 bumble bee species found in Michigan and quantified their pollen diets using museum specimens. We also extensively resurveyed the state to understand their contemporary status and distribution. Compared to a pre-2000 baseline, six species remain relatively common and widespread, whereas six species show range contractions of over 50%. There was a significant relationship between dietary breadth and distributional range change, with declined or declining species collecting around one-third fewer pollen types than stable species. Though there were significant compositional differences, we found no differences in the number of pollen types collected by species with differing tongue lengths. Overall, these results support the hypothesis that species with narrower dietary niches are at greater risk of decline. However, it is not clear if narrow dietary niches are a cause of declines, or if both are driven by an underlying factor such as proximity to the edge of climatic niches. Further research is needed to improve our understanding of dietary niche in bumble bees, and how it interacts with other factors to influence population trajectories of stable and at-risk species.

Joint species distribution models with species correlations and imperfect detection

Abstract: Spatiotemporal patterns in biological communities are typically driven by environmental factors and species interactions. Spatial data from communities are naturally described by stacking models for all species in the community. Two important considerations in such multispecies or joint species distribution models (JSDMs) are measurement errors and correlations between species. Up to now, virtually all JSDMs have included either one or the other, but not both features simultaneously, even though both measurement errors and species correlations may be essential for achieving unbiased inferences about the distribution of communities and species co-occurrence patterns. We developed two presence-absence JSDMs for modeling pairwise species correlations while accommodating imperfect detection: one using a latent variable and the other using a multivariate probit approach. We conducted three simulation studies to assess the performance of our new models and to compare them to earlier latent variable JSDMs that did not consider imperfect detection. We illustrate our models with a large Atlas data set of 62 passerine bird species in Switzerland. Under a wide range of conditions, our new latent variable JSDM with imperfect detection and species correlations yielded estimates with little or no bias for occupancy, occupancy regression coefficients, and the species correlation matrix. In contrast, with the multivariate probit model we saw convergence issues with large data sets (many species and sites) resulting in very long run times and larger errors. A latent variable model that ignores imperfect detection produced correlation estimates that were consistently negatively biased, that is, underestimated. We found that the number of latent variables required to represent the species correlation matrix adequately may be much greater than previously suggested, namely around n/2, where n is community size. The analysis of the Swiss passerine data set exemplifies how not accounting for imperfect detection will lead to negative bias in occupancy estimates and to attenuation in the estimated covariate coefficients in a JSDM. Furthermore, spatial heterogeneity in detection may cause spurious patterns in the estimated species correlation matrix if not accounted for. Our new JSDMs represent an important extension of current approaches to community modeling to the common case where species presence-absence cannot be detected with certainty.

Measuring continuous compositional change using decline and decay in zeta diversity

Abstract: Incidence, or compositional, matrices are generated for a broad range of research applications in biology. Zeta diversity provides a common currency and conceptual framework that links incidence-based metrics with multiple patterns of interest in biology, ecology, and biodiversity science. It quantifies the variation in species (or OTU) composition of multiple assemblages (or cases) in space or time, to capture the contribution of the full suite of narrow, intermediate, and wide-ranging species to biotic heterogeneity. Here we provide a conceptual framework for the application and interpretation of patterns of continuous change in compositional diversity using zeta diversity. This includes consideration of the survey design context, and the multiple ways in which zeta diversity decline and decay can be used to examine and test turnover in the identity of elements across space and time. We introduce the zeta ratio-based retention rate curve to quantify rates of compositional change. We illustrate these applications using 11 empirical data sets from a broad range of taxa, scales, and levels of biological organization-from DNA molecules and microbes to communities and interaction networks-including one of the original data sets used to express compositional change and distance decay in ecology. We show (1) how different sample selection schemes used during the calculation of compositional change are appropriate for different data types and questions, (2) how higher orders of zeta may in some cases better detect shifts and transitions, and (3) the relative roles of rare vs. common species in driving patterns of compositional change. By exploring the application of zeta diversity decline and decay, including the retention rate, across this broad range of contexts, we demonstrate its application for understanding continuous turnover in biological systems.

Toward a mechanistic understanding of "peat collapse" and its potential contribution to coastal wetland loss.

Abstract: Coastal wetlands are susceptible to loss in both health and extent via stressors associated with global climate change and anthropogenic disturbance. Peat collapse may represent an additional phenomenon contributing to coastal wetland loss in organic-rich soils through rapid vertical elevation decline. However, the term "peat collapse" has been inconsistently used in the literature, leading to ambiguities regarding the mechanisms, timing, and spatial extent of its contribution to coastal wetland loss. For example, it is unclear whether peat collapse is distinct from general subsidence, or what biogeochemical changes or sequence of events may constitute peat collapse. A critical analysis of peer-reviewed literature related to peat collapse was supplemented with fundamental principles of soil physics and biogeochemistry to develop a conceptual framework for coastal wetland peat collapse. We propose that coastal wetland peat collapse is a specific type of shallow subsidence unique to highly organic soils in which a loss of soil strength and structural integrity contributes to a decline in elevation, over the course of a few months to a few years, below the lower limit for emergent plant growth and natural recovery. We further posit that coastal wetland peat collapse is driven by severe stress or death of the vegetation, which compromises the supportive structure roots provide to low-density organic soils and shifts the carbon balance of the ecosystem toward a net source, as mineralization is no longer offset by sequestration. Under these conditions, four mechanisms may contribute to peat collapse: (1) compression of gas-filled pore spaces within the soil during dry-down conditions; (2) deconsolidation of excessively waterlogged peat, followed by transport; (3) compaction of aerenchyma tissue in wetland plant roots, and possibly collapse of root channels; and (4) acceleration of soil mineralization due to the addition of labile carbon (dying roots), oxygen (decreased flooding), nutrients (eutrophication), or sulfate (saltwater intrusion). Scientists and land managers should focus efforts on monitoring vegetation health across the coastal landscape as an indicator for peat collapse vulnerability and move toward codifying the term "peat collapse" in the scientific literature. Once clarified, the contribution of peat collapse to coastal wetland loss can be evaluated.

Plants alter their vertical root distribution rather than biomass allocation in response to changing precipitation

Abstract: Elucidating the variation of allocation pattern of ecosystem net primary productivity (NPP) and its underlying mechanisms is critically important for understanding the changes of aboveground and belowground ecosystem functions. Under optimal partitioning theory, plants should allocate more NPP to the organ that acquires the most limiting resource, and this expectation has been widely used to explain and predict NPP allocation under changing precipitation. However, confirmatory evidence for this theory has mostly come from observed spatial variation in the relationship between precipitation and NPP allocation across ecosystems, rather than directly from the influences of changing precipitation on NPP allocation within systems. We performed a 6-yr five-level precipitation manipulation experiment in a semiarid steppe to test whether changes in NPP allocation can be explained by the optimal partitioning theory, and how water requirement of plant community is maintained if NPP allocation is unaltered. The 30 precipitation levels (5 levels × 6 yr) were divided into dry, nominal, and wet precipitation ranges, relative to historical precipitation variation over the past six decades. We found that NPP in both aboveground (ANPP) and belowground (BNPP) increased nonlinearly as precipitation increased, while the allocation of NPP to BNPP (fBNPP ) showed a concave quadratic relationship with precipitation. The declined fBNPP as precipitation increased in the dry range supported the optimal partitioning theory. However, in the nominal range, NPP allocation was not influenced by the changed precipitation; instead, BNPP was distributed more in the surface soil horizon (0-10 cm) as precipitation increased, and conversely more in the deeper soil layers (10-30 cm) as precipitation decreased. This response in root foraging appears to be a strategy to satisfy plant water requirements and partially explains the stable NPP allocation patterns. Overall, our results suggest that plants can adjust their vertical BNPP distribution in response to drought stress, and that only under extreme drought does the optimal partitioning theory strictly apply, highlighting the context dependency of the adaption and growth of plants under changing precipitation.

The unprecedented loss of Florida's reef-building corals and the emergence of a novel coral-reef assemblage.

Abstract: Over the last half century, climate change, coral disease, and other anthropogenic disturbances have restructured coral‐reef ecosystems on a global scale. The disproportionate loss of once‐dominant, reef‐building taxa has facilitated relative increases in the abundance of “weedy” or stress‐tolerant coral species. Although the recent transformation of coral‐reef assemblages is unprecedented on ecological timescales, determining whether modern coral reefs have truly reached a novel ecosystem state requires evaluating the dynamics of reef composition over much longer periods of time. Here, we provide a geologic perspective on the shifting composition of Florida's reefs by reconstructing the millennial‐scale spatial and temporal variability in reef assemblages using 59 Holocene reef cores collected throughout the Florida Keys Reef Tract (FKRT). We then compare the relative abundances of reef‐building species in the Holocene reef framework to data from contemporary reef surveys to determine how much Florida's modern reef assemblages have diverged from long‐term baselines. We show that the composition of Florida's reefs was, until recently, remarkably stable over the last 8000 yr. The same corals that have dominated shallow‐water reefs throughout the western Atlantic for hundreds of thousands of years, Acropora palmata, Orbicella spp., and other massive coral taxa, accounted for nearly 90% of Florida's Holocene reef framework. In contrast, the species that now have the highest relative abundances on the FKRT, primarily Porites astreoides and Siderastrea siderea, were rare in the reef framework, suggesting that recent shifts in species assemblages are unprecedented over millennial timescales. Although it may not be possible to return coral reefs to pre‐Anthropocene states, our results suggest that coral‐reef management focused on the conservation and restoration of the reef‐building species of the past, will optimize efforts to preserve coral reefs, and the valuable ecosystem services they provide into the future.

Overcompensation for insect herbivory: a review and meta-analysis of the evidence.

Abstract: Not all herbivory is detrimental to plants. In some cases, plants can compensate for herbivory, maintain growth and fitness following damage, or even overcompensate for herbivory and perform better than if left undamaged. Examples of overcompensation to vertebrate herbivory are well known, but here we review the literature for examples of reproductive overcompensation (i.e., increased production of traits associated with fitness) and increased vegetative growth (i.e., vegetative overcompensation) following insect herbivory. We used a meta-analysis to explore the effects of plant growth form, evolutionary history, herbivore feeding guild, and other plant and insect traits on the expression of reproductive and vegetative overcompensation by plants. Our literature search revealed 86 studies documenting examples of overcompensation for insect herbivory by 67 plant species representing 26 families. These plants included monocots and dicots, annuals and perennials, and woody and herbaceous plants. We also found that varied insect herbivores induce overcompensation, including 75 insect species in six orders representing 27 families and myriad feeding guilds. In our meta-analysis, we calculated 53 effect sizes from 21 publications documenting reproductive overcompensation and 89 effect sizes from 40 publications documenting vegetative overcompensation. Variation in reproductive overcompensation was seen among plant growth forms, functional groups, cultivation, herbivore feeding sites, and plant and herbivore families. Variation in vegetative overcompensation was seen among plant families, herbivore families, and latitudinal gradients. We suggest overcompensation for insect herbivory may be far more prevalent than previously thought. Additional research focusing on the mechanisms, patterns, and ecological and evolutionary consequences of overcompensation for insect herbivory is likely to provide exciting new insights into this poorly understood and largely overlooked outcome of plant-insect interactions.

Behavior-specific habitat selection by African lions may promote their persistence in a human-dominated landscape

Abstract: Co-occurrence with humans presents substantial risks for large carnivores, yet human-dominated landscapes are increasingly crucial to carnivore conservation as human land use continues to encroach on wildlife habitat. Flexibility in large carnivore behavior may be a primary factor mediating coexistence with people, allowing carnivores to calibrate their activity and habitat use to the perceived level of human risk. However, our understanding of how large carnivores adjust the timing and location of behaviors in response to variations in human activity across the landscape remains limited, impacting our ability to identify important habitat for populations outside of protected areas. Here we examine whether African lions (Panthera leo) modify their behavior and habitat use in response to risk of a human encounter, and whether behavior-specific habitat selection allows lions to access feeding opportunities in a human-dominated landscape in Kenya. We determined fine-scale behavioral states for lions using high-resolution GPS and accelerometer data, and then investigated behavior-specific habitat selection at multiple temporal and spatial scales (ranging from 15 minutes to 12 hours and from approximately 200 meters to several kilometers). We found that lions exhibit substantial differences in habitat selection with respect to humans based on behavioral state and time of day. During the day, when risk of human encounter is highest, lions avoided areas of high human use when resting, meandering, and feeding. However, lions specifically selected for habitat near people when feeding at night. Flexible habitat use by lions thus permits access to prey, which appear to concentrate in areas near humans. The importance of habitat near people for feeding was only apparent when analyses explicitly accounted for lion behavioral state and spatiotemporal scale, highlighting the necessity of incorporating such information when investigating human impacts on large carnivore habitat use. Our results support the contention that behavior-specific habitat selection promotes carnivore persistence in human-dominated landscapes, demonstrating the importance of considering not just whether but how large carnivores use habitat near humans when managing vulnerable populations.

Trait probability density (TPD): measuring functional diversity across scales based on TPD with R.

Abstract: Functional diversity (FD) has the potential to address many ecological questions, from impacts of global change on biodiversity to ecological restoration. There are several methods estimating the different components of FD. However, most of these methods can only be computed at limited spatial scales and cannot account for intraspecific trait variability (ITV), despite its significant contribution to FD. Trait probability density (TPD) functions (which explicitly account for ITV) reflect the probabilistic nature of niches. By doing so, the TPD approach reconciles existing methods for estimating FD within a unifying framework, allowing FD to be partitioned seamlessly across multiple scales (from individuals to species, and from local to global scales), and accounting for ITV. We present methods to estimate TPD functions at different spatial scales and probabilistic implementations of several FD concepts, including the primary components of FD (functional richness, evenness, and divergence), functional redundancy, functional rarity, and solutions to decompose beta FD into nested and unique components. The TPD framework has the potential to unify and expand analyses of functional ecology across scales, capturing the probabilistic and multidimensional nature of FD. The R package TPD (https://CRAN.R-project.org/package=TPD) will allow users to achieve more comparative results across regions and case studies.

Kelp beds and their local effects on seawater chemistry, productivity, and microbial communities.

Abstract: Kelp forests are known as key habitats for species diversity and macroalgal productivity; however, we know little about how these biogenic habitats interact with seawater chemistry and phototroph productivity in the water column. We examined kelp forest functions at three locales along the Olympic Peninsula of Washington state by quantifying carbonate chemistry, nutrient concentrations, phytoplankton productivity, and seawater microbial communities inside and outside of kelp beds dominated by the canopy kelp species Nereocystis luetkeana and Macrocystis pyrifera. Kelp beds locally increased the pH, oxygen, and aragonite saturation state of the seawater, but lowered seawater inorganic carbon content and total alkalinity. Although kelp beds depleted nitrate and phosphorus concentrations, ammonium and dissolved organic carbon (DOC) concentrations were enhanced. Kelp beds also decreased chlorophyll concentrations and carbon fixed by phytoplankton, although kelp carbon fixation more than compensated for any difference in phytoplankton production. Kelp beds entrained distinct microbial communities, with higher taxonomic and phylogenetic diversity compared to seawater outside of the kelp bed. Kelp forests thus had significant effects on seawater chemistry, productivity and the microbial assemblages in their proximity. Thereby, the diversity of pathways for carbon and nitrogen cycling was also enhanced. Overall, these observations suggest that the contribution of kelp forests to nearshore carbon and nitrogen cycling is greater than previously documented.

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

Abstract: Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life, OTL). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel's λ and Blomberg's K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman's ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, was also highly correlated with estimates of Blomberg's K or close to Pagel's λ from purpose-built phylogenies when traits were simulated under Brownian motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

Coexistence and competitive exclusion in mutualism

Abstract: The competitive exclusion principle is fundamental to understanding coexistence. Well-established theories predict the conditions for coexistence in consumer-resource interactions. Given that species often compete for commodities offered by mutualists, competitive exclusion theory should also be critical to understanding how mutualisms function. We explicitly apply the competitive exclusion principle to mutualism and derive a rule analogous to Tilman's R* rule for exploitative competition. Coexistence is impossible when competitors compete solely for a shared partner-provided commodity because superior competitors deplete that commodity sufficiently to exclude inferior competitors. We then investigate how competition between two guild members for a partner-provided commodity and a resource external to the mutualism affects competitor coexistence. There are three key results. First, coexistence is possible via partitioning of a partner-provided commodity and another resource. Second, unlike in classic R* Theory, competitive outcomes are influenced both by species' abilities to obtain commodities and their mutualisms with the shared commodity-providing partner, which can indirectly alleviate competitors' commodity limitation. Third, the outcome of competition has important consequences for the commodity-providing partner, which depend on the type of mutualism and the competitive abilities of competing mutualists. This theory provides a novel framework for investigating how competitors for mutualistic commodities coexist in nature.

Multiple abiotic and biotic pathways shape biomass demographic processes in temperate forests

Abstract: Forests play a key role in regulating the global carbon cycle, and yet the abiotic and biotic conditions that drive the demographic processes that underpin forest carbon dynamics remain poorly understood in natural ecosystems. To address this knowledge gap, we used repeat forest inventory data from 92,285 trees across four large permanent plots (4-25 ha in size) in temperate mixed forests in northeast China to ask the following questions: (1) How do soil conditions and stand age drive biomass demographic processes? (2) How do vegetation quality (i.e., functional trait diversity and composition) and quantity (i.e., initial biomass stocks) influence biomass demographic processes independently from soil conditions and stand age? (3) What is the relative contribution of growth, recruitment, and mortality to net biomass change? Using structural equation modeling, we showed that all three demographic processes were jointly constrained by multiple abiotic and biotic factors and that mortality was the strongest determinant on net biomass change over time. Growth and mortality, as well as functional trait diversity and the community-weighted mean of specific leaf area (CWM SLA), declined with stand age. By contrast, high soil phosphorous concentrations were associated with greater functional diversity and faster dynamics (i.e., high growth and mortality rates), but associated with lower CWM SLA and initial biomass stock. More functionally diverse communities also had higher recruitment rates, but did not exhibit faster growth and mortality. Instead, initial biomass stocks and CWM SLA were stronger predictors of biomass growth and mortality, respectively. By integrating the full spectrum of abiotic and biotic drivers of forest biomass dynamics, our study provides critical system-level insights needed to predict the possible consequences of regional changes in forest diversity, composition, structure and function in the context of global change.

ATLANTIC-PRIMATES: a dataset of communities and occurrences of primates in the Atlantic Forests of South America.

Abstract: Primates play an important role in ecosystem functioning and offer critical insights into human evolution, biology, behavior, and emerging infectious diseases. There are 26 primate species in the Atlantic Forests of South America, 19 of them endemic. We compiled a dataset of 5,472 georeferenced locations of 26 native and 1 introduced primate species, as hybrids in the genera Callithrix and Alouatta. The dataset includes 700 primate communities, 8,121 single species occurrences and 714 estimates of primate population sizes, covering most natural forest types of the tropical and subtropical Atlantic Forest of Brazil, Paraguay and Argentina and some other biomes. On average, primate communities of the Atlantic Forest harbor 2 ± 1 species (range = 1-6). However, about 40% of primate communities contain only one species. Alouatta guariba (N = 2,188 records) and Sapajus nigritus (N = 1,127) were the species with the most records. Callicebus barbarabrownae (N = 35), Leontopithecus caissara (N = 38), and Sapajus libidinosus (N = 41) were the species with the least records. Recorded primate densities varied from 0.004 individuals/km2 (Alouatta guariba at Fragmento do Bugre, Parana, Brazil) to 400 individuals/km2 (Alouatta caraya in Santiago, Rio Grande do Sul, Brazil). Our dataset reflects disparity between the numerous primate census conducted in the Atlantic Forest, in contrast to the scarcity of estimates of population sizes and densities. With these data, researchers can develop different macroecological and regional level studies, focusing on communities, populations, species co-occurrence and distribution patterns. Moreover, the data can also be used to assess the consequences of fragmentation, defaunation, and disease outbreaks on different ecological processes, such as trophic cascades, species invasion or extinction, and community dynamics. There are no copyright restrictions. Please cite this Data Paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.

Statistical modeling of patterns in annual reproductive rates

Abstract: Reproduction by individuals is typically recorded as count data (e.g., number of fledglings from a nest or inflorescences on a plant) and commonly modeled using Poisson or negative binomial distributions, which assume that variance is greater than or equal to the mean. However, distributions of reproductive effort are often underdispersed (i.e., variance < mean). When used in hypothesis tests, models that ignore underdispersion will be overly conservative and may fail to detect significant patterns. Here we show that generalized Poisson (GP) and Conway-Maxwell-Poisson (CMP) distributions are better choices for modeling reproductive effort because they can handle both overdispersion and underdispersion; we provide examples of how ecologists can use GP and CMP distributions in generalized linear models (GLMs) and generalized linear mixed models (GLMMs) to quantify patterns in reproduction. Using a new R package, glmmTMB, we construct GLMMs to investigate how rainfall and population density influence the number of fledglings in the warbler Oreothlypis celata and how flowering rate of Heliconia acuminata differs between fragmented and continuous forest. We also demonstrate how to deal with zero-inflation, which occurs when there are more zeros than expected in the distribution, e.g., due to complete reproductive failure by some individuals.

Post-fire forest regeneration shows limited climate tracking and potential for drought-induced type conversion.

Abstract: Disturbance such as wildfire may create opportunities for plant communities to reorganize in response to climate change. The interaction between climate change and disturbance may be particularly important in forests, where many of the foundational plant species (trees) are long-lived and where poor initial tree establishment can result in conversion to shrub- or graminoid-dominated systems. The response of post-disturbance vegetation establishment to post-disturbance weather conditions, particularly to extreme weather, could therefore provide useful information about how forest communities will respond to climate change. We examined the effect of post-fire weather conditions on post-fire tree, shrub, and graminoid recruitment in fire-adapted forests in northern California, USA, by surveying regenerating vegetation in severely burned areas 4-5 yr after 14 different wildfires that burned between 2004 and 2012. This time period (2004-2016) encompassed a wide range of post-fire weather conditions, including a period of extreme drought. For the most common tree species, we observed little evidence of disturbance-mediated community reorganization or range shifts but instead either (1) low sensitivity of recruitment to post-fire weather or (2) weak but widespread decreases in recruitment under unusually dry post-fire conditions, depending on the species. The occurrence of a single strong drought year following fire was more important than a series of moderately dry years in explaining tree recruitment declines. Overall, however, post-fire tree recruitment patterns were explained more strongly by long-term climate and topography and local adult tree species abundance than by post-fire weather conditions. This observation suggests that surviving adult trees can contribute to a "biological inertia" that restricts the extent to which tree community composition will track changes in climate through post-disturbance recruitment. In contrast to our observations in trees, we observed substantial increases in shrub and graminoid establishment under post-fire drought, suggesting that shifts in dominance between functional groups may become more likely in a future with more frequent and intense drought.

Local adaptation of photoperiodic plasticity maintains life cycle variation within latitudes in a butterfly.

Abstract: The seasonal cycle varies geographically and organisms are under selection to express life cycles that optimally exploit their spatiotemporal habitats. In insects, this often means producing an annual number of generations (voltinism) appropriate to the local season length. Variation in voltinism may arise from variation in environmental factors (e.g., temperature or photoperiod) acting on a single reaction norm shared across populations, but it may also result from local adaptation of reaction norms. However, such local adaptation is poorly explored at short geographic distances, especially within latitudes. Using a combination of common-garden rearing and life cycle modeling, we have investigated the causal factors behind voltinism variation in Swedish populations of the butterfly Pararge aegeria, focusing on a set of populations that lie within a single degree of latitude but nonetheless differ in season length and voltinism. Despite considerable differences in ambient temperature between populations, modeling suggested that the key determinant of local voltinism was in fact interpopulation differences in photoperiodic response. These include differences in the induction thresholds for winter diapause, as well as differences in photoperiodic regulation of larval development, a widespread but poorly studied phenomenon. Our results demonstrate previously neglected ways that photoperiodism may mediate insect phenological responses to temperature, and emphasize the importance of local adaptation in shaping phenological patterns in general, as well as for predicting the responses of populations to changes in climate.

Plant–herbivore coevolution and plant speciation

Abstract: More than five decades ago, Ehrlich and Raven proposed a revolutionary idea-that the evolution of novel plant defense could spur adaptive radiation in plants. Despite motivating much work on plant-herbivore coevolution and defense theory, Ehrlich and Raven never proposed a mechanism for their "escape and radiate" model. Recent intriguing mechanisms proposed by Marquis et al. include sympatric divergence, pleiotropic effects of plant defense traits on reproductive isolation, and strong postzygotic isolation, but these may not be general features of herbivore-mediated speciation. An alternate view is that herbivores may impose strong divergent selection on defenses in allopatric plant populations, with plant-herbivore coevolution driving local adaptation resulting in plant speciation. Building on these ideas, we propose three scenarios that consider the role of herbivores in plant speciation. These include (1) vicariance, subsequent coevolution within populations and adaptive divergence between geographically isolated populations, (2) colonization of a new habitat lacking effective herbivores followed by loss of defense and then re-evolution and coevolution of defense in response to novel herbivores, and (3) evolution of a new defense followed by range expansion, vicariance, and coevolution. We discuss the general role of coevolution in plant speciation and consider outstanding issues related to understanding: (1) the mechanisms behind cospeciation of plants and insects, (2) geographic variation in defense phenotypes, (3) how defensive traits and geography map on plant phylogenies, and (4) the role of herbivores in driving character displacement in defense phenotypes of related species in sympatry.

Quantifying evenness and linking it to diversity, beta diversity, and similarity.

Abstract: An enormous number of measures based on different criteria have been proposed to quantify evenness or unevenness among species relative abundances in an assemblage. However, a unified approach that can encompass most of the widely used indices is still lacking. Here, we first present some basic requirements for an evenness measure. We then propose that unevenness among species relative abundances in an assemblage can be measured by a normalized divergence between the vector of species relative abundances and the mean vector, where the mean vector represents the species relative abundances of a completely even assemblage. Thus, evenness among species relative abundances is measured by the corresponding normalized extent of closeness between these two vectors. We consider five divergence measures, leading to five classes of evenness indices. All our evenness measures are in terms of diversity (Hill number) of order q > 0 (here q controls the weighting of species relative abundances) and species richness (diversity of order q = 0). We propose quantifying evenness through a continuous profile that depicts evenness as a function of diversity order q > 0. The profiles can be easily and visually compared across multiple assemblages. Our evenness indices satisfy all the requirements presented in this paper and encompass many widely used evenness measures as special cases. When there are multiple assemblages, the abundance-based Jaccard- and Sorensen-type dissimilarity measures (which are monotonic functions of beta diversity) can be expressed as weighted averages of the individual species' compositional unevenness values; here, each individual species' compositional unevenness is calculated based on that species' abundances among assemblages. The contribution of a species to each dissimilarity measure can be clearly disentangled and quantified in terms of this single species' compositional unevenness among assemblages. Thus, our framework links the concepts of evenness, diversity, beta diversity, and similarity. Moreover, the framework can be readily extended to a phylogenetic version. A real data example is used to illustrate our approach. We also discuss some criteria and other measures that were previously proposed in the literature.

The Australian National Rabbit Database: 50 yr of population monitoring of an invasive species.

Abstract: With ongoing introductions into Australia since the 1700s, the European rabbit (Oryctolagus cuniculus) has become one of the most widely distributed and abundant vertebrate pests, adversely impacting Australia's biodiversity and agroeconomy. To understand the population and range dynamics of the species and its impacts better, occurrence and abundance data have been collected by researchers and citizens from sites covering a broad spectrum of climatic and environmental conditions in Australia. The lack of a common and accessible repository for these data has, however, limited their use in determining important spatiotemporal drivers of the structure and dynamics of the geographical range of rabbits in Australia. To meet this need, we created the Australian National Rabbit Database, which combines more than 50Â yr of historical and contemporary survey data collected from throughout the range of the species in Australia. The survey data, obtained from a suite of complementary monitoring methods, were combined with high-resolution weather, climate, and environmental information, and an assessment of data quality. The database provides records of rabbit occurrence (689,265 records) and abundance (51,241 records, >120 distinct sites) suitable for identifying the spatiotemporal drivers of the rabbit's distribution and for determining spatial patterns of variation in its key life-history traits, including maximum rates of population growth. Because all data are georeferenced and date stamped, they can be coupled with information from other databases and spatial layers to explore the potential effects of rabbit occurrence and abundance on Australia's native wildlife and agricultural production. The Australian National Rabbit Database is an important tool for understanding and managing the European rabbit in its invasive range and its effects on native biodiversity and agricultural production. It also provides a valuable resource for addressing questions related to the biology, success, and impacts of invasive species more generally. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.