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The successful movement of individuals is fundamental to life. Facilitating these movements by promoting ecological connectivity has become a central theme in ecology and conservation. Urban areas contain more than half of the world's human population, and their potential to support biodiversity and to connect their citizens to nature is increasingly recognized. Promoting ecological connectivity within these areas is essential to reaching this potential. However, our current understanding of ecological connectivity within urban areas appears limited., We reviewed the published scientific literature to assess the state-of-the-art of ecological connectivity research in urban areas, summarized trends in study attributes and highlighted knowledge gaps., We found 174 papers that investigated ecological connectivity within urban areas. These papers addressed either structural (48) or functional connectivity (111), and some addressed both (15), but contained substantial geographic and taxonomic biases. These papers rarely defined the aspect of connectivity they were investigating and objective descriptions of the local urban context were uncommon. Formulated hypotheses or a priori predictions were typically unstated and many papers used suboptimal study designs and methods., We suggest future studies explicitly consider and quantify the landscape within their analyses and make greater use of available and rapidly developing tools and methods for measuring functional connectivity (e.g. biotelemetry or landscape genetics). We also highlight the need for studies to clearly define how the terms ' urban' and ' connectivity' have been applied., Knowledge gaps in ecological connectivity in urban areas remain, partly because the field is still in its infancy and partly because we must better capitalize on the state-of-the-art technological and analytical techniques that are increasingly available. Well-designed studies that employed high-resolution data and powerful analytical techniques highlight our abilities to quantify ecological connectivity in urban areas. These studies are exemplary, setting the standards for future research to facilitate data-driven and evidence-based biodiversity-friendly infrastructure planning in urban areas. [ABSTRACT FROM AUTHOR]

When we launched the journal in 2010, we did so because of feedback from the community that there was a need for a journal that promoted the publication of new methods. In 2010, there was no existing journal that specialized in publishing methods papers in ecology or evolutionary biology. I Methods in Ecology and Evolution i set out to publish across the disciplines of ecology and evolutionary biology. [Extracted from the article]

Defining mathematical terms and objects is a constant issue in ecology; often definitions are absent, erroneous, or imprecise. Through a bibliographic prospection, we show that this problem appears in macro‐ecology (biogeography and community ecology) where the lack of definition for the sigmoid class of functions results in difficulties of interpretation and communication. In order to solve this problem and to help harmonize papers that use sigmoid functions in ecology, herein we propose a comprehensive definition of these mathematical objects. In addition, to facilitate their use, we classified the functions often used in the ecological literature, specifying the constraints on the parameters for the function to be defined and the curve shape to be sigmoidal. Finally, we interpreted the different properties of the functions induced by the definition through ecological hypotheses in order to support and explain the interest of such functions in ecology and more precisely in biogeography. [ABSTRACT FROM AUTHOR]

There are many barriers to fieldwork including cost, time, and physical ability. Unfortunately, these barriers disproportionately affect minority communities and create a disparity in access to fieldwork in the natural sciences. Travel restrictions, concerns about our carbon footprint, and the global lockdown have extended this barrier to fieldwork across the community and led to increased anxiety about gaps in productivity, especially among graduate students and early‐career researchers. In this paper, we discuss agent‐based modeling as an open‐source, accessible, and inclusive resource to substitute for lost fieldwork during COVID‐19 and for future scenarios of travel restrictions such as climate change and economic downturn. We describe the benefits of Agent‐Based models as a teaching and training resource for students across education levels. We discuss how and why educators and research scientists can implement them with examples from the literature on how agent‐based models can be applied broadly across life science research. We aim to amplify awareness and adoption of this technique to broaden the diversity and size of the agent‐based modeling community in ecology and evolutionary research. Finally, we discuss the challenges facing agent‐based modeling and discuss how quantitative ecology can work in tandem with traditional field ecology to improve both methods. [ABSTRACT FROM AUTHOR]

In tribute to Dr. Robert N. Ginsburg (1925–2017), we examine his 1991 seminal paper Controversies about Stromatolites: Vices and Virtues, which summarized current ideas about stromatolites including controversies of definition, whether ancient stromatolites should be interpreted as sedimentary structures and mechanisms of carbonate fixation. The accepted model of stromatolite morphogenesis in 1991 was that biology controls microscale internal structure whereas environment controls macroscale morphology. Ginsburg, however, predicted that biology and environmental influences on stromatolite growth were closely coupled at macro, meso and micro scales. Recent research in Hamelin Pool and the Bahamas has advanced our understanding of the inherent duality of stromatolites and associated controversies. These studies suggest that at the macroscale, when physical forces are strong, the environment is the main control on the morphology; however, when physical forces are weak, biological communities become the main drivers of morphology. Therefore, stromatolites can be considered both as fossils and as sedimentary structures dependent on the energy in the environment of deposition. At the mesoscale, as predicted by Trompette, stromatolite fabrics are influenced equally by environment and biology. As the degree of lamination is often unknown or heterogeneous, a generic genetic term such as 'microbialite' is considered the most appropriate terminology for structures of probable microbial origin. At the microscale, stromatolite microfabrics reflect environmentally driven cycling of microbial communities, reflecting both biology and environment. With respect to carbonate fixation, research on modern stromatolites provides a model for biofilm precipitation of micritic laminae lacking microfossils in ancient stromatolites. As pointed out by Ginsburg, the inherent duality of environmental and biological controls of morphogenesis at all scales is at the root of many long‐standing controversies. Recent investigations corroborate the foresight of Ginsburg nearly 30 years ago, further confirming well‐preserved stromatolites can provide insight into both biology and environmental factors in ancient ecosystems. [ABSTRACT FROM AUTHOR]

The modeling of ecological data that include both abiotic and biotic factors is fundamental to our understanding of ecosystems. Repositories of biodiversity data, such as GBIF, iDigBio, Atlas of Living Australia, and SNIB (Mexico's National System of Biodiversity Information), contain a great deal of information that can lead to knowledge discovery about ecosystems. However, there is a lack of tools with which to efficiently extract such knowledge. In this paper, we present SPECIES, an open, web‐based platform designed to extract implicit information contained in large scale sets of ecological data. SPECIES is based on a tested methodology, wherein the correlations of variables of arbitrary type and spatial resolution, both biotic and abiotic, discrete and continuous, may be explored from both niche and network perspectives. In distinction to other modeling systems, SPECIES is a full stack exploratory tool that integrates the three basic components: data (which is incrementally growing), a statistical modeling and analysis engine, and an interactive visualization front end. Combined, these components provide a powerful tool that may guide ecologists toward new insights. SPECIES is optimized to support fast hypothesis prototyping and testing, analyzing thousands of biotic and abiotic variables, and presenting descriptive results to the user at different levels of detail. SPECIES is an open‐access platform available online (http://species.conabio.gob.mx), that is, powerful, flexible, and easy to use. It allows for the exploration and incorporation of ecological data and its subsequent integration into predictive models for both potential ecological niche and geographic distribution. It also provides an ecosystemic, network‐based analysis that may guide the researcher in identifying relations between different biota, such as the relation between disease vectors and potential disease hosts. SPECIES, an open web‐based platform designed for the exploratory analysis of large‐scale ecological datasets. SPECIES provides two perspectives: one based on ecological niche and geographic distribution modeling, and the other on ecological networks. SPECIES is optimized to support fast hypotheses prototyping and testing, analyzing thousands of biotic and abiotic variables and presenting descriptive results to the user at different levels of detail. [ABSTRACT FROM AUTHOR]

Information on yellow perch Perca flavescens population dynamics and responses to various abiotic and biotic factors in oligotrophic, north‐temperate inland lakes is limited. Water level fluctuations are known to influence available habitat and biological communities within the littoral zones of lakes, yet research is lacking for yellow perch in Wisconsin. The goal of our study was to characterize yellow perch population‐level responses to natural water level fluctuations in four northern Wisconsin lakes using a 39‐year time series. On average, increasing water level periods correlated with lower mean fyke net and gill net relative abundances (catch‐per‐unit‐effort), though generally not statistically significant. Yellow perch mean relative weight varied among lakes and was significantly greater during increasing water level periods for all lakes except one. The lack of statistically significant findings potentially suggests a buffering mechanism of north‐temperate oligotrophic lakes due to their small surface area to volume ratios, relative lack of nutrients, and(or) littoral structural habitat compared to other systems (e.g., shallow eutrophic lakes). Our results suggest that natural water level fluctuations may not be an environmental concern for yellow perch populations in some north‐temperate oligotrophic inland lakes. [ABSTRACT FROM AUTHOR]

Robert M. "Bob" May, Lord May of Oxford, O.M., who was the second recipient of the Ecological Society of America's Robert H. MacArthur Award, passed away at the age of 84 in Oxford, UK, on April 28, after a long illness. After a brief return to Australia, May was hired at Princeton to be a colleague of MacArthur and others; but sadly, he became in effect MacArthur's replacement after the latter's untimely death. Both Birch, who won the ESA's Eminent Ecologist Award in 1988, and the brilliant physicist Freeman Dyson, who was at the Princeton Institute for Advanced Study when May visited on a sabbatical in 1971, had suggested that Bob talk with MacArthur about whether he should change fields and become a theoretical ecologist. Bob continued to retain a Visiting Professorship at Princeton, where he would visit Princeton colleagues and friends and lecture on almost an annual basis until his declining health made that impossible; he received an honorary degree along with President Bill Clinton at Princeton's 250th anniversary in 1996. [Extracted from the article]

Copyright of African Journal of Ecology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Summary: Genome size varies 2400‐fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat 'communities' are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective.We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors.We show that palm genome size and repeat 'community' composition are best explained by aridity. Specifically, Ty3‐gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1‐copia and LINE elements were more abundant in drier environments.Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress‐response genes (e.g. Ty1‐copia) have amplified in arid‐adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat 'communities'. [ABSTRACT FROM AUTHOR]

A survey was distributed to members of the Ecological Society of America in 2014, which asked respondents to rate the usefulness of 131 of the most common, current ecological concepts. As part of the survey, key demographic and professional information was requested from respondents, including age, gender, education level, sector of employment, and primary area (i.e., domain) of interest in ecology. This paper reports how those factors interacted and affected concept ratings. Comprehensive analysis revealed many significant patterns. Among these, we discovered that concept ratings almost invariably increased with age, often dramatically. Also, there was a very strong tendency for males to rate concepts, in general, higher than did females, but the magnitudes of these differences were small. Furthermore, there was a significant gulf between the academic and government employment categories, characterized by academic respondents having rated most concepts higher. This research is important to the ecological community as a quantitative description of the kinds of variation existing among its constituents in terms of types and degrees of concept utility. Self‐knowledge is critical for understanding the discipline and for advancing its educational, research, and environmental initiatives. [ABSTRACT FROM AUTHOR]

Ecology and environmental science graduate degrees often involve fieldwork, frequently led by the graduate student. Few formal resources exist to support graduate students in successfully planning and implementing a data collection field campaign, even though this experience may be fundamental to completing a graduate degree. Graduate fieldwork requires leading and managing a team, often in unique circumstances (including long hours, remote regions, etc.), and therefore can be challenging even for those with previous leadership or field experience. Our objectives were to (1) collect general advice for graduate students on leading fieldwork safely and effectively, (2) solicit specific suggestions on resources and actions to take before, during, and after the field season, and (3) develop a series of recommendations for labs, departments, and universities to better prepare and support their students. We developed a survey to solicit community input and distributed it widely to the ecological sciences community via email LISTSERVs and social media. Here, we present results from the survey responses, including a summary of the perceived challenges that graduate students face while leading their own fieldwork, suggestions for how to prepare and complete fieldwork successfully, and a compilation of resources. Graduate field leaders can improve success via clear communication, risk assessment and procedural planning implemented before, during, and after the field season. Labs, principal investigators, departments, and professional societies can support graduate field leaders by formalizing institutional resources, financial support, and incentivizing skill development. Field leadership is a critical skill to develop during graduate education, and contributes to the success, retention, and advancement of researchers in the natural sciences. [ABSTRACT FROM AUTHOR]

Next‐Generation Sequencing (NGS) is a powerful tool that has been rapidly adopted by many ecologists studying microbial communities. Despite the exciting demonstration of NGS technology as a tool for ecological research, cryptic pitfalls inherent to its use can obscure correct interpretation of NGS data. Here, we provide an accessible overview of a NGS process that uses marker gene amplicon sequences (MGAS) that will allow scientists, particularly community ecologists, to make appropriate methodological choices and understand limits on inference about community composition and diversity that can be drawn from MGAS data.We describe the MGAS pipeline, focusing specifically on cryptic sources of variation that have received less emphasis in the ecological literature, but which may substantially impact inference about microbial community diversity and composition. By simulating communities from published microbiome data, we demonstrate how these sources of variation can generate inaccurate or misleading patterns.We specifically highlight sample dilution without researcher awareness and lane‐to‐lane variability, two cryptic sources of variation arising during the MGAS pipeline. These sources of variation affect estimates of species presence and relative abundance, particularly for species with moderate to low abundances. Each of these sources of bias can lead to errors in the estimation of both absolute and relative abundance within, and turnover among, microbial communities.Awareness and understanding of what happens and, specifically, why it happens during MGAS generation is key to generating a strong dataset and building a robust community matrix. Requesting sample dilution information from the sequencing centre, including technical replicates across sequencing lanes, and understanding how sampling intensity and community taxa distribution patterns shape the measurement of community richness, evenness and diversity are critical for drawing correct ecological inferences using MGAS data. [ABSTRACT FROM AUTHOR]

As we build a more diverse, equitable, and inclusive culture in the ecological research community, we must work to support new ecologists by empowering them with the knowledge, tools, validation, and sense of belonging in ecology to succeed. Undergraduate research experiences (UREs) are critical for a student's professional and interpersonal skill development and key for recruiting and retaining students from diverse groups to ecology. However, few resources exist that speak directly to an undergraduate researcher on the diversity, equity, and inclusion (DEI) dimensions of embarking on a first research experience. Here, we write primarily for undergraduate readers, though a broader audience of readers, especially URE mentors, will also find this useful. We explain many of the ways a URE benefits undergraduate researchers and describe how URE students from different positionalities can contribute to an inclusive research culture. We address three common sources of anxiety for URE students through a DEI lens: imposter syndrome, communicating with mentors, and safety in fieldwork. We discuss the benefits as well as the unique vulnerabilities and risks associated with fieldwork, including the potential for harassment and assault. Imposter syndrome and toxic field experiences are known to drive students, including students from underrepresented minority groups, out of STEM. Our goal is to encourage all students, including those from underrepresented groups, to apply for UREs, build awareness of their contributions to inclusion in ecology research, and provide strategies for overcoming known barriers. [ABSTRACT FROM AUTHOR]

R is an open‐source programming environment for statistical computing and graphics structured by numerous contributed packages. The current packages used for biodiversity research focus on limited, particular aspects of biodiversity. Most packages focus on the number and abundance of species.I present an r package named adiv that provides additional methods to measure and analyse biodiversity. adiv contains approaches to quantify species‐based, trait‐based (functional) and phylogenetic diversity (a) within communities (α diversity), (b) between communities (β diversity) and (c) to partition it over space and time (α, β and γ levels of diversity). Partitioning approaches allow evaluating whether the levels of α and β diversity could have been obtained by chance. Moreover, groups of biological entities (e.g. species of the same clade or with similar biological characteristics) that drive each level of diversity (α, β and γ) can be identified via ordination analyses.Although the package focuses on interspecific diversity in its current state, the developed approaches can also be applied to analyse intraspecific diversity or, at another level, ecosystem diversity. More generally, the functions can be applied in any discipline interested in the concept of diversity, such as economics or linguistics. Indeed, all available approaches can be easily applied at other scales and to other disciplines provided that the data have the required format: a matrix of abundance or presence/absence data of some entities in some collections and information on the differences between the entities.adiv aims to complement existing r packages to provide scientists with a wide variety of diversity indices, as each index reflects a very specific facet of biodiversity. adiv will grow in the future to integrate as many validated approaches for biodiversity analysis as possible, not yet available in r. As it includes both traditional and recent viewpoints on how biodiversity should be evaluated, adiv offers a promising platform where methods to analyse biodiversity can be developed and compared in terms of their statistical behaviour and biological relevance. Applications of the most relevant tools for a given study aim will eventually improve research on human‐driven variations in biodiversity. [ABSTRACT FROM AUTHOR]

Cancer is a disease of single cells that expresses itself at the population level. The striking similarities between initiation and growth of tumors and dynamics of biological populations, and between metastasis and ecological invasion and community dynamics suggest that oncology can benefit from an ecological perspective to improve our understanding of cancer biology. Tumors can be viewed as complex, adaptive, and evolving systems as they are spatially and temporally heterogeneous, continually interacting with each other and with the microenvironment and evolving to increase the fitness of the cancer cells. We argue that an eco-evolutionary perspective is essential to understand cancer biology better. Furthermore, we suggest that ecologically informed therapeutic approaches that combine standard of care treatments with strategies aimed at decreasing the evolutionary potential and fitness of neoplastic cells, such as disrupting cell-to-cell communication and cooperation, and preventing successful colonization of distant organs by migrating cancer cells, may be effective in managing cancer as a chronic condition. [ABSTRACT FROM AUTHOR]

The global movement of species by humans to non-native ranges has provided important resources for food, fiber, and fuel but has, at times, resulted in widespread invasions that cause significant ecological and economic impacts (Pysek et al.). However, the impacts of invasions on native species varied according to a complex interplay between local site characteristic and invasive species' density (Franzese et al.). And (2) to what extent will native species responses to invader removal depend on invasive species density at the time of management initiation?. [Extracted from the article]

Functional traits have long been considered the 'holy grail' in community ecology due to their potential to link phenotypic variation with ecological processes. Advancements across taxonomic disciplines continue to support functional ecology's objective to approach generality in community assembly. However, a divergence of definitions, aims and methods across taxa has created discord, limiting the field's predictive capacity. Here, we provide a guide to support functional ecological comparisons across taxa. We describe advances in cross‐taxa functional research, identify gaps in approaches, synthesize definitions and unify methodological considerations. When deciding which traits to compare, particularly response traits, we advocate selecting functionally analogous traits that relate to community assembly processes. Finally, we describe at what scale and for which questions functional comparisons across taxa are useful and when other approaches may be more constructive. Our approach promotes standardized methods for integrative research across taxa to identify broad trends in community assembly. [ABSTRACT FROM AUTHOR]

Descriptions of ecological networks typically assume that the same interspecific interactions occur each time a community is observed. This contrasts with the known stochasticity of ecological communities: community composition, species abundances and link structure all vary in space and time. Moreover, finite sampling generates variation in the set of interactions actually observed. For interactions that have not been observed, most datasets will not contain enough information for the ecologist to be confident that unobserved interactions truly did not occur.Here, we develop the conceptual and analytical tools needed to capture uncertainty in the estimation of pairwise interactions. To define the problem, we identify the different contributions to the uncertainty of an interaction. We then outline a framework to quantify the uncertainty around each interaction by combining data on observed co‐occurrences with prior knowledge. We illustrate this framework using perhaps the most extensively sampled network to date.We found significant uncertainty in estimates for the probability of most pairwise interactions. This uncertainty can, however, be constrained with informative priors. This uncertainty scaled up to summary measures of network structure such as connectance and nestedness. Even with informative priors, we are likely to miss many interactions that may occur rarely or under different local conditions.Overall, we demonstrate the importance of acknowledging the uncertainty inherent in network studies, and the utility of treating interactions as probabilities in pinpointing areas where more study is needed. Most importantly, we stress that networks are best thought of as systems constructed from random variables, the stochastic nature of which must be acknowledged for an accurate representation. Doing so will fundamentally change network analyses and yield greater realism. [ABSTRACT FROM AUTHOR]

In the last decades, thousands of investigations confirmed the detrimental effects of species translocated by man outside of their native ranges (nonindigenous species, or NIS). However, results concluding that many NIS have null, neutral, or positive impacts on the biota and on human interests are as common in the scientific literature as those that point at baneful impacts. Recently, several scholars confronted the stand that origin per se is not a reliable indicator of negative effects, suggesting that such conclusions are the expression of scientific denialism, often led by spurious purposes, and that their numbers are increasing. When assessed in the context of the growing interest in introduced species, the proportion of academic publications claiming that NIS pose no threats to the environment and to social and economic interests is extremely low, and has not increased since 1990. The widely prevailing notion that many NIS are effectively or potentially harmful does not conflict with the fact that most have mixed (negative, neutral, and positive) impacts. When based on solid grounds, reports of positive or neutral impacts should not be labeled as manipulative or misleading unless proven otherwise, even if they may hamper interest in‐ and funding of research and control bioinvasion programs. Upon introduction, some species may have large effects on the recipient ecosystems, but these effects are not necessarily all harmful (upper panel). Most introduced species have mixed effects, negative for some resident species or processes and positive for others (middle panel). Many introduced species have no major impacts, which does not entail that their small effects are not favorable for some resident species and deleterious for others. There is no evidence in the scientific literature that the negative effects of NIS are systematically ignored or dismissed (pink background). [ABSTRACT FROM AUTHOR]

Understanding species’ responses to environmental conditions, and how these ­species–environment associations shape spatial distributions, are longstanding goals in ecology and biogeography. However, an essential component of species–environment relationships – the spatial unit, or grain, at which they operate – remains unresolved. We identify three components of scale‐dependence in analyses of species–environment associations: 1) response grain, the grain at which species respond most strongly to their environment; 2) environment spatial structure, the pattern of spatial autocorrelation intrinsic to an environmental factor; and 3) analysis grain, the grain at which analyses are conducted and ecological inferences are made. We introduce a novel conceptual framework that defines these scale components in the context of analyzing species–environment relationships, and provide theoretical examples of their interactions for species with various ecological attributes. We then use a virtual species approach to investigate the impacts of each component on common methods of measuring and predicting species–environment relationships. We find that environment spatial structure has a substantial impact on the ability of even simple, univariate species distribution models (SDMs) to recover known species–­environment associations at coarse analysis grains. For simulated environments with ‘fine’ and ‘intermediate’ spatial structure, model explanatory power, and the frequency with which simple SDMs correctly estimated a virtual species’ response to the simulated environment, dramatically declined as analysis grain increased. Informed by these results, we use a scaling analysis to identify maximum analysis grains for individual environmental factors, and a scale optimization procedure to determine the grain of maximum predictive accuracy. Implementing these analysis grain thresholds and model performance standards in an example east African study system yields more accurate distribution predictions, compared to SDMs independently constructed at arbitrary analysis grains. Finally, we integrate our conceptual framework with virtual and empirical results to provide practical recommendations for researchers asking common questions about species–environment relationships. [ABSTRACT FROM AUTHOR]

Abstract: Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition vs. plant–soil feedback (PSF) on plant performance is poorly understood. Using a meta‐analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter‐ vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide‐treated soil) depended on treatments but were predominantly negative, broadly comparable in magnitude, and additive or synergistic. Stronger competitors experienced more negative PSF than weaker competitors when controlling for density (inter‐ to intraspecific competition), suggesting that PSF could prevent competitive dominance and promote coexistence. When competition was measured against plants growing singly, the strength of competition overwhelmed PSF, indicating that the relative importance of PSF may depend not only on neighbour identity but also density. We evaluate how competition and PSFs might interact across resource gradients; PSF will likely strengthen competitive interactions in high resource environments and enhance facilitative interactions in low‐resource environments. Finally, we provide a framework for filling key knowledge gaps and advancing our understanding of how these biotic interactions influence community structure. [ABSTRACT FROM AUTHOR]

Theory predicts that interspecific tradeoffs are primary determinants of coexistence and community composition. Using information from empirically observed tradeoffs to augment the parametrisation of mechanism-based models should therefore improve model predictions, provided that tradeoffs and mechanisms are chosen correctly. We developed and tested such a model for 35 grassland plant species using monoculture measurements of three species characteristics related to nitrogen uptake and retention, which previous experiments indicate as important at our site. Matching classical theoretical expectations, these characteristics defined a distinct tradeoff surface, and models parameterised with these characteristics closely matched observations from experimental multi-species mixtures. Importantly, predictions improved significantly when we incorporated information from tradeoffs by 'snapping' characteristics to the nearest location on the tradeoff surface, suggesting that the tradeoffs and mechanisms we identify are important determinants of local community structure. This 'snapping' method could therefore constitute a broadly applicable test for identifying influential tradeoffs and mechanisms. [ABSTRACT FROM AUTHOR]

The article discusses history and evolution of ecological sciences. Topics discussed includes role of botanist Johannes Warming on the study of plant-communities, influence of inanimate environments upon plant communities, and study of A. J. Lotka on regulation of ecosystem function in terms of ecological relationships of the component populations.

Species establishment within a community depends on their interactions with the local environment and resident community. Such environmental and biotic filtering is frequently inferred from functional trait and phylogenetic patterns within communities; these patterns may also predict which additional species can establish. However, differentiating between environmental and biotic filtering can be challenging, which may complicate establishment predictions. Creating a habitat-specific species pool by identifying which absent species within the region can establish in the focal habitat allows us to isolate biotic filtering by modeling dissimilarity between the observed and biotically excluded species able to pass environmental filters. Similarly, modeling the dissimilarity between the habitat-specific species pool and the environmentally excluded species within the region can isolate local environmental filters. Combined, these models identify potentially successful phenotypes and why certain phenotypes were unsuccessful. Here, we present a framework that uses the functional dissimilarity among these groups in logistic models to predict establishment of additional species. This approach can use multivariate trait distances and phylogenetic information, but is most powerful when using individual traits and their interactions. It also requires an appropriate distance-based dissimilarity measure, yet the two most commonly used indices, nearest neighbor (one species) and mean pairwise (all species) distances, may inaccurately predict establishment. By iteratively increasing the number of species used to measure dissimilarity, a functional neighborhood can be chosen that maximizes the detection of underlying trait patterns. We tested this framework using two seed addition experiments in calcareous grasslands. Although the functional neighborhood size that best fits the community's trait structure depended on the type of filtering considered, selecting these functional neighborhood sizes allowed our framework to predict up to 50% of the variation in actual establishment from seed. These results indicate that the proposed framework may be a powerful tool for studying and predicting species establishment. [ABSTRACT FROM AUTHOR]

Plant distributions are expected to shift in response to climate change, and range expansion dynamics will be shaped by the performance of individuals at the colonizing front. These plants will encounter new biotic communities beyond their range edges, and the net outcome of these encounters could profoundly affect colonization success. However, little is known about how biotic interactions vary across range edges and this has hindered efforts to predict changes in species distributions in response to climate change. In contrast, a rich literature documents how biotic interactions within species ranges vary according to distance to and density of conspecific individuals. Here, we test whether this framework can be extended to explain how biotic interactions differ beyond range edges, where conspecific adults are basically absent. To do so, we planted seven species of trees along a 450-km latitudinal gradient that crossed the current distributional range of five of these species and monitored foliar disease and invertebrate herbivory over 5 yr. Foliar disease and herbivory were analyzed as a function of distance to and density of conspecific and congeneric trees at several spatial scales. We found that within species ranges foliar disease was lower for seedlings that were farther from conspecific adults for Acer rubrum, Carya glabra, Quercus alba, and Robinia pseudoacacia. Beyond range edges, there was even less foliar disease for C. glabra, Q. alba, and R. pseudoacacia ( A. rubrum was not planted outside its range). Liriodendron tulipifera did not experience reduced disease within or beyond its range. In contrast, Quercus velutina displayed significant but idiosyncratic patterns in disease at varying distances from conspecifics. Patterns of distance dependent herbivory across spatial scales was generally weak and in some cases negative (i.e., seedlings farther from conspecific adults had more herbivory). Overall, we conclude that differences in biotic interactions across range edges can be thought of as a spatial extension to the concept of distance dependent biotic interactions. This framework also provides the basis for general predictions of how distance dependent biotic interactions will change across range edges in other systems. [ABSTRACT FROM AUTHOR]

Model-based methods have emerged as a powerful approach for analysing multivariate abundance data in community ecology. Key applications include model-based ordination, modelling the various sources of correlations across species, and making inferences while accounting for these between species correlations., boral (version 0.9.1, licence GPL-2) is an r package available on cran for model-based analysis of multivariate abundance data, with estimation performed using Bayesian Markov chain Monte Carlo methods. A key feature of the boral package is the ability to incorporate latent variables as a parsimonious method of modelling between species correlation., Pure latent variable models offer a model-based approach to unconstrained ordination, for visualizing sites and the indicator species characterizing them on a low-dimensional plot., Correlated response models consist of fitting generalized linear models to each species, while including latent variables to account for residual correlation between species, for example, due to unmeasured covariates. [ABSTRACT FROM AUTHOR]

Urban transmission of arthropod-vectored disease has increased in recent decades. Understanding and managing transmission potential in urban landscapes requires integration of sociological and ecological processes that regulate vector population dynamics, feeding behaviour and vector-pathogen interactions in these unique ecosystems. Vectorial capacity is a key metric for generating predictive understanding about transmission potential in systems with obligate vector transmission. This review evaluates how urban conditions, specifically habitat suitability and local temperature regimes, and the heterogeneity of urban landscapes can influence the biologically relevant parameters that define vectorial capacity: vector density, survivorship, biting rate, extrinsic incubation period and vector competence., Incidence of vector-borne disease in urban host populations is rarely, if ever, evenly distributed across an urban area. The persistence and quality of vector habitat can vary significantly across socio-economic boundaries to influence vector species composition and abundance, often generating socio-economically distinct gradients of transmission potential across neighbourhoods., Urban regions often experience unique temperature regimes, broadly termed urban heat islands ( UHI). Arthropod vectors are ectothermic organisms, and their growth, survival and behaviour are highly sensitive to environmental temperatures. Vector response to UHI conditions is dependent on regional temperature profiles relative to the vector's thermal performance range. In temperate climates, UHI can facilitate increased vector development rates while having countervailing influence on survival and feeding behaviour. Understanding how urban heat island ( UHI) conditions alter thermal and moisture constraints across the vector life cycle to influence transmission processes is an important direction for both empirical and modelling research., There remain persistent gaps in understanding of vital rates and drivers in mosquito-vectored disease systems, and vast holes in understanding for other arthropod-vectored diseases. Empirical studies are needed to better understand the physiological constraints and socio-ecological processes that generate heterogeneity in critical transmission parameters, including vector survival and fitness. Likewise, laboratory experiments and transmission models must evaluate vector response to realistic field conditions, such as variability in sociological and environmental conditions. [ABSTRACT FROM AUTHOR]

900I.900II.901III.901IV.902V.905VI.908909References909 Summary: Integrative concepts of the biosphere, ecosystem, biogeocenosis and, recently, Earth's critical zone embrace scientific disciplines that link matter, energy and organisms in a systems‐level understanding of our remarkable planet. Here, we assert the congruence of Tansley's (1935) venerable ecosystem concept of ‘one physical system’ with Earth science's critical zone. Ecosystems and critical zones are congruent across spatial–temporal scales from vegetation‐clad weathering profiles and hillslopes, small catchments, landscapes, river basins, continents, to Earth's whole terrestrial surface. What may be less obvious is congruence in the vertical dimension. We use ecosystem metabolism to argue that full accounting of photosynthetically fixed carbon includes respiratory CO2 and carbonic acid that propagate to the base of the critical zone itself. Although a small fraction of respiration, the downward diffusion of CO2 helps determine rates of soil formation and, ultimately, ecosystem evolution and resilience. Because life in the upper portions of terrestrial ecosystems significantly affects biogeochemistry throughout weathering profiles, the lower boundaries of most terrestrial ecosystems have been demarcated at depths too shallow to permit a complete understanding of ecosystem structure and function. Opportunities abound to explore connections between upper and lower components of critical‐zone ecosystems, between soils and streams in watersheds, and between plant‐derived CO2 and deep microbial communities and mineral weathering. See also the Commentary by Dan Binkley [ABSTRACT FROM AUTHOR]

Hundreds of experiments have now manipulated species richness ( SR) of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity (PD) among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than SR because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis., Here, we reanalyse data from 16 experiments that have manipulated plant SR in grassland ecosystems and examined the impact on above-ground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the PD of plants impacts average community biomass production as well as the stability of community biomass production through time., Using four complementary analyses, we show that, after statistically controlling for variation in SR, PD (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. However, after controlling for SR, PD was positively related to variation in community biomass over time due to an increase in the variances of individual species, but this relationship was not strong enough to influence community stability., In contrast to the non-significant relationships between PD, biomass and stability, our analyses show that SR per se tends to increase the mean biomass production of plant communities, after controlling for PD. The relationship between SR and temporal variation in community biomass was either positive, non-significant or negative depending on which analysis was used. However, the increases in community biomass with SR, independently of PD, always led to increased stability. These results suggest that PD is no better as a predictor of ecosystem functioning than SR., Synthesis. Our study on grasslands offers a cautionary tale when trying to relate PD to ecosystem functioning suggesting that there may be ecologically important trait and functional variation among species that is not explained by phylogenetic relatedness. Our results fail to support the hypothesis that the conservation of evolutionarily distinct species would be more effective than the conservation of SR as a way to maintain productive and stable communities under changing environmental conditions. [ABSTRACT FROM AUTHOR]

The author discusses the various aspects of ecosystems in four dimensions. He talks about the classical importance of defining spatial boundaries with the development of geographical information systems and mathematical approaches for dealing with gradients of change. Also tackled is the relationship between plants and soils.

The microbes contained within free‐living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across four mesic prairies in the central United States. Composition of fungal endophyte communities differed among sites and among individuals within a site, but was not consistently affected by experimental manipulation of nutrient supply to hosts (A. gerardii) or herbivore reduction via fencing. In contrast, mean fungal diversity was similar among sites but was limited by total plant biomass at the plot scale. Our work demonstrates that distributed experiments motivated by ecological theory are a powerful tool to unravel the multiscale processes governing microbial community composition and diversity. [ABSTRACT FROM AUTHOR]

The diversity–stability relationship is a long‐standing, central focus of community ecology. Two major challenges have impeded studies of the diversity–stability relationship (DSR): the difficulty in obtaining high‐quality longitudinal data sets; and the lack of a general theoretical framework that can encompass the enormous complexity inherent in "diversity," "stability," and their many interactions. Metagenomic "Big Data" now provide high quality longitudinal data sets, and the human microbiome project (HMP) offers an unprecedented opportunity to reinvigorate investigations of DSRs. We introduce a new framework for exploring DSRs that has three parts: (1) a cross‐scale measure of dominance with a simple mathematical form that can be applied simultaneously to individual species and entire communities and can be used to construct species dominance networks (SDNs); (2) analysis of SDNs based on special trio motifs, core‐periphery, rich‐club, and nested structures, and high salience skeletons; and (3) a synthesis of coarse‐scale core/periphery/community‐level stability modeling with fine‐scale analysis of SDNs that further reveals the stability properties of the community structures. We apply this new approach to data from the human vaginal microbiome of the HMP, simultaneously illustrating its utility in developing and testing theories of diversity and stability while providing new insights into the underlying ecology and etiology of a human microbiome‐associated disease. [ABSTRACT FROM AUTHOR]

Historical, evolutionary, and ecological processes jointly shape the structure of communities, and the relative influence of such process may vary from one region to another. Nevertheless, much of community ecology focuses on one or several communities in a given region. To assess the relative importance and the context‐dependency of processes shaping communities, studies in community ecology must be conducted across regions and along broad‐scale environmental gradients. Regionally, historical colonization and extinction events, as well as diversification, can influence community structure by shaping the pool of potential community members (i.e., the regional species pool). Locally, a suite of deterministic and stochastic processes can influence community structure. We constructed a large time‐calibrated phylogenetic tree for North American odonates and used analyses of phylogenetic community structure with explicit species pool definitions to assess the predominant processes structuring assemblages along a north–south environmental gradient spanning two biomes and 8° of latitude in eastern Canada. Phylogenetic analyses of 39 lentic (i.e., lake) odonate communities revealed that co‐occurring species were on average more closely related than expected by chance, but only in the temperate biome. In addition, site‐to‐site variation in phylogenetic structure across the temperate and boreal biomes was most strongly related to variation in water pH. The most alkaline lakes were in the temperate biome and were also the most phylogenetically clustered, suggesting that water pH acts as a main environmental filter of odonate communities. An alternative explanation was that the recent radiation of damselflies increased the diversity of this group relative to that of dragonflies in the temperate species pool, thereby leaving a signature of clustering in that biome. However, our comparative null model analyses with explicit species pool definitions at least partially ruled out this explanation. Somewhat contrary to previous hypotheses regarding the assembly of odonate communities, our results suggest that stochastic processes alone cannot account for community structure in odonates and that deterministic, niche‐based processes have a strong influence. [ABSTRACT FROM AUTHOR]