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Showing papers on "Ecology (disciplines) published in 2009"


Journal ArticleDOI
TL;DR: It is suggested that, similar to the manifold that tree species leaf traits cluster around the 'leaf economics spectrum', a similar 'wood economics spectrum' may be defined.
Abstract: Wood performs several essential functions in plants, including mechanically supporting aboveground tissue, storing water and other resources, and transporting sap. Woody tissues are likely to face physiological, structural and defensive trade-offs. How a plant optimizes among these competing functions can have major ecological implications, which have been under-appreciated by ecologists compared to the focus they have given to leaf function. To draw together our current understanding of wood function, we identify and collate data on the major wood functional traits, including the largest wood density database to date (8412 taxa), mechanical strength measures and anatomical features, as well as clade-specific features such as secondary chemistry. We then show how wood traits are related to one another, highlighting functional trade-offs, and to ecological and demographic plant features (growth form, growth rate, latitude, ecological setting). We suggest that, similar to the manifold that tree species leaf traits cluster around the 'leaf economics spectrum', a similar 'wood economics spectrum' may be defined. We then discuss the biogeography, evolution and biogeochemistry of the spectrum, and conclude by pointing out the major gaps in our current knowledge of wood functional traits.

2,408 citations


Journal ArticleDOI
TL;DR: Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation.
Abstract: The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earths biota in a time of rapid global change.

1,867 citations


Journal ArticleDOI
TL;DR: A citizen scientist is a volunteer who collects and/or processes data as part of a scientific enquiry, particularly in ecology and the environmental sciences.
Abstract: A citizen scientist is a volunteer who collects and/or processes data as part of a scientific enquiry. Projects that involve citizen scientists are burgeoning, particularly in ecology and the environmental sciences, although the roots of citizen science go back to the very beginnings of modern science itself.

1,822 citations


Journal ArticleDOI
TL;DR: Here, the principles of biophysical ecology can be used to link spatial data to the physiological responses and constraints of organisms, which provides a mechanistic view of the fundamental niche which can then be mapped to the landscape to infer range constraints.
Abstract: Species distribution models (SDMs) use spatial environmental data to make inferences on species' range limits and habitat suitability. Conceptually, these models aim to determine and map components of a species' ecological niche through space and time, and they have become important tools in pure and applied ecology and evolutionary biology. Most approaches are correlative in that they statistically link spatial data to species distribution records. An alternative strategy is to explicitly incorporate the mechanistic links between the functional traits of organisms and their environments into SDMs. Here, we review how the principles of biophysical ecology can be used to link spatial data to the physiological responses and constraints of organisms. This provides a mechanistic view of the fundamental niche which can then be mapped to the landscape to infer range constraints. We show how physiologically based SDMs can be developed for different organisms in different environmental contexts. Mechanistic SDMs have different strengths and weaknesses to correlative approaches, and there are many exciting and unexplored prospects for integrating the two approaches. As physiological knowledge becomes better integrated into SDMs, we will make more robust predictions of range shifts in novel or non-equilibrium contexts such as invasions, translocations, climate change and evolutionary shifts.

1,821 citations


Journal ArticleDOI
01 Sep 2009-Ecology
TL;DR: PanTHERIA as mentioned in this paper is a species-level data set compiled for analysis of life history, ecology, and geography of all known extant and recently extinct mammalian species, collected over a period of three years by 20 individuals.
Abstract: Analyses of life-history, ecological, and geographic trait differences among species, their causes, correlates, and likely consequences are increasingly important for understanding and conserving biodiversity in the face of rapid global change. Assembling multispecies trait data from diverse literature sources into a single comprehensive data set requires detailed consideration of methods to reliably compile data for particular species, and to derive single estimates from multiple sources based on different techniques and definitions. Here we describe PanTHERIA, a species-level data set compiled for analysis of life history, ecology, and geography of all known extant and recently extinct mammals. PanTHERIA is derived from a database capable of holding multiple geo-referenced values for variables within a species containing 100 740 lines of biological data for extant and recently extinct mammalian species, collected over a period of three years by 20 individuals. PanTHERIA also includes spatial databases o...

1,372 citations



Book
01 Jun 2009
TL;DR: The mussel form and habit C. M. Yonge, the biology of mussel larvae B. L. Bayne, R. Widdows and R. Levinton, and population genetics J. J. Thompson are reviewed.
Abstract: Preface 1. The mussel form and habit C. M. Yonge 2. Ecology R. Seed 3. Mussels and pollution D. Roberts 4. The biology of mussel larvae B. L. Bayne 5. Physiology I B. L. Bayne, R. J. Thompson and J. Widdows 6. Physiology II B. L. Bayne, R. J. Thompson and J. Widdows 7. Physiological integrations B. L. Bayne, J. Widdows and R. J. Thompson 8. Energy metabolism P. A. Gabbott 9. Population genetics J. S. Levinton and R. K. Koehn 10. Cultivation J. Mason References Index.

973 citations


Journal ArticleDOI
TL;DR: It is argued that a top-down approach that focuses on PAB maximizes research efficiency and identifies the most influential factors first, and subsequently narrows the number of potential causal mechanisms.
Abstract: Aim Invasion ecology includes many hypotheses Empirical evidence suggests that most of these can explain the success of some invaders to some degree in some circumstances If they all are correct, what does this tell us about invasion? We illustrate the major themes in invasion ecology, and provide an overarching framework that helps organize research and foster links among subfields of invasion ecology and ecology more generally Location Global Methods We review and synthesize 29 leading hypotheses in plant invasion ecology Structured around propagule pressure (P), abiotic characteristics (A) and biotic characteristics (B), with the additional influence of humans (H) on P, A and B (hereon PAB), we show how these hypotheses fit into one paradigm P is based on the size and frequency of introductions, A incorporates ecosystem invasibility based on physical conditions, and B includes the characteristics of invading species (invasiveness), the recipient community and their interactions Having justified the PAB framework, we propose a way in which invasion research could progress Results By highlighting the common ground among hypotheses, we show that invasion ecology is encumbered by theoretical redundancy that can be removed through integration Using both holistic and incremental approaches, we show how the PAB framework can guide research and quantify the relative importance of different invasion mechanisms Main conclusions If the prime aim is to identify the main cause of invasion success, we contend that a top-down approach that focuses on PAB maximizes research efficiency This approach identifies the most influential factors first, and subsequently narrows the number of potential causal mechanisms By viewing invasion as a multifaceted process that can be partitioned into major drivers and broken down into a series of sequential steps, invasion theory can be rigorously tested, understanding improved and effective weed management techniques identified

923 citations


Book
15 Aug 2009
TL;DR: This major work, written by one of the best-known investigators of Anolis, reviews and synthesizes an immense literature and illustrates how different scientific approaches to the questions of adaptation and diversification can be integrated and examines evolutionary and ecological questions of interest to a broad range of biologists.
Abstract: Adaptive radiation, which results when a single ancestral species gives rise to many descendants, each adapted to a different part of the environment, is possibly the single most important source of biological diversity in the living world. One of the best-studied examples involves Caribbean Anolis lizards. With about 400 species, Anolis has played an important role in the development of ecological theory and has become a model system exemplifying the integration of ecological, evolutionary, and behavioral studies to understand evolutionary diversification. This major work, written by one of the best-known investigators of Anolis, reviews and synthesizes an immense literature. Jonathan B. Losos illustrates how different scientific approaches to the questions of adaptation and diversification can be integrated and examines evolutionary and ecological questions of interest to a broad range of biologists.

907 citations


Journal ArticleDOI
TL;DR: In this article, the authors identified four major areas of inquiry: (1) the dynamics of isotopic incorporation, (2) mixing models, (3) routing, and (4) trophic discrimination factors.
Abstract: About 10 years ago, reviews of the use of stable isotopes in animal ecology predicted explosive growth in this field and called for laboratory experiments to provide a mechanistic foundation to this growth. They identified four major areas of inquiry: (1) the dynamics of isotopic incorporation, (2) mixing models, (3) the problem of routing, and (4) trophic discrimination factors. Because these areas remain central to isotopic ecology, we use them as organising foci to review the experimental results that isotopic ecologists have collected in the intervening 10 years since the call for laboratory experiments. We also review the models that have been built to explain and organise experimental results in these areas.

828 citations


Journal ArticleDOI
TL;DR: In this paper, the authors argue that bats have enormous potential as bioindicators: they show taxonomic stability, trends in their populations can be monitored, short-and long-term effects on populations, and they are distributed widely around the globe.
Abstract: The earth is now subject to climate change and habitat deterioration on unprecedented scales. Monitoring climate change and habitat loss alone is insufficient if we are to understand the effects of these factors on complex biological communities. It is therefore important to identify bioindicator taxa that show measurable responses to climate change and habitat loss and that reflect wider-scale impacts on the biota of interest. We argue that bats have enormous potential as bioindicators: they show taxonomic stability, trends in their populations can be monitored, shortand longterm effects on populations can be measured and they are distributed widely around the globe. Because insectivorous bats occupy high trophic levels, they are sensitive to accumulations of pesticides and other toxins, and changes in their abundance may reflect changes in populations of arthropod prey species. Bats provide several ecosystem services, and hence reflect the status of the plant populations on which they feed and pollinate as well as the productivity of insect communities. Bat populations are affected by a wide range of stressors that affect many other taxa. In particular, changes in bat numbers or activity can be related to climate change (including extremes of drought, heat, cold and precipitation, cyclones and sea level rise), deterioration of water quality, agricultural intensification, loss and fragmentation of forests, fatalities at wind turbines, disease, pesticide use and overhunting. There is an urgent need to implement a global network for monitoring bat populations so their role as bioindicators can be used to its full potential.

Journal ArticleDOI
TL;DR: This review provides a comprehensive and current overview of environmental metabolomics research, and critically evaluates the contribution that metabolomics has made to the environmental sciences, and highlights and discusses recommendations to advance the understanding of the environment, ecology and evolution using a metabolomics approach.
Abstract: Environmental metabolomics is the application of metabolomics to characterise the interactions of organisms with their environment. This approach has many advantages for studying organism–environment interactions and for assessing organism function and health at the molecular level. As such, metabolomics is finding an increasing number of applications in the environmental sciences, ranging from understanding organismal responses to abiotic pressures, to investigating the responses of organisms to other biota. These interactions can be studied from individuals to populations, which can be related to the traditional fields of ecophysiology and ecology, and from instantaneous effects to those over evolutionary time scales, the latter enabling studies of genetic adaptation. This review provides a comprehensive and current overview of environmental metabolomics research. We begin with an overview of metabolomic studies into the effects of abiotic pressures on organisms. In the field of ecophysiology, studies on the metabolic responses to temperature, water, food availability, light and circadian rhythms, atmospheric gases and season are reviewed. A section on ecotoxicogenomics discusses research in aquatic and terrestrial ecotoxicology, assessing organismal responses to anthropogenic pollutants in both the laboratory and field. We then discuss environmental metabolomic studies of diseases and biotic–biotic interactions, in particular herbivory. Finally, we critically evaluate the contribution that metabolomics has made to the environmental sciences, and highlight and discuss recommendations to advance our understanding of the environment, ecology and evolution using a metabolomics approach.

Journal ArticleDOI
TL;DR: OCBIL theory aims to develop an integrated series of hypotheses explaining the evolution and ecology of, and best conservation practices for, biota on very old, climatically buffered, infertile landscapes (OCBILs), and lays a foundation for future research and for better informed conservation management.
Abstract: OCBIL theory aims to develop an integrated series of hypotheses explaining the evolution and ecology of, and best conservation practices for, biota on very old, climatically buffered, infertile landscapes (OCBILs). Conventional theory for ecology and evolutionary and conservation biology has developed primarily from data on species and communities from young, often disturbed, fertile landscapes (YODFELs), mainly in the Northern Hemisphere. OCBILs are rare, but are prominent in the Southwest Australian Floristic Region, South Africa’s Greater Cape, and Venezuela’s Pantepui Highlands. They may have been more common globally before Pleistocene glaciations. Based on the premise that natural selection has favoured limited dispersability of sedentary organisms, OCBILs should have elevated persistence of lineages (Gondwanan Heritage Hypothesis) and long-lived individuals (Ultimate Self Hypothesis), high numbers of localised rare endemics and strongly differentiated population systems. To counter such natural fragmentation and inbreeding due to small population size, ecological, cytogenetic and genetic mechanisms selecting for the retention of heterozygosity should feature (the James Effect). The climatic stability of OCBILs should be paralleled by persistence of adjacent semi-arid areas, conducive to speciation (Semiarid Cradle Hypothesis). Special nutritional and other biological traits associated with coping with infertile lands should be evident, accentuated in plants, for example, through water-foraging strategies, symbioses, carnivory, pollination and parasitism. The uniquely flat landscapes of southwestern Australia have had prolonged presence of saline lakes along palaeoriver systems favouring evolution of accentuated tolerance to salinity. Lastly, unusual resiliences and vulnerabilities might be evident among OCBIL organisms, such as enhanced abilities to persist in small fragmented populations but great susceptibility to major soil disturbances. In those places where it is most pertinent, OCBIL theory hopefully lays a foundation for future research and for better informed conservation management.

Journal ArticleDOI
TL;DR: It is suggested that the distinctive feature of nutritional ecology is its integrative nature, and that the field would benefit from more attention to formalizing a theoretical and quantitative framework for developing this.
Abstract: Summary 1. The science of nutritional ecology spans a wide range of fields, including ecology, nutrition, behaviour, morphology, physiology, life history and evolutionary biology. But does nutritional ecology have a unique theoretical framework and research program and thus qualify as a field of research in its own right? 2. We suggest that the distinctive feature of nutritional ecology is its integrative nature, and that the field would benefit from more attention to formalizing a theoretical and quantitative framework for developing this. 3. Such a framework, we propose, should satisfy three minimal requirements: it should be nutritionally explicit, organismally explicit, and ecologically explicit. 4. We evaluate against these criteria four existing frameworks (Optimal Foraging Theory, Classical Insect Nutritional Ecology, the Geometric Framework for nutrition, and Ecological Stoichiometry), and conclude that each needs development with respect to at least one criterion. 5. We end with an initial attempt at assessing the expansion of our own contribution, the Geometric Framework, to better satisfy the criterion of ecological explicitness.

Book
15 Jan 2009
TL;DR: The goal of this book is to contribute to the knowledge of ecology and its role in the management and restoration of ecosystems.
Abstract: Preface 1. Introduction 2. Systematics and Evolution 3. Ecological Morphology and Anatomy 4. Physiology 5. Population Ecology 6. Community Ecology 7. Ecosystem Ecology 8. World Grasslands 9. Disturbance 10. Management and Restoration References

Journal ArticleDOI
TL;DR: It is posited that sex-ratio distorting microorganisms sometimes dominate their host's microevolution and reproductive ecology, driving extremely rapid natural selection, altering the molecular evolution landscape, and potentially causing evolution in conserved systems such as sex determination.
Abstract: Inherited microorganisms that manipulate the reproduction of their host are a common feature in arthropod biology. Although research initially concentrated on why these manipulations were observed, more recent study has emphasized the profound effects they may have on the ecology and evolution of their host. We review the natural history and evolutionary ecology of inherited reproductive parasites, before examining their impact on host ecology and evolution. We posit that sex-ratio distorting microorganisms sometimes dominate their host's microevolution and reproductive ecology, driving extremely rapid natural selection, altering the molecular evolution landscape, and potentially causing evolution in conserved systems such as sex determination. The evolutionary importance of symbionts inducing cytoplasmic incompatibility lies more in the barriers to gene flow they can produce, which may then contribute to reproductive isolation and speciation. Throughout, we link theory with empirical data, point to areas of ignorance, and identify promising avenues of future research.

Journal ArticleDOI
TL;DR: Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community.
Abstract: The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.


Journal ArticleDOI
TL;DR: The current understanding of the role of microorganisms in coral health and disease is reviewed, and the pressing interdisciplinary research priorities required to elucidate the mechanisms of disease are highlighted.

Book
01 Jan 2009
TL;DR: Fully illustrated and featuring contributions from the world’s leading experts in bat biology, this reference contains everything bat researchers and natural resource managers need to know for the study and conservation of this wide-ranging, ecologically vital, and diverse taxon.
Abstract: First published in 1988, Ecological and Behavioral Methods for the Study of Bats is widely acknowledged as the primary reference for both amateur and professional bat researchers. Bats are the second most diverse group of mammals on the earth. They live on every continent except Antarctica, ranging from deserts to tropical forests to mountains, and their activities have a profound effect on the ecosystems in which they live. Despite their ubiquity and importance, bats are challenging to study. This volume provides researchers, conservationists, and consultants with the ecological background and specific information essential for studying bats in the wild and in captivity. Chapters detail many of the newest and most commonly used field and laboratory techniques needed to advance the study of bats, describe how these methods are applied to the study of the ecology and behavior of bats, and offer advice on how to interpret the results of research. The book includes forty-three chapters, fourteen of which are new to the second edition, with information on molecular ecology and evolution, bioacoustics, chemical communication, flight dynamics, population models, and methods for assessing postnatal growth and development. Fully illustrated and featuring contributions from the world's leading experts in bat biology, this reference contains everything bat researchers and natural resource managers need to know for the study and conservation of this wide-ranging, ecologically vital, and diverse taxon.

Journal ArticleDOI
TL;DR: Eco-hydromorphological expertise is currently fragmented across the main contributory disciplines (ecology, hydrology, geomorphology, flood risk management, civil engineering), potentially restricting research and development.
Abstract: 1. The assessment of links between ecology and physical habitat has become a major issue in river research and management. Key drivers include concerns about the conservation implications of human modifications (e.g. abstraction, climate change) and the explicit need to understand the ecological importance of hydromorphology as prescribed by the EU's Water Framework Directive. Efforts are focusing on the need to develop eco-hydromorphology at the interface between ecology, hydrology and fluvial geomorphology. Here, the scope of this emerging field is defined, some research and development issues are suggested, and a path for development is sketched out. 2. In the short term, major research priorities are to use existing literature or data better to identify patterns among organisms, ecological functions and river hydromorphological character. Another early priority is to identify model systems or organisms to act as research foci. In the medium term, the investigation of pattern-processes linkages, spatial structuring, scaling relationships and system dynamics will advance mechanistic understanding. The effects of climate change, abstraction and river regulation, eco-hydromorphic resistance/resilience, and responses to environmental disturbances are likely to be management priorities. Large-scale catchment projects, in both rural and urban locations, should be promoted to concentrate collaborative efforts, to attract financial support and to raise the profile of eco-hydromorphology. 3. Eco-hydromorphological expertise is currently fragmented across the main contributory disciplines (ecology, hydrology, geomorphology, flood risk management, civil engineering), potentially restricting research and development. This is paradoxical given the shared vision across these fields for effective river management based on good science with social impact. A range of approaches is advocated to build sufficient, integrated capacity that will deliver science of real management value over the coming decades.


Journal ArticleDOI
TL;DR: This selective review addressing the ecology of herbivore-induced plant volatiles (HIPVs) by integrating information on mechanisms and ecological functions is addressed.
Abstract: Plants respond to insect herbivory with the production of volatiles that attract carnivorous enemies of the herbivores, a phenomenon called indirect defence or 'plants crying for help' Plants are under selection to maximize Darwinian fitness, and this can be done by making the right 'decisions' (ie by responding to environmental stress in ways that maximize seed production) Plant decisions related to the response to herbivory in terms of the emission of herbivore-induced volatiles include 'to respond or not to respond', 'how fast to respond', 'how to respond' and 'when to stop responding' In this review, the state-of-the-art of the research field is presented in the context of these decisions that plants face New questions and directions for future research are identified To understand the consequences of plant responses in a community context, it is important to expand research from individual interactions to multispecies interactions in a community context To achieve this, detailed information on underlying mechanisms is essential and first steps on this road have been made This selective review addresses the ecology of herbivore-induced plant volatiles (HIPVs) by integrating information on mechanisms and ecological functions New questions are identified as well as challenges for extending current information to community ecology

Book
01 Jan 2009
TL;DR: In the second edition of the book as discussed by the authors, the authors provide a detailed overview of the methods used for the study of the ecology and behavior of bats in the wild and in captivity, including molecular ecology and evolution, bioacoustics, chemical communication, flight dynamics, population models, and postnatal growth and development.
Abstract: "First published in 1988, Ecological and Behavioral Methods for the Study of Bats is widely acknowledged as the primary reference for both amateur and professional bat researchers Bats are the second most diverse group of mammals on the earth They live on every continent except Antarctica, ranging from deserts to tropical forests to mountains, and their activities have a profound effect on the ecosystems in which they live Despite their ubiquity and importance, bats are challenging to study This volume provides researchers, conservationists, and consultants with the ecological background and specific information essential for studying bats in the wild and in captivity Chapters detail many of the newest and most commonly used field and laboratory techniques needed to advance the study of bats, describe how these methods are applied to the study of the ecology and behavior of bats, and offer advice on how to interpret the results of research The book includes forty-three chapters, fourteen of which are new to the second edition, with information on molecular ecology and evolution, bioacoustics, chemical communication, flight dynamics, population models, and methods for assessing postnatal growth and development Fully illustrated and featuring contributions from the world’s leading experts in bat biology, this reference contains everything bat researchers and natural resource managers need to know for the study and conservation of this wide-ranging, ecologically vital, and diverse taxon"--Publisher website

Book
17 Sep 2009
TL;DR: This paper presents a meta-anatomy of phytochemical ecology and discusses its role in human evolution, as well as some of the mechanisms behind its development and its applications.
Abstract: PART 1. INTRODUCTION PART 2. LARVAE PART 3. JUVENILES AND ADULTS PART 4. AMPHIBIAN POPULATIONS PART 5. AMPHIBIAN COMMUNITIES PART 6. PHYSIOLOGICAL ECOLOGY AND GENETICS PART 7. MONITORING, STATUS AND TRENDS

Journal ArticleDOI
TL;DR: This methodological diversity of genetic tools provides a great variety of potential solutions to measuring dispersal, and is reviewed here to help (molecular) ecologists find their way toward dispersal inference and interpretation and to stimulate further developments.
Abstract: The dispersal process, by which individuals or other dispersing agents such as gametes or seeds move from birthplace to a new settlement locality, has important consequences for the dynamics of genes, individuals, and species. Many of the questions addressed by ecology and evolutionary biology require a good understanding of species’ dispersal patterns. Much effort has thus been devoted to overcoming the difficulties associated with dispersal measurement. In this context, genetic tools have long been the focus of intensive research, providing a great variety of potential solutions to measuring dispersal. This methodological diversity is reviewed here to help (molecular) ecologists find their way toward dispersal inference and interpretation and to stimulate further developments.

Book ChapterDOI
TL;DR: This paper draws together information on the state of the art in multistate mark–recapture models (MSMR), which first appeared in the 1970s but have undergone substantial development in the last 15 years, and provides a modeling philosophy and a series of general principles on how to conduct analyses.
Abstract: Summary Many fields of science begin with a phase of exploration and description, followed by investigations of the processes that account for observed patterns. The science of ecology is no exception, and recent decades have seen a focus on understanding key processes underlying the dynamics of ecological systems. In population ecology, emphasis has shifted from the state variable of population size to the demographic processes responsible for changes in this state variable: birth, death, immigration, and emigration. In evolutionary ecology, some of these same demographic processes, rates of birth and death, are also the determinants of fitness. In animal population ecology, the estimation of state variables and their associated vital rates is especially problematic because of the difficulties in sampling such populations and detecting individual animals. Indeed, early capture–recapture models were developed for the purpose of estimating population size, given the reality that all animals are not caught or detected at any sampling occasion. More recently, capture–recapture models for open populations were developed to draw inferences about survival in the face of these same sampling problems. The focus of this paper is on multi‐state mark–recapture models (MSMR), which first appeared in the 1970s but have undergone substantial development in the last 15 years. These models were developed to deal explicitly with biological variation, in that animals in different “states” (classes defined by location, physiology, behavior, reproductive status, etc.) may have different probabilities of survival and detection. Animal transitions between states are also stochastic and themselves of interest. These general models have proven to be extremely useful and provide a way of thinking about a remarkably wide range of important ecological processes. These methods are now at a stage of refinement and sophistication where they can readily be used by biologists to tackle a wide range of important issues in ecology. In this paper, we draw together information on the state of the art in multistate mark–recapture methods, explaining the models and illustrating their use. We provide a modeling philosophy and a series of general principles on how to conduct analyses. We cover key issues and features, and we anticipate the ways in which we expect the models to develop in the years ahead. In particular: – MSMR can now be used in a straightforward fashion by population biologists, thanks to the development of sound goodness‐of‐fit procedures, reliable parameter identifiability diagnostics, and robust user‐friendly computer software.Constrained models and model selection procedures can be used in the ANOVA‐like philosophy commonly used over the last 15 years for survival models, to answer a variety of biological questions. We develop as an example a treatment of meadow vole Microtus pennsylvanicus data. – As in survival models, random effects should be an integral part of this philosophy. Some simple approaches to random effects are illustrated. – States can be defined in a very general way, for example, by combining several criteria, such as sites and reproductive states, and can include nonobservable states. We develop as an example a multisite recruitment model of roseate terns Sterna dougallii . – MSMR models appear as a natural framework for combining different sources of information, viewed as different events that can be organized into mutually exclusive alternatives. – With the available developments, MSMR models are becoming a standard tool in population biology, as shown by a rapid growth of their use in the literature. In particular, given the ease with which a variety of constrained models can now be developed, MSMR models appear as less data hungry than was often feared. – MSMR models make it also possible to unify a large array of methodology, and, as such, are both a step towards further unification in a “mother of all” model, and a sound basis for further generalizations. – Future developments concern a variety of generalizations such as the reverse time approach and population size estimation. “Multievent” models, accounting for uncertainty in state determination, and integrated state–space models are key generalizations already in full development.

Journal ArticleDOI
TL;DR: In this paper, the authors provide a conceptual framework for the continued development of macrophysiology, which is subdivided into three major components: the establishment of macophysiological patterns, determining the form of those patterns, and understanding the mechanisms that give rise to them.
Abstract: Widespread recognition of the importance of biological studies at large spatial and temporal scales, particularly in the face of many of the most pressing issues facing humanity, has fueled the argument that there is a need to reinvigorate such studies in physiological ecology through the establishment of a macrophysiology. Following a period when the fields of ecology and physiological ecology had been regarded as largely synonymous, studies of this kind were relatively commonplace in the first half of the twentieth century. However, such large-scale work subsequently became rather scarce as physiological studies concentrated on the biochemical and molecular mechanisms underlying the capacities and tolerances of species. In some sense, macrophysiology is thus an attempt at a conceptual reunification. In this article, we provide a conceptual framework for the continued development of macrophysiology. We subdivide this framework into three major components: the establishment of macrophysiological patterns, determining the form of those patterns (the very general ways in which they are shaped), and understanding the mechanisms that give rise to them. We suggest ways in which each of these components could be developed usefully.

Journal ArticleDOI
TL;DR: The ecological relevance of manipulative parasites in ecosystems is reviewed, directions for further research are proposed, and phenotypic alterations in parasitised hosts modify host population ecology, apparent competition processes, food web structure and energy and nutrient flow between habitats.
Abstract: The diversity of ways in which host manipulation by parasites interferes with ecological and evolutionary processes governing biotic interactions has been recently documented, and indicates that manipulative parasites are full participants in the functioning of ecosystems. Phenotypic alterations in parasitised hosts modify host population ecology, apparent competition processes, food web structure and energy and nutrient flow between habitats, as well as favouring habitat creation. As is usually the case in ecology, these phenomena can be greatly amplified by a series of secondary consequences (cascade effects). Here we review the ecological relevance of manipulative parasites in ecosystems and propose directions for further research.

Journal ArticleDOI
TL;DR: This article reviewed evidence from six complementary approaches to understand possible changes: plant physiology experiments, long-term monitoring plots, ecosystem flux techniques, atmospheric measurements, Earth observations, and global-scale vegetation models.
Abstract: Global environmental changes may be altering the ecology of tropical forests. Long-term monitoring plots have provided much of the evidence for large-scale, directional changes in tropical forests, but the results have been controversial. Here we review evidence from six complementary approaches to understanding possible changes: plant physiology experiments, long-term monitoring plots, ecosystem flux techniques, atmospheric measurements, Earth observations, and global-scale vegetation models. Evidence from four of these approaches suggests that large-scale, directional changes are occurring in the ecology of tropical forests, with the other two approaches providing inconclusive results. Collectively, the evidence indicates that both gross and net primary productivity has likely increased over recent decades, as have tree growth, recruitment, and mortality rates, and forest biomass. These results suggest a profound reorganization of tropical forest ecosystems. We evaluate the most likely drivers of the su...