Showing papers in "Trends in Ecology and Evolution in 2003"

Farmland biodiversity: is habitat heterogeneity the key?

Abstract: Agricultural intensification has led to a widespread decline in farmland biodiversity measured across many different taxa. The changes in agricultural practices affect many different aspects of the farmland habitat, but agricultural industry, policy and much previous research has tended to be concerned with specific sectors or practices (e.g. pesticide use or cereal husbandry). Here, we review the empirical literature to synthesize the research effort that has been directed to investigate specific practices or goals to make general statements regarding the causes and consequences of farmland biodiversity decline. We argue that the loss of ecological heterogeneity at multiple spatial and temporal scales is a universal consequence of multivariate agricultural intensification and, therefore, that future research should develop cross-cutting policy frameworks and management solutions that recreate that heterogeneity as the key to restoring and sustaining biodiversity in temperate agricultural systems.

Inclusion of facilitation into ecological theory

Abstract: Investigations of the role of competition, predation and abiotic stress in shaping natural communities were a staple for previous generations of ecologists and are still popular themes. However, more recent experimental research has uncovered the largely unanticipated, yet striking influence of facilitation (i.e. positive species interactions) on the organization of terrestrial and aquatic communities. Modern ecological concepts and theories were well established a decade before the current renaissance of interest in facilitation began, and thus do not consider the importance of a wide variety of facilitative interactions. It is time to bring ecological theory up to date by including facilitation. This process will not be painless because it will fundamentally change many basic predictions and will challenge some of our most cherished paradigms. But, ultimately, revising ecological theory will lead to a more accurate and inclusive understanding of natural communities.

Catastrophic regime shifts in ecosystems: linking theory to observation

Abstract: Occasionally, surprisingly large shifts occur in ecosystems. Theory suggests that such shifts can be attributed to alternative stable states. Verifying this diagnosis is important because it implies a radically different view on management options, and on the potential effects of global change on such ecosystems. For instance, it implies that gradual changes in temperature or other factors might have little effect until a threshold is reached at which a large shift occurs that might be difficult to reverse. Strategies to assess whether alternative stable states are present are now converging in fields as disparate as desertification, limnology, oceanography and climatology. Here, we review emerging ways to link theory to observation, and conclude that although, field observations can provide hints of alternative stable states, experiments and models are essential for a good diagnosis.

Landscape genetics: combining landscape ecology and population genetics

Abstract: Understanding the processes and patterns of gene flow and local adaptation requires a detailed knowledge of how landscape characteristics structure populations. This understanding is crucial, not only for improving ecological knowledge, but also for managing properly the genetic diversity of threatened and endangered populations. For nearly 80 years, population geneticists have investigated how physiognomy and other landscape features have influenced genetic variation within and between populations. They have relied on sampling populations that have been identified beforehand because most population genetics methods have required discrete populations. However, a new approach has emerged for analyzing spatial genetic data without requiring that discrete populations be identified in advance. This approach, landscape genetics, promises to facilitate our understanding of how geographical and environmental features structure genetic variation at both the population and individual levels, and has implications for ecology, evolution and conservation biology. It differs from other genetic approaches, such as phylogeography, in that it tends to focus on processes at finer spatial and temporal scales. Here, we discuss, from a population genetic perspective, the current tools available for conducting studies of landscape genetics.

Evolution by gene duplication: an update

Abstract: The importance of gene duplication in supplying raw genetic material to biological evolution has been recognized since the 1930s. Recent genomic sequence data provide substantial evidence for the abundance of duplicated genes in all organisms surveyed. But how do newly duplicated genes survive and acquire novel functions, and what role does gene duplication play in the evolution of genomes and organisms? Detailed molecular characterization of individual gene families, computational analysis of genomic sequences and population genetic modeling can all be used to help us uncover the mechanisms behind the evolution by gene duplication.

From space to species: ecological applications for remote sensing

Abstract: A variety of ecological applications require data from broad spatial extents that cannot be collected using field-based methods. Remote sensing data and techniques address these needs, which include identifying and detailing the biophysical characteristics of species' habitats, predicting the distribution of species and spatial variability in species richness, and detecting natural and human-caused change at scales ranging from individual landscapes to the entire world. Such measurements are subject to substantial errors that can be difficult to overcome, but corrected data are readily available and can be of sufficiently high resolution to be integrated into traditional field-based studies. Ecologists and conservation biologists are finding new ways to approach their research with the powerful suite of tools and data from remote sensing.

Remote sensing for biodiversity science and conservation

Abstract: Remote-sensing systems typically produce imagery that averages information over tens or even hundreds of square meters – far too coarse to detect most organisms – so the remote sensing of biodiversity would appear to be a fool’s errand. However, advances in the spatial and spectral resolutions of sensors now available to ecologists are making the direct remote sensing of certain aspects of biodiversity increasingly feasible; for example, distinguishing species assemblages or even identifying species of individual trees. In cases where direct detection of individual organisms or assemblages is still beyond our grasp, indirect approaches offer valuable information about diversity patterns. Such approaches derive meaningful environmental parameters from biophysical characteristics that

Contemporary evolution meets conservation biology

Abstract: Recent research has revealed that evolution often occurs on contemporary timescales, often within decades. Contemporary evolution is associated with the same factors that are driving the current extinction crisis: habitat loss and degradation, overharvesting and exotic species. Thus, it is relevant to many conservation situations. First, habitat fragmentation might influence the potential of a population to adapt in response environmental degradation. Second, certain harvesting strategies can result in the evolution of life-history traits, ultimately resulting in negative impacts on harvestable yield. Third, the establishment of exotic species can be influenced by their adaptive potential and our ability to limit that potential. Furthermore, contemporary evolution is of concern for intensively managed species, because it might reduce their fitness in native habitats. Ultimately, contemporary evolution is influenced by complex interactions among population size, genetic variation, the strength of selection, and gene flow, making most management scenarios unique. In a world filled with contemporary evolution, conservation efforts that ignore its implications will be less efficient and perhaps even risk prone. Humans have become an evolutionary force of extraordinary influence [1], evidenced most obviously by an unprecedented extinction rate that is attributable to their activities [2]. Human activities are also associated with evolutionary changes that can occur within a few hundred years, otherwise known as CONTEMPORARY EVOLUTION (see Glossary) [3‐5].

Benefits beyond boundaries: the fishery effects of marine reserves

Abstract: Marine reserves are areas of the sea where fishing is not allowed. They provide refuges where populations of exploited species can recover and habitats modified by fishing can regenerate. In some places, closed areas have been used for fisheries management for centuries [1] and, until recently, natural refugia also existed, inaccessible through depth, distance or adverse conditions. Developments in technology have left few areas of fishing interest beyond our reach. Recently, the idea of marine reserves as fisheries management tools has re-emerged with developing interest in ecosystembased management, and observations of incidental fisheries benefits from reserves established for conservation. In light of new evidence, we argue that, by integrating large-scale networks of marine reserves into fishery management, we could reverse global fishery declines and provide urgently needed protection for

A plea for DNA taxonomy

Abstract: Taxonomy underpins all biological research, with implications for many basic scientific and applied fields. Insights into the stability or change of animal and plant guilds require species identification on a broad scale and biodiversity questions have become a major public issue. But this comes at a time when taxonomy is facing a crisis, because ever fewer specialists are available. Here, we explore the possibility of using DNA-based methodology to overcome these problems. The utility of DNA sequences for taxonomic purposes is well established. However, all current taxonomic approaches intend to use DNA, at best, as an auxiliary criterion for identifying a species or a taxon, but have not given it a central role. We propose a scheme in which DNA would be the scaffold of a taxonomic reference system, whilst maintaining the importance of the morphological information associated with whole specimens.

Phenotypic flexibility and the evolution of organismal design

Abstract: Evolutionary biologists often use phenotypic differences between species and between individuals to gain an understanding of organismal design. The focus of much recent attention has been on developmental plasticity - the environmentally induced variability during development within a single genotype. The phenotypic variation expressed by single reproductively mature organisms throughout their life, traditionally the subject of many physiological studies, has remained under-exploited in evolutionary biology. Phenotypic flexibility, the reversible within-individual variation, is a function of environmental conditions varying predictably (e.g. with season), or of more stochastic fluctuations in the environment. Here, we provide a common framework to bring the different categories of phenotypic plasticity together, and emphasize perspectives on adaptation that reversible types of plasticity might provide. We argue that better recognition and use of the various levels of phenotypic variation will increase the scope for phenotypic experimentation, comparison and integration.

Plant ecotypes: genetic differentiation in the age of ecological restoration

Abstract: Recent studies illustrate the emerging field of restoration genetics, which is a synthesis of restoration ecology and population genetics. The translocation of organisms during the restoration of native ecosystems has provoked new questions concerning the consequences of sampling protocols and of intraspecific hybridization between locally adapted and transplanted genotypes. Studies are now underway to determine both the extent of local adaptation among focal populations and the potential risks of introducing foreign genotypes, including founder effects, genetic swamping and outbreeding depression. Data are needed to delineate ‘seed transfer zones', or regions within which plants can be moved with little or no consequences for population fitness. Here, we address the revival of transplant and common garden studies, the use of novel molecular markers to predict population genetic consequences of translocation, and their combined power for determining appropriate seed transfer zones in restoration planning for native plant populations.

Species diversity: from global decreases to local increases

Abstract: Current patterns of global change can strongly affect biodiversity at global, regional and local scales. At global scales, habitat destruction and the introduction of exotic species are contributing to declines in species diversity. At regional and local scales, evidence for declines in diversity is mixed, and recent work suggests that diversity might commonly be increasing. In spite of these trends, considerable research continues to consider explicitly the effects of declines in diversity on processes that operate at regional and local scales (such as ecosystem functioning), without explicitly considering the converse set of questions, namely the effects of increases in diversity. Here, we examine evidence that indicates how species diversity is changing across spatial scales and argue that global decreases in diversity are commonly contrasted by increases in diversity at regional and local scales.

The adaptive significance of insect gall morphology

Abstract: Insect galls are dramatic examples of extended phenotypes: although composed of host plant tissues, their development is largely controlled by insect genes. Adaptive explanations for gall traits should thus be expressed in terms of impacts on insect fitness, but the extent to which interspecific variation in gall structure is adaptive, and the possible selective pressures driving diversification in gall form remain controversial. In colonial aphids and thrips, gall structures probably diversified in response to selection for enhancement of the surface area available for feeding. In other taxa, such as gall wasps and gall midges, diversity is expressed predominantly in non-nutritive tissues, particularly those on the gall surface. All natural enemies attack the occupants of closed galls by penetrating gall tissue, and modifications that reduce enemy attack rates should thus be favoured. Recent studies of intraspecific variation in gall form strongly support a defensive role for several traits, but, to date, there is little empirical support for enemies as a cause of interspecific variation in gall form. Selection imposed by enemies nevertheless remains the most probable adaptive explanation for the evolution of diversity. We suggest that this hypothesis has yet to be tested explicitly, and discuss the requirements for an appropriate cross-species analysis.

Wild meat: the bigger picture

Abstract: Massive overhunting of wildlife for meat across the humid tropics is now causing local extinctions of numerous species. Rural people often rely heavily on wild meat, but, in many areas, this important source of food and income is either already lost or is being rapidly depleted. The problem can only be tackled by looking at the wider economic and institutional context within which such hunting occurs, from household economics to global terms of trade. Conservation efforts must be placed within a landscape context; a mosaic of hunted and no-take areas might balance conservation with continued subsistence use. Successful conservation of hunted wildlife requires collaboration at all scales, involving local people, resource extraction companies, governments and scientists.

Delimiting species: a Renaissance issue in systematic biology

Abstract: The literature about species concepts might be larger than that about any other subject in evolutionary biology, but the issue of empirically testing species boundaries has been given little attention relative to seemingly endless debates over what species are. The practical issue of delimiting species boundaries is nevertheless of central importance to many areas of evolutionary biology. The number of recently described methods for delimiting species suggests renewed interest in the topic, and some methods are explicitly quantitative. Here, we review nine of these methods by summarizing the relevant biological properties of species amenable to empirical evaluation, the classes of data required and some of the strengths and limitations of each.

DNA-based methods for pedigree reconstruction and kinship analysis in natural populations

Abstract: The widespread use of microsatellite loci has spurred the recent development of many new statistical methods for inferring kin relationships from molecular data. We now have an unprecedented ability to infer detailed genealogical information about individuals in natural populations, but the best approach for a given problem is not always obvious. Researchers in different fields have also been deriving similar methods independently. Thus, some biologists might not be aware of what is even possible. By adopting these new methods, researchers in ecology and evolution could extract far more pedigree information from natural populations than is currently being exploited.

From spatial orientation to food acquisition in echolocating bats

Abstract: Field research on echolocation behavior in bats has emphasized studies of food acquisition, and the adaptive value of sonar signal design as been considered largely in the context of foraging. However, echolocation tasks related to spatial orientation also differ among bats and are relevant to understanding signal structure. Here, we argue that the evolution of echolocation in bats is characterized by two key innovations: first, the evolution of echolocation for spatial orientation and, second, a later transition for prey acquisition. This conceptual framework calls for a new view on field data from bats orienting and foraging in different types of habitats. According to the ecological constraints in which foraging bats operate, four distinct functional groups or guilds can be defined. Within each group, signal design and echolocation behavior are rather similar.

The utility of single nucleotide polymorphisms in inferences of population history

Abstract: Single nucleotide polymorphisms (SNPs) represent the most widespread type of sequence variation in genomes, yet they have only emerged recently as valuable genetic markers for revealing the evolutionary history of populations. Their occurrence throughout the genome also makes them ideal for analyses of speciation and historical demography, especially in light of recent theory suggesting that many unlinked nuclear loci are needed to estimate population genetic parameters with statistical confidence. In spite of having lower variation compared with microsatellites, SNPs should make the comparison of genomic diversities and histories of different species (the core goal of comparative biogeography) more straightforward than has been possible with microsatellites. The most pervasive, but correctable, complication to SNP analysis is a bias towards analyzing only the most variable loci, an artifact that is usually introduced by the limited number of individuals used to screen initially for polymorphisms. Although the use of SNPs as markers in population studies is still new, innovative methods for SNP identification, automated screening, haplotype inference and statistical analysis might quickly make SNPs the marker of choice. Traditionally, phylogeography has used gene trees of nonrecombining, uniparentally inherited LOCI (see Glossary), such as mitochondrial DNA or the vertebrate Y chromosome, to study the geographical distribution of genetic variation within species [1]. As evolutionary biologists have started to examine variation in recombining, biparentally inherited loci, a natural outgrowth of phylogeography is a shift from gene trees to analyses, based on COALESCENT THEORY, of multi-locus, recombining histories. This new discipline, dubbed historical demography [2,3] or statistical phylogeography [4], is concerned less with gene trees than with estimating population parameters such as genetic diversities, divergence times, growth rates and gene flow between populations. The shift in focus is, in part, a result of recent advances in population genetics, which suggest that, from a statistical standpoint, the ability of single-locus phylogeography to determine the timing of speciation events and the historical demography of populations has been overestimated [3‐7]. The errors surrounding estimates of divergence times, rates of gene flow and population-size changes during speciation are all reduced substantially when information from multiple unlinked loci is combined [8,9]. With the move to analyses of multiple loci, phylogeographers must re-learn an old lesson: that the number of loci required to estimate the preceding parameters with statistical confidence can be soberingly large because of the high stochasticity of the gene tree of any single locus [10]. What is required is a suite of unlinked nuclear genetic markers that can capture a genome-wide picture of the population history [3,11‐14]. The polymerase chain reaction (PCR) as well as fluorescent sequencing and fragment analysis technologies have catalyzed a revolution in the development of genetic markers for the analysis of natural populations. Emphasizing discoveries in nonmodel species, we discuss one emerging marker of great relevance to historical demography: single nucleotide polymorphisms (SNPs).

Plant height and evolutionary games

Abstract: In plants, investment in height improves access to light, but incurs costs in construction and maintenance of the stem. Because the benefits of plant height depend on which other height strategies are present, competition for light can usefully be framed as a game-theoretic problem. The vertical structure of the world's vegetation, which is inefficient for plant growth, can then be understood as the outcome of evolutionary and ecological arms races. In addition, game-theoretic models predict taller vegetation on sites of higher leaf area index, and allocation to reproduction only after an initial period of height growth. However, of 14 game-theoretic models for height reviewed here, only one predicts coexistence of a mix of height strategies, a conspicuous feature of most vegetation. We suggest that game-theoretic models could help account for observed mixtures of height strategies if they incorporated processes for coexistence along spectra of light income and time since disturbance.

Population diversity and ecosystem services

Abstract: The current rate of biodiversity loss threatens to disrupt greatly the functioning of ecosystems, with potentially significant consequences for humanity. The magnitude of the loss is generally measured with the use of species extinction rates, an approach that understates the severity of the problem and masks some of its most important consequences. Here, we propose a major expansion of this focus to include population diversity: considering changes in the size, number, distribution and genetic composition of populations and the implications of those changes for the functioning of ecosystems and the provision of ecosystem services. We also outline the key components of population diversity and describe a new approach to delineating a population unit that explicitly links it to the services that it provides

Response to Eberhard and Cordero, and Córdoba-Aguilar and Contreras-Garduño: sexual conflict and female choice

Abstract: Response to Eberhard and Cordero, and Cordoba-Aguilar and Contreras-Garduno: sexual conflict and female choice

Rapid evolutionary dynamics and disease threats to biodiversity

Abstract: Existing and emerging pathogens pose unusual challenges for conservation because of their potential to drive rapid changes in the numerical abundance and genetic composition of wild host populations. An increasing number of studies indicate that host genetic diversity plays an important role in buffering populations against widespread epidemics, and that parasites represent powerful selective agents in natural populations. The observation that infectious diseases might be both mitigated by and rapidly change the genetic composition of host populations gives new significance to the role of host genetic diversity in species conservation. Less clear is the role that pathogen evolutionary change plays in the emergence and spread of new diseases, but recent examples indicate that humans might be selecting unknowingly for rapid changes in pathogen biology through habitat fragmentation, climate shifts and environmental pollution. Although the risks they pose to endangered species are apparent, pathogens and other natural enemies can be a driving force behind species and genetic diversity in natural populations, and preserving interacting networks of coevolving populations should enable hosts to respond better to future disease threats.

On the evolutionary ecology of specific immune defence

Abstract: Evolutionary ecology has developed along two major conceptual avenues, starting from the observation that hosts vary in their immune defence against parasites The first avenue, rooted in life-history theory, assumes fitness costs of immune defence and tradeoffs in the face of limited resources, rather than specific host–parasite interactions. The second avenue focuses on specific responses, especially those generated by genotype–genotype interaction between and within host and parasite species. Specificity in the interactions between hosts and parasites play a crucial role in the field but analysis is difficult. Here, we classify concepts about host–parasite interactions into these two families and discuss their reconciliation with the help of a defence component model and two-dimensional classification scheme of the individual components. This helps to clarify some of the confusing terminology and might guide further research in the field.

Tradeoffs and the evolution of thermal reaction norms

Abstract: Tradeoffs have played a prominent role in the development of theories describing the evolution of reaction norms Different classes of tradeoffs are known to constrain the evolution of phenotypes, but current theories incorporate only a subset of these tradeoffs Consequently, these theories cannot account for some of the variation in reaction norms that has been observed within and among species Empirical studies of thermal reaction norms for physiological and life historical traits have shown that different proximate mechanisms can produce similar reaction norms As a consequence, certain tradeoffs can be circumvented when the fitness costs imposed by these tradeoffs are severe We argue that a unified theory that includes all classes of tradeoffs would provide a better understanding of the mechanisms that drive the evolution of reaction norms

How to kill (almost) all life: the end-Permian extinction event

Abstract: The biggest mass extinction of the past 600 million years (My), the end-Permian event (251My ago), witnessed the loss of as much as 95% of all species on Earth. Key questions for biologists concern what combination of environmental changes could possibly have had such a devastating effect, the scale and pattern of species loss, and the nature of the recovery. New studies on dating the event, contemporary volcanic activity, and the anatomy of the environmental crisis have changed our perspectives dramatically in the past five years. Evidence on causation is equivocal, with support for either an asteroid impact or mass volcanism, but the latter seems most probable. The extinction model involves global warming by 6°C and huge input of light carbon into the ocean-atmosphere system from the eruptions, but especially from gas hydrates, leading to an ever-worsening positive-feedback loop, the ‘runaway greenhouse'.

Costs and consequences of evolutionary temperature adaptation.

Abstract: Temperature affects everything that an organism does. Although we have an increasingly sophisticated understanding of evolutionary adaptation to temperature at the molecular level for some cellular processes, we still know little about evolutionary temperature adaptation in gene expression, cell-cycle control or growth, all of which influence organism performance and fitness. Recent studies have shown that the physiological costs of evolutionary temperature adaptation vary with body temperature. Here, I argue that this macroecological pattern has powerful consequences for life-history theory, and probably also for food-web dynamics, biological diversity and biotic response to climate change. The relationships among evolution, temperature and ecology are multivariate, hierarchical and complex making evolutionary physiology at the macroecological scale an exciting and challenging agenda for the next decade.

Thermal biology in insect-parasite interactions

Abstract: Recently, several applied studies exploring the use of pathogens for insect biocontrol have demonstrated significant effects of environmental temperature on the outcome of infection. For example, host resistance, host recovery, pathogen virulence and replication can alter considerably with sometimes very small changes in temperature. Moreover, the effectiveness of certain insect parasitoids and the activity of endosymbionts can vary across the range of realistic temperatures experienced in the field. These responses are not necessarily linear or immediately predictable, because they derive from a complex ‘genotype-by-genotype-by-environment' interaction. Given the importance of parameters such as virulence and resistance in determining the course of a host–parasite interaction, such effects of temperature could have profound implications for host–parasite dynamics and coevolution.

Insects at low temperatures: an ecological perspective

Abstract: Modern climate change has precipitated widespread interest in the responses of organisms to the thermal environment. In insects, it is not only changes in mean environmental temperature and growing season length that are important, but also their responses to environmental extremes. Much is now known about the ways in which insects cope with the ice–water threshold, and with the low temperatures that precede it. Recent work has demonstrated a diversity of physiological responses to cooling and freezing in insects, with extremes of temperature, rates of temperature change, the numbers of freeze–thaw transitions, climatic unpredictability and the state of the surrounding microhabitat being important factors determining the cold tolerance strategy adopted by an insect. Insect low temperature biology now integrates techniques ranging from laboratory-based functional genomics to climatology, making it not only intrinsically fascinating, but also of considerable relevance to investigations of the biological implications of climate change.

Functional diversity revealed by removal experiments

Abstract: The dominant protocol to study the effects of plant diversity on ecosystem functioning has involved synthetically assembled communities, in which the experimental design determines species composition. By contrast, the composition of naturally assembled communities is determined by environmental filters, species recruitment and dispersal, and other assembly processes. Consequently, natural communities and ecosystems can differ from synthetic systems in their reaction to changes in diversity. Removal experiments, in which the diversity of naturally assembled communities is manipulated by removing various components, complement synthetic-assemblage experiments in exploring the relationship between diversity and ecosystem functioning. Results of recent removal experiments suggest that they are more useful for understanding the ecosystem effects of local, nonrandom extinctions, changes in the natural abundance of species, and complex interspecific interactions. This makes removal experiments a promising avenue for progress in ecological theory and an important source of information for those involved in making land-use and conservation decisions. Current extinction rates caused by human activities are orders of magnitude higher than natural background levels [1], and it is crucial that we understand the functional consequences of such extinctions. Terrestrial plants provide the basis for many fundamental ecosystem processes and services; therefore, many initiatives have been launched in the past decade to address this issue by documenting the possible effects of terrestrial plant diversity on ecosystem processes. Most of these studies are based on experiments using synthetic communities, in