Showing papers in "Trends in Ecology and Evolution in 2009"

Generalized linear mixed models: a practical guide for ecology and evolution

Abstract: How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize 'best-practice' data analysis procedures for scientists facing this challenge.

A new dawn for citizen science.

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.

Eutrophication science: where do we go from here?

Abstract: Cultural eutrophication has become the primary water quality issue for most of the freshwater and coastal marine ecosystems in the world. However, despite extensive research during the past four to five decades, many key questions in eutrophication science remain unanswered. Much is yet to be understood concerning the interactions that can occur between nutrients and ecosystem stability: whether they are stable or not, alternate states pose important complexities for the management of aquatic resources. Evidence is also mounting rapidly that nutrients strongly influence the fate and effects of other non-nutrient contaminants, including pathogens. In addition, it will be important to resolve ongoing debates about the optimal design of nutrient loading controls as a water quality management strategy for estuarine and coastal marine ecosystems.

Gene tree discordance, phylogenetic inference and the multispecies coalescent

Abstract: The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome. Recent advances in genealogical modeling suggest that resolving close species relationships is not quite as simple as applying more data to the problem. Here we discuss the complexities of genealogical discordance and review the issues that new methods for multilocus species tree inference will need to address to account successfully for naturally occurring genomic variability in evolutionary histories.

Novel ecosystems: implications for conservation and restoration

Abstract: Many ecosystems are rapidly being transformed into new, non-historical configurations owing to a variety of local and global changes. We discuss how new systems can arise in the face of primarily biotic change (extinction and/or invasion), primarily abiotic change (e.g. land use or climate change) and a combination of both. Some changes will result in hybrid systems retaining some original characteristics as well as novel elements, whereas larger changes will result in novel systems, which comprise different species, interactions and functions. We suggest that these novel systems will require significant revision of conservation and restoration norms and practices away from the traditional place-based focus on existing or historical assemblages.

Alien species in a warmer world: risks and opportunities

Abstract: Climate change and biological invasions are key processes affecting global biodiversity, yet their effects have usually been considered separately. Here, we emphasise that global warming has enabled alien species to expand into regions in which they previously could not survive and reproduce. Based on a review of climate-mediated biological invasions of plants, invertebrates, fishes and birds, we discuss the ways in which climate change influences biological invasions. We emphasise the role of alien species in a more dynamic context of shifting species' ranges and changing communities. Under these circumstances, management practices regarding the occurrence of 'new' species could range from complete eradication to tolerance and even consideration of the 'new' species as an enrichment of local biodiversity and key elements to maintain ecosystem services.

Invasive species, ecosystem services and human well-being.

Abstract: Although the effects of invasive alien species (IAS) on native species are well documented, the many ways in which such species impact ecosystem services are still emerging. Here we assess the costs and benefits of IAS for provisioning, regulating and cultural services, and illustrate the synergies and tradeoffs associated with these impacts using case studies that include South Africa, the Great Lakes and Hawaii. We identify services and interactions that are the least understood and propose a research and policy framework for filling the remaining knowledge gaps. Drawing on ecology and economics to incorporate the impacts of IAS on ecosystem services into decision making is key to restoring and sustaining those life-support services that nature provides and all organisms depend upon.

Extinction debt: a challenge for biodiversity conservation.

Abstract: Local extinction of species can occur with a substantial delay following habitat loss or degradation. Accumulating evidence suggests that such extinction debts pose a significant but often unrecognized challenge for biodiversity conservation across a wide range of taxa and ecosystems. Species with long generation times and populations near their extinction threshold are most likely to have an extinction debt. However, as long as a species that is predicted to become extinct still persists, there is time for conservation measures such as habitat restoration and landscape management. Standardized long-term monitoring, more high-quality empirical studies on different taxa and ecosystems and further development of analytical methods will help to better quantify extinction debt and protect biodiversity.

DNA barcoding for ecologists

Abstract: DNA barcoding - taxon identification using a standardized DNA region - has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcoding techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism's remains but also determine the species composition of environmental samples. Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples. Here we review the new avenues offered to ecologists by DNA barcoding, particularly in the context of new sequencing technologies.

Impacts of roads and linear clearings on tropical forests.

Abstract: Linear infrastructure such as roads, highways, power lines and gas lines are omnipresent features of human activity and are rapidly expanding in the tropics. Tropical species are especially vulnerable to such infrastructure because they include many ecological specialists that avoid even narrow (<30-m wide) clearings and forest edges, as well as other species that are susceptible to road kill, predation or hunting by humans near roads. In addition, roads have a major role in opening up forested tropical regions to destructive colonization and exploitation. Here, we synthesize existing research on the impacts of roads and other linear clearings on tropical rainforests, and assert that such impacts are often qualitatively and quantitatively different in tropical forests than in other ecosystems. We also highlight practical measures to reduce the negative impacts of roads and other linear infrastructure on tropical species.

Something in the way you move: dispersal pathways affect invasion success

Abstract: Biological invasions are caused by human-mediated extra-range dispersal and, unlike natural extra-range dispersal, are often the result of multiple introductions from multiple sources to multiple locations. The processes and opportunities that result in propagules moving from one area to another can be used more broadly to differentiate all types of extra-range dispersal. By examining key properties of dispersal pathways (notably propagule pressure, genetic diversity and the potential for simultaneous movement of coevolved species), the establishment and evolutionary trajectories of extra-range dispersal can be better understood. Moreover, elucidation of the mechanistic properties of dispersal pathways is crucial for scientists and managers who wish to assist, minimise or prevent future movements of organisms.

Do baseline glucocorticoids predict fitness

Abstract: Baseline glucocorticoid (cort) levels are increasingly employed as physiological indices of the relative condition or health of individuals and populations. Often, high cort levels are assumed to indicate an individual or population in poor condition and with low relative fitness (the Cort–Fitness Hypothesis). We review empirical support for this assumption, and find that variation in levels of baseline cort is positively, negatively, or non-significantly related to estimates of fitness. These relationships between levels of baseline cort and fitness can vary within populations and can even shift within individuals at different times in their life history. Overall, baseline cort can predict the relative fitness of individuals and populations, but the relationship is not always consistent or present.

The jellyfish joyride: causes, consequences and management responses to a more gelatinous future

Abstract: Human-induced stresses of overfishing, eutrophication, climate change, translocation and habitat modification appear to be promoting jellyfish (pelagic cnidarian and ctenophore) blooms to the detriment of other marine organisms. Mounting evidence suggests that the structure of pelagic ecosystems can change rapidly from one that is dominated by fish (that keep jellyfish in check through competition or predation) to a less desirable gelatinous state, with lasting ecological, economic and social consequences. Management actions needed to stop such changes require tactical coping strategies and longer-term preventative responses based on fundamental and targeted research on this understudied group.

Gene flow and species delimitation.

Abstract: A defining feature of species is that their constituting populations are connected by gene flow. However, interspecific gene flow (introgression) can affect species integrity. If some genome components were less prone to introgression than others, they should be particularly suitable to delimitate species. Recent simulation studies have predicted a negative correlation between intra- and interspecific gene flow, suggesting that markers associated with the most dispersing sex should better delimitate species. A review of studies of introgression in species with sex-biased dispersal largely confirms this prediction. Hence, species delimitation should be more effective with markers experiencing high levels of gene flow, a simple but not widely appreciated prediction.

Intralocus sexual conflict.

Abstract: Intralocus sexual conflict occurs when selection on a shared trait in one sex displaces the other sex from its phenotypic optimum. It arises because many shared traits have a common genetic basis but undergo contrasting selection in the sexes. A recent surge of interest in this evolutionary tug of war has yielded evidence of such conflicts in laboratory and natural populations. Here we highlight outstanding questions about the causes and consequences of intralocus sexual conflict at the genomic level, and its long-term implications for sexual coevolution. Whereas recent thinking has focussed on the role of intralocus sexual conflict as a brake on sexual coevolution, we urge a broader appraisal that also takes account of its potential to drive adaptive evolution and speciation.

Adaptive monitoring: a new paradigm for long-term research and monitoring.

Abstract: Long-term research and monitoring can provide important ecological insights and are crucial for the improved management of ecosystems and natural resources. However, many long-term research and monitoring programs are either ineffective or fail completely owing to poor planning and/or lack of focus. Here we propose the paradigm of adaptive monitoring, which aims to resolve many of the problems that have undermined previous attempts to establish long-term research and monitoring. This paradigm is driven by tractable questions, rigorous statistical design at the outset, a conceptual model of the ecosystem or other entity being examined and a human need to know about ecosystem change. An adaptive monitoring framework enables monitoring programs to evolve iteratively as new information emerges and research questions change.

Ecological explanations for (incomplete) speciation

Abstract: Divergent natural selection has been shown to promote speciation in many taxa. However, although divergent selection often initiates the process of speciation, it often fails to complete it. Several time-based, geographic and genetic factors have been recognized to explain this variability in how far speciation proceeds. We review here recent evidence indicating that variability in the completeness of speciation can also be associated with the nature of divergent selection itself, with speciation being greatly promoted by (i) stronger selection on a given, single trait (the 'stronger selection' hypothesis) and (ii) selection on a greater number of traits (the 'multifarious selection' hypothesis). However, evidence for each selective hypothesis is still scarce, and further work is required to determine their relative importance.

Ecological thresholds and regime shifts: approaches to identification.

Abstract: There is an apparent gap between the prominence of present theoretical frameworks involving ecological thresholds and regime shifts, and the paucity of efforts to conduct simple tests and quantitative inferences on the actual appearance of such phenomena in ecological data. A wide range of statistical methods and analytical techniques are now available that render these questions tractable, some of them even dating back half a century. Yet, their application has been sparse and confined within a narrow subset of cases of ecological regime shifts. Our objective is to raise awareness on the range of techniques available, and to their principles and limitations, to promote a more operational approach to the identification of ecological thresholds and regime shifts.

Threshold models in restoration and conservation: a developing framework

Abstract: The recognition that a system can appear resilient to changes in the environment, only to reach a critical threshold of rapid and unexpected change, is spurring work to apply threshold models in conservation and restoration. Here we address the relevance of threshold models to habitat management. Work to date indicates these concepts are highly applicable: human impacts can widen the range of habitats where threshold dynamics occur and shift communities into new states that are difficult to reverse. However, in many applied settings, threshold concepts are being adopted without evaluation of evidence and uncertainty. We suggest a framework for incorporating threshold models that reflects an emphasis on applicability to decision making and management on relatively short timescales and in human-impacted systems.

Emerging horizons in biodiversity and ecosystem functioning research

Abstract: Two decades of intensive research have provided compelling evidence for a link between biodiversity and ecosystem functioning (B-EF). Whereas early B-EF research concentrated on species richness and single processes, recent studies have investigated different measures of both biodiversity and ecosystem functioning, such as functional diversity and joint metrics of multiple processes. There is also a shift from viewing assemblages in terms of their contribution to particular processes toward placing them within a wider food web context. We review how the responses and predictors in B-EF experiments are quantified and how biodiversity effects are shaped by multitrophic interactions. Further, we discuss how B-EF metrics and food web relations could be addressed simultaneously. We conclude that addressing traits, multiple processes and food web interactions is needed to capture the mechanisms that underlie B-EF relations in natural assemblages.

Assisted colonization is not a viable conservation strategy

Abstract: A potential conservation strategy increasingly discussed by conservation biologists is the translocation of species to favorable habitat beyond their native range to protect them from human-induced threats, such as climate change. Even if preceded by careful risk assessment, such action is likely to produce myriad unintended and unpredictable consequences. Accurate risk assessment is impeded by contingency: the impacts of introduced species vary over time and space under the influence of local environmental variables, interspecific interactions and evolutionary change. Some impacts, such as native species extinctions, are large and irrevocable. Here we argue that conservation biologists have not yet developed a sufficient understanding of the impacts of introduced species to make informed decisions regarding species translocations.

Speed-accuracy tradeoffs in animal decision making.

Abstract: The traditional emphasis when measuring performance in animal cognition has been overwhelmingly on accuracy, independent of decision time. However, more recently, it has become clear that tradeoffs exist between decision speed and accuracy in many ecologically relevant tasks, for example, prey and predator detection and identification; pollinators choosing between flower species; and spatial exploration strategies. Obtaining high-quality information often increases sampling time, especially under noisy conditions. Here we discuss the mechanisms generating such speed–accuracy tradeoffs, their implications for animal decision making (including signalling, communication and mate choice) and the significance of differences in decision strategies among species, populations and individuals. The ecological relevance of such tradeoffs can be better understood by considering the neuronal mechanisms underlying decision-making processes.

Relaxed selection in the wild

Abstract: Natural populations often experience the weakening or removal of a source of selection that had been important in the maintenance of one or more traits. Here we refer to these situations as 'relaxed selection,' and review recent studies that explore the effects of such changes on traits in their ecological contexts. In a few systems, such as the loss of armor in stickleback, the genetic, developmental and ecological bases of trait evolution are being discovered. These results yield insights into whether and how fast a trait is reduced or lost under relaxed selection. We provide a prospectus and a framework for understanding relaxed selection and trait loss in natural populations. We also examine its implications for applied issues, such as antibiotic resistance and the success of invasive species.

Adaptive radiation, nonadaptive radiation, ecological speciation and nonecological speciation.

Abstract: Radiations of ecologically and morphologically differentiated sympatric species can exhibit the pattern of a burst of diversification, which might be produced by ecological divergence between populations, together with the acquisition of reproductive isolation ('ecological speciation'). Here we suggest that this pattern could also arise if speciation precedes significant ecological differentiation (i.e. through geographical isolation and nonadaptive radiation). Subsequently, species ecologically differentiate and spread into sympatry. Alternative routes to producing ecologically differentiated sympatric species are difficult to detect in old radiations. However, nonadaptive radiations are common and might therefore regularly be responsible for currently ecologically differentiated sympatric species (e.g. among groups that are not susceptible to ecological speciation). Species evolving nonadaptively over long periods might eventually replace young, ecologically produced species.

Coral bleaching: the role of the host

Abstract: Coral bleaching caused by global warming is one of the major threats to coral reefs. Very recently, research has focused on the possibility of corals switching symbionts as a means of adjusting to accelerating increases in sea surface temperature. Although symbionts are clearly of fundamental importance, many aspects of coral bleaching cannot be readily explained by differences in symbionts among coral species. Here we outline several potential mechanisms by which the host might influence the bleaching response, and conclude that predicting the fate of corals in response to climate change requires both members of the symbiosis to be considered equally.

The altitude-for-latitude disparity in the range retractions of woody species

Abstract: Increasing temperatures are driving rapid upward range shifts of species in mountains. An altitudinal range retreat of 10 m is predicted to translate into a ∼10-km latitudinal retreat based on the rate at which temperatures decline with increasing altitude and latitude, yet reports of latitudinal range retractions are sparse. Here, we examine potential climatic, biological, anthropogenic and methodological explanations for this disparity. We argue that the lack of reported latitudinal range retractions stems more from a lack of research effort, compounded by methodological difficulties, rather than from their absence. Given the predicted negative impacts of increasing temperatures on wide areas of the latitudinal distributions of species, the investigation of range retractions should become a priority in biogeographical research.

Pelagic protected areas: the missing dimension in ocean conservation

Abstract: Fewer protected areas exist in the pelagic ocean than any other ecosystem on Earth. Although there is increasing support for marine protected areas (MPAs) as a tool for pelagic conservation, there have also been numerous criticisms of the ecological, logistical and economic feasibility of place-based management in the dynamic pelagic environment. Here we argue that recent advances across conservation, oceanography and fisheries science provide the evidence, tools and information to address these criticisms and confirm MPAs as defensible and feasible instruments for pelagic conservation. Debate over the efficacy of protected areas relative to other conservation measures cannot be resolved without further implementation of MPAs in the pelagic ocean.

On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota.

Abstract: Ediacara fossils document an important evolutionary episode just before the Cambrian explosion and hold critical information about the early evolution of macroscopic and complex multicellular life. They also represent an enduring controversy in paleontology. How are the Ediacara fossils related to living animals? How did they live? Do they share any evolutionary patterns with other life forms? Recent developments indicate that Ediacara fossils epitomize a phylogenetically diverse biosphere, probably including animals, protists, algae, fungi and others. Their simple ecology is dominated by epibenthic osmotrophs, deposit feeders and grazers, but few if any predators. Their evolution started with an early morphospace expansion followed by taxonomic diversification within confined morphospace, and concluded by extinction of many taxa at the Ediacaran–Cambrian boundary.

The evolution of restricted recombination in sex chromosomes

Abstract: In species with separate sexes, sex determination often has a genetic basis, and in a wide diversity of taxa a pair of cytologically distinguishable 'sex chromosomes' are found such that the chromosome complements of males and females differ (males are often XY and females XX, but sometimes females are ZW whereas males are ZZ). Recent evidence from sequences of sex-linked genes confirms classical genetic evidence that these chromosomes are a homologous pair, evolved from a normal chromosome pair, between which recombination stopped. We discuss why sex chromosomes evolve reduced recombination and why different parts of the chromosomes stopped recombining at different times, and outline some of the consequences of suppressed recombination, including the evolution of chromosome heteromorphism.

Detecting range shifts from historical species occurrences: new perspectives on old data

Abstract: The difficulty of making valid comparisons between historical and contemporary data is an obstacle to documenting range change in relation to environmental modifications. Recent statistical advances use occupancy modeling to estimate simultaneously the probability of detection and the probability of occupancy, and enable unbiased comparisons between historical and modern data; however, they require repeated surveys at the same locations within a time period. We present two models for explicitly comparing occupancy between historical and modern eras, and discuss methods to measure range change. We suggest that keepers of historical data have crucial roles in curating and aiding accessibility to data, and we recommend that collectors of contemporary specimen data organize their sampling efforts to include repeated surveys to estimate detection probabilities.