Hot off the presses! Apr 01 Trends in Ecology & Evolution

The Apr 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 26(4):i (2011)
  
• Natural history collections as sources of long-term datasets
  - Trends in Ecology and Evolution 26(4):153-154 (2011)
  In the otherwise excellent special issue of Trends in Ecology and Evolution on long-term ecological research (TREE 25(10), 2010), none of the contributors mentioned the importance of natural history collections (NHCs) as sources of data that can strongly complement past and ongoing survey data. Whereas very few field surveys have operated for more than a few decades, NHCs, conserved in museums and other institutions, comprise samples of the Earth's biota typically extending back well into the nineteenth century and, in some cases, before this time. They therefore span the period of accelerated anthropogenic habitat destruction, climate warming and ocean acidification, in many cases reflecting baseline conditions before the major impact of these factors.
• The costs of describing the entire animal kingdom
  - Trends in Ecology and Evolution 26(4):154-155 (2011)
  
• Why research on traits of invasive plants tells us very little
  - Trends in Ecology and Evolution 26(4):155-156 (2011)
  
• Unfortunately, linguistic injustice matters
  - Trends in Ecology and Evolution 26(4):156-157 (2011)
  
• Social networking in the world of ants
  - Trends in Ecology and Evolution 26(4):157-158 (2011)
  
• Aboveground–belowground interactions: the way forward
  - Trends in Ecology and Evolution 26(4):158-159 (2011)
  
• The genes underlying the process of speciation
  - Trends in Ecology and Evolution 26(4):160-167 (2011)
  The long-standing goal of finding genes causing reproductive isolation is being achieved. To better link the genetics with the process of speciation, we propose that 'speciation gene' be defined as any gene contributing to the evolution of reproductive isolation. Characterizing a speciation gene involves establishing that the gene affects a component of reproductive isolation; demonstrating that divergence at the locus occurred before completion of speciation; and quantifying the effect size of the gene (i.e. the increase in total reproductive isolation caused by its divergence). Review of a sample of candidate speciation genes found that few meet these criteria. Improved characterization of speciation genes will clarify how numerous they are, their properties and how they affect genome-wide patterns of divergence.
• Addressing the threat to biodiversity from botanic gardens
  - Trends in Ecology and Evolution 26(4):168-174 (2011)
  Increasing evidence highlights the role that botanic gardens might have in plant invasions across the globe. Botanic gardens, often in global biodiversity hotspots, have been implicated in the early cultivation and/or introduction of most environmental weeds listed by IUCN as among the worst invasive species worldwide. Furthermore, most of the popular ornamental species in living collections around the globe have records as alien weeds. Voluntary codes of conduct to prevent the dissemination of invasive plants from botanic gardens have had limited uptake, with few risk assessments undertaken of individual living collections. A stronger global networking of botanic gardens to tackle biological invasions involving public outreach, information sharing and capacity building is a priority to prevent the problems of the past occurring in the future.
• Peto's Paradox: evolution's prescription for cancer prevention
  - Trends in Ecology and Evolution 26(4):175-182 (2011)
  The evolution of multicellularity required the suppression of cancer. If every cell has some chance of becoming cancerous, large, long-lived organisms should have an increased risk of developing cancer compared with small, short-lived organisms. The lack of correlation between body size and cancer risk is known as Peto's paradox. Animals with 1000 times more cells than humans do not exhibit an increased cancer risk, suggesting that natural mechanisms can suppress cancer 1000 times more effectively than is done in human cells. Because cancer has proven difficult to cure, attention has turned to cancer prevention. In this review, similar to pharmaceutical companies mining natural products, we seek to understand how evolution has suppressed cancer to develop ultimately improved cancer prevention in humans.
• Why intraspecific trait variation matters in community ecology
  - Trends in Ecology and Evolution 26(4):183-192 (2011)
  Natural populations consist of phenotypically diverse individuals that exhibit variation in their demographic parameters and intra- and inter-specific interactions. Recent experimental work indicates that such variation can have significant ecological effects. However, ecological models typically disregard this variation and focus instead on trait means and total population density. Under what situations is this simplification appropriate? Why might intraspecific variation alter ecological dynamics? In this review we synthesize recent theory and identify six general mechanisms by which trait variation changes the outcome of ecological interactions. These mechanisms include several direct effects of trait variation per se and indirect effects arising from the role of genetic variation in trait evolution.
• Evolution in structured populations: beyond the kin versus group debate
  - Trends in Ecology and Evolution 26(4):193-201 (2011)
  Much of the literature on social evolution is pervaded by the old debate about the relative merits of kin and group selection. In this debate, the biological interpretation of processes occurring in real populations is often conflated with the mathematical methodology used to describe these processes. Here, we highlight the distinction between the two by placing this discussion within the broader context of evolution in structured populations. In this review we show that the current debate overlooks important aspects of the interplay between genetic and demographic structuring, and argue that a continued focus on the relative merits of kin versus group selection distracts attention from moving the field forward.
• New paradigms for the evolution of beneficial infections
  - Trends in Ecology and Evolution 26(4):202-209 (2011)
  A longstanding paradigm predicts that microbial parasites and mutualists exhibit disparate evolutionary patterns. Parasites are predicted to promote arms races with hosts, rapid evolution and sexual recombination. By contrast, mutualists have been linked with beneficial coadaptation, evolutionary stasis and asexuality. In this review we discuss the recent surge of molecular data on microbes that are being used to test and reshape these ideas. New analyses reveal that beneficial microbes often share mechanisms of infection and defense with parasites, and can also exhibit rapid evolution and extensive genetic exchange. To explain these patterns, new paradigms must take into account the varied population biology of beneficial microbes, their potential conflicts with hosts, and the mosaic nature of genome evolution that requires locus-based tests to analyze the genetics of host adaptation.

Hot off the presses! Jan 01 Trends in Ecology & Evolution

The Jan 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 26(1):i (2011)
  
• The social side of Homo economicus
  - Trends in Ecology and Evolution 26(1):1-3 (2011)
  Many recent experiments in the field of behavioural economics appear to demonstrate a willingness of humans to behave altruistically, even when it is not in their interest to do so. This has led to the assertion that humans have evolved a special predisposition towards altruism. Recent studies have questioned this, and demonstrated that selfless cooperation does not hold up in controlled experiments. As I discuss here, this calls for more economic 'field experiments' and highlights the need for greater integration of the evolutionary and economic sciences.
• What is long-term in ecology?
  - Trends in Ecology and Evolution 26(1):3-4 (2011)
  
• New technology facilitates the study of social networks
  - Trends in Ecology and Evolution 26(1):5-6 (2011)
  
• Continuing sculpting
  - Trends in Ecology and Evolution 26(1):6-7 (2011)
  
• Selection as a unifying process in the biological and social sciences
  - Trends in Ecology and Evolution 26(1):7-8 (2011)
  
• The most intensively studied area on Earth
  - Trends in Ecology and Evolution 26(1):8-9 (2011)
  
• Horizon scan of global conservation issues for 2011
  - Trends in Ecology and Evolution 26(1):10-16 (2011)
  This review describes outcomes of a 2010 horizon-scanning exercise building upon the first exercise conducted in 2009. The aim of both horizon scans was to identify emerging issues that could have substantial impacts on the conservation of biological diversity, and to do so sufficiently early to encourage policy-relevant, practical research on those issues. Our group included professional horizon scanners and researchers affiliated with universities and non- and inter-governmental organizations, including specialists on topics such as invasive species, wildlife diseases and coral reefs. We identified 15 nascent issues, including new greenhouse gases, genetic techniques to eradicate mosquitoes, milk consumption in Asia and societal pessimism.
• Experiments with genitalia: a commentary
  - Trends in Ecology and Evolution 26(1):17-21 (2011)
  There has been a recent burst of studies of the function of genitalia, many of which share several important shortcomings. Given that further studies on this topic are likely (there are probably millions of species showing rapid genital divergence), I discuss the studies critically to promote clear formulation of hypotheses and interpretation of results in the future. I also emphasize some possibly important but neglected variables, including female stimulation, phylogenetic contexts, and the behavior of male genitalia, and outline simple techniques that could improve future studies.
• Pleiotropy, apparent stabilizing selection and uncovering fitness optima
  - Trends in Ecology and Evolution 26(1):22-29 (2011)
  Evolutionary theory has emphasized that the evolution of single traits cannot be understood in isolation when pleiotropy is present. Widespread pleiotropy causes the appearance of stabilizing selection on metric traits owing to joint effects with fitness, and results in the genetic variation being concentrated in relatively few combinations of the measured traits. In this review, we show how trait combinations with high levels of genetic variation can be used to uncover fitness optima that are defined by apparent stabilizing selection. Defining fitness optima in this way could provide one avenue by which researchers can overcome the problem posed by measuring the myriad of traits that must influence fitness, or by measuring total fitness itself.
• Conservation paleobiology: putting the dead to work
  - Trends in Ecology and Evolution 26(1):30-37 (2011)
  Geohistorical data and analyses are playing an increasingly important role in conservation biology practice and policy. In this review, we discuss examples of how the near-time and deep-time fossil record can be used to understand the ecological and evolutionary responses of species to changes in their environment. We show that beyond providing crucial baseline data, the conservation paleobiology perspective helps us to identify which species will be most vulnerable and what kinds of responses will be most common. We stress that inclusion of geohistorical data in our decision-making process provides a more scientifically robust basis for conservation policies than those dependent on short-term observations alone.
• Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition
  - Trends in Ecology and Evolution 26(1):38-44 (2011)
  The new field of 'stoichiogenomics' integrates evolution, ecology and bioinformatics to reveal surprising patterns of the differential usage of key elements [e.g. nitrogen (N)] in proteins and nucleic acids. Because the canonical amino acids as well as nucleotides differ in element counts, natural selection owing to limited element supplies might bias monomer usage to reduce element costs. For example, proteins that respond to N limitation in microbes use a lower proportion of N-rich amino acids, whereas proteome- and transcriptome-wide element contents differ significantly for plants as compared with animals, probably because of the differential severity of element limitations. In this review, we show that with these findings, new directions for future investigations are emerging, particularly via the increasing availability of diverse metagenomic and metatranscriptomic data sets.
• Exploring vegetation in the fourth dimension
  - Trends in Ecology and Evolution 26(1):45-52 (2011)
  Much ecological research focuses on changes in vegetation on spatial scales from stands to landscapes; however, capturing data on vegetation change over relevant timescales remains a challenge. Pollen analysis offers unrivalled access to data with global coverage over long timescales. Robust techniques have now been developed that enable pollen data to be converted into vegetation data in terms of individual taxa, plant communities or biomes, with the possibility of deriving from those data a range of plant attributes and ecological indicators. In this review, I discuss how coupling pollen with macrofossil, charcoal and genetic data opens up the extensive pollen databases to investigation of the drivers of vegetation change over time and also provides extensive data sets for testing hypotheses with wide ecological relevance.

Hot off the presses! Feb 01 Trends in Ecology & Evolution

The Feb 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 26(2):i (2011)
  
• Basic research in evolution and ecology enhances forensics
  - Trends in Ecology and Evolution 26(2):53-55 (2011)
  In 2009, the National Research Council recommended that the forensic sciences strengthen their grounding in basic empirical research to mitigate against criticism and improve accuracy and reliability. For DNA-based identification, this goal was achieved under the guidance of the population genetics community. This effort resulted in DNA analysis becoming the 'gold standard' of the forensic sciences. Elsewhere, we proposed a framework for streamlining research in decomposition ecology, which promotes quantitative approaches to collecting and applying data to forensic investigations involving decomposing human remains. To extend the ecological aspects of this approach, this review focuses on forensic entomology, although the framework can be extended to other areas of decomposition.
• Academic strategies in a funding crisis: research competitor, ruderal or university teacher?
  - Trends in Ecology and Evolution 26(2):56-57 (2011)
  
• Recent developments in sociobiology and the scientific method
  - Trends in Ecology and Evolution 26(2):57-58 (2011)
  
• 'Linguistic injustice' is not black and white
  - Trends in Ecology and Evolution 26(2):58-59 (2011)
  
• Conservation science must engender hope to succeed
  - Trends in Ecology and Evolution 26(2):59-60 (2011)
  
• Data archiving in ecology and evolution: best practices
  - Trends in Ecology and Evolution 26(2):61-65 (2011)
  Many ecology and evolution journals have recently adopted policies requiring that data from their papers be publicly archived. I present suggestions on how data generators, data re-users, and journals can maximize the fairness and scientific value of data archiving. Data should be archived with enough clarity and supporting information that they can be accurately interpreted by others. Re-users should respect their intellectual debt to the originators of data through citation both of the paper and of the data package. In addition, journals should consider requiring that all data for published papers be archived, just as DNA sequences must be deposited in GenBank. Data are another valuable part of the legacy of a scientific career and archiving them can lead to new scientific insights. Archiving also increases opportunities for credit to be given to the scientists who originally collected the data.
• Hypothesis testing in biogeography
  - Trends in Ecology and Evolution 26(2):66-72 (2011)
  Often, biogeography is applied only as a narrative addition to phylogenetic studies and lacks scientific rigour. However, if research questions are framed as hypotheses, biogeographical scenarios become testable. In this review, we explain some problems with narrative biogeography and show how the use of explicit hypotheses is changing understanding of how organisms came to be distributed as they are. Developing synergies between biogeography, ecology, molecular dating and palaeontology are providing novel data and hypothesis-testing opportunities. New approaches are challenging the classic 'Gondwana' paradigm and a more complicated history of the Southern Hemisphere is emerging, involving not only general drivers such as continental drift and niche conservatism, but also drowning and re-emergence of landmasses, biotic turnover and long-distance colonization.
• Vacant habitats in the Universe
  - Trends in Ecology and Evolution 26(2):73-80 (2011)
  The search for life on other planets usually makes the assumption that where there is a habitat, it will contain life. On the present-day Earth, uninhabited habitats (or vacant habitats) are rare, but might occur, for example, in subsurface oils or impact craters that have been thermally sterilized in the past. Beyond Earth, vacant habitats might similarly exist on inhabited planets or on uninhabited planets, for example on a habitable planet where life never originated. The hypothesis that vacant habitats are abundant in the Universe is testable by studying other planets. In this review, I discuss how the study of vacant habitats might ultimately inform an understanding of how life has influenced geochemical conditions on Earth.
• Animals and the invention of the Phanerozoic Earth system
  - Trends in Ecology and Evolution 26(2):81-87 (2011)
  Animals do not just occupy the modern biosphere, they permeate its structure and define how it works. Their unique combination of organ-grade multicellularity, motility and heterotrophic habit makes them powerful geobiological agents, imposing myriad feedbacks on nutrient cycling, productivity and environment. Most significantly, animals have 'engineered' the biosphere over evolutionary time, forcing the diversification of, for example, phytoplankton, land plants, trophic structure, large body size, bioturbation, biomineralization and indeed the evolutionary process itself. This review surveys how animals contribute to the modern world and provides a basis for reconstructing ancient ecosystems. Earlier, less animal-influenced biospheres worked quite differently from the one currently occupied, with the Ediacaran–Cambrian radiation of organ-grade animals marking a fundamental shift in macroecological and macroevolutionary expression.
• The evolution of the worldwide leaf economics spectrum
  - Trends in Ecology and Evolution 26(2):88-95 (2011)
  The worldwide leaf economic spectrum (WLES) is a strikingly consistent pattern of correlations among leaf traits. Although the WLES effectively summarizes variation in plant ecological strategies, little is known about its evolution. We reviewed estimates of natural selection and genetic variation for leaf traits to test whether the evolution of the WLES was limited by selection against unfit trait combinations or by genetic constraints. There was significant selection for leaf traits on both ends of the WLES spectrum, as well as significant genetic variation for these traits. In addition, genetic correlations between WLES traits were variable in strength and direction. These data suggest that genetic constraints have had a smaller role than selection in the evolution of the WLES.
• Dynamic disequilibrium of the terrestrial carbon cycle under global change
  - Trends in Ecology and Evolution 26(2):96-104 (2011)
  In this review, we propose a new framework, dynamic disequilibrium of the carbon cycles, to assess future land carbon-sink dynamics. The framework recognizes internal ecosystem processes that drive the carbon cycle toward equilibrium, such as donor pool-dominated transfer; and external forces that create disequilibrium, such as disturbances and global change. Dynamic disequilibrium within one disturbance–recovery episode causes temporal changes in the carbon source and sink at yearly and decadal scales, but has no impacts on longer-term carbon sequestration unless disturbance regimes shift. Such shifts can result in long-term regional carbon loss or gain and be quantified by stochastic statistics for use in prognostic modeling. If the regime shifts result in ecosystem state changes in regions with large carbon reserves at risk, the global carbon cycle might be destabilized.

Hot off the presses! Mar 01 Trends in Ecology & Evolution

The Mar 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 26(3):i (2011)
  
• A reckoning for reckoning
  - Trends in Ecology and Evolution 26(3):105-106 (2011)
  
• Seeing only REDD? A response to Law et al.
  - Trends in Ecology and Evolution 26(3):106-107 (2011)
  
• Monitoring decisions: not as simple as they seem?
  - Trends in Ecology and Evolution 26(3):107 (2011)
  
• Should we implement monitoring or research for conservation?
  - Trends in Ecology and Evolution 26(3):108-109 (2011)
  
• Tortured genius
  - Trends in Ecology and Evolution 26(3):109-110 (2011)
  
• Endangered species and a threatened discipline: behavioural ecology
  - Trends in Ecology and Evolution 26(3):111-118 (2011)
  Behavioural ecologists often see little connection between the current conservation crisis and the future of their discipline. This view is myopic because our abilities to investigate and interpret the adaptive significance and evolutionary histories of behaviours are increasingly being compromised in human-dominated landscapes because of species extinctions, habitat destruction, invasive species, pollution, and climate change. In this review, we argue that many central issues in behavioural ecology will soon become prohibitively difficult to investigate and interpret, thus impeding the rapid progress that characterizes the field. To address these challenges, behavioural ecologists should design studies not only to answer basic scientific questions but also to provide ancillary information for protection and management of their study organisms and habitats, and then share their biological insights with the applied conservation community.
• Four opportunities for studies of ecological succession
  - Trends in Ecology and Evolution 26(3):119-123 (2011)
  Lessons learned from the study of ecological succession have much to offer contemporary environmental problem solving but these lessons are being underutilized. As anthropogenic disturbances increase, succession is more relevant than ever. In this review, we suggest that succession is particularly suitable to address concerns about biodiversity loss, climate change, invasive species, and ecological restoration. By incorporating modern experimental techniques and linking results across environmental gradients with meta-analyses, studies of succession can substantially improve our understanding of other ecological phenomena. Succession can help predict changes in biodiversity and ecosystem services impacted by invasive species and climate change and guide manipulative responses to these disruptions by informing restoration efforts. Succession is still a critical, integrative concept that is central to ecology.
• Dark diversity: shedding light on absent species
  - Trends in Ecology and Evolution 26(3):124-128 (2011)
  Ecological theory and nature conservation have traditionally relied solely on observed local diversity. In this review, we recommend including those species that are absent from an ecosystem but which belong to its species pool; that is, all species in the region that can potentially inhabit those particular ecological conditions. We call the set of absent species 'dark diversity'. Relating local and dark diversities enables biodiversity comparisons between regions, ecosystems and taxonomic groups, and the evaluation of the roles of local and regional processes in ecological communities. Dark diversity can also be used to counteract biodiversity loss and to estimate the restoration potential of ecosystems. We illustrate the dark diversity concept by globally mapping plant dark diversity and the local:dark diversity ratio.
• Scavenging: how carnivores and carrion structure communities
  - Trends in Ecology and Evolution 26(3):129-135 (2011)
  Recent advances in the ecology of food webs underscore the importance of detritus and indirect predator–prey effects. However, most research considers detritus as an invariable pool and predation as the only interaction between carnivores and prey. Carrion consumption, scavenging, is a type of detrital feeding that should have widespread consequences for the structure and stability of food webs. Providing access to high-quality resources, facultative scavenging is a ubiquitous and phylogenetically widespread strategy. In this review, we argue that scavenging is underestimated by 16-fold in food-web research, producing inflated predation rates and underestimated indirect effects. Furthermore, more energy is generally transferred per link via scavenging than predation. Thus, future food-web research should consider scavenging, especially in light of how major global changes can affect scavengers.
• Evergreens favored by higher responsiveness to increased CO2
  - Trends in Ecology and Evolution 26(3):136-142 (2011)
  Physical CO2 diffusion from sub-stomatal cavities to the chloroplasts where photosynthesis takes place is an important limitation of photosynthesis largely neglected in research related to global climate change. This limitation is particularly important in leaves with robust structures such as evergreen sclerophylls. In these leaves, photosynthesis is less sensitive to changes in stomatal openness, which is considered to be the primary limitation of photosynthesis. In this review we state that, because of large limitations in internal diffusion in C3 plants, photosynthesis and the intrinsic efficiency of the use of plant water responds more strongly to elevated levels of CO2 in leaves with more robust structures. This provides an additional explanation for the current apparent expansion of evergreen sclerophylls in many Earth ecosystems, and adds a new perspective to research of the biological effects of increasing atmospheric CO2.
• Genes as leaders and followers in evolution
  - Trends in Ecology and Evolution 26(3):143-151 (2011)
  A major question for the study of phenotypic evolution is whether intra- and interspecific diversity originates directly from genetic variation, or instead, as plastic responses to environmental influences initially, followed later by genetic change. In species with discrete alternative phenotypes, evolutionary sequences can be inferred from transitions between environmental and genetic phenotype control, and from losses of phenotypic alternatives. From the available evidence, sequences appear equally probable to start with genetic polymorphism as with polyphenism, with a possible dominance of one or the other for specific trait types. We argue in this review that to evaluate the prevalence of each route, an investigation of both genetic and environmental cues for phenotype determination in several related rather than in isolated species is required.

Hot off the presses! Nov 01 Trends in Ecology & Evolution

The Nov 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 25(11):i (2010)
  
• Transdisciplinary research is needed to predict plant invasions in an era of global change
  - Trends in Ecology and Evolution 25(11):619-620 (2010)
  
• Biodiversity "surpluses" and "deficits" are not novel issues
  - Trends in Ecology and Evolution 25(11):620-621 (2010)
  
• Response to 'Biodiversity "surpluses" and "deficits" are not novel issues': We agree
  - Trends in Ecology and Evolution 25(11):621-622 (2010)
  
• Artifacts of the evolving mind: what tool use tells us about early human cognition
  - Trends in Ecology and Evolution 25(11):622-623 (2010)
  
• Popular ants with style and substance
  - Trends in Ecology and Evolution 25(11):623-624 (2010)
  
• Aliens, globalization, and biodiversity
  - Trends in Ecology and Evolution 25(11):624-625 (2010)
  
• Three roads diverged? Routes to phylogeographic inference
  - Trends in Ecology and Evolution 25(11):626-632 (2010)
  Phylogeographic methods facilitate inference of the geographical history of genetic lineages. Recent examples explore human migration and the origins of viral pandemics. There is longstanding disagreement over the use and validity of certain phylogeographic inference methodologies. In this paper, we highlight three distinct frameworks for phylogeographic inference to give a taste of this disagreement. Each of the three approaches presents a different viewpoint on phylogeography, most fundamentally on how we view the relationship between the inferred history of a sample and the history of the population the sample is embedded in. Satisfactory resolution of this relationship between history of the tree and history of the population remains a challenge for all but the most trivial models of phylogeographic processes. Intriguingly, we believe that some recent methods that entirely avoid inference about the history of the population will eventually help to reach a resolution .
• Rising to the challenge of sustaining coral reef resilience
  - Trends in Ecology and Evolution 25(11):633-642 (2010)
  Phase-shifts from one persistent assemblage of species to another have become increasingly commonplace on coral reefs and in many other ecosystems due to escalating human impacts. Coral reef science, monitoring and global assessments have focused mainly on producing detailed descriptions of reef decline, and continue to pay insufficient attention to the underlying processes causing degradation. A more productive way forward is to harness new theoretical insights and empirical information on why some reefs degrade and others do not. Learning how to avoid undesirable phase-shifts, and how to reverse them when they occur, requires an urgent reform of scientific approaches, policies, governance structures and coral reef management.
• Stochastic models of population extinction
  - Trends in Ecology and Evolution 25(11):643-652 (2010)
  Theoretical ecologists have long sought to understand how the persistence of populations depends on biotic and abiotic factors. Classical work showed that demographic stochasticity causes the mean time to extinction to increase exponentially with population size, whereas variation in environmental conditions can lead to a power-law scaling. Recent work has focused especially on the influence of the autocorrelation structure ('color') of environmental noise. In theoretical physics, there is a burst of research activity in analyzing large fluctuations in stochastic population dynamics. This research provides powerful tools for determining extinction times and characterizing the pathway to extinction. It yields, therefore, sharp insights into extinction processes and has great potential for further applications in theoretical biology.
• Do consistent individual differences in metabolic rate promote consistent individual differences in behavior?
  - Trends in Ecology and Evolution 25(11):653-659 (2010)
  Consistent individual differences (CIDs) in behavior are a widespread phenomenon in animals, but the proximate reasons for them are unresolved. We discuss evidence for the hypothesis that CIDs in energy metabolism, as reflected by resting metabolic rate (RMR), promote CIDs in behavior patterns that either provide net energy (e.g. foraging activity), and/or consume energy (e.g. courtship activity). In doing so, we provide a framework for linking together RMR, behavior, and life-history productivity. Empirical studies suggest that RMR is (a) related to the capacity to generate energy, (b) repeatable, and (c) correlated with behavioral output (e.g. aggressiveness) and productivity (e.g. growth). We conclude by discussing future research directions to clarify linkages between behavior and energy metabolism in this emerging research area.
• Chromosomal speciation revisited: rearranging theory with pieces of evidence
  - Trends in Ecology and Evolution 25(11):660-669 (2010)
  The suggestion that chromosomal rearrangements play a role in speciation resulted from the observation that heterokaryotypes are often infertile. However, the first chromosomal speciation models were unsatisfactory and data available to test them was scarce. Recently, large amounts of data have become available and new theoretical models have been developed explaining how rearrangements facilitate speciation in the face of gene flow. Here, we re-examine theoretical predictions and revisit different sources of data. Although rearrangements are often associated with increased levels of divergence, unequivocal demonstration that their role in suppressing recombination results in speciation is often lacking. Finally, we question some previous predictions and suggest new empirical and theoretical approaches to understanding the relevance of rearrangements in the origin of species.
• How understanding aboveground–belowground linkages can assist restoration ecology
  - Trends in Ecology and Evolution 25(11):670-679 (2010)
  The topic of aboveground–belowground linkages has seen much recent activity, resulting in several conceptual advances regarding plant–soil feedbacks, multitrophic interactions, and how organisms drive ecosystem processes. Although restoration ecology has been rapidly evolving as a scientific discipline, the principles that have developed regarding aboveground–belowground linkages have yet to be thoroughly integrated into it. In this review, we conceptually integrate the role of aboveground–belowground linkages with the principles of restoration ecology through a framework that transcends multiple levels of ecological organization, and illustrate its application through three examples: restoration of abandoned land, reversal of biological invasions, and restoration of natural disturbances. We conclude that this integration can greatly assist restoration ecology, through aiding identification of effective invention practices and prediction of ecosystem recovery.

Hot off the presses! Dec 01 Trends in Ecology & Evolution

The Dec 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 25(12):i (2010)
  
• Light pollution as a biodiversity threat
  - Trends in Ecology and Evolution 25(12):681-682 (2010)
  
• Swarm intelligence in plant roots
  - Trends in Ecology and Evolution 25(12):682-683 (2010)
  
• Astrobiology in Antarctica
  - Trends in Ecology and Evolution 25(12):683-684 (2010)
  
• Community ecology: stasis, evolution or revolution?
  - Trends in Ecology and Evolution 25(12):684-685 (2010)
  
• Names are key to the big new biology
  - Trends in Ecology and Evolution 25(12):686-691 (2010)
  Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution and ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a 'big science'. Informatics devices will exploit this 'big new biology', revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory and semantic Global Names Architecture.
• Assessing rapid evolution in a changing environment
  - Trends in Ecology and Evolution 25(12):692-698 (2010)
  Climate change poses a serious threat to species persistence. Effective modelling of evolutionary responses to rapid climate change is therefore essential. In this review we examine recent advances in phylogenetic comparative methods, techniques normally used to study adaptation over long periods, which allow them to be applied to the study of adaptation over shorter time scales. This increased applicability is largely due to the emergence of more flexible models of character evolution and the parallel development of molecular technologies that can be used to assess adaptive variation at loci scattered across the genome. The merging of phylogenetic and population genetic approaches to the study of adaptation has significant potential to advance our understanding of rapid responses to environmental change.
• Making statistics biologically relevant in fragmented landscapes
  - Trends in Ecology and Evolution 25(12):699-704 (2010)
  The biological impacts of habitat fragmentation are routinely assessed using standard statistical modelling techniques that are used across many ecological disciplines. However, to assess the biological relevance of fragmentation impacts, we must consider an extra, spatial dimension to the standard statistical model: the biological importance of a significant and well supported model with large effect sizes crucially depends on the configuration of habitat within the study area. We argue that mapping the outputs from statistical models across a study area generates biologically meaningful estimates of fragmentation impacts. Integrating traditional statistical approaches with geographic information systems will facilitate rigorous comparisons of fragmentation impacts between taxa, studies and ecosystems.
• Adaptation genomics: the next generation
  - Trends in Ecology and Evolution 25(12):705-712 (2010)
  Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?
• Species differences in responses to captivity: stress, welfare and the comparative method
  - Trends in Ecology and Evolution 25(12):713-721 (2010)
  Approximately 26 billion animals, spanning over 10 000 species, are kept on farms and in zoos, conservation breeding centers, research laboratories and households. Captive animals are often healthier, longer-lived and more fecund than free-living conspecifics, but for some species the opposite is true. Captivity is a very long way from the ideal 'common garden' often assumed by evolutionary and ecological researchers using data for captive animals. The use of comparative methods to investigate the fundamental biological causes of these species differences would help to improve husbandry and enclosure design, and might even reveal relationships between susceptibilities to poor captive welfare and susceptibilities to anthropogenic threat in the wild. Studies of these species differences could also inspire and facilitate 'evo-mecho' research into the functions of behavioral control mechanisms.

Hot off the presses! Oct 01 Trends in Ecology & Evolution

The Oct 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 25(10):i (2010)
  
• Monitoring does not always count
  McDonald-Madden E Baxter PW Fuller RA Martin TG Game ET Montambault J Possingham HP - Trends in Ecology and Evolution 25(10):547-550 (2010)
  The gross under-resourcing of conservation endeavours has placed an increasing emphasis on spending accountability. Increased accountability has led to monitoring forming a central element of conservation programs. Although there is little doubt that information obtained from monitoring can improve management of biodiversity, the cost (in time and/or money) of gaining this knowledge is rarely considered when making decisions about allocation of resources to monitoring. We present a simple framework allowing managers and policy advisors to make decisions about when to invest in monitoring to improve management.
• Uniting marine and terrestrial modelling of biodiversity under climate change
  Mokany K Richardson AJ Poloczanska ES Ferrier S The CSIRO CAF Biodiversity Working Group - Trends in Ecology and Evolution 25(10):550-551 (2010)
  
• "Awkward wording. Rephrase": linguistic injustice in ecological journals
  Clavero M - Trends in Ecology and Evolution 25(10):552-553 (2010)
  
• The balancing act of conservation
  - Trends in Ecology and Evolution 25(10):553-554 (2010)
  
• Landscapes of hope, oceans of promise: trophic cascades
  - Trends in Ecology and Evolution 25(10):554-555 (2010)
  
• Environmental myopia: a diagnosis and a remedy
  Silvertown J Tallowin J Stevens C Power SA Morgan V Emmett B Hester A Grime PJ Morecroft M Buxton R Poulton P Jinks R Bardgett R - Trends in Ecology and Evolution 25(10):556-561 (2010)
  Long-term ecological observation affords a picture of the past that uniquely informs our understanding of present and future ecological communities and processes. Without a long-term perspective, our vision is prone to environmental myopia. Long-term experiments (LTEs) in particular can reveal the mechanisms that underlie change in communities and ecosystem functioning in a way that cannot be understood by long-term monitoring alone. Despite the urgent need to know more about how climate change will affect ecosystems and their functioning, the continued existence of LTEs is extremely precarious and we believe that dedicated funds are needed to support them. A new non-profit organization called the Ecological Continuity Trust seeks to provide a solution to this problem by establishing an endowment that will be specifically earmarked to sustain LTEs as a scientific tool for the benefit of future generations.
• Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology
  Clutton-Brock T Sheldon BC - Trends in Ecology and Evolution 25(10):562-573 (2010)
  Many important questions in ecology and evolutionary biology can only be answered with data that extend over several decades and answering a substantial proportion of questions requires records of the life histories of recognisable individuals. We identify six advantages that long-term, individual based studies afford in ecology and evolution: (i) analysis of age structure; (ii) linkage between life history stages; (iii) quantification of social structure; (iv) derivation of lifetime fitness measures; (v) replication of estimates of selection; (vi) linkage between generations, and we review their impact on studies in six key areas of evolution and ecology. Our review emphasises the unusual opportunities and productivity of long-term, individual-based studies and documents the important role that they play in research on ecology and evolutionary biology as well as the difficulties they face.
• Long-term datasets in biodiversity research and monitoring: assessing change in ecological communities through time
  Magurran AE Baillie SR Buckland ST Dick JM Elston DA Scott EM Smith RI Somerfield PJ Watt AD - Trends in Ecology and Evolution 25(10):574-582 (2010)
  The growing need for baseline data against which efforts to reduce the rate of biodiversity loss can be judged highlights the importance of long-term datasets, some of which are as old as ecology itself. We review methods of evaluating change in biodiversity at the community level using these datasets, and contrast whole-community approaches with those that combine information from different species and habitats. As all communities experience temporal turnover, one of the biggest challenges is distinguishing change that can be attributed to external factors, such as anthropogenic activities, from underlying natural change. We also discuss methodological issues, such as false alerts and modifications in design, of which users of these data sets need to be aware.
• Biodiversity baselines, thresholds and resilience: testing predictions and assumptions using palaeoecological data
  Willis KJ Bailey RM Bhagwat SA Birks HJ - Trends in Ecology and Evolution 25(10):583-591 (2010)
  Fossil records are replete with examples of long-term biotic responses to past climate change. One particularly useful set of records are those preserved in lake and marine sediments, recording both climate changes and corresponding biotic responses. Recently there has been increasing focus on the need for conservation of ecological and evolutionary processes in the face of climate change. We review key areas where palaeoecological archives contribute to this conservation goal, namely: (i) determination of rates and nature of biodiversity response to climate change; (ii) climate processes responsible for ecological thresholds; (iii) identification of ecological resilience to climate change; and (iv) management of novel ecosystems. We stress the importance of long-term palaeoecological data in fully understanding contemporary and future biotic responses.
• Accessible ecology: synthesis of the long, deep, and broad
  Peters DP - Trends in Ecology and Evolution 25(10):592-601 (2010)
  Large volumes of data have been collected to document the many ways that ecological systems are responding to changing environmental drivers. A general buy-in on solutions to these problems can be reached only if these and future data are made easily accessible to and understood by a broad audience that includes the public, decision-makers, and other scientists. A developing framework for synthesis is reviewed that integrates three main strategies of ecological research (long-term studies; short-term, process-based studies; and broad-scale observations) with derived data products and additional sources of knowledge. This framework focuses on making data from multiple sources and disciplines easily understood by many, a prerequisite for finding synthetic solutions and predicting future dynamics in a changing world.
• Multi-decadal oceanic ecological datasets and their application in marine policy and management
  Edwards M Beaugrand G Hays GC Koslow JA Richardson AJ - Trends in Ecology and Evolution 25(10):602-610 (2010)
  Long-term biological time-series in the oceans are relatively rare. Using the two longest of these we show how the information value of such ecological time-series increases through space and time in terms of their potential policy value. We also explore the co-evolution of these oceanic biological time-series with changing marine management drivers. Lessons learnt from reviewing these sequences of observations provide valuable context for the continuation of existing time-series and perspective for the initiation of new time-series in response to rapid global change. Concluding sections call for a more integrated approach to marine observation systems and highlight the future role of ocean observations in adaptive marine management.
• Never mind the length, feel the quality: the impact of long-term epidemiological data sets on theory, application and policy
  Rohani P King AA - Trends in Ecology and Evolution 25(10):611-618 (2010)
  Infectious diseases have been a prime testing ground for ecological theory. However, the ecological perspective is increasingly recognized as essential in epidemiology. Long-term, spatially resolved reliable data on disease incidence and the ability to test them using mechanistic models have been critical in this cross-fertilization. Here, we review some of the key intellectual developments in epidemiology facilitated by long-term data. We identify research frontiers at the interface of ecology and epidemiology and their associated data needs.