Showing papers in "Trends in Ecology and Evolution in 2005"
TL;DR: The use of the NDVI in recent ecological studies is reviewed and its possible key role in future research of environmental change in an ecosystem context is outlined.
Abstract: Assessing how environmental changes affect the distribution and dynamics of vegetation and animal populations is becoming increasingly important for terrestrial ecologists to enable better predictions of the effects of global warming, biodiversity reduction or habitat degradation. The ability to predict ecological responses has often been hampered by our rather limited understanding of trophic interactions. Indeed, it has proven difficult to discern direct and indirect effects of environmental change on animal populations owing to limited information about vegetation at large temporal and spatial scales. The rapidly increasing use of the Normalized Difference Vegetation Index (NDVI) in ecological studies has recently changed this situation. Here, we review the use of the NDVI in recent ecological studies and outline its possible key role in future research of environmental change in an ecosystem context.
2,493 citations
TL;DR: Propagule pressure is proposed as a key element to understanding why some introduced populations fail to establish whereas others succeed and how the study of propagule pressure can provide an opportunity to tie together disparate research agendas within invasion ecology.
Abstract: Human-mediated species invasions are a significant component of current global environmental change. There is every indication that the rate at which locations are accumulating non-native species is accelerating as free trade and globalization advance. Thus, the need to incorporate predictive models in the assessment of invasion risk has become acute. However, finding elements of the invasion process that provide consistent explanatory power has proved elusive. Here, we propose propagule pressure as a key element to understanding why some introduced populations fail to establish whereas others succeed. In the process, we illustrate how the study of propagule pressure can provide an opportunity to tie together disparate research agendas within invasion ecology.
2,288 citations
TL;DR: The recent literature is reviewed, drawing parallels between fire and herbivores as alternative consumers of vegetation, and pointing to the common questions and some surprisingly different answers that emerge from viewing fire as a globally significant consumer that is analogous to herbivory.
Abstract: It is difficult to find references to fire in general textbooks on ecology, conservation biology or biogeography, in spite of the fact that large parts of the world burn on a regular basis, and that there is a considerable literature on the ecology of fire and its use for managing ecosystems. Fire has been burning ecosystems for hundreds of millions of years, helping to shape global biome distribution and to maintain the structure and function of fire-prone communities. Fire is also a significant evolutionary force, and is one of the first tools that humans used to re-shape their world. Here, we review the recent literature, drawing parallels between fire and herbivores as alternative consumers of vegetation. We point to the common questions, and some surprisingly different answers, that emerge from viewing fire as a globally significant consumer that is analogous to herbivory.
1,942 citations
TL;DR: This work surveys studies of natural interspecific hybridization in plants and a variety of animals to show that limited invasions of the genome are widespread, with potentially important consequences in evolutionary biology, speciation, biodiversity, and conservation.
Abstract: Hybridization between species is commonplace in plants, but is often seen as unnatural and unusual in animals. Here, I survey studies of natural interspecific hybridization in plants and a variety of animals. At least 25% of plant species and 10% of animal species, mostly the youngest species, are involved in hybridization and potential introgression with other species. Species in nature are often incompletely isolated for millions of years after their formation. Therefore, much evolution of eventual reproductive isolation can occur while nascent species are in gene-flow contact, in sympatry or parapatry, long after divergence begins. Although the relative importance of geographic isolation and gene flow in the origin of species is still unknown, many key processes involved in speciation, such as 'reinforcement' of post-mating isolation by the evolution of assortative mating, will have ample opportunity to occur in the presence of continuing gene flow. Today, DNA sequence data and other molecular methods are beginning to show that limited invasions of the genome are widespread, with potentially important consequences in evolutionary biology, speciation, biodiversity, and conservation.
1,897 citations
TL;DR: Reanalyzed the extinctions included in the IUCN Red List database on a species-by-species basis and reassessed the role of invasive species in those extinctions, finding that the results agree with those of recent statistical analyses.
Abstract: In a recent Opinion article in TREE [1xAre invasive species a major cause of extinctions?. Gurevitch, J. and Padilla, D.K. Trends Ecol. Evol. 2004; 19: 470–474Abstract | Full Text | Full Text PDF | PubMed | Scopus (572)See all References[1], Gurevitch and Padilla concluded that the importance of invasive species in causing declines and extinctions of species is unproven. They analyzed the IUCN Red List database [2xSee all References[2] and stated that only 6% of the taxa are threatened with extinction as a result of invasion by alien species and <2% (ten terrestrial plants and no animal species) of the 762 extinctions were the result of the introduction of alien species. We believe that these figures and the message of the article are misleading.The IUCN database includes a searchable hierarchical classification of threats to wildlife (e.g. habitat loss, invasive alien species, harvesting, and so on), which was used by Gurevitch and Padilla in their article [1xAre invasive species a major cause of extinctions?. Gurevitch, J. and Padilla, D.K. Trends Ecol. Evol. 2004; 19: 470–474Abstract | Full Text | Full Text PDF | PubMed | Scopus (572)See all References[1]. However, this classification system is used in only 5.1% (39 out of 762) of the extinct species (e.g. there are 129 extinct species of birds, but none of them has been assigned a extinction cause, despite the fact that many are among the best documented cases of extinction) and detailed information about the causes of extinction is provided in other fields of the database (e.g. the robust white-eye Zosterops strenuus, endemic to Lord Howe Island, Australia, ‘was common before 1918, but plummeted to extinction following the arrival of black rat’). We reanalyzed the extinctions included in the IUCN Red List database on a species-by-species basis and reassessed the role of invasive species in those extinctions.The conclusion is radically different from that reached by Gurevitch and Padilla. Of the 680 extinct animal species, causes could be compiled for 170 (25%), of which 91 (54%) included the effects of invasive species. For 34 cases (20%), invasive species were the only cited cause of extinction. Habitat destruction and harvesting (hunting and/or gathering) were cited for 82 and 77 species, respectively.Our results agree with those of recent statistical analyses [3xAvian extinction and mammalian introductions on oceanic islands. Blackburn, T.M. et al. Science. 2004; 305: 1955–1958Crossref | PubMed | Scopus (345)See all References, 4xMammal extinctions on Australian islands: causes and conservation implications. Burbidge, A.A. and Manly, F.J. J. Biogeogr. 2002; 29: 465–473Crossref | Scopus (73)See all References], modelling of future scenarios [5xBiodiversity – Global biodiversity scenarios for the year 2100. Sala, O.E. et al. Science. 2000; 287: 1770–1774Crossref | PubMed | Scopus (3430)See all References[5], and several reviews of particular taxa by expert groups that have concluded that invasive species are the leading cause of extinction of birds (65 out of 129 spp.) [6xThreatened Birds of the World. BirdLife International. See all References[6] and the second cause of the extinction of North American fish (27 out of 40 spp. [7xExtinctions of North American fishes during the past century. Miller, R.R. et al. Fisheries. 1989; 14: 22–38Crossref | Scopus (264)See all References[7]), world fish (11 out of 23 spp. [8xSee all References[8]) and mammals (12 out of 25 spp. [9xSee all References[9]). Although extinction is often the end result of invasions, there are other ecological and evolutionary impacts of biotic homogenization that are less understood [10xEcological and evolutionary consequences of biotic homogenization. Olden, J.D. et al. Trends Ecol. Evol. 2004; 19: 18–24Abstract | Full Text | Full Text PDF | PubMed | Scopus (477)See all References, 11xThe evolutionary impact of invasive species. Mooney, H.A. and Cleland, E.E. Proc. Natl. Acad. Sci. U. S. A. 2001; 98: 5446–5451Crossref | PubMed | Scopus (687)See all References], thus prevention and the precautionary principle are of particular relevance to invasive species.
1,381 citations
TL;DR: A quantitative framework, based on statistical decision theory, for analysing animal information use in evolutionary ecology is proposed, to promote an integrative approach to studying information use by animals, which is itself integral to adaptive animal behaviour and organismal biology.
Abstract: Information is a crucial currency for animals from both a behavioural and evolutionary perspective. Adaptive behaviour relies upon accurate estimation of relevant ecological parameters; the better informed an individual, the better it can develop and adjust its behaviour to meet the demands of a variable world. Here, we focus on the burgeoning interest in the impact of ecological uncertainty on adaptation, and the means by which it can be reduced by gathering information, from both 'passive' and 'responsive' sources. Our overview demonstrates the value of adopting an explicitly informational approach, and highlights the components that one needs to develop useful approaches to studying information use by animals. We propose a quantitative framework, based on statistical decision theory, for analysing animal information use in evolutionary ecology. Our purpose is to promote an integrative approach to studying information use by animals, which is itself integral to adaptive animal behaviour and organismal biology.
1,188 citations
TL;DR: The interactions between climate change and plankton communities are reviewed, focusing on systematic changes in plankton community structure, abundance, distribution and phenology over recent decades, to consider the potential socioeconomic impacts.
Abstract: Understanding how climate change will affect the planet is a key issue worldwide. Questions concerning the pace and impacts of climate change are thus central to many ecological and biogeochemical studies, and addressing the consequences of climate change is now high on the list of priorities for funding agencies. Here, we review the interactions between climate change and plankton communities, focusing on systematic changes in plankton community structure, abundance, distribution and phenology over recent decades. We examine the potential socioeconomic impacts of these plankton changes, such as the effects of bottom-up forcing on commercially exploited fish stocks (i.e. plankton as food for fish). We also consider the crucial roles that plankton might have in dictating the future pace of climate change via feedback mechanisms responding to elevated atmospheric CO 2 levels. An important message emerges from this review: ongoing plankton monitoring programmes worldwide will act as sentinels to identify future changes in marine ecosystems.
1,093 citations
TL;DR: Some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions, and issues, such as the costs, are currently at the forefront of research in this field.
Abstract: The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where additional effort is required. I suggest that some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions. Other issues, such as the costs of plasticity are currently at the forefront of research in this field, and are likely to be areas of major future development.
1,060 citations
TL;DR: In this paper, the authors propose a new framework to describe the structure and functioning of ecological networks and to assess the probable consequences of biodiversity change, by incorporating body size into theoretical models that explore food web stability and the patterning of energy fluxes.
Abstract: Body size determines a host of species traits that can affect the structure and dynamics of food webs, and other ecological networks, across multiple scales of organization. Measuring body size provides a relatively simple means of encapsulating and condensing a large amount of the biological information embedded within an ecological network. Recently, important advances have been made by incorporating body size into theoretical models that explore food web stability, the patterning of energy fluxes, and responses to perturbations. Because metabolic constraints underpin body-size scaling relationships, metabolic theory offers a potentially useful new framework within which to develop novel models to describe the structure and functioning of ecological networks and to assess the probable consequences of biodiversity change.
1,041 citations
TL;DR: If there is to be broad-based public support for biodiversity conservation, the places where people live and work should be designed so as to provide opportunities for meaningful interactions with the natural world.
Abstract: Biodiversity loss is a matter of great concern among conservation scientists, but the wherewithal to reverse this trend is generally lacking. One reason is that nearly half of the world's people live in urban areas and are increasingly disconnected from nature. If there is to be broad-based public support for biodiversity conservation, the places where people live and work should be designed so as to provide opportunities for meaningful interactions with the natural world. Doing so has the potential not only to engender support for protecting native species, but also to enhance human well-being. Accomplishing these goals will necessitate conservation scientists forging new collaborations with design professionals, health practitioners and social scientists, as well as encouraging the participation of the general public.
1,039 citations
TL;DR: The emergence of a complex systems approach for sustaining and repairing marine ecosystems, linking ecological resilience to governance structures, economics and society is highlighted.
Abstract: Resource managers and scientists from disparate disciplines are rising to the challenge of understanding and moderating human impacts on marine ecosystems. Traditional barriers to communication between marine ecologists, fisheries biologists, social scientists and economists are beginning to break down, and the distinction between applied and basic research is fading. These ongoing trends arise, in part, from an increasing awareness of the profound influence of people on the functioning of all marine ecosystems, an increased focus on spatial and temporal scale, and a renewed assessment of the role of biodiversity in the sustainability of ecosystem goods and services upon which human societies depend. Here, we highlight the emergence of a complex systems approach for sustaining and repairing marine ecosystems, linking ecological resilience to governance structures, economics and society.
TL;DR: The science is reviewed, the most crucial gaps are identified, and ways to fill them are suggested so that a promising management tool can help meet the growing challenges faced by coastal marine fisheries.
Abstract: As well as serving valuable biodiversity conservation roles, functioning no-take fishery reserves protect a portion of the fishery stock as insurance against future overfishing. So long as there is adequate compliance by the fishing community, it is likely that they will also sustain and even enhance fishery yields in the surrounding area. However, there are significant gaps in scientific knowledge that must be filled if no-take reserves are to be used effectively as fishery management tools. Unfortunately, these gaps are being glossed over by some uncritical advocacy. Here, we review the science, identify the most crucial gaps, and suggest ways to fill them, so that a promising management tool can help meet the growing challenges faced by coastal marine fisheries.
TL;DR: Recent applications of network thinking to the evolution of networks at the gene and protein level and to the dynamics and stability of communities are reviewed.
Abstract: Although pairwise interactions have always had a key role in ecology and evolutionary biology, the recent increase in the amount and availability of biological data has placed a new focus on the complex networks embedded in biological systems. The increased availability of computational tools to store and retrieve biological data has facilitated wide access to these data, not just by biologists but also by specialists from the social sciences, computer science, physics and mathematics. This fusion of interests has led to a burst of research on the properties and consequences of network structure in biological systems. Although traditional measures of network structure and function have started us off on the right foot, an important next step is to create biologically realistic models of network formation, evolution, and function. Here, we review recent applications of network thinking to the evolution of networks at the gene and protein level and to the dynamics and stability of communities. These studies have provided new insights into the organization and function of biological systems by applying existing techniques of network analysis. The current challenge is to recognize the commonalities in evolutionary and ecological applications of network thinking to create a predictive science of biological networks.
TL;DR: It is proposed that a temporal framework is crucial to the authors' understanding of the nature and ecological significance of relationships between aboveground and belowground communities.
Abstract: Ecologists are becoming increasingly aware of the role of aboveground–belowground relationships in controlling ecosystem processes and properties. Here, we review recent studies that show that relationships between aboveground and belowground communities operate over a hierarchy of temporal scales, ranging from days to seasons, to millennia, with differing consequences for ecosystem structure and function. We propose that a temporal framework is crucial to our understanding of the nature and ecological significance of relationships between aboveground and belowground communities.
TL;DR: An expanding body of work is highlighted that examines how plasticity can affect all levels of ecological organization through effects on demographic parameters, direct and indirect species interactions, such as competition, predation, and coexistence, and ultimately carbon and nutrient cycles.
Abstract: Phenotypic plasticity is widespread in nature, and often involves ecologically relevant behavioral, physiological, morphological and life-historical traits. As a result, plasticity alters numerous interactions between organisms and their abiotic and biotic environments. Although much work on plasticity has focused on its patterns of expression and evolution, researchers are increasingly interested in understanding how plasticity can affect ecological patterns and processes at various levels. Here, we highlight an expanding body of work that examines how plasticity can affect all levels of ecological organization through effects on demographic parameters, direct and indirect species interactions, such as competition, predation, and coexistence, and ultimately carbon and nutrient cycles.
TL;DR: In a new paper, MacDougall and Turkington provide the first direct test of whether invasive species are the drivers of community change, or merely 'passengers' along for the environmental ride.
Abstract: Invasive species are widely accepted as one of the leading direct causes of biodiversity loss. However, much of the evidence for this contention is based on simple correlations between exotic dominance and native species decline in degraded systems. Although appealing, direct causality is not the only possible interpretation. A plausible alternative hypothesis is that exotic dominance could be the indirect consequence of habitat modification driving native species loss. In a new paper, MacDougall and Turkington now provide the first direct test of whether invasive species are the drivers of community change, or merely 'passengers' along for the environmental ride.
TL;DR: It is concluded that consensus decision making is common in non-human animals, and that cooperation between group members in the decision-making process is likely to be the norm, even when the decision involves significant conflict of interest.
Abstract: Individual animals routinely face decisions that are crucial to their fitness. In social species, however, many of these decisions need to be made jointly with other group members because the group will split apart unless a consensus is reached. Here, we review empirical and theoretical studies of consensus decision making, and place them in a coherent framework. In particular, we classify consensus decisions according to the degree to which they involve conflict of interest between group members, and whether they involve either local or global communication; we ask, for different categories of consensus decision, who makes the decision, what are the underlying mechanisms, and what are the functional consequences. We conclude that consensus decision making is common in non-human animals, and that cooperation between group members in the decision-making process is likely to be the norm, even when the decision involves significant conflict of interest.
TL;DR: How to match the appropriate methods with the underlying biological questions for several common problems in ecology and conservation are discussed and several topics for future research are identified that should ensure that this field remains dynamic and productive.
Abstract: Assignment methods, which use genetic information to ascertain population membership of individuals or groups of individuals, have been used in recent years to study a wide range of evolutionary and ecological processes. In applied studies, the first step of articulating the biological question(s) to be addressed should be followed by selection of the method(s) best suited for the analysis. However, this first step often receives less attention than it should, and the recent proliferation of assignment methods has made the selection step challenging. Here, we review assignment methods and discuss how to match the appropriate methods with the underlying biological questions for several common problems in ecology and conservation (assessing population structure; measuring dispersal and hybridization; and forensics and mixture analysis). We also identify several topics for future research that should ensure that this field remains dynamic and productive.
TL;DR: In this paper, the structure and dynamics of old-growth forests appear to be rapidly changing, suggesting that there is a pantropical response to global anthropogenic forcing, although the evidence comes almost exclusively from censuses of tree plots and is controversial.
Abstract: Understanding and mitigating the impact of an ever-increasing population and global economic activity on tropical forests is one of the great challenges currently facing biologists, conservationists and policy makers. Tropical forests currently face obvious regional changes, both negative and positive, and uncertain global changes. Although deforestation rates have increased to unprecedented levels, natural secondary succession has reclaimed approximately 15% of the area deforested during the 1990s. Governments have also protected 18% of the remaining tropical moist forest; however, unsustainable hunting continues to threaten many keystone mammal and bird species. The structure and dynamics of old-growth forests appear to be rapidly changing, suggesting that there is a pantropical response to global anthropogenic forcing, although the evidence comes almost exclusively from censuses of tree plots and is controversial. Here, I address ongoing anthropogenic change in tropical forests and suggest how these forests might respond to increasing anthropogenic pressure.
TL;DR: It is proposed that resistance to herbivores is likely to change during plant development in a non-linear fashion and the role of ontogeny should be incorporated as an important factor in new syntheses of plant defense theory.
Abstract: As plants develop from seeds to seedlings, juveniles and mature stages, their ontogeny can constrain the expression of resistance to herbivore damage. Nevertheless, ecological and evolutionary theories regarding interactions between plants, herbivores and their natural enemies are largely based on observations and experiments conducted at a single ontogenetic stage. Owing to resource allocation and architectural constraints in plants, and the influence of herbivore foraging behavior, resistance to herbivores is likely to change during plant development. We propose that such changes are likely to occur in a non-linear fashion and suggest that the role of ontogeny should be incorporated as an important factor in new syntheses of plant defense theory.
TL;DR: This work briefly describes approaches to spatial epidemiology that are spatially implicit, such as metapopulation models of disease transmission, and focuses on research in spatial Epidemiology that is spatially explicit,such as the creation of risk maps for particular geographical areas.
Abstract: Spatial epidemiology is the study of spatial variation in disease risk or incidence. Several ecological processes can result in strong spatial patterns of such risk or incidence: for example, pathogen dispersal might be highly localized, vectors or reservoirs for pathogens might be spatially restricted, or susceptible hosts might be clumped. Here, we briefly describe approaches to spatial epidemiology that are spatially implicit, such as metapopulation models of disease transmission, and then focus on research in spatial epidemiology that is spatially explicit, such as the creation of risk maps for particular geographical areas. Although the spatial dynamics of infectious diseases are the subject of intensive study, the impacts of landscape structure on epidemiological processes have so far been neglected. The few studies that demonstrate how landscape composition (types of elements) and configuration (spatial positions of those elements) influence disease risk or incidence suggest that a true integration of landscape ecology with epidemiology will be fruitful.
TL;DR: It is argued that PARs have had an important role in human evolution, and that their recognition and interpretation has major significance for public health.
Abstract: The importance of a single genotype being able to produce different phenotypes in different environments (phenotypic plasticity) is widely recognized in evolutionary theory and its adaptive significance is clear. In most cases, the developing organism responds to an environmental cue by producing a selectively and immediately appropriate phenotype. One subset of phenotypic responses to environmental stimuli, however, does not necessarily provide an immediate selective advantage. Rather, these kinds of responses, which we call 'predictive adaptive responses' (PARs), act primarily to improve fitness at a later stage of development. We argue that PARs have had an important role in human evolution, and that their recognition and interpretation has major significance for public health.
TL;DR: It is concluded that, although pathogen emergence is inherently unpredictable, emerging pathogens tend to share some common traits, and that directly transmitted RNA viruses might be the pathogens that are most likely to jump between host species.
Abstract: Novel pathogens continue to emerge in human, domestic animal, wildlife and plant populations, yet the population dynamics of this kind of biological invasion remain poorly understood. Here, we consider the epidemiological and evolutionary processes underlying the initial introduction and subsequent spread of a pathogen in a new host population, with special reference to pathogens that originate by jumping from one host species to another. We conclude that, although pathogen emergence is inherently unpredictable, emerging pathogens tend to share some common traits, and that directly transmitted RNA viruses might be the pathogens that are most likely to jump between host species.
TL;DR: The resurrection of oceanic dispersal is the most striking aspect of a major shift in historical biogeography toward a more even balance between vicariance and dispersal explanations and implies that biotas are more dynamic and have more recent origins than had been thought previously.
Abstract: Geographical distributions of terrestrial or freshwater taxa that are broken up by oceans can be explained by either oceanic dispersal or vicariance in the form of fragmentation of a previously contiguous landmass. The validation of plate-tectonics theory provided a global vicariance mechanism and, along with cladistic arguments for the primacy of vicariance, helped create a view of oceanic dispersal as a rare phenomenon and an explanation of last resort. Here, I describe recent work that suggests that the importance of oceanic dispersal has been strongly underestimated. In particular, molecular dating of lineage divergences favors oceanic dispersal over tectonic vicariance as an explanation for disjunct distributions in a wide variety of taxa, from frogs to beetles to baobab trees. Other evidence, such as substantial gene flow among island populations of Anolis lizards, also indicates unexpectedly high frequencies of oceanic dispersal. The resurrection of oceanic dispersal is the most striking aspect of a major shift in historical biogeography toward a more even balance between vicariance and dispersal explanations. This new view implies that biotas are more dynamic and have more recent origins than had been thought previously. A high frequency of dispersal also suggests that a fundamental methodological assumption of many biogeographical studies – that vicariance is a priori a more probable explanation than dispersal – needs to be re-evaluated and perhaps discarded.
TL;DR: To understand how postcopulatory sexual selection influences sperm traits, future research should determine sex-specific interactions that influence paternity, identify genetic correlations between ejaculate characters, quantify the relative costs of producing different sperm trait, and test assumptions of models of sperm quality evolution.
Abstract: The outcome of sperm competition is mediated largely by the relative numbers of sperm from competing males. However, substantial variation in features of sperm morphology and behaviour, such as length, longevity and motility, exists and researchers have suggested that this variation functions in postcopulatory sexual selection. Recent studies have determined the effect of these sperm-quality traits on fertilization success and a synthesis of this literature reveals that they are important in both sperm competition and cryptic female choice. To understand how postcopulatory sexual selection influences sperm traits, future research should determine sex-specific interactions that influence paternity, identify genetic correlations between ejaculate characters, quantify the relative costs of producing different sperm traits, and test assumptions of models of sperm quality evolution. Such research will shed light on what evolutionary pressures are responsible for the diversity in sperm morphometry and behaviour.
TL;DR: Recent progress in assembling the tree of eukaryotes is reviewed, describing the major evidence for each supergroup, and where gaps in the authors' knowledge remain.
Abstract: Recent advances in resolving the tree of eukaryotes are converging on a model composed of a few large hypothetical 'supergroups', each comprising a diversity of primarily microbial eukaryotes (protists, or protozoa and algae). The process of resolving the tree involves the synthesis of many kinds of data, including single-gene trees, multigene analyses, and other kinds of molecular and structural characters. Here, we review the recent progress in assembling the tree of eukaryotes, describing the major evidence for each supergroup, and where gaps in our knowledge remain. We also consider other factors emerging from phylogenetic analyses and comparative genomics, in particular lateral gene transfer, and whether such factors confound our understanding of the eukaryotic tree.
TL;DR: It is argued here that researchers in this field must take a more cognitive and self-critical approach, and in place of checking criteria off lists, researchers must explain, in sufficient enough detail, how the data were obtained, and why they should be believed to be authentic.
Abstract: The study of ancient DNA has the potential to make significant and unique contributions to ecology and evolution. However, the techniques used contain inherent problems, particularly with regards to the generation of authentic and useful data. The solution currently advocated to reduce contamination and artefactual results is to adopt criteria for authentication. Nevertheless, these criteria are not foolproof, and we believe that they have, in practice, replaced the use of thought and prudence when designing and executing ancient DNA studies. We argue here that researchers in this field must take a more cognitive and self-critical approach. Specifically, in place of checking criteria off lists, researchers must explain, in sufficient enough detail to dispel doubt, how the data were obtained, and why they should be believed to be authentic.
TL;DR: It is shown here that belowground organisms can also induce defense responses aboveground and vice versa, which could contribute to a better understanding of the costs and benefits involved in the selection for induced responses in plants.
Abstract: Plants have a variety of chemical defenses that often increase in concentration following attack by herbivores. Such induced plant responses can occur aboveground, in the leaves, and also belowground in the roots. We show here that belowground organisms can also induce defense responses aboveground and vice versa. Indirect defenses are particularly sensitive to interference by induced feeding activities in the other compartment, and this can disrupt multitrophic interactions. Unravelling the involvement of induced plant responses in the interactions between aboveground and belowground communities associated with plants is likely to benefit from comprehensive metabolomic analyses. Such analyses are likely to contribute to a better understanding of the costs and benefits involved in the selection for induced responses in plants.
TL;DR: It is demonstrated that older individuals of some fish species produce larvae that have substantially better survival potential than do larvae from younger fishes, augmenting established knowledge that larger individuals usually have exponentially greater fecundity.
Abstract: Research by Berkeley et al. and by Bobko and Berkeley has recently demonstrated that older individuals of some fish species produce larvae that have substantially better survival potential than do larvae from younger fishes. These new findings augment established knowledge that larger individuals usually have exponentially greater fecundity. This is important because commercial fisheries and especially recreational fishing often target the larger fish. The protection of larger or older individuals is necessary for the sustainability of species currently exploited by humans.
TL;DR: It is argued that these ancient polyploidy events might have also had an important role in the origin and diversification of the angiosperms.
Abstract: Despite intensive research, little is known about the origin of the angiosperms and their rise to ecological dominance during the Early Cretaceous. Based on whole-genome analyses of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for the creation of many important developmental and regulatory genes found in extant angiosperm genomes. Here, we argue that these ancient polyploidy events might have also had an important role in the origin and diversification of the angiosperms.