Jack of all trades,master of some? On the role of phenotypic plasticity in plant invasions

Invasion biologists often suggest that phenotypic plasticity plays an important role in successful plant invasions. Assuming that plasticity enhances ecological niche breadth and therefore confers a fitness advantage, recent studies have posed two main hypotheses: (1) invasive species are more plastic than non-invasive or native ones; (2) populations in the introduced range of an invasive species have evolved greater plasticity than populations in the native range. These two hypotheses largely reflect the disparate interests of ecologists and evolutionary biologists. Because these sciences are typically interested in different temporal and spatial scales, we describe what is required to assess phenotypic plasticity at different levels. We explore the inevitable tradeoffs of experiments conducted at the genotype vs. species level, outline components of experimental design required to identify plasticity at different levels, and review some examples from the recent literature. Moreover, we suggest that a successful invader may benefit from plasticity as either (1) a Jack-of-all-trades, better able to maintain fitness in unfavourable environments; (2) a Master-of-some, better able to increase fitness in favourable environments; or (3) a Jack-and-master that combines some level of both abilities. This new framework can be applied when testing both ecological or evolutionary oriented hypotheses, and therefore promises to bridge the gap between the two perspectives.     

Perspective: Time scales in scientific research with an emphasis on microbial cellular and molecular research

Scientists use time to describe and research the universe in which humans live. Geologists and evolutionary biologists often use time scales in the millions to billions of years while biochemists and molecular biologists use time scales in the milliseconds or less. The atom smashers use time scales that are almost the speed of light. However, in some areas of research such as molecular-based activities in cells, it is very challenging to obtain data sets in molecular time scales. This has been a challenge to obtaining accurate and precise measurements at the cell and molecular levels of organization in living organisms. Measurements of specific cellular and molecular activities are often made over time scales longer than the actual molecular events. The data sets obtained become estimates over seconds, minutes and hours and not measurements over milli- and nanoseconds. The question can then be posed — how representative and accurate are our data sets when the time scales are not synchronized with the actual living events? In this article, the role of time scales in scientific research and our understanding of living microorganisms are examined with an emphasis on cell and molecular time scales.     

Eco-evolutionary dynamics

Evolutionary ecologists and population biologists have recently considered that ecological and evolutionary changes are intimately linked and can occur on the same time-scale. Recent theoretical developments have shown how the feedback between ecological and evolutionary dynamics can be linked, and there are now empirical demonstrations showing that ecological change can lead to rapid evolutionary change. We also have evidence that microevolutionary change can leave an ecological signature. We are at a stage where the integration of ecology and evolution is a necessary step towards major advances in our understanding of the processes that shape and maintain biodiversity. This special feature about ‘eco-evolutionary dynamics’ brings together biologists from empirical and theoretical backgrounds to bridge the gap between ecology and evolution and provide a series of contributions aimed at quantifying the interactions between these fundamental processes.     

Conflicts in maintaining biodiversity at multiple scales

Biodiversity consists of multiple scales, including functional diversity in ecological traits, species diversity and genetic diversity within species, and is declining across the globe, largely in response to human activities. While species extinctions are the most obvious aspect of this, there has also been a more insidious loss of genetic diversity within species. While a vast literature concerns each of these scales of biodiversity, less is known about how different scales affect one another. In particular, genetic and species diversity may influence each other in numerous ways, both positively and negatively. However, we know little about the mechanism behind these patterns. In this issue of Molecular Ecology, Nestmann et al. (2011) experimentally explore the effect of species and functional diversity and composition of grassland plant communities on the genetic structure of one of the component species. Increasing species richness led to greater changes in the genetic composition of the focal populations over 4 years, primarily because of genetic drift in smaller population sizes. However, there were also genetic changes in response to particular plant functional groups, indicating selective differences driven by plant community composition. These results suggest that different levels of biodiversity can trade-off in communities, which may prove a challenge for conservation biologists seeking to preserve all aspects of biodiversity.     

Discrepancies in occupancy and abundance approaches to identifying and protecting habitat for an at‐risk species

Predicting how environmental factors affect the distribution of species is a fundamental goal of conservation biology. Conservation biologists rely on species distribution and abundance models to identify key habitat characteristics for species. Occupancy modeling is frequently promoted as a practical alternative to use of abundance in identifying habitat quality. While occupancy and abundance are potentially governed by different limiting factors operating at different scales, few studies have directly compared predictive models for these approaches in the same system. We evaluated how much occupancy and abundance are driven by the same environmental factors for a species of conservation concern, the greater short‐horned lizard (Phrynosoma hernandesi). Occupancy was most strongly dictated by precipitation, temperature, and density of ant mounds. While these factors were also in the best‐supported predictive models for lizard abundance, the magnitude of the effects varied, with the sign of the effect changing for temperature and precipitation. These discrepancies show that while occupancy modeling can be an efficient approach for conservation planning, predictors of occupancy probability should not automatically be equated with predictors of population abundance. Understanding the differences in factors that control occupancy versus abundance can help us to identify habitat requirements and mitigate the loss of threatened species.     

Integrating ecology and developmental biology to explain the timing of frog metamorphosis

Amphibian metamorphosis has long intrigued ecologists and developmental biologists, yet the two research programs have progressed separately and toward different goals. Plasticity in metamorphic timing has profound effects on fitness, which has prompted ecologists to develop and test models for predicting how environmental factors affect the size and age of metamorphosis. These models rely upon untested assumptions about the mechanisms for regulating growth and development. Whereas developmental biologists explicitly investigate these mechanisms at the hormonal and genetic levels, they largely ignore the role of environmental input. Recent developments in our understanding of the molecular biology of frog metamorphosis are revealing how these two research programs could be integrated. Here, I review these developments to test ecologists' assumptions about frog metamorphosis, and to present strategies for both research fields to investigate the mechanistic basis of metamorphic plasticity.     

The drought environment: physical, biological and agricultural perspectives

'Drought' has many meanings in relation to crop production. These range from: statistical (say, the lowest decile of annual rainfall) to a meteorologist; through yield being limited by too little water to an agronomist; to sudden severe water deficits to many molecular biologists. To a farmer, the corresponding management issues, respectively, are risk management (how best to manage a meteorologically drought-prone farm over several years), how best to match cultivar and agronomic operations to the developing growing season, and how best to minimize possible major damage to (say) floral fertility induced by severe water deficits during flowering. All these definitions and the issues they imply are relevant to improving crop production when water is limiting. How can scientists best help? The answers depend on the scales (temporal and spatial) being addressed. Agronomists and breeders, interacting, can help improve components of seasonal water balance in the field, for example, minimizing evaporative losses from the soil surface by better matching the development of a crop to its environment. Physiologists, biochemists, and molecular biologists can help by identifying ways of improving the competence of particular organs. A promising target is floral infertility resulting from water deficits, which results from lesions in tissue, and cellular and molecular processes. Choosing problems whose solutions will have implications in the field and be attractive to farmers requires knowledge of what is important in the field.     

Habitat selection behaviour links local and regional scales in aquatic systems

The role of habitat selection behaviour in the assembly of natural communities is an increasingly important theme in ecology. At the same time, ecologists and conservation biologists are keenly interested in scale and how processes at scales from local to regional interact to determine species distributions and patterns of biodiversity. How important is habitat selection in generating observed patterns of distribution and diversity at multiple spatial scales? In theory, habitat selection in response to interacting species can generate both positive and negative covariances among species distributions and create the potential to link processes of community assembly across multiple scales. Here I demonstrate that habitat selection by treefrogs in response to the distribution of fish predators functions at both the regional scale among localities and the local scale among patches within localities, implicating habitat selection as a critical link between local communities and the regional dynamics of metacommunities in complex landscapes.     

Genetic analysis of spatial foraging patterns and resource sharing in bumble bee pollinators

Conservation biologists, evolutionary ecologists and agricultural biologists require an improved understanding of how pollinators utilize space and share resources. Using microsatellite markers, we conducted a genetic analysis of space use and resource sharing at several spatial scales among workers of two ecologically dissimilar bumble bee species (Bombus terrestris and B. pascuorum) foraging in an urban landscape (London, UK). At fine scales, the relatedness of workers visiting small patches of flowers did not differ significantly from zero. Therefore, colonies shared flower patches randomly with other colonies, suggesting that worker scent-marks deterring visits to unrewarding flowers have not evolved as signals benefiting nestmates. To investigate space use at intermediate scales, we developed a program based on Thomas & Hill's maximum likelihood sibship reconstruction method to estimate the number of colonies utilizing single sites. The average number of colonies (95% confidence limits) sending workers to forage at sites of approximately 1 ha in area was 96 colonies (84-118) in B. terrestris and 66 colonies (61-76) in B. pascuorum. These values are surprisingly high and suggested that workers travelled far from their colonies to visit the sites. At the landscape scale, there was little or no genetic differentiation between sites. We conclude that urban habitats support large bumble bee populations and are potentially valuable in terms of bumble bee conservation. In addition, bumble bee-mediated gene flow in plants is likely to occur over large distances and plant-bumble bee conservation requires landscape-scale action.     

Wrapping and interoperating bioinformatics resources using CORBA

Bioinformaticians seeking to provide services to working biologists are faced with the twin problems of distribution and diversity of resources. Bioinformatics databases are distributed around the world and exist in many kinds of storage forms, platforms and access paradigms. To provide adequate services to biologists, these distributed and diverse resources have to interoperate seamlessly within single applications. The Common Object Request Broker Architecture (CORBA) offers one technical solution to these problems. The key component of CORBA is its use of object orientation as an intermediate form to translate between different representations. This paper concentrates on an explanation of object orientation and how it can be used to overcome the problems of distribution and diversity by describing the interfaces between objects.     

Creating parts that allow for rational design: Synthetic biology and the problem of context-sensitivity

The parts-based engineering approach in synthetic biology aims to create pre-characterised biological parts that can be used for the rational design of novel functional systems. Given the context-sensitivity of biological entities, a key question synthetic biologists have to address is what properties these parts should have so that they give a predictable output even when they are used in different contexts. In the first part of this paper I will analyse some of the answers that synthetic biologists have given to this question and claim that the focus of these answers on parts and their properties does not allow us to tackle the problem of context-sensitivity. In the second part of the paper, I will argue that we might have to abandon the notions of parts and their properties in order to understand how independence in biology could be achieved. Using Robert Cummins’ account of functional analysis, I will then develop the notion of a capacity and its condition space and show how these notions can help to tackle the problem of context-sensitivity in biology.     

Extending the range of additivity in using inclusive fitness

Inclusive fitness is a concept widely utilized by social biologists as the quantity organisms appear designed to maximize. However, inclusive fitness theory has long been criticized on the (uncontested) grounds that other quantities, such as offspring number, predict gene frequency changes accurately in a wider range of mathematical models. Here, we articulate a set of modeling assumptions that extend the range of scenarios in which inclusive fitness can be applied. We reanalyze recent formal analyses that searched for, but did not find, inclusive fitness maximization. We show (a) that previous models have not used Hamilton''s definition of inclusive fitness, (b) a reinterpretation of Hamilton''s definition that makes it usable in this context, and (c) that under the assumption of probabilistic mixing of phenotypes, inclusive fitness is indeed maximized in these models. We also show how to understand mathematically, and at an individual level, the definition of inclusive fitness, in an explicit population genetic model in which exact additivity is not assumed. We hope that in articulating these modeling assumptions and providing formal support for inclusive fitness maximization, we help bridge the gap between empiricists and theoreticians, which in some ways has been widening, demonstrating to mathematicians why biologists are content to use inclusive fitness, and offering one way to utilize inclusive fitness in general models of social behavior.     

Bridging the gaps in systems biology

Systems biology aims at creating mathematical models, i.e., computational reconstructions of biological systems and processes that will result in a new level of understanding—the elucidation of the basic and presumably conserved “design” and “engineering” principles of biomolecular systems. Thus, systems biology will move biology from a phenomenological to a predictive science. Mathematical modeling of biological networks and processes has already greatly improved our understanding of many cellular processes. However, given the massive amount of qualitative and quantitative data currently produced and number of burning questions in health care and biotechnology needed to be solved is still in its early phases. The field requires novel approaches for abstraction, for modeling bioprocesses that follow different biochemical and biophysical rules, and for combining different modules into larger models that still allow realistic simulation with the computational power available today. We have identified and discussed currently most prominent problems in systems biology: (1) how to bridge different scales of modeling abstraction, (2) how to bridge the gap between topological and mechanistic modeling, and (3) how to bridge the wet and dry laboratory gap. The future success of systems biology largely depends on bridging the recognized gaps.     

When enough is enough: genetic diseases associated with transcriptional derepression

For many human genetic diseases, the underlying genetic defect has been determined. Thus, although traditionally a field only for researchers in medicine or human genetics, human diseases are now opening up to molecular biologists, cell biologists and biochemists. Here we discuss four human genetic disorders, Familial Alzheimer's disease, Rett syndrome, Klippel-Trenaunay syndrome and Facioscapulohumeral muscular dystrophy, and how investigations into these diseases are providing important lessons about human biology.     

Orchid diversity: an evolutionary consequence of deception?

The Orchidaceae are one of the most species-rich plant families and their floral diversity and pollination biology have long intrigued evolutionary biologists. About one-third of the estimated 18,500 species are thought to be pollinated by deceit. To date, the focus has been on how such pollination evolved, how the different types of deception work, and how it is maintained, but little progress has been made in understanding its evolutionary consequences. To address this issue, we discuss here how deception affects orchid mating systems, the evolution of reproductive isolation, speciation processes and neutral genetic divergence among species. We argue that pollination by deceit is one of the keys to orchid floral and species diversity. A better understanding of its evolutionary consequences could help evolutionary biologists to unravel the reasons for the evolutionary success of orchids.     

The importance of integration and scale in the arbuscular mycorrhizal symbiosis

The arbuscular mycorrhizal (AM) fungus contributes to system processes and functions at various hierarchical organizational levels, through their establishment of linkages and feedbacks between whole-plants and nutrient cycles. Even though these fungal mediated feedbacks and linkages involve lower-organizational level processes (e.g. photo-assimilate partitioning, interfacial assimilate uptake and transport mechanisms, intraradical versus extraradical fungal growth), they influence higher-organizational scales that affect community and ecosystem behavior (e.g. whole-plant photosynthesis, biodiversity, nutrient and carbon cycling, soil structure). Hence, incorporating AM fungi into research directed at understanding many of the diverse environmental issues confronting society will require knowledge of how these fungi respond to or initiate changes in vegetation dynamics, soil fertility or both. Within the last few years, the rapid advancement in the development of analytical tools has increased the resolution by which we are able to quantify the mycorrhizal symbiosis. It is important that these tools are applied within a conceptual framework that is temporally and spatially relevant to fungus and host. Unfortunately, many of the studies being conducted on the mycorrhizal symbiosis at lower organizational scales are concerned with questions directed solely at understanding fungus or host without awareness of what the plant physiologist or ecologist needs for integrating the mycorrhizal association into larger organizational scales or process levels. We show by using the flow of C from plant-to-fungus-to-soil, that through thoughtful integration, we have the ability to bridge different organizational scales. Thus, an essential need of mycorrhizal research is not only to better integrate the various disciplines of mycorrhizal research, but also to identify those relevant links and scales needing further investigation for understanding the larger-organizational level responses. The U.S. Government's right to retain a non-exclusive, royalty-free licence in and to any copyright is acknowledged. This revised version was published online in June 2006 with corrections to the Cover Date.     

When Local Extinction and Colonization of River Fishes Can Be Predicted by Regional Occupancy: the Role of Spatial Scales

Background

Predicting which species are likely to go extinct is perhaps one of the most fundamental yet challenging tasks for conservation biologists. This is particularly relevant for freshwater ecosystems which tend to have the highest proportion of species threatened with extinction. According to metapopulation theories, local extinction and colonization rates of freshwater subpopulations can depend on the degree of regional occupancy, notably due to rescue effects. However, relationships between extinction, colonization, regional occupancy and the spatial scales at which they operate are currently poorly known.

Methods

And Findings: We used a large dataset of freshwater fish annual censuses in 325 stream reaches to analyse how annual extinction/colonization rates of subpopulations depend on the regional occupancy of species. For this purpose, we modelled the regional occupancy of 34 fish species over the whole French river network and we tested how extinction/colonization rates could be predicted by regional occupancy described at five nested spatial scales. Results show that extinction and colonization rates depend on regional occupancy, revealing existence a rescue effect. We also find that these effects are scale dependent and their absolute contribution to colonization and extinction tends to decrease from river section to larger basin scales.

Conclusions

In terms of management, we show that regional occupancy quantification allows the evaluation of local species extinction/colonization dynamics and reduction of local extinction risks for freshwater fish species implies the preservation of suitable habitats at both local and drainage basin scales.     

How the spatial scales of dispersal, competition, and environmental heterogeneity interact to affect coexistence

Spatial coexistence depends on a variety of biological and physical processes, and the relative scales of these processes may promote or suppress coexistence. We model plant competition in a spatially varying environment to show how shifting scales of dispersal, competition, and environmental heterogeneity affect coexistence. Spatial coexistence mechanisms are partitioned into three types: the storage effect, nonlinear competitive variance, and growth-density covariance. We first describe how the strength of each of these mechanisms depends on covariances between population densities and between population densities and the environment, and we then explain how changes in the scales of dispersal, competition, and environmental heterogeneity should affect these covariances. Our quantitative approach allows us to show how changes in the scales of biological and physical processes can shift the relative importance of different classes of spatial coexistence mechanisms and gives us a more complete understanding of how environmental heterogeneity can enable coexistence. For example, we show how environmental heterogeneity can promote coexistence even when competing species have identical responses to the environment.     

Local Scale Effects of Disease on Biodiversity

To date, ecologists and conservation biologists have focused much of their attention on the population and ecosystem effects of disease at regional scales and the role that diseases play in global species extinction. Far less research has been dedicated to identifying the effects that diseases can have on local scale species assemblages. We examined the role of infectious disease in structuring local biodiversity. Our intention was to illustrate how variable outcomes can occur by focusing on three case studies: the influence of chestnut blight on forest communities dominated by chestnut trees, the influence of red-spot disease on urchin barrens and kelp forests, and the influence of sylvatic plague on grassland communities inhabited by prairie dogs. Our findings reveal that at local scales infectious disease seems to play an important, though unpredictable, role in structuring species diversity. Through our case studies, we have shown that diseases can cause drastic population declines or local extirpations in keystone species, ecosystem engineers, and otherwise abundant species. These changes in local diversity may be very important, particularly when considered alongside potentially corresponding changes in community structure and function, and we believe that future efforts to understand the importance of disease to species diversity should have an increased focus on these local scales.     

One cell, two cell, red cell, blue cell: The persistence of a unicellular stage in multicellular life histories

As developmental biologists come closer to understanding at the molecular and genetic levels how a zygote becomes an adult, it is easy to forget that the very phenomenon that gives them an occupation remains a vexing problem to evolutionary biologists: why do unicellular stages persist in life histories of multicellular organisms? There are two explanatory hypotheses. One is that a unicellular stage purges multicellular organisms of deleterious mutations by exposing offspring that are each uniformly of one genotype to selection. Another is that a one-cell stage reduces conflicts of interest among genetically different replicators within an organism.