Ecological and evolutionary genetics of Arabidopsis

The crucifer Arabidopsis thaliana has been the subject of intense research into molecular and developmental genetics. One of the consequences of having this wealth of physiological and molecular data available, is that ecologists and evolutionary biologists have begun to incorporate this model system into their studies. Current research on A. thaliana and its close relatives ably illustrates the potential for synergy between mechanistic and organismal biology. On the one hand, mechanistically oriented research can be placed in an historical context, which takes into account the particular phylogenetic history and ecology of these species. This helps us to make sense of redundancies, anomalies and sub-optimalities that would otherwise be difficult to interpret. On the other hand, ecologists and evolutionary biologists now have the opportunity to investigate the physiological and molecular basis for the phenotypic changes they observe. This provides new insight into the mechanisms that influence evolutionary change.     

The role of ethics in experimental marine biology and ecology

Although most countries have ethical guidelines for research involving human subjects and other sentient animals, the ethical issues associated with field research have received little attention. Most experimental marine biologists and ecologists operate without ethical guidelines or scrutiny, despite intermittent community concern about their activities. We offer suggestions on how marine biologists and ecologists can protect the future of research involving the field collection and experimental manipulation of organisms by developing mechanisms to address community concerns that such research is ethically responsible. We urge experimental marine biologists and ecologists to take pre-emptive initiatives by encouraging: (1) institutional animal ethics committees to broaden their terms of reference to include environmental ethics; (2) scientific societies to develop codes of ethics to guide the environmental research conducted by their members; (3) editorial boards of journals to require the research they publish to conform to an appropriate code of ethics, and (4) management agencies that issue permits for field research to establish an ethics committee to advise them on the ethical issues raised by specific research proposals. We conclude that the resultant administrative burden on scientists would be low but that the penalties of operating without such protection can be high.     

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.     

生态位分化与森林群落物种多样性维持研究展望

一直以来,生态学家和进化生物学家对森林群落物种多样格局及其形成机制持有不同的观点。虽然Robert Ricklefs将进化和生态过程整合的观点已经被群落生态学家广泛接受,但是区域物种进化历史以及局域群落微进化过程是否能够影响群落生态学过程以及这些过程如何影响群落结构和动态还有待商榷。经典的生态位理论同时强调了种间和种内生态位分化对群落多样性维持的影响。但是生态学家普遍认为种间差异足以代表群落内个体间的相互作用关系,并且由于进化过程导致的种内分化往往涉及较长的时间尺度,因此,虽然种内差异是自然选择的重要材料,物种对环境的适应性进化过程所导致的种内分化对群落构建的影响往往被生态学家所忽视。为此,通过回顾种间和个体生态位分化的研究历史,对两类研究分别进行简要阐述,强调在今后的群落生态学研究中需要考虑个体分化对局域群落构建的影响。     

Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010

This report summarizes the proceedings of the 2(nd) Annual Argonne Soils Workshop held at Argonne National Laboratory October 6-8, 2010. The workshop assembled a diverse group of soil ecologists, microbiologists, molecular biologists, and computational scientists to discuss the challenges and opportunities related to implementation of metagenomics approaches in soil microbial ecology. The overarching theme of the workshop was "designing ecologically meaningful soil metagenomics research", which encouraged presentations on both ecological and computational topics. The workshop fostered valuable cross-discipline communication and delivered the message that soil metagenomics research must be based on an iterative process between biological inquiry and bioinformatics tools.     

Crosstalk between plant responses to pathogens and herbivores: a view from the outside in

Plants encounter numerous pests and pathogens in the natural environment. An appropriate response to attack by such organisms can lead to tolerance or resistance mechanisms that enable the plant to survive. Many studies concentrate on the signalling pathways that enable plants to recognize and respond to attack, and measure the downstream effect in either biochemical or molecular terms. At the whole plant level, ecologists examine the fitness costs of attack not only for the plant but also over a range of trophic levels. The links between these differing levels of study are beginning to be addressed by the adoption of molecular approaches in more ecologically relevant settings. This review will describe the different approaches used by ecologists and cell biologists in this field and will try to address the question of how we can explore the response to, and consequences, of attack by multiple enemies.     

What processes must we understand to forecast regional-scale population dynamics?

An urgent challenge facing biologists is predicting the regional-scale population dynamics of species facing environmental change. Biologists suggest that we must move beyond predictions based on phenomenological models and instead base predictions on underlying processes. For example, population biologists, evolutionary biologists, community ecologists and ecophysiologists all argue that the respective processes they study are essential. Must our models include processes from all of these fields? We argue that answering this critical question is ultimately an empirical exercise requiring a substantial amount of data that have not been integrated for any system to date. To motivate and facilitate the necessary data collection and integration, we first review the potential importance of each mechanism for skilful prediction. We then develop a conceptual framework based on reaction norms, and propose a hierarchical Bayesian statistical framework to integrate processes affecting reaction norms at different scales. The ambitious research programme we advocate is rapidly becoming feasible due to novel collaborations, datasets and analytical tools.     

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.     

Reducing ambiguity in describing plant–insect interactions: "preference", "acceptability" and "electivity"

Ecologists and evolutionary biologists have a common interest in plant–insect interactions. Ecologists develop terminology describing patterns of association between plants and insects, while evolutionary biologists use the same words to denote potentially heritable traits of individuals. Use of the same terms to describe both traits of the interaction and traits of the organisms hinders communication. An example is "preference", often used by ecologists to denote properties of the plant–insect interaction and by behavioural or evolutionary biologists to denote insect traits. The existing term "electivity" could be incorporated into the lexicon of plant–insect interactions to supplant the ecological use of "preference". The term "preference" would then denote a behavioural trait of the insect. The mirror-image trait of the plant would be "acceptability". This could be a step towards a common terminology that would be usable by both ecologists and evolutionists.     

Ecology, sexual selection and speciation

The spectacular diversity in sexually selected traits among animal taxa has inspired the hypothesis that divergent sexual selection can drive speciation. Unfortunately, speciation biologists often consider sexual selection in isolation from natural selection, even though sexually selected traits evolve in an ecological context: both preferences and traits are often subject to natural selection. Conversely, while behavioural ecologists may address ecological effects on sexual communication, they rarely measure the consequences for population divergence. Herein, we review the empirical literature addressing the mechanisms by which natural selection and sexual selection can interact during speciation. We find that convincing evidence for any of these scenarios is thin. However, the available data strongly support various diversifying effects that emerge from interactions between sexual selection and environmental heterogeneity. We suggest that evaluating the evolutionary consequences of these effects requires a better integration of behavioural, ecological and evolutionary research.     

Life in the colonies: learning the alien ways of colonial organisms

Who needs to go to outer space to study alien beings when the oceans of our own planet abound with bizarre and unknown creatures? Many of them belong to sessile clonal and colonial groups, including sponges, hydroids, corals, octocorals, ascidians, bryozoans, and some polychaetes. Their life histories, in many ways unlike our own, are a challenge for biologists. Studying their ecology, behavior, and taxonomy means trying to “think like a colony” to understand the factors important in their lives. Until the 1980s, most marine ecologists ignored these difficult modular organisms. Plant ecologists showed them ways to deal with the two levels of asexually produced modules and genetic individuals, leading to a surge in research on the ecology of clonal and colonial marine invertebrates. Bryozoans make excellent model colonial animals. Their life histories range from ephemeral to perennial. Aspects of their lives such as growth, reproduction, partial mortality due to predation or fouling, and the behavior of both autozooids and polymorphs can be studied at the level of the colony, as well as that of the individual module, in living colonies and over time.     

Targeted sequence capture as a powerful tool for evolutionary analysis1

Next-generation sequencing technologies (NGS) have revolutionized biological research by significantly increasing data generation while simultaneously decreasing the time to data output. For many ecologists and evolutionary biologists, the research opportunities afforded by NGS are substantial; even for taxa lacking genomic resources, large-scale genome-level questions can now be addressed, opening up many new avenues of research. While rapid and massive sequencing afforded by NGS increases the scope and scale of many research objectives, whole genome sequencing is often unwarranted and unnecessarily complex for specific research questions. Recently developed targeted sequence enrichment, coupled with NGS, represents a beneficial strategy for enhancing data generation to answer questions in ecology and evolutionary biology. This marriage of technologies offers researchers a simple method to isolate and analyze a few to hundreds, or even thousands, of genes or genomic regions from few to many samples in a relatively efficient and effective manner. These strategies can be applied to questions at both the infra- and interspecific levels, including those involving parentage, gene flow, divergence, phylogenetics, reticulate evolution, and many more. Here we provide a brief overview of targeted sequence enrichment, and emphasize the power of this technology to increase our ability to address a wide range of questions of interest to ecologists and evolutionary biologists, particularly for those working with taxa for which few genomic resources are available.     

First synthesize new viruses then regulate their release? The case of the wild rabbit

European wild rabbits originated in southwestern Europe but have been introduced into many other countries world-wide, becoming serious pests in many instances. As a consequence of rabbits being regarded so differently, applied research for their management often has opposing goals, namely their conservation or their control. Furthermore, modern gene technology has led to the concept of using genetically modified myxoma viruses for rabbit management, again with quite contrary aims in mind. In this paper we explain the possible ecological and economic consequences of using these genetically modified viruses inappropriately and we consider whether national and international regulations are sufficient to prevent improper use. If international regulations are inadequate, molecular biologists and ecologists must consider the consequences of their research and advice beyond their own country to avoid unwanted impacts.     

Railway ecology: Underrepresented in science?

Over the past two decades, the effects of roads on wildlife have been extensively studied. Theoretically, railways cause similar effects as well, yet ecologists do not understand the magnitude of these effects. Despite the field of road ecology rapidly expanding and the large footprint created by railways, there is a prominent lack of research related to railways and their effects on wildlife. To emphasize gaps between road and railway wildlife studies, we performed a thorough systematic review of twelve peer-reviewed journals in which ecologists and conservation biologists commonly publish. We found a clear underrepresentation of railway studies despite the potential negative ecological effects associated with this important anthropogenic feature. We found 259 road-wildlife articles and only 17 railway-wildlife articles in the journals we assessed with the majority of road studies focused in North America and the majority of railway studies in Europe. Although road-wildlife studies have increased through time, railway-wildlife studies have remained stagnant. In our opinion, the development of research pertaining to ‘Railway Ecology’ is long overdue.     

Recognizing and Interpreting the Fossils of Early Eukaryotes

Using molecular sequence data, biologists cangenerate hypotheses of protistan phylogeny and divergence times. Fossils, however, provide our only direct constraints on the timingand environmental context of early eukaryotic diversification. Forthis reason, recognition of eukaryotic fossils in Proterozoic rocksis key to the integration of geological and comparative biologicalperspectives on protistan evolution. Microfossils preserved in shales of the ca. 1500 Ma Roper Group, northern Australia, display characters that ally them to the Eucarya, but, at present, attribution to any particular protistan clade is uncertain. Continuing research on wall ultrastructure and microchemistry promises new insights into the nature and systematic relationshipsof early eukaryotic fossils.     

Compensation for a bad start: grow now, pay later?

Nutritional conditions during key periods of development, when the architecture and modus operandi of the body become established, are of profound importance in determining the subsequent life-history trajectory of an organism. If developing individuals experience a period of nutritional deficit, they can subsequently show accelerated growth should conditions improve, apparently compensating for the initial setback. However, recent research suggests that, although compensatory growth can bring quick benefits, it is also associated with a surprising variety of costs that are often not evident until much later in adult life. Clearly, the nature of these costs, the timescale over which they are incurred and the mechanisms underlying them will play a crucial role in determining compensatory strategies. Nonetheless, such effects remain poorly understood and largely neglected by ecologists and evolutionary biologists.     

Molecular phylogeny and systematics of oligochaeta: Pro et contra

The systematics of oligochaete worms was discussed by experts for the entire 20th century. The development of computing and molecular techniques hold promise for the construction of a phylogenetically reasonable system. However, the eliminating of some paraphyletic lineages did not result in unanimous approval among a wide range of biologists (mainly morphologists and ecologists). Molecular systematics has helped clear up the position of many controversial species and genera, while causing doubts about the classification of higher rank taxa, which seemed to be logical and stable until recently.     

Hierarchal gene trees and molecular phylogeny of the Rotifera: use of the Polymerase Chain Reaction (PCR) to dissect ecological and evolutionary patterns

The study of rotifer phylogenies and the analysis of population-level processes historically have been disjunct. This is despite a growing recognition that there are many ways in which rotifer population biologists and ecologists might profit from the availability of a comprehensive phylogeny of the group. New molecular methods which can be applied to a wide range of genetic systems and systematic grades will shortly eliminate the methodological (and perhaps conceptual) distinction between these fields. Of particular importance is the development of the Polymerase Chain Reaction (PCR), a technique of synthetic DNA amplification which produces concentrated preparations of selected genes from complex mixtures of nuclear and mitochondrial genomes. Analysis of PCR products can provide hierarchal genetic comparisons from the level of local rotifer populations through broad evolutionary (at least molecular) phylogenies.