Chance as an explanatory factor in evolutionary biology.

Darwinian evolutionary biology has often been criticized for appealing to the notion of 'chance' in its explanations. According to some critics, such appeals exhibit the explanatory poverty of evolutionary theory. In response, defenders of Darwinism sometimes downplay the importance of 'chance' in evolution. I believe that both of these approaches are mistaken. The main thesis of this paper is that the term 'chance' encompasses a number of distinct concepts, and that at least some of these concepts serve essential explanatory functions in evolutionary biology. This claim is defended by way of an historical survey of the major concepts of 'chance' in the history of evolutionary biology, especially the concepts used by Jean Baptiste Lamarck, Charles Darwin, and Sewall Wright. An examination of their biologies shows how the concepts of 'chance' used cohere with their major scientific objectives and methods. These concepts survive and continue to function as important explanatory factors in contemporary evolutionary biology. Examples of such usage are given, and the explanatory status of 'chance' assessed.     

Robustness as an evolutionary principle.

We suggest simulating evolution of complex organisms using a model constrained solely by the requirement of robustness in its expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence for dynamical features in the evolved networks is found that can be related to biological observables.     

The uncertainty principle as an evolutionary engine.

Heisenberg's uncertainty principle in quantum mechanics underlies the genesis of evolutionary variability. When the uncertainty principle is coupled with the incontrovertible principle of the conservation of energy and material resources, there appears an uncertainty relationship between local fluctuations in the quantities to be conserved on a global scale and the rate of their local variation. Since the local fluctuations are accompanied by the non-vanishing rate of variation because of the uncertainty relationship, they generate subsequent fluctuations. Generativity latent in the uncertainty relationship is non-random and ubiquitous all through various evolutionary stages from abiotic synthesis of monomers and polymers up to the emergence of behavior-induced variability of organisms.     

A limits-oriented approach to evolutionary ecology

Evolutionary ecology focuses on optimal traits to provide a mechanistic understanding of ecological patterns. For some issues, however, It might be a mismatch to marry optimality and ecology. Given that many ecological questions involve limits (to species distributions and abundances; to species diversity), it might be useful to focus on `limiting traits' rather than optimal traits; that is, to understand ecological limits it might be useful to identify the things that organisms do poorly, and to study constraints on the evolution of these limiting traits. While a limiting-traits approach has a long history in ecology, relatively few studies have fully applied the approach, and some ecological issues have only recently been examined from this view.     

Elasticity analysis as an important tool in evolutionary and population ecology

Elasticity analysis estimates the proportional change in the population growth rate for a proportional change in a vital rate (i.e. survival, growth or reproduction). It can be used to pinpoint those parts of an organism’s life history that should be the focus of management effort, or those that contribute most to fitness. Recent theoretical work has emphasized some limitations of the technique, has overcome other problems, and has shown that it is robust to some violations of its underlying assumptions. Thus, although care is needed, elasticity analysis is a simple first step in answering important questions in evolutionary and population ecology.     

Niche conservatism as an emerging principle in ecology and conservation biology

The diversity of life is ultimately generated by evolution, and much attention has focused on the rapid evolution of ecological traits. Yet, the tendency for many ecological traits to instead remain similar over time [niche conservatism (NC)] has many consequences for the fundamental patterns and processes studied in ecology and conservation biology. Here, we describe the mounting evidence for the importance of NC to major topics in ecology (e.g. species richness, ecosystem function) and conservation (e.g. climate change, invasive species). We also review other areas where it may be important but has generally been overlooked, in both ecology (e.g. food webs, disease ecology, mutualistic interactions) and conservation (e.g. habitat modification). We summarize methods for testing for NC, and suggest that a commonly used and advocated method (involving a test for phylogenetic signal) is potentially problematic, and describe alternative approaches. We suggest that considering NC: (1) focuses attention on the within‐species processes that cause traits to be conserved over time, (2) emphasizes connections between questions and research areas that are not obviously related (e.g. invasives, global warming, tropical richness), and (3) suggests new areas for research (e.g. why are some clades largely nocturnal? why do related species share diseases?).     

Innateness as an explanatory concept

Although many of the issues surrounding innateness have received a good deal of attention lately, the basic concept of token innateness has been largely ignored. In the present paper, I try to correct this imbalance by offering an account of the innateness of token traits. I begin by explaining Stephen Stich's account of token innateness and offering a counterexample to that account. I then clarify why the contemporary biological approaches to innateness will not be able to resolve the problems that beset Stich's account. From there, I develop an alternative understanding of the innateness of token traits, what I call a causal/explanatory account. The argument to be made is that token innateness is both a causal, and an explanatory, concept. After clarifying this understanding of innateness, and showing how it handles several counterexamples to other accounts, I end with some comments on what the causal/explanatory account suggests for our understanding of innateness in general.     

Towards an evolutionary ecology of life in soil

The soil-microbe system is one of the most diverse components of the terrestrial ecosystem. The origin of this diversity, and its relation to the life-sustaining processes that are mediated by the resident microbial community, is still poorly understood. The inherent complexities necessitate a theoretical framework that integrates ecological and evolutionary approaches and which embraces the physical heterogeneity of the soil environment. Such a framework is currently lacking, although recent advances in theory and experimentation are beginning to identify the essential ingredients. Here, we review and evaluate the relevance of current modelling approaches, and propose a new synthesis of an evolutionary ecology of life in soil. Key elements include an account of dispersal, horizontal gene transfer, and the consideration of the physical and biological components of soil as an integrated complex adaptive system.     

Toll-like receptors--taking an evolutionary approach

The Toll receptor was initially identified in Drosophila melanogaster for its role in embryonic development. Subsequently, D. melanogaster Toll and mammalian Toll-like receptors (TLRs) have been recognized as key regulators of immune responses. After ten years of intense research on TLRs and the recent accumulation of genomic and functional data in diverse organisms, we review the distribution and functions of TLRs in the animal kingdom. We provide an evolutionary perspective on TLRs, which sheds light on their origin at the dawn of animal evolution and suggests that different TLRs might have been co-opted independently during animal evolution to mediate analogous immune functions.     

A standardized approach to estimate life history tradeoffs in evolutionary ecology

As tradeoffs limit the maximum Darwinian fitness individuals can reach, measuring reliably the strength of tradeoffs using appropriate metrics is of prime importance to understand the evolution of traits under constraints. Tradeoffs involving phenotypic traits and fitness components, however, are difficult to quantify in free‐ranging populations because of confounding effects due to environmental variation and individual heterogeneity. Furthermore, although some methods have been used previously to quantify tradeoffs, these methods cannot be applied with respect to binary traits, which are common to describe life histories (e.g. probability of reproduction, nesting success, offspring survival). Here, we demonstrate how to measure reliably the strength of tradeoffs involving binary traits using (auto)correlation estimates obtained from generalized linear (mixed) models. We first propose a standardized approach that accounts for the variation in the nature of the tradeoffs being compared (e.g. continuous/binary traits, repeated/non‐repeated measures), and then apply this method to longitudinal data from two contrasting species of large herbivores. Empirical estimates of tradeoffs varied among traits, and between‐species comparisons suggested that reproductive tradeoffs between successive breeding attempts might only occur in capital breeders. The empirical results we obtained clearly demonstrate that the method we provide allows measuring reliably the strength of tradeoffs under most circumstances, including tradeoffs on binary traits. Our original approach therefore offers an important first step for comparing the strength and, hence, the relative importance of different tradeoffs, and opens the door to a better understanding of the evolution of life history traits in free‐ranging populations.     

Variation in immune defence as a question of evolutionary ecology

The evolutionary-ecology approach to studying immune defences has generated a number of hypotheses that help to explain the observed variance in responses. Here, selected topics are reviewed in an attempt to identify the common problems, connections and generalities of the approach. In particular, the cost of immune defence, response specificity, sexual selection, neighbourhood effects and questions of optimal defence portfolios are discussed. While these questions still warrant further investigation, future challenges are the development of synthetic concepts for vertebrate and invertebrate systems and also of the theory that predicts immune responses based on a priori principles of evolutionary ecology.     

Pike Esox lucius as an emerging model organism for studies in ecology and evolutionary biology: a review

The pike Esox lucius is a large, long‐lived, iteroparous, top‐ predator fish species with a circumpolar distribution that occupies a broad range of aquatic environments. This study reports on a literature search and demonstrates that the publication rate of E. lucius research increases both in absolute terms and relative to total scientific output, and that the focus of investigation has changed over time from being dominated by studies on physiology and disease to being gradually replaced by studies on ecology and evolution. Esox lucius can be exploited as a model in future research for identifying causes and consequences of phenotypic and genetic variation at the levels of individuals, populations and species as well as for investigating community processes.     

The evolutionary ecology of metacommunities

Research on the interactions between evolutionary and ecological dynamics has largely focused on local spatial scales and on relatively simple ecological communities. However, recent work demonstrates that dispersal can drastically alter the interplay between ecological and evolutionary dynamics, often in unexpected ways. We argue that a dispersal-centered synthesis of metacommunity ecology and evolution is necessary to make further progress in this important area of research. We demonstrate that such an approach generates several novel outcomes and substantially enhances understanding of both ecological and evolutionary phenomena in three core research areas at the interface of ecology and evolution.     

The evolutionary ecology of myco-heterotrophy

Nonphotosynthetic mycorrhizal plants have long attracted the curiosity of botanists and mycologists, and they have been a target for unabated controversy and speculation. In fact, these puzzling plants dominated the very beginnings of the field of mycorrhizal biology. However, only recently has the mycorrhizal biology of this diverse group of plants begun to be systematically unravelled, largely following a landmark Tansley review a decade ago and crucial developments in the field of molecular ecology. Here I explore our knowledge of these evolutionarily and ecologically diverse plant-fungal symbioses, highlighting areas where there has been significant progress. The focus is on what is arguably the best understood example, the monotropoid mycorrhizal symbiosis, and the overarching goal is to lay out the questions that remain to be answered about the biology of myco-heterotrophy and epiparasitism.     

Microbial metabolism as an evolutionary response: the cybernetic approach to modeling

The growth and metabolic capabilities of microorganisms depend on their interactions with the culture medium. Many media contain two or more key substrates, and an organism may have different preferences for the components. Microorganisms adjust their preferences according to the prevailing conditions so as to favor their own survival. Cybernetic modeling describes this evolutionary strategy by defining a goal that an organism tries to attain optimally at all times. The goal is often, but not always, maximization of growth, and it may require the cells to manipulate their metabolic processes in response to changing environmental conditions. The cybernetic approach overcomes some of the limitations of metabolic control analysis (MCA), but it does not substitute MCA. Here we review the development of the cybernetic modeling of microbial metabolism, how it may be combined with MCA, and what improvements are needed to make it a viable technique for industrial fermentation processes.     

The evolutionary ecology of Plasmodium

Plasmodium, the aetiological agent of malaria, imposes a substantial public health burden on human society and one that is likely to deteriorate. Hitherto, the recent Darwinian medicine movement has promoted the important role evolutionary biology can play in issues of public health. Recasting the malaria parasite two‐host life cycle within an evolutionary framework has generated considerable insight into how the parasite has adapted to life within both vertebrate and insect hosts. Coupled with the rapid advances in the molecular basis to host–parasite interactions, exploration of the evolutionary ecology of Plasmodium will enable identification of key steps in the life cycle and highlight fruitful avenues of research for developing malaria control strategies. In addition, elucidating the extent to which Plasmodium can respond to short‐ and long‐term changes in selection pressures, i.e. its adaptive capacity, is even more crucial in predicting how the burden of malaria will alter with our rapidly evolving ecology.     

The evolutionary ecology of deception

Through dishonest signals or actions, individuals often misinform others to their own benefit. We review recent literature to explore the evolutionary and ecological conditions for deception to be more likely to evolve and be maintained. We identify four conditions: (1) high misinformation potential through perceptual constraints of perceiver; (2) costs and benefits of responding to deception; (3) asymmetric power relationships between individuals and (4) exploitation of common goods. We discuss behavioural and physiological mechanisms that form a deception continuum from secrecy to overt signals. Deceptive tactics usually succeed by being rare and are often evolving under co‐evolutionary arms races, sometimes leading to the evolution of polymorphism. The degree of deception can also vary depending on the environmental conditions. Finally, we suggest a conceptual framework for studying deception and highlight important questions for future studies.     

The evolutionary ecology of corals

Corals display a wide range of complex life histories. The evolutionary consequences of factors such as clonality, indeterminate growth, asexual reproduction coupled with various (sexual) breeding systems, different levels of gene flow, and strongly overlapping generations have only just begun to be explored. We identify a series of problems and areas for new research that may be resolved b y the application of novel theoretical approaches (including nonequilibrium population genetic models and demographic models incorporating modular processes such as colony fission and polyp mortality), greater in situ experimentation, long-term monitoring of population dynamics and the use of new genetic techniques.