The generality of Constructive Neutral Evolution

Constructive Neutral Evolution (CNE) is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic and molecular structures or processes, such as retained gene duplications, the spliceosome, and RNA editing. Here we aim to expand the scope of such explanation beyond the molecular level, integrating CNE with Multi-Level Selection theory, and arguing that several popular higher-level selection scenarios are in fact instances of CNE. Suitably contextualized, CNE occurs at any level in the biological hierarchy at which natural selection as normally construed occurs. As examples, we focus on modularity in protein–protein interaction networks or “interactomes,” the origin of eukaryotic cells and the evolution of co-dependence in microbial communities—a variant of the “Black Queen Hypothesis” which we call the “Gray Queen Hypothesis”.     

Overcoming Allee effects through evolutionary,genetic, and demographic rescue

Despite the amplified threats of extinction facing small founder populations, successful colonization sometimes occurs, bringing devastating ecological and economic consequences. One explanation may be rapid evolution, which can increase mean fitness in populations declining towards extinction, permitting persistence and subsequent expansion. Such evolutionary rescue may be particularly important, given Allee effects. When a population is introduced at low density, individuals often experience a reduction in one or more components of fitness due to novel selection pressures that arise from diminished intraspecific interactions and positive density dependence (i.e. component Allee effects). A population can avoid extinction if it can adapt and recover on its own (i.e. evolutionary rescue), or if additional immigration sustains the population (i.e. demographic rescue) or boosts its genetic variation that facilitates adaptation (i.e. genetic rescue). These various forms of rescue have often been invoked as possible mechanisms for specific invasions, but their relative importance to invasion is not generally understood. Within a spatially explicit modelling framework, we consider the relative impact of each type of rescue on the probability of successful colonization, when there is evolution of a multi-locus quantitative trait that influences the strength of component Allee effects. We demonstrate that when Allee effects are important, the effect of demographic rescue via recurrent immigration overall provides the greatest opportunity for success. While highlighting the role of evolution in the invasion process, we underscore the importance of the ecological context influencing the persistence of small founder populations.     

Constraining the adaptationism debate

This contribution to the adaptationism debate elaborates the nature of constraints and their importance in evolutionary explanation and argues that the adaptationism debate should be limited to the issue of how to privilege causes in evolutionary explanation. I argue that adaptationist explanations are deeply conceptually dependent on developmental constraints, and explanations that appeal to constraints are dependant on the results of natural selection. I suggest these explanations should be integrated into the framework of historical causal explanation. Each strategy explicitly appeals to some aspect of the evolutionary process, while implicitly appealing to others. Thus, adaptationists and anti-adaptationists can offer complementary causal explanations of the same explanandum. This eliminates much of the adaptationism debate and explains why its adversaries regularly agree with each other more than they would like. The adaptationism issue that remains is a species of the general issue of how to privilege causes in explanation. I show how a proposed solution to this general problem might be brought to bear on evolutionary explanations, and investigate some difficulties that might arise due to the nature of the evolutionary process.     

Comparative chemical anatomy of the brain: concepts and methods

The study of neuropeptides represents an appropriate playground for comparative and evolutionary research. Comparative analysis can give insight into the conservative pattern of intercellular transmission molecules, possibly bound both to some evolutionary antiquity and to cellular constraints. In the same time it can teach us how modulation has occurred at molecular, cellular, multicellular levels in order to give the species-specific functional organization. Using some examples from vertebrate central neurons system (CNS) immunocytochemical analyses, the results so far obtained suggest the rise of a new comparative chemical neuroanatomy. The rationale of "what" and "why" we are comparing is, however, needed in order to understand constancy, heterogeneity or else trends toward complexity in the distribution of neuropeptides.     

Non-adaptive complexity and biochemical function

Intricate biochemical structures are usually thought to be useful, because natural selection preserves them from degradation by a constant hail of destructive mutations. Biochemists therefore often deliberately disrupt them to understand how complexity improves protein function or fitness. However, evolutionary theory suggests that even useless complexity that never improved fitness can become completely essential if a simple set of evolutionary conditions is fulfilled. We review evidence that stable protein complexes, protein–chaperone interactions, and complexes consisting of several paralogs all fulfill these conditions. This makes reverse genetics or destructive mutagenesis unsuitable for assigning functions to these kinds of complexity. Instead, we advocate that incorporating evolutionary approaches into biochemistry overcomes this difficulty and allows us to distinguish useless from useful biochemical complexity.     

Evolutionary Change and Epistemology

This paper is concerned with the debate in evolutionary epistemology about the nature of the evolutionary process at work in the development of science: whether it is Darwinian or Lamarckian. It is claimed that if we are to make progress through the many arguments that have grown up around this issue, we must return to an examination of the concepts of change and evolution, and examine the basic kinds of mechanism capable of bringing evolution about. This examination results in two kinds of processes being identified, dubbed direct and indirect, and these are claimed to exhaust all possibilities. These ideas are then applied to a selection of the debates within evolutionary epistemology. It is shown that while arguments about the pattern and rate of evolutionary change are necessarily inconclusive, those concerning the origin of novel variations and the mode of inheritance can be resolved by means of the distinctions made here. It is claimed that the process of selection in the evolution of science can also be clarified. The conclusion is that the main process producing the evolution of science is a direct or Lamarckian one although, if realism is correct, an indirect or Darwinian process plays a vital role.     

How evolution generates complexity without design: language as an instructional metaphor

One of the major stumbling blocks to understanding evolution is the difficulty in reconciling the emergence of complexity with the apparently undirected forces that drive evolutionary processes. This difficulty was originally framed as the "Watch and Watchmaker" argument and more recently revived by proponents of "intelligent design." Undergraduates in particular often attribute purpose and forethought as the driving force behind biological phenomena, and have difficulty understanding evolutionary processes. To demonstrate that complexity can arise solely through mutations that fix in populations via natural selection or drift, we can use analogies where processes can be observed across short time frames and where the key data are accessible to those without specialized biological knowledge. The evolution of language provides such an example. Processes of natural selection, mutation, genetic drift, acquisition of new functions, punctuated equilibria, and lateral gene transfer can be illustrated using examples of changing spellings, neologism, and acquisition of words from other languages. The examples presented in this article are readily accessible, and demonstrate to students that languages have dynamically increased in complexity, simply driven by the usage patterns of their speakers.     

From pattern to process: identifying predator–prey models from time-series data

Fitting nonlinear models to time-series is a technique of increasing importance in population ecology. In this article, we apply it to assess the importance of predator dependence in the predation process by comparing two alternative models of equal complexity (one with and one without predator dependence) to predator–prey time-series. Stochasticities in such data come from both observation error and process error. We consider how these errors must be taken into account in the fitting process, and we develop eight different model selection criteria. Applying these criteria to laboratory data on simple protozoan and arthropod predator–prey systems shows that little predator dependence is present, with one interesting exception. Field data are more ambiguous (either selection depends on the particular criterion or no significant differences can be detected), and we show that both models fit reasonably well. We conclude that, within our modeling framework, predator dependence is in general insignificant in simple systems in homogeneous environments. Relatively complex systems show significant predator dependence more often than simple ones but the data are also often inconclusive. The analysis of such systems should rely on several models to detect predictions that are sensitive to predator dependence and to direct further research if necessary. Received: July 13, 2000 / Accepted: September 25, 2001     

Selektion und Evolutionstheorie: Müssen »altdarwinistische Dogmen« durch eine kritische Evolutionstheorie ersetzt werden?

Some authors (mainlyBonik, Gutmann, andPeters) have tried to revise current evolutionary concepts, fraught — in their opinion — with “1paleodarwinistic dogmas”. Some points of their theories are reviewed critically in the present paper: (1) Evolution is of course inimaginable without selection, but an “internal selection” eliminating misshaped embryos has nothing to do with evolution. This is stabilizing selection which reduces genetic variation and would even block evolutionary change completely if it was perfect. When this kind of internal selection was “neglected” by earlier authors, this cannot be qualified as paleodarwinistic dogmatism being in contradiction with the premises of evolutionary theory. — (2) Energetic rationalisation of organisms is certainly an important factor in selection but not an absolute law explaining everything about evolution. There are many adaptive processes resulting in less “economic” formations; e.g. heavy armors like those of tortoises, ankylosaurs, and stegosaurs. Among others, protective functions justify a certain waste of energy. — (3) Comparing organisms with technical machines provides an interesting analogy, but again this cannot be considered as the only possible approach for evolutionary models. »Maschinenanalogie« combined with a generalized »internal selection« (i.e. with the nature of adaptive changes determined by the internal construction of organisms) leads inevitably to an underestimation of selective pressures resulting from the ecologic and biocoenotic context. The simple fact of diverging evolutionary lineages shows that the same species (“machine”) can be improved in different ways under the influence of different external factors.     

The nonribosomal peptide biosynthetic system — on the origins of structural diversity of peptides,cyclopeptides and related compounds

A variety of peptides have been detected in microorganisms. Some have found applications in various fields, for example the classical -lactam antibiotics, immunosuppressors like cyclosporin, promising new antibacterials like teichoplanin or daptomycin and antifungals like echinocandin. For none of these has it been established how their complicated biosynthetic pathways have evolved or what functions they fulfill within or for their producers. So it is unclear what selection processes limit the range of their structural analogues within various groups of microorganisms. We here consider recent data in the field of biosynthesis and how they may suggest mechanisms of genetic diversity. These may illustrate the complexity of genetic and intracellular organization of biosynthetic pathways and indicate the cellular context of some metabolites related to the complex background of the production of each metabolite. Research focusing on various targets like the increase of productivity of fermentations or the spread of resistances to antibacterials is slowly being understood.This paper belongs to the Special edition ofAntonie van Leeuwenhoek Vol 64, No 2, on Diversity of Genetic Systems, edited by T. Beppu     

Can You Sequence Ecology? Metagenomics of Adaptive Diversification

Few areas of science have benefited more from the expansion in sequencing capability than the study of microbial communities. Can sequence data, besides providing hypotheses of the functions the members possess, detect the evolutionary and ecological processes that are occurring? For example, can we determine if a species is adapting to one niche, or if it is diversifying into multiple specialists that inhabit distinct niches? Fortunately, adaptation of populations in the laboratory can serve as a model to test our ability to make such inferences about evolution and ecology from sequencing. Even adaptation to a single niche can give rise to complex temporal dynamics due to the transient presence of multiple competing lineages. If there are multiple niches, this complexity is augmented by segmentation of the population into multiple specialists that can each continue to evolve within their own niche. For a known example of parallel diversification that occurred in the laboratory, sequencing data gave surprisingly few obvious, unambiguous signs of the ecological complexity present. Whereas experimental systems are open to direct experimentation to test hypotheses of selection or ecological interaction, the difficulty in “seeing ecology” from sequencing for even such a simple system suggests translation to communities like the human microbiome will be quite challenging. This will require both improved empirical methods to enhance the depth and time resolution for the relevant polymorphisms and novel statistical approaches to rigorously examine time-series data for signs of various evolutionary and ecological phenomena within and between species.     

Neutrale Mutationen und evolutionäre Fortentwicklung

Neutral mutation and evolutionary progress The process and causes of regressive evolution are still under debate. Contrary to DARWIN'S original assumption, Neo-Darwinian proponents make selection responsible for reduction. Biologically functionless structures like eye and pigmentation in cave animals deliver excellent material to study this problem. Comparison of regressive (eye, pigmentation, aggression, dorsal light reaction) and constructive traits (gustatory equipment, egg yolk content, feeding behavior) in epigean and cave fish (Astyanax fasciatus, Characidae) reveal a high variability of the regressive features in the cave forms. Contrary to this, the constructive traits are characterized by a low variability in epigean and cave fish. This difference is attributed to the lack of selection on regressive structures. The existence of an intermediate cave population between epigean and true cave fish of A. fasciatus makes possible the study of evolutionary rates. It is shown that the regressive traits do not evolve more quickly than the constructive ones do. On the contrary, constructive traits like egg yolk content are even more rapid because they are of great biological value in the cave biotope. Especially energy economy is claimed by Neo-Darwinists to play a decisive role as a selective force. Comparison of the development of epi- and hypogean larvae of A. fasciatus shows that the formation of a smaller and less differentiated eye in the cave specimens has no effect on body growth. Furthermore, even behavioral traits like aggressiveness, schooling, dorsal light reaction, or negative phototaxis, which all are not performed in darkness by the epigean ancestor, become genetically reduced in the cave fish. The principles of regressive evolution, loss of selection and increase in variability, play a central role in evolution in general. When biota with empty niches are colonized, stabilizing selection relaxes from the special adaptations to the niche inhabited before by the invading species. Variability may arise in these and is permitted as long as fitness is guaranteed. Such processes characterize adaptive radiation. Examples are given by the species flocks on isolated islands or in chemically abnormal lakes like those of the East African Rift Valley. Only secondarily, on the basis of the arisen variability, does directional selection promote the newly developing species into different niches. The loss of stabilizing selection is an important factor for the evolutionary process to be open for evolutionary progress.     

Artificial life and living systems: Insight into artificial life and its implications in life science research

Advanced technology has made it possible to build machines and systems like robots, which are capable of making intelligent decisions. Robots capable of self-replication and perform human functions are also available. The current challenge is to design evolutionary systems with high complexity comparable to that of biological networks. This is proposed to be achieved by ALife (Artificial Life). Here, we describe the promises provided by ALife for life sciences.     

The Relationship between Sexual Selection and Sexual Conflict

Evolutionary conflicts of interest arise whenever genetically different individuals interact and their routes to fitness maximization differ. Sexual selection favors traits that increase an individual’s competitiveness to acquire mates and fertilizations. Sexual conflict occurs if an individual of sex A’s relative fitness would increase if it had a “tool” that could alter what an individual of sex B does (including the parental genes transferred), at a cost to B’s fitness. This definition clarifies several issues: Conflict is very common and, although it extends outside traits under sexual selection, sexual selection is a ready source of sexual conflict. Sexual conflict and sexual selection should not be presented as alternative explanations for trait evolution. Conflict is closely linked to the concept of a lag load, which is context-dependent and sex-specific. This makes it possible to ask if one sex can “win.” We expect higher population fitness if females win.Many published studies ask if sexual selection or sexual conflict drives the evolution of key reproductive traits (e.g., mate choice). Here we argue that this is an inappropriate question. By analogy, G. Evelyn Hutchinson (1965) coined the phrase “the ecological theatre and the evolutionary play” to capture how factors that influence the birth, death, and reproduction of individuals (studied by ecologists) determine which individuals reproduce, and “sets the stage” for the selective forces that drive evolutionary trajectories (studied by evolutionary biologists). The more modern concept of “eco-evolutionary feedback” (Schoener 2011) emphasizes that selection changes the character of the actors over time, altering their ecological interactions. No one would sensibly ask whether one or the other shapes the natural world, when obviously both interact to determine the outcome.So why have sexual conflict and sexual selection sometimes been elevated to alternate explanations? This approach is often associated with an assumption that sexual conflict affects traits under direct selection, favoring traits that alter the likelihood of a potential mate agreeing or refusing to mate because it affects the bearer’s immediate reproductive output, whereas “traditional” sexual selection is assumed to favor traits that are under indirect selection because they increase offspring fitness. These “traditional” models are sometimes described as “mutualistic” (e.g., Pizzari and Snook 2003; Rice et al. 2006), although this term appears to be used only when contrasting them with sexual conflict models. The investigators of the original models never describe them as “mutualistic,” which is hardly surprising given that some males are rejected by females.In this review, we first define sexual conflict and sexual selection. We then describe how the notion of a “lag load” can reveal which sex currently has greater “power” in a sexual conflict over a specific resource. Next, we discuss why sexual conflict and sexual selection are sometimes implicitly (or explicitly) presented as alternative explanations for sexual traits (usually female mate choice/resistance). To illustrate the problems with the assumptions made to take this stance, we present a “toy model” of snake mating behavior based on a study by Shine et al. (2005). We show that empirical predictions about the mating behavior that will be observed if females seek to minimize direct cost of mating or to obtain indirect genetic benefits were overly simplistic. This allows us to make the wider point that whom a female is willing to mate with and how often she mates are often related questions. Finally, we discuss the effect of sexual conflict on population fitness.     

Limiting relationships between selection and recombination

It is difficult to directly observe processes like natural selection at the genetic level, but relatively easy to estimate genetic frequencies in populations. As a result, genetic frequency data are widely used to make inferences about the underlying evolutionary processes. However, multiple processes can generate the same patterns of frequency data, making such inferences weak. By studying the limits to the underlying processes, one can make inferences from frequency data by asking how strong selection (or some other process of interest) would have to be to generate the observed pattern. Here we present results of a study of the limits to the relationship between selection and recombination in two-locus, two-allele systems in which we found the limiting relationships for over 30 000 sets of parameters, effectively covering the range of two-locus, two-allele problems. Our analysis relates T _min—the minimum time for a population to evolve from the initial to the final conditions—to the strengths of selection and recombination, the amount of linkage disequilibrium, and the Nei distance between the initial and final conditions. T _min can be large with either large disequilibrium and small Nei distance, or the reverse. The behavior of T _min provides information about the limiting relationships between selection and recombination. Our methods allow evolutionary inferences from frequency data when deterministic processes like selection and recombination are operating; in this sense they complement methods based entirely on drift.     

The evolution of resource specialization through frequency-dependent and frequency-independent mechanisms

Levins's fitness set approach has shaped the intuition of many evolutionary ecologists about resource specialization: if the set of possible phenotypes is convex, a generalist is favored, while either of the two specialists is predicted for concave phenotype sets. An important aspect of Levins's approach is that it explicitly excludes frequency-dependent selection. Frequency dependence emerged in a series of models that studied the degree of character displacement of two consumers coexisting on two resources. Surprisingly, the evolutionary dynamics of a single consumer type under frequency dependence has not been studied in detail. We analyze a model of one evolving consumer feeding on two resources and show that, depending on the trait considered to be subject to evolutionary change, selection is either frequency independent or frequency dependent. This difference is explained by the effects different foraging traits have on the consumer-resource interactions. If selection is frequency dependent, then the population can become dimorphic through evolutionary branching at the trait value of the generalist. Those traits with frequency-independent selection, however, do indeed follow the predictions based on Levins's fitness set approach. This dichotomy in the evolutionary dynamics of traits involved in the same foraging process was not previously recognized.     

Phylogenetic signal, evolutionary process, and rate

A recent advance in the phylogenetic comparative analysis of continuous traits has been explicit, model-based measurement of "phylogenetic signal" in data sets composed of observations collected from species related by a phylogenetic tree. Phylogenetic signal is a measure of the statistical dependence among species' trait values due to their phylogenetic relationships. Although phylogenetic signal is a measure of pattern (statistical dependence), there has nonetheless been a widespread propensity in the literature to attribute this pattern to aspects of the evolutionary process or rate. This may be due, in part, to the perception that high evolutionary rate necessarily results in low phylogenetic signal; and, conversely, that low evolutionary rate or stabilizing selection results in high phylogenetic signal (due to the resulting high resemblance between related species). In this study, we use individual-based numerical simulations on stochastic phylogenetic trees to clarify the relationship between phylogenetic signal, rate, and evolutionary process. Under the simplest model for quantitative trait evolution, homogeneous rate genetic drift, there is no relation between evolutionary rate and phylogenetic signal. For other circumstances, such as functional constraint, fluctuating selection, niche conservatism, and evolutionary heterogeneity, the relationship between process, rate, and phylogenetic signal is complex. For these reasons, we recommend against interpretations of evolutionary process or rate based on estimates of phylogenetic signal.     

Simulation of the evolution of genomic complexity.

A general evolutionary trend is the generation of organisms of increasing complexity, notwithstanding that reduction and simplification phenomena do occur in the evolutionary process. This paper proposes an evolutionary model incorporating the mechanisms of gene amplification and deletion. The evolutionary process leading to genomic complexity and the coexistence of simpler organisms with complicated ones were both simulated using the proposed model. The model was also used to investigate the influence of various factors on the evolution of complexity. The simulations indicated that the evolution of complexity is largely influenced by adaptation to complicated environments. Nevertheless, complex organisms require relatively more resources for survival and replication, which limits the on going tendency towards complexity. Moreover, the analysis showed that if the environment varies rapidly and the profit obtained from complexity is greater than the resources consumed, selection will tend to favor complexity. However, high living cost will tend to limit the trend of complexity and if the environment is relatively stable, reduction and simplification will become the dominant trends.     

The genotypic complexity of evolved fault-tolerant and noise-robust circuits

Noise and component failure is an increasingly difficult problem in modern electronic design. Bio-inspired techniques is one approach that is applied in an effort to solve such issues, motivated by the strong robustness and adaptivity often observed in nature. Circuits investigated herein are designed to be tolerant to faults or robust to noise, using an evolutionary algorithm. A major challenge is to improve the scalability of the approach. Earlier results have indicated that the evolved circuits may be suited for the application of artificial development, an approach to indirect mapping from genotype to phenotype that may improve scalability. Those observations were based on the genotypic complexity of evolved circuits. Herein, we measure the genotypic complexity of circuits evolved for tolerance to faults or noise, in order to uncover how that tolerance affects the complexity of the circuits. The complexity is analysed and discussed with regards to how it relates to the potential benefits to the evolutionary process of introducing an indirect genotype-phenotype mapping such as artificial development.