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The mechanism of evolutionary change can be studied directly through selection experiments in laboratory microcosms. This chapter begins by describing the experimental approach to evolution, and goes on to analyse adaptation over different time scales. The first section in this chapter is about microcosmologica. Subsections here concern Dallinger's experiment; the laboratory microcosm; the inhabitants of the microcosm; the selection experiment; fitness and adaptedness; and microcosm genealogy. The second section is all about sorting (in other words selection of pre-existing variation) and includes subsection on a single episode of selection; the sorting of a single type; the mixture of discrete types; the Fundamental Theorem of Natural Selection; the sorting in finite populations; drift and selection; and fluctuating population size. The third section is on purifying selection (defined as maintaining adaptedness despite genetic deterioration) and this section discusses the following: mutation-drift balance; mutation-selection equilibrium; and Muller's Ratchet. The fourth section is about directional selection (this is restoring adaptedness despite environmental deterioration) and details the probability that a beneficial mutation will be fixed; periodic selection; Fisher's geometrical analogy; the variable-mutation model; the extreme-value mode; clonal interference; the distribution of fitness effects; genetic interference; and the genetic basis of adaptation. The fifth section is about successive substitution and includes detail on phenotypic evolution towards the optimum; adaptive walks; transitivity; and clonal interference. The sixth section, Cumulative adaptation, includes the following: the protein matrix; connectance; synthetic beneficial mutations; functional interaction in a protein structure; the evolution of RNA sequences; reversibility; cumulation; cumulative construction of novel amidases; diminishing returns; and contingency. The last section called Successive substitution at several loci explains genetic interactions; the adaptive landscape; the allele matrix; compensatory mutations; compound structures; processing chains; the effect of mutation in a simple processing chain; the pattern of adaptation; the evolution of metabolic pathways; in vitro selection; genetic changes during adaptation; and repeated adaptation.

This concluding chapter argues that experimental evolution with microbes has emerged as a very attractive alternative to overcome the problem of long time scales in empirical studies of evolution. This is exemplified by the long-term evolution experiments of Richard Lenski, whose experimental Escherichia coli lines have evolved for more than 40,000 generations to date. Lenski and his many collaborators convincingly argued that the diversified strains have coexisted over long time periods, and hence that this diversification represents a case of asexual speciation. The ecological mechanism for diversification in this case appears to be related to crossfeeding, a scenario in which one strain or species persists by scavenging on nutrients that accumulate in the environment as metabolic byproducts of the coexisting strain. With crossfeeding, polymorphisms can be maintained even in simple environments with a single limiting resource such as glucose. This is an excellent example of frequency-dependent selection, as the fitness of the crossfeeder depends on the presence or absence of the glucose specialist.

The action of selection is based on a few simple principles that are general to all self-replicating systems, and which constitute a distinct branch of science. This introductory chapter presents a brief overview of some of these principles in a wide range of systems. It is divided into various sections on the following discussion topics: RNA viruses are the simplest self-replicators; exponential growth can be maintained by serial transfer; replication is always imprecise; imprecise replication leads to differential growth; selection acts directly on rates of replication; selection may act indirectly on other characters; the indirect response to selection is often antagonistic; evolution typically involves a sequence of alterations; the evolution of increased complexity is a contingent process; very improbable structures rapidly arise through the cumulation of alterations; competitors are an important part of the environment; evolution through selection is a property of self-replicators; self-replicating algorithms evolve in computers; and finally evolution through selection is governed by a set of general principles.

This chapter reviews traditional and newer approaches to the empirical study of biological form, highlighting the contribution of experimental evolution to an improved understanding of why and how particular transformations in animal shape occur. It begins by reviewing different mathematical methods for quantifying and comparing organismal shape, focusing on one methodology in particular: the scaling relationship between two traits. The chapter also examines the biology of shape expression and evolution, and presents case studies where experimental evolution has been used to explore various aspects of scaling relationship evolution.

This final chapter epitomizes some of the material presented in the bulk of the text under headings which reflect the introductory section by consisting of declaratory sentences. This chapter aims to provide a framework for discussion that will help to move the field into the next stage of evolutionary studies.

This chapter explores recent examples where experimental evolution, empowered by genomic technologies and increasingly informed by systems biology, has fundamentally advanced our understanding of adaptive evolution. It focuses on genomically enabled insights into the following issues: how prevalent adaptive parallelism is; what the relative contributions of structural versus regulatory mutations are to the adaptive process; whether trade offs inevitably result from pleiotropy; how and why loss of function occurs under strong selection; and how much and how often adaptations arise from large-scale structural changes, such as gene duplications, deletions, and translocations. The chapter also offers perspective on how whole-genome sequencing and bioinformatics have been and can be fruitfully applied in the context of experimental evolution.

The adaptive landscape has had a major role in shaping and motivating many experimental evolution studies. In return, these studies have made important contributions to our understanding of the nature of adaptive landscapes. The simplest findings come from studies that have examined the similarity of evolutionary outcomes from initially identical replicate populations. Comparison of resulting evolutionary trajectories has allowed experimenters to examine the repeatability of evolution, a reflection of the relative influence of chance and selection on the outcome of evolution. Other experiments have addressed the evolution of diversity within (usually) initially homogeneous populations — an outcome determined by the availability of distinct adaptive peaks and the existence of ecological conditions that allow the maintenance of subpopulations at different peaks. Experiments can be carefully designed and controlled to assess the effect of environment — e.g. spatial structure, resource complexity — on the likelihood that distinct peaks will be reached. This chapter discusses how bacterial experimental evolution studies can and have contributed to our understanding of the form of adaptive landscapes.

This chapter discusses the role of field experiments in experimental evolution. Field experiments come in different forms, but the most widely discussed method in the context of evolution is field introduction. The chapter provides a practical guide for researchers interested in experimental evolution and field introductions. It begins by differentiating different kinds of field experiment (replacement experimental methods and live-animal introductions) with regard to the study of evolution, and then discusses specific considerations for these different kinds of study. The chapter also examines the unique advantages of field introductions for addressing evolutionary issues.

This chapter considers the place of experimental studies in evolutionary biology, first describing the advantages of experimental evolution and contrasting it with other approaches. The special strengths of experimental evolution lie in the essence of any experiment: replication and control. By replicating the number of populations exposed to the novel environment, an investigator can, in effect, repeat the opportunity for evolutionary change and determine whether the outcome has consistency. The novel experimental populations can be statistically compared with the group of control populations with the number of degrees of freedom determined by the number of independent replicates of each. The chapter also discusses two areas of evolutionary thought and theory to which experimental studies have made substantial contributions: the presence and generality of trade-offs, and the role of genetic drift during adaptation.

This chapter looks critically at a particular type of experimental evolution, often called laboratory natural selection (LNS). In this protocol, stocks of organisms are reared chronically under different conditions and allowed to evolve by natural selection over many generations. The chapter discusses the difficulties of balancing simplicity and realism in laboratory studies of natural selection, especially when they are intended to simulate selection in the wild. Because LNS experiments have strengths and weaknesses, researchers contemplating one face the classic catch-22 (or double-bind) situation. They may well decide that LNS is the best way to test a given evolutionary hypothesis, but simultaneously they must accept that some of the inferences they draw from their LNS experiment may be of uncertain validity.

This chapter focuses on empirical tests of evolutionary theory using viruses, specifically bacteriophage or phage, beginning by reviewing phage biology and the phage life cycle, and then describing laboratory procedures for cultivating phage and assaying fitness. It also reviews the theoretical models that have been used to describe phage ecology and evolution, in order to emphasize the advantages of using phage experimental systems to test theoretical predictions. The chapter then discusses recent phage experiments that have investigated the genetic basis and molecular mechanisms underlying adaptation. Finally, it emphasizes that the insights gained from experimental evolution studies with phage have important implications not only for phage ecology and evolution, but also for predator–prey and host–parasite interactions in general.

This chapter examines how botanical investigators in the early twentieth century used radium to induce or control biological evolution. Explicitly linking the transmutation of the physical species of radium with the transmutation of biological species, Daniel Trembley MacDougal and Charles Stuart Gager of the New York Botanic Garden and the Brooklyn Botanical Garden, respectively, independently irradiated plants with radium in an attempt to study the physiological effects induced as well as to provide experimental confirmation of Hugo de Vries’ new “mutation theory.” Metaphors of radium’s powers were put to experimental test at this moment and passed. Even among those plants that happened not to mutate, radium was seen to have “stimulated” and “accelerated” their growth toward an “early senescence.” What would later be taken as a clear sign of mutagenic damage was at this time clear proof of radium’s relevance in the novel early twentieth-century quest to experimentally induce and ultimately control evolution.

This chapter provides an overview of the ways to model experimental evolution. There are three approaches to modeling the evolution of quantitative traits: (1) population-based models, (2) Mendelian-based models, and (3) variance-components models. The chapter focuses on variance-components models and discusses how to implement them for both single- and multiple-trait cases. To illustrate how multiple traits can be dealt with in a laboratory evolution model, it presents a case study of the laboratory evolution in the sand cricket, Gryllus firmus.

This chapter presents some of the methods in experimental evolution that can be used to study the evolution of behavior, illustrating how these can be applied toward understanding the origin and mechanisms of behavioral diversity. One method is artificial selection, a powerful tool used to explore the question of how behavior evolves; another is mass selection, which relies on an experimental setup that sorts individuals into groups depending on a particular behavior. An alternative approach for identifying mechanisms of behavioral evolution is to use experimental methods to explore genetics and physiology of real behavioral shifts that occurred among populations or species in nature. The chapter describes how laboratory experimental tools, such as genetic engineering and pharmacology, were used to discover the evolution of mating systems in voles.

This chapter discusses many of the varied attempts to study the evolution of sex. It suggests that a wide range of biological systems have been usefully harnessed to explore questions pertaining to the evolution and maintenance of sex by reviewing experimental evolution studies involving viruses, unicellular organisms, and multicellular organisms.

Darwin's erroneous reasoning concerning heredity was influenced by his gradualist prejudices. This style of thinking prevented Darwin from giving appropriate attention to the hypothesis of discrete inheritance, leading evolutionary biology up a blind alley of blending inheritance. Darwin's other mistake also came from his gradualist preconceptions. Darwin repeatedly emphasized that natural selection acts only by slow accretion and is slow, which implies that natural selection is difficult to observe. This book emphasizes that the Darwinian inhibition about experimental research on evolution should now be resolutely discarded. Its goal is to foster selection experiments and experimental evolution as a central component of evolutionary biology.

This chapter discusses the meaning of adaptedness, and examines its relation both to natural selection and to the conditions for existence. Adaptedness means a certain appropriateness or fit between the various aspects of an organism's morphology, physiology, lifestyle, and environment. The chapter provides examples to explain how the adaptedness of a trait relates to its evolutionary history and how it relates to the process of adaptation. It also examines the experimental evolution of bacteria, peppered moths, and Darwin's finches, which shows that natural selection in evolution is a factor maintaining the adaptedness in the face of environmental change and associated changes in the mode of adaptedness.

Parallel evolution has been used as “proof” of a bewildering array of sometimes contradictory assertions: that Darwinism is wrong, that selection is all powerful, that the modern synthesis is incomplete, that chance matters, or that chance does not matter. Perhaps most importantly, parallel evolution is a source of fascination, as the evolution of a particular life form is seen as one of the least probable chains of events imaginable. Our stance is that both chance and history do matter in evolution. Beyond reasserting these well-known points, the central question is what parallel evolution (or the lack thereof) tells us about evolutionary processes. First, we argue that the topic of parallel evolution crystallizes a series of unsolved issues that have fueled recurrent debates throughout the history of evolutionary genetics. Second, we discuss the implications of parallel evolution at different biological levels. Third, we review the causes of genotypic and phenotypic parallel evolution. Fourth, we show how parallel evolution can be modeled and the additional insights brought by theory. We conclude with a series of questions for future work, and by stressing that using explicit phenotypic landscape models is a useful way to resolve controversies emerging from the observation of parallel evolution.