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Diversification occurs readily in asexual populations, but is obstructed by recombination in outcrossed sexual organisms. Species may arise because sexual isolation permits diversification, or because sexual isolation follows diversification; this chapter takes the former view. The first section in this final chapter is called Speciation and diversification and it details allopatric and sympatric divergence; asexual diversification; the poverty of the protists; and speciation in macrobes. The second section is called Experimental speciation and is about sexual divergence by drift; disruptive natural selection; the evolution of isolating mechanisms; divergent natural selection in complete isolation; reinforcement; artificial selection for sexual isolation; sexual divergence; and offers a new species of yeast. The final section entitled Emerging species is all about sticklebacks; whitefish; and sedges.

This chapter examines how populations in different environments can fall at different stages along a continuum of progress toward ecological speciation. It traces how variation can be used to infer ecological speciation through either of two general approaches: (1) integrated signatures of reproductive isolation based on measures of gene flow, and (2) confirmation of the ecological basis of reproductive barriers. The chapter also addresses the rapidity of ecological speciation (rapid speciation), at what point progress toward ecological speciation becomes irreversible (speciation reversal), to what extent ecological speciation is driven by competitive (adaptive speciation) or reproductive (reinforcement) interactions, and how many traits (magic traits) and selective pressures (dimensionality) are involved.

This chapter defines ecological speciation as the process by which barriers to gene flow evolve between populations as a result of ecologically based divergent selection between environments. It provides a brief history of the ecological speciation hypothesis, dating back to Charles Darwin's On the Origin of Species in 1895. It also examines alternatives to ecological speciation, saying that they tend to involve stochastic events, such as random changes in gene frequencies and stochastic differences among populations in which mutations arise. These alternatives can be classified into two main categories. The first one considers mechanisms of speciation that do not involve selection, and the second considers mechanisms that do not involve selection, but in which, selection is not divergent between ecological environments.

Although the contribution of natural selection to speciation was not an explicit empirical focus of most of the twentieth century, it was often assumed to be an important factor in the evolutionary diversification of lineages. A challenging task is identifying the potential contributions of ecological divergence to reproductive barriers that are not inherently ecological, including sexual isolation, cryptic postmating isolation, and intrinsic hybrid inviability. This chapter shows how particular comparative approaches can be used to identify and quantify ecological contributions to reproductive isolation and speciation, focusing on herbivorous insects. First, it discusses the nature and study of ecological speciation, and presents some advantages of evaluating herbivorous insect systems for such investigations. The chapter then describes recently developed comparative approaches that have provided insights on this topic. It also analyzes available herbivore data sets to illustrate these methods and the evidence they provide on ecology's role in herbivore speciation, highlights important issues pertaining to the conduct and interpretation of these comparative studies, and suggests future directions for advancing the multidimensional study of ecological speciation through the creative application of comparative approaches.

This chapter reviews five classes of approaches for testing ecological speciation. The explicit predictions, associated with each approach, allow ecological speciation to be distinguished from alternative mechanisms of speciation. All methods assume that relevant ecological variables or traits are measured. The chapter notes that it is important to ensure that further tests meet the criteria and assumptions of the methods used. It also states that manipulative field experiments testing the extent to which adaptive divergence reduces gene flow are the ‘final frontier’ in tests for ecological speciation.

This chapter deals with the conditions under which pleitropy versus linkage disequilibrium can drive ecological speciation. It considers just how tight physical linkage needs to be for linkage disequilibrium to be an effective mechanism for speciation. It concludes by looking at the number of loci underlying ecological speciation and the specific genes driving the process. It identifies a number of factors that might make linkage disequilibrium an effective mechanism of speciation, including physical linkage, structural features that reduce recombination, one-allele assortative mating mechanisms, and strong selection.

This chapter concentrates on the degree to which ecological speciation unfolds once it is initiated. Its central concept is that speciation is often an extended and continuous process. It details on the evidence for the continuum of speciation, noting examples of partial reproductive isolation, and exploring the extent to which they represent a stable outcome versus an intermediate state that is bound to progress to complete reproductive isolation. It also explains how far speciation proceeds, starting with non-selective hypotheses, and then turning to hypotheses based upon the specific nature of divergent selection itself, namely how strong selection is and how many traits or genes it acts on.

This chapter summarizes what is known about ecological speciation, focusing on findings with strong support. It outlines the key missing components in the understanding of ecological speciation, thereby outlining clear avenues for further research. It examines aspects of ecological speciation that were not thoroughly treated in this book. It states that the study of ecological speciation is yet to enter a truly experimental phase, where manipulations are commonly employed to isolate causal associations between the factors driving and constraining speciation. The future holds promise, particularly as rapidly developing genomic methodologies continue to be further integrated with classical ecological approaches.

This chapter focuses on the geographic component of ecological speciation. It begins by giving different definitions of the geography of speciation and then studies the effects of geography on the sources of divergent selection. It considers how geographic contact between populations might constrain or promote ecological speciation, and how speciation can involve multiple geographic modes of divergence. It also assesses the empirical problem of detecting gene flow, through consideration of comparative geographic, coalescent-based, and genomic approaches. It concludes with a consideration of speciation along continuous environmental gradients versus between discrete patches and the unresolved issue of the spatial scale of speciation.

As diversity accumulation reflects the balance between speciation and extinction through time, the high biotic diversity of the Cape likely results from high speciation and/or low extinction rates. In the past century numerous authors have speculated about the extrinsic aspects of the Cape environment or the intrinsic properties of its biota which may have tipped the scales towards continued diversification. Usually some combination of complex environmental conditions and relative climatic stability is invoked. This chapter critically assesses the predominant correlative phylogenetic evidence for various drivers of diversification in the Cape but focuses mainly on work from population level studies which more directly addresses the process of speciation itself. Within the ecological speciation theoretical framework factors promoting divergent selection and reducing gene flow between populations are explored. The chapter also reviews the little that is known about extinction in the Cape biota and suggests future research avenues and approaches which will enhance the understanding of the processes that underlie the well-established patterns of hyperdiversity in the Cape.

This chapter discusses the genomic basis of ecological speciation. It empirically and theoretically explores the genomic perspective of speciation, leading to a more integrative understanding of ecological speciation. The main concept of this chapter is that genetic differentiation between populations is expected to be highly variable across the genome, possibly ranging from some regions with little or no differentiation through to fixed differences. It considers the expectations for genomic divergence at equilibrium and treats the transient effects of selective sweeps, both form new mutations and standing genetic variation. It also highlights key conceptual and theoretical points, and illustrates these points with empirical examples.

This chapter examines case studies of various types of reproductive isolation during ecological speciation. It considers the contributions of individual reproductive barriers to levels of total reproductive isolation that exist at any one point in time. It tackles the issue of how commonly different barriers are observed during ecological speciation. It also observes the evolution of different barriers during speciation. It states that the explicit theory concerning the timing of evolution of different reproductive barriers, and how different barriers might affect each other, is scarce, explaining that it is difficult to predict which barriers are most likely to drive ecological speciation.

This chapter details the nature of plasticity and how it can be studied, focusing in particular on the “reaction norm” approach. The subsequent key questions first evaluate whether or not plasticity is typically adaptive, with the main alternative being maladaptive physiological responses to stress. The next question informs the costs and limits to plasticity, without which any environment-phenotype mismatch could be easily bridged. The chapter considers when adaptive plasticity should be strongest, such as when environments are variable in space or time, when gene flow is high, and when reliable cues exist. Also considered are alternative hypotheses for how genetic change and plasticity interact: that is, plasticity might enhance or constrain genetic evolution and ecological speciation.