TABLE OF CONTENTS
Chapter 1: The Theory of Evolution - David P. Mindell, Samuel M. Scheiner
DOI: 10.7208/chicago/9780226671338.003.0001
[constitutive theory;general theory;metaphor;pragmatism;theory integration]
The increasing breadth of evolutionary science, operating across genes and genomes, whole organisms, clades and ecosystems, makes ongoing integration for principles, concepts and methods, both challenging and necessary. This chapter discusses the general theory of evolution - its role, its principles and scientific rationale - as well as how it relates to its constitutive theories and other general theories within biology. It reviews aspects of recent growth for evolution, including expanding on the Modern Synthesis, reticulate evolution, abundant host-symbiont systems and increasingly sophisticated phylogenetic methods. The overall diversity of explanatory aims among evolutionary biologists, in seeking to understand evolution across taxa, at multiple levels of biological organization, and due to many different causes, requires a pluralistic approach to understanding evolutionary theory. This is consistent with the philosophical approach known as pragmatism, allowing flexibility for syntheses across disciplines and countering any tendency towards an overly proscribed general theory. The role of metaphor is also discussed. (pages 1 - 22)
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Chapter 2: Historicizing the Synthesis: Critical Insights and Pivotal Moments in the Long History of Evolutionary Theory - Vassiliki Betty Smocovitis
DOI: 10.7208/chicago/9780226671338.003.0002
[history of evolution;Darwin-Wallace theory;Mendelian genetics;eclipse of Darwin;theoretical population genetics;synthetic theory;modern synthesis;Darwin Centennial;extended synthesis]
This paper focuses on pivotal moments in the long history of evolutionary biology in the way of understanding some of the major developments leading to the synthetic theory of evolution. It tracks the early history of our understanding of evolution leading to establishment of the Darwin-Wallace theory of evolution, the rise of Mendelian genetics, the eclipse of Darwin, and the origins of theoretical population genetics. It pays special attention to the evolutionary synthesis and the establishment of the modern synthetic theory of evolution, the discipline of evolutionary biology,and its subsequent success around the time of Darwin Centennial of 1959, and its challenges in the 1980s. The extent to which more recentdevelopments necessitate the need for an extended synthesis is also assessed. (pages 25 - 45)
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Chapter 3: Philosophy of Evolutionary Theory: Risky Inferences of Process from Pattern - Patrick Forber
DOI: 10.7208/chicago/9780226671338.003.0003
[philosophy of science;testing holism;phenotypic selection;molecular sequence;biological hierarchy]
An important task in philosophy of science is the analysis of testing methods deployed in different scientific disciplines. Evolutionary biology provides an excellent focal case because it aims to reconstruct the deep past by using a variety of methods. This chapter discusses the general philosophical challenges that face risky inferences to past evolutionary processes from extant patterns in biological populations and molecular sequences. Different methods for detecting phenotypic versus molecular signatures of selection are examined, and contrasting challenges facing different detection methods are identified. The chapter concludes that while the same evolutionary processes may operate across the biological hierarchy, they tend to leave different signatures on the phenotypic versus molecular levels. (pages 46 - 63)
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Chapter 4: Modeling Evolutionary Theories - Patrick C. Phillips
DOI: 10.7208/chicago/9780226671338.003.0004
[genetics;genomics;hypothesis test;mathematical model;natural selection;statistics]
Models are a critical component of nearly every theory in evolutionary biology. Over the last 100 years, most models in evolutionary biology have transitioned from verbal approaches, as exemplified by Darwin, to precise mathematical models, usually based upon our increasing understanding of underlying genetic processes. This chapter explores two phases of the transition to increasingly quantitative approaches to evolutionary theory. The first phase was the focus on understanding general evolutionary mechanisms, such as natural selection, mutation, recombination, and migration. The second phase was the recent shift from abstract models of mechanism to concrete statistical models being used to analyze the emerging onslaught of genetic and genomic data being generated across the tree of life. No matter how precise the model, however, tests of specific hypotheses will nearly always be limited by the historical nature of evolution and the dependence of statistical tests of evolutionary change on assumptions about the underlying structure of the evolutionary processes. The role of explicit mathematical models in evolutionary biology is now unassailable, and their sophistication is likely to continue to increase over the foreseeable future. (pages 64 - 83)
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Chapter 5: Traits and Homology - James O. Mcinerney
DOI: 10.7208/chicago/9780226671338.003.0005
[homology;genetic network;developmental biology;recombination;common ancestor;phylogeny reconstruction;gene sharing]
Homology has been a contentious topic for discussion for almost 200 years and the debate is ongoing. In its simplest definition, homology means “descended from a common ancestor.” Because of genetic recombination, or the replacement of one kind of character or trait with a different kind that can fulfil the same role, identifying homologs and indeed defining homology in detail is fraught with difficulty. In this chapter, I detail some of the history of the concept and link the concept to its uses in phylogeny reconstruction, developmental biology and networks of gene sharing. (pages 84 - 101)
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Chapter 6: The Nature of Species in Evolution - Marco J. Nathan, Joel Cracraft
DOI: 10.7208/chicago/9780226671338.003.0006
[species;species problem;units of classification;units of evolution;ontology]
Much has been written about the so-called“speciesproblem," which can be broadly characterized as the task of providing a functional species concept that picks out the “right” kind of entities. Yet, to date,no general consensus has been achieved on the individuation and definition of species, or whether a unique solution to the species problem exists. Some have gone as far as questioning whether contemporary biology requires species concepts at all. The goal of this chapter is to shed some light on the sources of the disagreement. It begins by drawing attention to two distinct ways species figure in biology, namely, as units of classification and units of evolution. Next, it introduces the so-called species problem and discusses a variety of ontological issues that pertain to the nature and role of species in evolutionary theory. The second part of the chapter explores the interface between philosophical considerations and how species are conceived and used in biology. (pages 102 - 122)
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Chapter 7: The Tree of Life and the Episodic Evolutionary Synthesis - Maureen Kearney
DOI: 10.7208/chicago/9780226671338.003.0007
[phylogeny;natural selection;Tree of Life;species;systematics;genes;organisms;evolutionary lineages;evolutionary history]
The Tree of Life depicts phylogenetic relationships of species lineages. Together with theories of phylogeny and natural selection, it explains common ancestry, descent with modification, and change within lineages. It had a profound influence on comparative biology, which continues to grow as species relationships and the history of biodiversity’s organization are increasingly recognized as critical to hypothesis-testing. Recent major expansion of genomic data has contributed to resolving phylogenetic relationships. With new knowledge of genetic diversity and non-divergent genetic evolutionary processes, the Tree of Life has been challenged as an inaccurate portrayal of the history of life. The debate about its reality stems from different ways of seeing organisms. Should organismal lineages be conceptualized as equivalent to their genomes, or as complex historical and biological systems that retain identity in spite of genetic exchange and other changes? Do organisms have any emergent reality beyond the sum of their genomes? The debate exemplifies the incomplete integration between major subdisciplines of evolutionary biology. Resolution will require further cross-disciplinary research and synthesis across systematics, ecology, genetics, paleontology, and organismal biology. Theory on the nature of organisms, species, and phylogeny must also be re-examined to assess the validity of a universal theory of phylogeny. (pages 123 - 143)
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Chapter 8: Situating Evolutionary Developmental Biology in Evolutionary Theory - Alan C. Love
DOI: 10.7208/chicago/9780226671338.003.0008
[abstract structure;concrete practice;evo-devo;explanation;morphology;novelty;theory structure]
Evolutionary developmental biology (evo-devo) is a complex array of research programs. The place of evo-devo within evolutionary theory is contested, especially with respect to the origin of novelty. For example, evo-devo research aimed at explaining novelties has been a locus for criticizing population genetic explanations. An additional difficulty is that the boundaries of evo-devo are debated. Taking these disagreements as a starting point, this chapter probes the value of a particular account of theory structure for situating evo-devo within evolutionary theory. This endeavor requires distinguishing two approaches for accomplishing the task: “abstract-structure first” and “concrete-practice first.” Using the former approach, evo-devo is situated in terms of distinctively explaining the evolution of morphology and the analysis shows how the framework respects evo-devo as a separate area of inquiry, provides an affirmative answer to the hierarchical ordering of evo-devo within evolutionary theory, and supplies a characterization of how that ordering operates. However, the payoff of these accomplishments is unclear. Two lessons can be derived from this result – one methodological, one substantive – and the chapter closes with reflections on strategies intended to advance scientific inquiry by explicating theoretical structure. (pages 144 - 168)
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Chapter 9: The Inductive Theory of Natural Selection - Steven A. Frank, Gordon A. Fox
DOI: 10.7208/chicago/9780226671338.003.0009
[causal analysis;inductive theory;deductive theory;prediction;explanation;natural selection]
The theory of natural selection has two forms. Deductive theory describes how populations change over time. One starts with an initial population and some rules for change. From those assumptions, one calculates the future state of the population. Deductive theory predicts how populations adapt to environmental challenge. Inductive theory describes the causes of change in populations. One starts with a given amount of change. One then assigns different parts of the total change to particular causes. Inductive theory analyzes alternative causal models for how populations have adapted to environmental challenge. This chapter emphasizes the inductive analysis of cause. (pages 171 - 193)
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Chapter 10: The Theory of Multilevel Selection - Charles Goodnight
DOI: 10.7208/chicago/9780226671338.003.0010
[multilevel selection;Price equation;contextual analysis;indirect genetic effects;genetic interaction;population structure;group selection;kin selection]
This chapter explores the modeling of multilevel selection (MLS) – and the related concepts of group selection and kin selection – using variance partitioning methods, using the Price equation to elucidate basic issues within MLS theory. An expansion of this theory, based on contextual analysis and direct fitness, is used to show that kin selection and MLS selection have the same mathematical roots, although they are not identical. Kin selection theory is oriented towards identifying the optimal group and individual level traits that maximize the fitness of an organism, while MLS theory is oriented towards identifying the rate of evolution of the group and individual level traits in a specified situation. Because of these differences, kin selection and group selection can be considered as complementary approaches. The chapter also addresses why heritable variation at one level often bears little relation to heritable variation at other levels. It is shown that interactions among units (e.g., individuals) cannot contribute to a response to selection at that level, but can contribute to response to selection at a higher level (e.g., the population). Thus, the response to selection at one level can be qualitatively different than the response to selection at other levels. (pages 194 - 210)
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Chapter 11: The Demography of Fitness: Life Histories and Their Evolution - Gordon A. Fox, Samuel M. Scheiner
DOI: 10.7208/chicago/9780226671338.003.0011
[life history trade-off;resource allocation;hierarchical allocation;bet-hedging]
Life histories are the schedules of births and deaths of individuals. The theory of life history evolution concerns how these schedules evolve. Trade-offs are central to the theory. Trade-offs - such as those between reproduction and survival - require a theory of the demography of fitness.The trade-offs are consequences of resource limitation as mediated by organismal traits. Resource allocation can be hierarchical, in the sense that allocating to a particular component of demographic performance can constrain additional components. Resource allocation may involve within-individual trade-offs (e.g., more resource allocated to current reproduction may reduce the amount of resource available to somatic growth and maintenance). It can also be between individuals, as under bet-hedging models for production of varied types of offspring that can succeed in different types of conditions. The purely demographic aspects of the theory are fairly mature. However, it remains a challenge to apply this theory in empirical settings to understand the response of populations to selection. This is because the genetic structure of the relevant traits in the population plays a large role in selection response, and we do not yet have the tools to predict the consequences of selection on demographic trade-offs with genetic correlation structures. (pages 211 - 231)
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Chapter 12: The Theory of Ecological Specialization - Timothée Poisot
DOI: 10.7208/chicago/9780226671338.003.0012
[ecological specificity;local adaptation;ecological niche;dispersal;biotic complexity]
Ecological specificity describes the affinity of an organism for a subset of every axis forming its ecological niche. It is a powerful concept that integrates concepts in evolutionary biology, such as local adaptation, with those in ecology, such as dispersal and biotic interactions. This chapter reviews the current perspective on the concept, and highlights areas where refinements of conceptual definitions are needed. In particular, it focuses on the potential of improving our understanding of ecological specificity as a way to gain more predictive ability on the evolution of ecological niches, species interactions, and species distributions. (pages 232 - 253)
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Chapter 13: The Theory of the Evolution of Phenotypic Plasticity - Samuel M. Scheiner
DOI: 10.7208/chicago/9780226671338.003.0013
[environmental heterogeneity;phenotypic plasticity;plasticity cost;plasticity limitation;local adaptation;genetic differentiation]
The theory of the evolution of phenotypic plasticity deals the role of the environment in determining the relationship between genotype and phenotype. The role of phenotypic plasticity in evolutionary processes was recognized as early as the 19th century, but did not rise to prominence until the 1980s. The chapter discussed the factors that promote and inhibit the evolution of adaptive phenotypic plasticity. For phenotypic plasticity to be favored by selection: (1) there must be a heterogeneous environment that affects the phenotypic expression of traits, (2) there must be spatial and/or temporal variation in the optimal phenotypic value of those plastic traits, (3) individuals or lineages must experience that environmental heterogeneity, and (4) those plastic traits must meet the other conditions required for evolution by natural selection. Three types of conditions can limit that evolution: (1) maintenance, production, or information-acquisition costs, (2) the lack of a reliable cue about the future state of the environment, and (3) developmental limitations. The chapter also examines the evolutionary consequences of phenotypic plasticity. The presence of phenotypic plasticity can act to either inhibit or enhance genetic differentiation, local adaptation, and species divergence. More information is needed on the prevalence of adaptive phenotypic plasticity. (pages 254 - 272)
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Chapter 14: The Evolution of Sex - Maria E. Orive
DOI: 10.7208/chicago/9780226671338.003.0014
[cost of sex;Fisher-Muller model;Red Queen model;recombination;Muller’s ratchet;modifier theory;evolutionary rate;linkage disequilibrium;epistasis;clonal interference]
The theory of the evolution of sex is one of the richest and most quantitatively sophisticated bodies of theory within evolutionary biology. While briefly introducing other biological phenomena described by the term “sex”, this chapter focuses on the theory of recombination. After a discussion of what is meant by the “cost of sex”, the chapter contrasts the two main theoretical approaches taken to explore the evolution of genetic recombination: optimality theory and modifier theory. Key optimality models are considered, such as the Fisher-Muller model, Muller’s ratchet, and the Red Queen model. Models of modifiers of recombination necessarily consider both short-term selection on offspring fitness and long-term selection on population fitness. At the core of modern theory for the evolution of sex is the build-up and break-down of linkage equilibrium, and the role that negative linkage disequilibrium plays in favoring the evolution of recombination. The roles that population structure, genetic drift, epistasis, genomic architecture, and fitness landscapes play in the evolution of sex are discussed, as well as advances in understanding provided by genetic computer algorithms. Finally, the chapter asks what the study of asexuality and of organisms lacking recombination can tell us about the evolution of sex and recombination. (pages 273 - 295)
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Chapter 15: Speciation - Scott V. Edwards, Robin Hopkins, James Mallet
DOI: 10.7208/chicago/9780226671338.003.0015
[reinforcement;postzygotic isolation;prezygotic isolation;post-mating isolation;pre-mating isolation;Haldane's rule;chromosomal rearrangement;polyploidy;hybrid]
Speciation is the foundational process ultimately producing the many branches across the Tree of Life. This chapter defines the use of the term “species” so as to provide a practical framework for discussing the process of divergence and the achievement of reproductive isolation. Divergence and speciation in allopatry, with little or no subsequent gene flow, is likely the most common form of speciation. Nonetheless, mathematical models of speciation producing speciation in the face of gene flow are readily constructed, and recent genomic data suggests that such processes are likely widespread in many groups. Three scenarios involving ecological divergence and pre-mating isolation are prevalent: microhabitat specialization can, like geographical isolation, reduce opportunities for mating with alternatively adapted forms; ecological or even neutral divergence in allopatry can yield pleiotropic effects on post-mating compatibility, including intrinsic postzygotic isolation, such as Haldane's Rule; and processes such as reinforcement can select for assortative mating. Sexual selection and genomic barriers such as inversions or polyploidy are additional drivers of speciation. Recent theories of speciation differ from those espoused 50 years ago in placing greater importance on ecological divergence among species and a greater role for gene flow in shaping lineage divergence. (pages 296 - 318)
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Chapter 16: The Theory of Evolutionary Biogeography - Rosemary G. Gillespie, Jun Y. Lim, Andrew J. Rominger
DOI: 10.7208/chicago/9780226671338.003.0016
[vicariance;dispersal;island biogeography;niche theory;species pump;plate tectonics;supercontinent cycles;climatological cycles]
Evolutionary biogeography lies at the intersection between two sets of highly dynamic processes. One set dictates the physical environment, in which changes in size, isolation, and overall suitability for supporting life, tend to occur in cycles of different frequencies. The second set of processes shapes the ecological and evolutionary trajectories of organisms that inhabit the physical environment. The chapter reviews some of the major biogeographic patterns, and summarize theories that have been developed to account for the different patterns, including vicariance, dispersal, island biogeography, ecophylogenetics, niche theory, and neutral theory. The chapter develops propositions for a synthetic theory of biogeography that integrates the dynamic nature of geographic space with the spatial and temporal dynamics of biodiversity. Specifically, it outlines how geological and climatological cycles lead to periods of isolation and fusion of organisms inhabiting a given area, with associated effects speciation and extinction. A synthetic theory of biogeography requires cross-domain consideration of how the cyclical nature of change in the physical environment affects the ecological and evolutionary processes of different taxa and at different scales of space and time. (pages 319 - 337)
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Chapter 17: Macroevolutionary Theory
DOI: 10.7208/chicago/9780226671338.003.0017
[developmental bias;disparity;diversity;epigenetics;extinction;hierarchy;macroevolution;novelty;origination;species selection]
Macroevolutionary theory incorporates issues of scale and hierarchy, and thus includes the origin and fates of evolutionary novelties, the evolutionary role of rare events ranging from the internal redeployment of gene regulatory networks to externally driven mass extinctions, and the potential for emergent properties or dynamics at different hierarchical levels to shape large-scale patterns. Developmental factors impose non-linear relationships between magnitudes of genetic change and their phenotypic expression, an uneven probability distribution of evolutionary changes around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. Large-scale sorting of these biased inputs – clade dynamics – are often shaped by differential origination and extinction, including strict-sense species selection, in which rate differentials are governed by emergent, species-level traits such as geographic range size, and effect macroevolution, in which rates are governed by organism-level traits such as body size. Both processes can create hitchhiking effects, indirectly causing proliferation or decline of other traits. The nonlinear, sometimes temporally discordant, relationships among macroevolutionary currencies (taxonomic, morphologic, functional) are crucial for understanding the nature of evolutionary diversification; e.g. taxonomic diversifications can lag behind, occur in concert with, or precede, increases in disparity.
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