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Reticulate evolution of disease vectors and diseases

Michael L. Arnold

in Reticulate Evolution and Humans: Origins and Ecology

A goal shared by this chapter with all the other parts of this book is to emphasize the ubiquity of reticulate evolution as an agent of genetic and evolutionary change. Another goal, unique to the ... More

A goal shared by this chapter with all the other parts of this book is to emphasize the ubiquity of reticulate evolution as an agent of genetic and evolutionary change. Another goal, unique to the topic in this chapter, is to address the hypothesis that genetic exchange events have impacted greatly the evolutionary trajectory of organisms that parasitize and kill humans. The first of these goals is accomplished as this chapter is considered in the context of the previous seven. The second objective is obvious from the examples given. The organisms that make up the lion-share of the pathogens that maim and kill humans are represented in the examples discussed.Less

Evolution of specificity and diversity

Denis C. Shields, Catriona R. Johnston, Iain M. Wallace, and Richard J. Edwards

in Ancestral Sequence Reconstruction

The divergence of proteins following gene duplication has long been recognized as an important process in the evolution of both new and specific protein functions. For functional divergence to occur, ... More

The divergence of proteins following gene duplication has long been recognized as an important process in the evolution of both new and specific protein functions. For functional divergence to occur, the duplicated gene has to survive duplication and avoid becoming a pseudogene (gene death). The mechanism by which a gene duplicates survive is still under some debate, but it is thought that maintenance of duplicate pairs can be accomplished by the evolution of novel functions, splitting ancestral functions between duplicate pairs called paralogs, or some combination of both neo- and subfunctionalization. Although no consensus has been reached as to which process plays a more dominant role in the generation and maintenance of duplicates at the genomic or protein level, the distinction is somewhat irrelevant for the bioinformatic prediction of individual specificity-determining sites; that is, those sites that are important for differences in gene function between paralogs. Instead, the evolutionary history and changing selective constraints for individual residues is important for the interpretation of results. This chapter examines the types of substitution that occur at these sites and the phylogenetic signals that they leave.Less

Detecting Positive Selection

Norman A. Johnson

in Darwinian Detectives: Revealing the Natural History of Genes and Genomes

Positive natural selection, though rare in comparison with negative selection, is the main evolutionary force responsible for adaptive evolutionary change. Using the neutral theory to generate null ... More

Positive natural selection, though rare in comparison with negative selection, is the main evolutionary force responsible for adaptive evolutionary change. Using the neutral theory to generate null hypotheses, evolutionary geneticists have developed tests for detecting positive selection. Several of these tests make use of DNA sequence data sets that contain information on both variation existing within a species (polymorphism) and differences accumulated between species (divergence). This chapter focuses on the McDonald-Krietman test, a powerful but relatively simple test of detecting positive selection. Also discussed is how inferences about the action of selection can be made through the examination of linkage disequilibrium, patterns of correlations of genetic variants at different (but linked) sites. The chapter concludes with a discussion of the legacy of Kimura and his neutral theory of molecular evolution.Less

Adaptive Dynamics: A Framework for Modeling the Long-Term Evolutionary Dynamics of Quantitative Traits

Michael Doebeli

in The Adaptive Landscape in Evolutionary Biology

To describe evolution in the general case of frequency-dependent selection, one needs a mathematical framework that describes how fitness landscapes change dynamically as a consequence of ... More

To describe evolution in the general case of frequency-dependent selection, one needs a mathematical framework that describes how fitness landscapes change dynamically as a consequence of evolutionary change. Adaptive dynamics provides such a framework. Adaptive dynamics can be derived from first principles governing individual-based ecological processes and is based on the notion of invasion fitness, a fitness definition that has a precise ecological meaning. Adaptive dynamics describes evolution as a dynamical system in phenotype space, with the evolving trait values as dynamic variables whose change is governed by dynamically changing fitness landscapes. This chapter reviews some fundamental definitions and properties of adaptive dynamics, including the definitions of the two central notions of stability: convergence stability and evolutionary stability. It presents examples that illustrate the definition of invasion fitness and the paradigmatic dynamic regimes that can occur when bifurcations lead to the loss of either convergence or evolutionary stability. Finally, it illustrates the importance of an ecologically based fitness definition by briefly describing the phenomenon of evolutionary suicide.Less

Evading predators

Anne E. Magurran

in Evolutionary Ecology: The Trinidadian Guppy

Trinidadian guppies provided one of the first experimental demonstrations that predators have a significant impact on behaviour and morphology. This chapter begins with a brief general introduction ... More

Trinidadian guppies provided one of the first experimental demonstrations that predators have a significant impact on behaviour and morphology. This chapter begins with a brief general introduction to predator prey interactions. The consequences of variation in predation risk for Trinidadian guppies, and the trade-offs linked to effective predator defences are then evaluated. It asks if and when adaptive differences can be classed as evolutionary change, and considers the pitfalls associated with such assumptions. Schooling behaviour, evasive tactics, crypsis and colour patterns, mating activity, foraging, and time budgets are examined as well as the relationship between learning skills and geographic variation anti-predator responses. Age-related changes in morphology and behaviour are explored. The chapter ends by examining differences between the sexes in response to predation.Less

The Experimental Study of Reverse Evolution

Suzanne Estes and Henrique Teotónio

in Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments

This chapter focuses on the experimental researches on reverse evolution, and discusses adaptive landscape models, which provide a useful framework to quantify contingencies of evolutionary change. ... More

This chapter focuses on the experimental researches on reverse evolution, and discusses adaptive landscape models, which provide a useful framework to quantify contingencies of evolutionary change. Studies that reveal general features of adaptive landscapes in the context of reverse evolution are also presented. The chapter furthermore discusses the genetic mechanisms of reverse evolution and effects of recombination on the likelihood of reverse evolution.Less

Introduction

Rama S. Singh, Jianping Xu, and Rob J. Kulathinal

in Rapidly Evolving Genes and Genetic Systems

Evolutionary rates not only reflect the tempo at which genotypes, phenotypes, and species lineages are transformed over time but also offer valuable insight into the evolutionary processes involved ... More

Evolutionary rates not only reflect the tempo at which genotypes, phenotypes, and species lineages are transformed over time but also offer valuable insight into the evolutionary processes involved in divergence. For the last century and a half, biologists have been, and to a large degree still remain, steeped in the paradigm of slow and steady gradual evolutionary change. New findings and technologies are beginning to change this view as significant rate variations are seen in a large number of examples across and within all levels of biological organization. This introductory chapter provides a brief historical account and broad survey of recent findings on evolution rates and highlights examples demonstrating rapid and/or non-gradual evolutionary change. What do these exceptions to slow and gradual rates of evolution tell us about higher-level processes? How does such episodic change fit into our neo-Darwinian notions of gradualism? And what exciting prospects do we expect to discover in the future?Less

Evolutionary rescue under environmental change?

Rowan D.H. Barrett and Andrew P. Hendry

in Behavioural Responses to a Changing World: Mechanisms and Consequences

This chapter considers the notion of evolutionary responses in mitigating the harmful effects of environmental change. It describes how the persistence of populations will depend of phenotypic ... More

This chapter considers the notion of evolutionary responses in mitigating the harmful effects of environmental change. It describes how the persistence of populations will depend of phenotypic responses that better suit individuals for new conditions as a result of rapid environmental global change. It discusses how these evolutionary responses occur through individual-level behavioural or plastic changes, or population-level evolutionary changes. It reviews studies that have documented adaptive phenotypic responses to environmental change, and highlights how these examples have not investigated their potential role in making the difference between population persistence and extirpation. It also highlights key issues about evolutionary rescue and the limitations of this process, and outlines pressing research questions and potential empirical approaches to their resolution.Less

Why Now?

Robert C. Berwick and Noam Chomsky

in Why Only Us: Language and Evolution

This chapter explains that the book is a collection of essays that address the evolution of language. It examines the tension between Darwinian infinitesimal evolutionary change and continuity, with ... More

This chapter explains that the book is a collection of essays that address the evolution of language. It examines the tension between Darwinian infinitesimal evolutionary change and continuity, with the goal of resolving it. It considers Charles Darwin's view that language is closely associated with thought, what the paleoneurologist Harry Jerison calls an “internal mental tool,” and provides empirical linguistic support for this position. It also explores three key properties of human language syntactic structure, all captured by minimalist system assumptions: human language syntax is hierarchical, and is blind to considerations of linear order, with linear ordering constraints reserved for externalization; the particular hierarchical structures associated with sentences affects their interpretation; and there is no upper bound on the depth of relevant hierarchical structure. The book concludes by assessing the biological basis for vocal learning from an evolutionary perspective. In the remainder of this chapter, contemporary evolutionary theory and theories about the evolution of language are discussed, along with vocal learning and production, as mediated by the sensorimotor interface, and genomics.Less

A synthesis of neutralism and selectionism

Andreas Wagner

in The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems

Neutralism and selectionism are two opposing perspectives on evolutionary change. In the broadest sense, they apply to all evolutionary change, including evolutionary innovation. Any theory of ... More

Neutralism and selectionism are two opposing perspectives on evolutionary change. In the broadest sense, they apply to all evolutionary change, including evolutionary innovation. Any theory of innovation thus needs to have a position towards them. This chapter first explains these two perspectives. It then provides some background material on the population dynamics of neutral change. It proposes a synthetic view on neutralism and selectionism that can resolve the tension between them. In this view, neutralism and selectionism capture complementary aspects of biological reality. Genotype networks play a central role in it. This view also clarifies the role of molecular exaptations in innovation.Less

Transformation and Transition Research: An Introduction

Wolfgang Merkel, Raj Kollmorgen, and Hans-Jürgen Wagener (eds)

in The Handbook of Political, Social, and Economic Transformation

Social institutions and governmental regimes are systems of action structured by values and norms. Within these systems, self-conscious actors communicate with each other using different material and ... More

Social institutions and governmental regimes are systems of action structured by values and norms. Within these systems, self-conscious actors communicate with each other using different material and symbolic resources. The systems develop and change in response to new knowledge, altered allocations of resources, and changes in values and institutions. ‘Transformation’ analyses radical systemic change from the intentional policy point of view while ‘transition’ describes the historical path along which such change is taking place. The pragmatic design of positive institutions, which is at the basis of the concept of transformation, is historically a rather recent phenomenon. Although these concepts gained prominence only with the great turnaround of 1989/90, they have a prehistory in social theory (Marx, Menger, Weber, Schumpeter, and Polanyi, for instance) and in historical development (the French and the Russian revolutions, Meiji Restoration, post-Civil War United States, for instance). Transformation research thus has at its disposal a wide field of cases and analytic levels.Less

Natural hybridization as a catalyst of rapid evolutionary change

Michael L. Arnold, Jennafer A.P. Hamlin, Amanda N. Brothers, and Evangeline S. Ballerini

in Rapidly Evolving Genes and Genetic Systems

Natural hybridization is a widespread phenomenon, detected among clades of fungi, plants, and animals. The potential outcomes of genetic exchange include adaptive trait evolution, speciation, and ... More

Natural hybridization is a widespread phenomenon, detected among clades of fungi, plants, and animals. The potential outcomes of genetic exchange include adaptive trait evolution, speciation, and even the radiation of entire species complexes. Not only does natural hybridization have the potential to affect evolutionary processes, it often does so very rapidly. Indeed, adaptations can be transferred in only a handful of hybrid generations. Likewise, entire species assemblages may arise from a hybrid swarm over the space of a few thousand years. This chapter tests these conclusions with examples from a diverse array of fungal, botanical, and zoological examples. Each example illustrates the potential for natural hybridization to provide the genetic and phenotypic variation necessary for rapid, adaptive, diversifying evolution.Less

Sexual Selection and the Politics of Mating

in From Man to Ape: Darwinism in Argentina, 1870-1920

This chapter examines the analogies of Charles Darwin's concept of sexual selection to the politics of mating in Argentina. It discusses attempts of such figures as Domingo Sarmiento and Eduardo ... More

This chapter examines the analogies of Charles Darwin's concept of sexual selection to the politics of mating in Argentina. It discusses attempts of such figures as Domingo Sarmiento and Eduardo Holmberg to show that nation and race can be considered to have emerged via sexual selection and thus subject cultural direction. This chapter highlights the important of sexual selection in the discussions of race and argues that the open-endedness of the constitutive analogies of Darwinism underwrote an ambitious generalization of the Darwinian account of evolutionary change and its application to a social and cultural realm now conceived as at least partially autonomous from the biological.Less

Genetic exchange and humans

Michael L. Arnold

in Divergence with Genetic Exchange

This chapter begins with information from analyses of genomic and phenotypic traits resulting in tests of alternative models of human evolution. The remaining sections illustrate how genetic exchange ... More

This chapter begins with information from analyses of genomic and phenotypic traits resulting in tests of alternative models of human evolution. The remaining sections illustrate how genetic exchange has also affected organisms upon which humans depend for food, companionship, and entertainment. The discussion of human evolutionary history begins with analogous cases of reticulate evolution in a limited set of nonhominine taxa. It then proceeds to data for the clade containing Gorilla, Pan, and Homo. The data sets for the hominin primates derive from numerous genomic studies and a more limited set of morphological analyses. However, the diverse types of data lead to the same inference—all hominine lineages analyzed to date, including Homo, likely possess genomes consisting of segments of DNA derived from multiple, divergent lineages. Likewise, animals and plants on which we depend for protein, mobility, and stimulation illustrate the various outcomes from natural hybridization, including adaptive evolutionary change.Less