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The Princeton Guide to Evolution

The Princeton Guide to Evolution

EDITOR IN CHIEF Jonathan B. Losos
David A. Baum
Douglas J. Futuyma
Hopi E. Hoekstra
Richard E. Lenski
Allen J. Moore
Catherine L. Peichel
Dolph Schluter
Michael J. Whitlock
Michael J. Donoghue
Simon A. Levin
Trudy F. C. Mackay
Loren Rieseberg
Joseph Travis
Gregory A. Wray
Copyright Date: 2014
Pages: 848
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  • Book Info
    The Princeton Guide to Evolution
    Book Description:

    The Princeton Guide to Evolution is a comprehensive, concise, and authoritative reference to the major subjects and key concepts in evolutionary biology, from genes to mass extinctions. Edited by a distinguished team of evolutionary biologists, with contributions from leading researchers, the guide contains some 100 clear, accurate, and up-to-date articles on the most important topics in seven major areas: phylogenetics and the history of life; selection and adaptation; evolutionary processes; genes, genomes, and phenotypes; speciation and macroevolution; evolution of behavior, society, and humans; and evolution and modern society. Complete with more than 100 illustrations (including eight pages in color), glossaries of key terms, suggestions for further reading on each topic, and an index, this is an essential volume for undergraduate and graduate students, scientists in related fields, and anyone else with a serious interest in evolution.

    Explains key topics in some 100 concise and authoritative articles written by a team of leading evolutionary biologists Contains more than 100 illustrations, including eight pages in color Each article includes an outline, glossary, bibliography, and cross-references Covers phylogenetics and the history of life; selection and adaptation; evolutionary processes; genes, genomes, and phenotypes; speciation and macroevolution; evolution of behavior, society, and humans; and evolution and modern society

    eISBN: 978-1-4008-4806-5
    Subjects: Ecology & Evolutionary Biology, General Science

Table of Contents

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  1. Front Matter
    (pp. i-iv)
  2. Table of Contents
    (pp. v-vi)
  3. Preface
    (pp. vii-viii)
    Jonathan B. Losos
  4. Contributors
    (pp. ix-xiv)
  5. Section I Introduction

    • I.1 What Is Evolution?
      (pp. 3-9)
      Jonathan Losos

      Evolution refers to change through time as species become modified and diverge to produce multiple descendant species. Evolution and natural selection are often conflated, but evolution is the historical occurrence of change, and natural selection is one mechanism—in most cases the most important—that can cause it. Recent years have seen a flowering in the field of evolutionary biology, and much has been learned about the causes and consequences of evolution. The two main pillars of our knowledge of evolution come from knowledge of the historical record of evolutionary change, deduced directly from the fossil record and inferred from...

    • I.2 The History of Evolutionary Thought
      (pp. 10-27)
      Garland E. Allen

      While philosophers and naturalists in the ancient world did not have a concept of “evolution” in the modern sense, certain traditions or schools of thought in Greece and Rome developed ideas about the origins of biological diversity by natural, as opposed to supernatural, processes. The basic idea that living organisms of one kind can become transformed into living organisms of another kind has its roots in the works of the Greek philosopher Epicurus (341–270 BCE) and his school (the “Epicureans”) in Athens. Epicureans were philosophical materialists who believed the world was composed of small particles, or atoms, that were...

    • I.3 The Evidence for Evolution
      (pp. 28-39)
      Gregory C. Mayer

      The evidence for evolution was first comprehensively assembled by Charles Darwin, who succeeded in convincing essentially all his scientific contemporaries of the fact of descent with modification. A signal factor in Darwin’s achievement was that he was able to weave together numerous strands of natural history—paleontology, systematics, embryology, morphology, biogeography—into a coherent framework. Since Darwin, genetics has joined this synthesis, and, in a development that might have surprised Darwin, evolution in natural populations has proven to occur sufficiently rapidly that it can be observed on human timescales. The most direct evidence of evolution comes from the fossil record,...

    • I.4 From DNA to Phenotypes
      (pp. 40-46)
      Michael C. Whitlock

      Genetic information is passed between generations in most organisms by DNA. Variation among individuals of the sequence of their DNA is the raw material of evolution. DNA codes for phenotype by sequences specifying proteins and RNAs and by regulatory elements that control when and by how much of each is made. Variation in DNA sequence can translate into variation in phenotype, which may cause fitness differences among individuals on which natural selection can act. This chapter describes the basics of how phenotypes are created from the instructions coded in DNA and introduces some of the descriptions of genetic variation used...

  6. Section II Phylogenetics and the History of Life

    • [II Introduction]
      (pp. 47-50)
      David A. Baum

      As laid out by Charles Darwin, evolutionary theory is built around two key postulates (see Section I: Introduction). First, features of living species were acquired over time by evolution along lineages that have branched to form the evolutionary tree of life. Second, the good fit between organisms and their current way of life is explained by natural selection (and variants such as sexual and group selection). Although evolutionary biology has grown significantly in the century and a half since the publication of On the Origin of Species, these two points still constitute the central canon of evolutionary biology. They are...

    • II.1 Interpretation of Phylogenetic Trees
      (pp. 51-59)
      Kevin E. Omland

      All organisms on earth share common ancestry; we are related to every species that has ever existed. Evolutionary biologists since Darwin have sought to infer a “tree of life,” a phylogenetic tree showing how all species are related to one another. The concept of phylogeny as the evolutionary history of organisms—and phylogenetic trees as a depiction of that history—is central to evolutionary biology. Phylogenies form the basis for our understanding of relationships among organisms, and they are key tools of modern evolutionary research; however, phylogenetic trees are frequently misinterpreted because of fundamental misconceptions about what trees can and...

    • II.2 Phylogenetic Inference
      (pp. 60-66)
      Mark Holder

      A phylogeny describes the genealogical relationships between different species. In the early 1960s, many biologists were openly skeptical about the prospects of inferring reliable phylogenies. The last 50 years have produced a rich variety of statistical approaches for estimating evolutionary relationships and quantifying the degree of statistical support for different aspects of phylogenetic hypotheses. Current methods use powerful models of biological characters changing over evolutionary time to tease apart historical signals from similarities due to convergence. Today, phylogenetic inference is a routine part of many evolutionary studies, and phylogenies often provide a crucial framework for testing hypotheses....

    • II.3 Molecular Clock Dating
      (pp. 67-74)
      Bruce Rannala and Ziheng Yang

      This chapter reviews the history of the molecular clock, its impact on molecular evolution, and the controversies surrounding mechanisms of evolutionary rate variation and the application of the clock to date species divergences. We review current molecular clock dating methods, including maximum likelihood and Bayesian methods, with an emphasis on relaxing the clock and on incorporating uncertainties into fossil calibrations....

    • II.4 Historical Biogeography
      (pp. 75-81)
      Michael J. Donoghue

      Historical biogeographers try to understand how life and the earth have evolved together, accounting for current geographic distribution patterns in terms of past events. They try to understand where lineages originated, and how, when, and why they have spread, adapted to new environments, and diversified. These spatially oriented questions are as central to evolutionary biology today as they were at the time of Darwin and Wallace. Although we are still analyzing patterns that were noted long ago, the landscape of ideas and methods has changed dramatically over the years. A key recent period, beginning in the 1970s, saw the rise...

    • II.5 Phylogeography
      (pp. 82-88)
      Michael E. Hellberg

      Phylogeography is the study of the history of populations within species. These studies emerged from analysis of mitochondrial DNA sampled from multiple populations, providing a genealogical perspective within species. Early studies helped identify geographical barriers that separated differentiated populations and suggest where recent range expansions had occurred. The development of coalescent theory led to analyses that could not only discern whether populations were isolated, and, if so, for how long, but also identify demographic changes since that point and past gene flow between populations. An emerging multilocus, model-testing framework places greater emphasis on identifying key factors in shaping population history...

    • II.6 Concepts in Character Macroevolution: Adaptation, Homology, and Evolvability
      (pp. 89-99)
      Allan Larson

      Evolutionary analysis requires deconstructing an organism into separately measurable parts that we call characters. This operation succeeds if the characters have biological validity, representing semiautonomous units of evolutionary change within the context of the organism as a whole. All empirical tests of Darwinian evolutionary theory rely on the biological validity of the characters constructed to test it. This article presents a critical analysis of the evolutionary character concepts used to test Darwinian evolutionary theory in a macro-evolutionary framework (comparisons among species encompassing millions of years of evolutionary time). The term macroevolution often carries connotations of a rejection of Darwinian evolutionary...

    • II.7 Using Phylogenies to Study Phenotypic Evolution: Comparative Methods and Tests of Adaptation
      (pp. 100-105)
      Richard Ree

      Phylogeny, in describing the genealogy of species, provides a historical framework for understanding the evolution of phenotypic diversity. Modern comparative biology uses the analysis of trait variation across species to infer the history of organic evolution and to elucidate evolutionary principles and processes. Comparative methods account for the fact that species are not entirely independent, but instead share evolutionary history by virtue of common ancestry. These methods commonly employ statistical models of trait evolution that can be used to estimate ancestral states, rates of change, directional trends, and correlations between traits. They can also be used to study the links...

    • II.8 Taxonomy in a Phylogenetic Framework
      (pp. 106-111)
      Julia Clarke

      In biology, naming of groups of organisms is a separate but linked enterprise to determining relationships among them. Although, historically, an array of properties of interest were considered relevant for clustering organisms and applying names, today most biologists are interested specifically in discovering and naming phylogenetic groups: organisms related by virtue of descent from common ancestry. Because named groups of organisms, or taxa, figure prominently in our evolutionary theories, many biologists are deeply invested in how names are applied. A major focus has been on naming clades, all the descendants of a common ancestor and that ancestor. Some workers have...

    • II.9 The Fossil Record
      (pp. 112-119)
      Noel A. Heim and Dana H. Geary

      The fossil record documents the history of life over the course of the past 3.5 billion years, demonstrates that evolution has occurred, and provides otherwise inaccessible insights into the evolutionary process. This chapter outlines briefly how the fossil record has been formed, and explores the nature of the fossil record in relation to its central role in understanding evolution. Evolutionary biology is a historical science, and the process of evolution is often played out over intervals of time much too long for direct observation. Thus the fossil record provides the dimension of time that is essential for a complete understanding of the process that unites all of biology....

    • II.10 The Origin of Life
      (pp. 120-126)
      David Deamer

      The prebiotic environment had a variety of simple carbon compounds and energy sources that could drive chemical reactions. These reactions produced ever more complex carbon compounds, some of which could assemble into membranous compartments, while others could link up to make polymeric chains. The polymers became encapsulated in the compartments, producing vast numbers of protocells. The variable protocellular compartments are a microscopic version of what is now called combinatorial chemistry; that is, each protocell contained a different mix of polymers and monomers, and represented a natural experiment. Some of the polymers happened to have potential catalytic abilities, while others could...

    • II.11 Evolution in the Prokaryotic Grade
      (pp. 127-135)
      J. Peter Gogarten and Lorraine Olendzenski

      Prokaryotes are defined as organisms that lack a double membrane-bounded nucleus, but comprise two separate evolutionary lineages, the Archaea (or Archaebacteria) and the Bacteria (or Eubacteria). In prokaryotes and in many single-celled eukaryotes, genes can be transferred between related and unrelated organisms. As a consequence, genes coexisting in a genome have different histories from one another, and organisms can acquire new traits not only through gradual modification of ancestral traits, but also through transfer of genetic material from unrelated organisms....

    • II.12 Origin and Diversification of Eukaryotes
      (pp. 136-142)
      Laura A. Katz and Laura Wegener Parfrey

      Eukaryotes are marked by tremendous diversity in terms of size, shape, ecology, and genome structure. Eukaryotes are defined by two evolutionary innovations: the nucleus and cytoskeleton. Although named for the presence of a nucleus (eu = true, karyon = kernel or seed), it is the cytoskeleton and related proteins that allowed for the dramatic variation in morphology (i.e., shape and size) among eukaryotes. As with Archaea and Bacteria, the other two domains of life, eukaryotes are predominantly single-celled microbes, with plants, animals, and fungi representing just three of approximately 75 major lineages. This chapter discusses the origin of eukaryotes and...

    • II.13 Major Events in the Evolution of Land Plants
      (pp. 143-151)
      Peter R. Crane and Andrew B. Leslie

      Although land plants represent merely one branch in the eukaryotic tree of life, they are essential to the energetics and functioning of terrestrial ecosystems. Land plants appear to have arisen from a single colonization of the land surface around 450 million years ago. In the early phases of this colonization, plant innovations centered on the elaboration of a new kind of plant body capable of withstanding the rigors of life on land and exploiting the new opportunities that terrestrial existence provided. Subsequently, this phase of vegetative innovation was followed by successive transformations of the reproductive system, for example, resulting in...

    • II.14 Major Events in the Evolution of Fungi
      (pp. 152-158)
      David S. Hibbett

      Fungi represent one of the few clades of eukaryotes that evolved complex multicellular forms and diversified extensively on land, the others being plants and animals. In the process, Fungi have become integral to the functioning of ecosystems. They are the master decayers of plant biomass, playing a pivotal role in the global carbon cycle. As parasites and pathogens, they attack plants, animals, and each other, but they have also evolved intricate mutualistic symbioses, such as mycorrhizae and associations with the fungus gardening leaf-cutter ants. The number of extant species of Fungi is a matter of conjecture; one commonly cited estimate...

    • II.15 Origin and Early Evolution of Animals
      (pp. 159-166)
      Paulyn Cartwright

      Around 600 million years ago, members of the animal clade were present but distinct from animals seen on earth today. The origin of most living animal lineages occurred relatively suddenly during the Cambrian period (543–510 Ma). The rapid appearance of animal phyla in the fossil record is referred to as the Cambrian explosion. Understanding the evolutionary relationships by reconstructing the animal tree of life is fundamental for unraveling key transitions in animal evolution. While much progress has been made, the phylogenetic position of many major animal lineages remains uncertain. Through the study of animals’ closest living relatives, the choanoflagellates,...

    • II.16 Major Events in the Evolution of Arthropods
      (pp. 167-173)
      Brian M. Wiegmann and Michelle D. Trautwein

      The animal phylum Arthropoda is by almost any measure the most successful clade of metazoan life. Its members occupy and often dominate all ecosystems on earth and have had a long and rich history of diversification beginning in or just prior to the Cambrian (546 million years ago, Ma).They can boast more species than any other animal group and include familiar and abundant forms—spiders, crustaceans, centipedes and millipedes, and insects, along with numerous unique, less well-known, or extinct types—trilobites, sea spiders, horseshoe crabs. Adaptations for exploiting nearly any food source make them a major component of the living...

    • II.17 Major Features of Tetrapod Evolution
      (pp. 174-182)
      Farish A. Jenkins Jr.

      Tetrapod evolution spans the last 375 million years, beginning with the origin of limbed terrestrial vertebrates from finned fishes. The earliest tetrapods were amphibians that radiated during the Late Paleozoic; only three groups of highly specialized amphibians survive today. The development of an amniotic egg provided novel mechanisms to enhance embryonic growth and allowed eggs to be laid on land. Amniotes came to dominate Mesozoic and Cenozoic terrestrial faunas worldwide, generated powered aerial flight three times, reverted to aquatic habitats and the marine realm repeatedly, created endothermic temperature controls, evolved limbs for running, digging, and climbing, flew in water with...

    • II.18 Human Evolution
      (pp. 183-188)
      John Hawks

      Living humans are the sole living representatives of a lineage, the hominins, which diverged from other living apes 5 to 7 million years ago. Hominins remained limited to Africa for two-thirds of their history. With chimpanzee-sized bodies and brains, early hominins diversified into several lineages with different dietary strategies. One of these found a path toward technology, food sharing, and hunting and gathering, giving rise to our genus, Homo, approximately 2 million years ago. As populations of Homo spread throughout the world, they gave rise to regional populations with their own anatomical and genetic distinctiveness. Within the last 100,000 years,...

  7. Section III Natural Selection and Adaptation

    • [III Introduction]
      (pp. 189-192)
      Douglas J. Futuyma

      Natural selection is the centerpiece of Darwin’s great book, and is prominent in its title: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. In fact, this book was a hastily written “abstract” of a book he had started, and intended to be much larger, titled simply Natural Selection. To be sure, Alfred Russel Wallace independently conceived the idea, but it was Darwin who deduced its many implications and followed its ramifications in detail, and with whom the concept is usually, and rightly, associated. Natural selection is the...

    • III.1 Natural Selection, Adaptation, and Fitness: Overview
      (pp. 193-199)
      Stephen C. Stearns

      This chapter defines natural selection, adaptation, and fitness, the core concepts in the process driving an important part of evolutionary change, discusses how they relate to each other, and comments on their appropriate and inappropriate use....

    • III.2 Units and Levels of Selection
      (pp. 200-205)
      Samir Okasha

      The levels-of-selection question asks at which level or levels of the biological hierarchy the process of natural selection takes place. After a brief historical introduction, this chapter sketches some of the more important positions in the levels-of-selection debate. Topics discussed include group selection and kin selection, the gene’s-eye view of evolution, species selection, and the major evolutionary transitions....

    • III.3 Theory of Selection in Populations
      (pp. 206-214)
      Kent E. Holsinger

      This chapter provides an introduction to the genetics of natural selection. It focuses on selection associated with differences in probability of survival determined by alternative alleles at a single locus, but it also illustrates some of the properties associated with natural selection when selection arises at other stages in the life cycle, when selection varies in space or time, when selection interacts with other evolutionary processes (like mutation, migration, and genetic drift), and when fitness depends on the genotype at more than one locus....

    • III.4 Kin Selection and Inclusive Fitness
      (pp. 215-220)
      David C. Queller and Joan E. Strassmann

      Kin selection is selection that operates via effects on relatives. It is the explanation for altruistic behavior, where an actor gives up fitness in order to help other individuals, because the trait can spread only through possession of the altruism gene by beneficiaries. It also applies to other forms of behavior toward relatives, including selfish behavior. Kin selection, and the associated but broader concept of inclusive fitness, is supported by many theoretical models and empirical studies....

    • III.5 Phenotypic Selection on Quantitative Traits
      (pp. 221-229)
      Edmund D. Brodie III

      Natural selection is the primary driver of adaptive evolution. Despite its power as a force of change over time, it is a remarkably simple process with only a few basic criteria. Whenever variation in a trait is associated with differences in reproductive success, selection occurs. This fundamental relationship between phenotype and fitness is measured as a covariance, and allows for a quantitative assessment of the strength of selection. Selection can occur in different modes that have distinct effects on the distributions of traits. While directional selection that changes the average character is most commonly considered, stabilizing and disruptive selection can...

    • III.6 Responses to Selection: Experimental Populations
      (pp. 230-237)
      Graham Bell

      Evolutionary biology has been an observational and comparative science for most of its history because “natural selection always acts with extreme slowness” (Darwin 1859, p. 121) and therefore produces adaptation “by minute steps, which, if useful, are augmented in the course of innumerable generations” (Weismann 1909, p. 24). Artificial selection in crop plants and domestic animals was from the first used to justify the general principle of modification, but the deliberate choice of breeding individuals by human agency made it only a simile for natural selection. A century passed before the invention of the chemostat led to the realization that...

    • III.7 Responses to Selection: Natural Populations
      (pp. 238-246)
      Joel G. Kingsolver and David W. Pfennig

      In On the Origin of Species, Darwin proposed a new mechanism that drives evolution and generates adaptation: natural selection (see chapter III.1). Yet despite the centrality of natural selection to his theory, Darwin never actually attempted to measure selection in nature. Furthermore, in the century following the publication of The Origin, selection was generally regarded as too weak, and evolutionary change too slow, to be observed directly in natural populations.

      Research in the past four decades has demonstrated that selection and evolution in natural populations can be faster and more dynamic than Darwin and other early evolutionary biologists thought possible. Selection...

    • III.8 Evolutionary Limits and Constraints
      (pp. 247-252)
      Ary Hoffmann

      Although evolution is a powerful process that leads to rapid changes in the characteristics of organisms, limits to evolution arise from a lack of genetic variation, a loss of well-adapted genotypes in populations due to gene flow, trait interactions leading to trade-offs, and/or the difficulty of evolving simultaneous changes in a number of traits. Signatures of genetic constraints at the molecular level include a loss of functional genes as a result of mutational decay....

    • III.9 Evolution of Modifier Genes and Biological Systems
      (pp. 253-260)
      Sarah P. Otto

      The features that define how an organism lives and reproduces—how its genes are transmitted over time and space—have been molded by evolution. Scientists study this process by tracking changes over time at genes that alter the biological system (so-called modifier genes). Genes that modify a particular feature evolve in response to both direct and indirect selection, where the former depends on which modifier allele(s) an individual carries, and the latter depends on genetic associations that develop between the modifier and other genes affecting fitness. This chapter reviews the philosophy of modifier models and how they are used to...

    • III.10 Evolution of Reaction Norms
      (pp. 261-267)
      Stephen C. Stearns

      Because the genetically identical members of clones can develop different phenotypes when they encounter different environments, we infer that one genotype can produce different phenotypes depending on the environment encountered. What difference does this make to the evolutionary process? To help answer that question, evolutionary biologists use the concepts of phenotypic plasticity, reaction norms, and canalization to describe the patterns observed. This chapter describes how those patterns are thought to evolve, what consequences they have for further evolution, whether they can be predicted and whether they are adaptive, nonadaptive, or maladaptive. It concludes with a discussion of the nature, origin,...

    • III.11 Evolution of Life Histories
      (pp. 268-275)
      David Reznick

      The life history is a composite of all the variables that contribute to the way in which an organism propagates itself. The most important variables are how old it is when it begins to reproduce, how much it invests in reproduction, as opposed to other activities or structures, and how it allocates resources to offspring (many small versus few large).We are interested in life histories from a theoretical perspective because these variables are closely allied to an organism’s fitness, or its ability to contribute offspring to the next generation. We are interested in life histories from a natural history perspective...

    • III.12 Evolution of Form and Function
      (pp. 276-281)
      Peter C. Wainwright

      Form and function are inextricably linked in living creatures because patterns of natural selection reflect the impact of alternative morphologies on the ability of the organism to perform the tasks determining its survival and reproduction. The details of construction of a lizard’s limbs and body will determine how fast it can run and how effectively it can evade specific predators. To the extent that limb dimensions affect maneuverability and sprint speed, they can be expected to evolve if a new sort of predator comes on the scene, favoring a different escape strategy; thus, the primary reason that lizard limb dimensions...

    • III.13 Biochemical and Physiological Adaptations
      (pp. 282-287)
      Michael J. Angilletta Jr.

      Organisms can thrive in diverse environments by evolving biochemical processes to tolerate extreme conditions or to avoid these extremes by regulating internal conditions. Both tolerance and regulation impose costs, often expressed as trade-offs with other traits that affect fitness. By analyzing these trade-offs, one can predict how natural selection will shape physiological strategies in particular environments. Our understanding of physiological adaptation has been tested through comparative analyses of populations along environmental clines and experimental evolution of populations in the laboratory. These approaches have often led to surprising insights, suggesting that we can better understand physiological adaptation by also considering processes...

    • III.14 Evolution of the Ecological Niche
      (pp. 288-297)
      Robert D. Holt

      Every species and clade has a niche characterizing the range of environments (including abiotic as well as biotic factors) within which it persists, and outside of which it goes extinct. The niche describes how an organism with a particular phenotype performs in its demography (birth and death rates) as a function of environmental conditions. Given genetic variation in these traits, niches can evolve, sometimes quite rapidly, but niches also can show surprising conservatism. To understand niche evolution, one must draw on and integrate many areas of knowledge, ranging from detailed mechanistic understanding of individual performance to the mapping of genes ...

    • III.15 Adaptation to the Biotic Environment
      (pp. 298-304)
      Sharon Y. Strauss

      Adaptation to the biotic environment describes the evolutionary response of a population to the web of interactions with other organisms that influence fitness....

  8. Section IV Evolutionary Processes

    • [IV Introduction]
      (pp. 305-306)
      Michael C. Whitlock

      As the great population geneticist (and statistician) Sir Ronald Fisher said in the first sentence of his foundational Genetical Theory of Evolution, “Natural selection is not evolution.” A population evolves when the frequencies of its genotypes change over time. The most important of these changes are typically caused by natural selection, but selection is not the only mechanism by which evolution occurs. When alleles are passed from one generation to the next, the next generation may by chance not exactly match the generation of its parents, especially if the population size is small. Alleles can mutate to new alleles, and...

    • IV.1 Genetic Drift
      (pp. 307-314)
      Philip Hedrick

      Genetic drift is the chance change in genetic variation resulting from small population size. The effective population size, which can incorporate unequal numbers of male and female parents, variation in progeny number, or variation in numbers over different generations, is a useful concept for understanding genetic drift. The neutral theory incorporates the effects of genetic drift and mutation to understand the amount and pattern of molecular genetic variation. Coalescent approaches provide a way to estimate the past population size and other evolutionary factors....

    • IV.2 Mutation
      (pp. 315-320)
      Charles F. Baer

      Evolution depends on genetic differences among individuals, and ultimately all genetic variation has its origins in mutation. There are many ways in which DNA can change in a heritable fashion—from changes in single nucleotides, to rearrangements, to wholesale insertion or deletion of new sequences of DNA—and many causes of these mutations. Mutation rates vary among individuals, among species, among regions of the genome, and according to environmental conditions, and these mutation rates themselves can evolve. It may be energetically expensive to minimize mutation rates, and lineages with low mutation rates may slow their rates of evolution. On the...

    • [Illustrations]
      (pp. None)
    • IV.3 Geographic Variation, Population Structure, and Migration
      (pp. 321-327)
      Ophélie Ronce

      Species are rarely genetically homogeneous sets of individuals, and genetic diversity is not distributed randomly through space within their ranges. Spatial patterns in genetic diversity can be observed at many different scales. At a very fine scale, within a continuous population, the genetic similarity between two individuals generally declines with increasing distance between them. For instance, in the annual plant Medicago truncatula, two individuals growing within 0.5m of each other in an old field were found to be on average about 10 times more likely to carry identical variants for some highly polymorphic DNA sequence than two individuals separated by ...

    • IV.4 Recombination and Sex
      (pp. 328-333)
      N. H. Barton

      Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on. Indeed, a substantial fraction of molecular evolution—as measured by the rate of protein...

    • IV.5 Genetic Load
      (pp. 334-339)
      Aneil F. Agrawal

      At a cursory level, evolution by natural selection is simple. Some genotypes are better than others. Those genotypes increase in frequency, wiping out the alternatives. The population then consists of only the best genotype(s). Once this has occurred, the population has achieved its maximum fitness. However, a number of phenomena—especially those processes that generate the variation necessary for adaptation—prevent populations from achieving this selective nirvana in which only the best genotype exists. In other words, nonoptimal genotypes persist at equilibrium. The presence of these nonoptimal genotypes means that the average fitness of individuals within the population is lower...

    • IV.6 Inbreeding
      (pp. 340-346)
      Deborah Charlesworth

      Inbreeding (mating between individuals with recent common ancestors) led to populations of organisms being more homozygous than predicted by the familiar Hardy- Weinberg formula for random-mating populations. Inbreeding is one form of nonrandom mating, and it can occur in populations where numbers of potential mates are limited because of small population size or restricted dispersal, or in species or populations with preferential mating with related individuals, either natural (e.g., in naturally self-fertilizing organisms such as many hermaphrodite plants and animals) or enforced (e.g., in sib-mated “inbred lines” of mice, or when inbred strains or breeds are created by crop breeders...

    • IV.7 Selfish Genetic Elements and Genetic Conflict
      (pp. 347-355)
      Lila Fishman and John Jaenike

      While all successful genes can be said to be selfish, the term selfish genetic element (SGE) refers to heritable units that spread despite their adverse effects on individuals and populations. SGEs are remarkably abundant and diverse, ranging from mitochondrial variants to transposable elements to heritable symbiotic microorganisms. Because the spread of such elements entails a cost to other components of an organism’s genome, there can be strong selection to suppress the action of SGEs. SGEs affect several important features of organisms and populations, including genome size and structure, mutational load and mean population fitness, sex ratio, and speciation. SGEs are...

    • IV.8 Evolution of Mating Systems: Outcrossing versus Selfing
      (pp. 356-362)
      Spencer C. H. Barrett

      Mating systems vary enormously among groups of organisms. This has led to diverse definitions and approaches for investigating their evolution and maintenance. Animal mating systems are characterized by different patterns of parental investment in offspring and variation in the extent to which sexual selection shapes male and female traits (see chapter VII.4). A primary focus of most studies is determining the causes and consequences of variation in mate number for females and males. In contrast, in hermaphrodite organisms, particularly plants, the emphasis is largely on determining the incidence of cross- and self-fertilization and its fitness consequences. Most studies of mating-system...

  9. Section V Genes, Genomes, Phenotypes

    • [V Introduction]
      (pp. 363-366)
      Hopi E. Hoekstra and Catherine L. Peichel

      Darwin’s 1859 theory of evolution by natural selection has three main tenets: (1) phenotypes vary among individuals, (2) phenotypic differences lead to differential fitness, and (3) these fitness-related phenotypes are heritable. Over decades, Darwin amassed huge amounts of data on natural variation and its effects on organismal fitness. By contrast, he knew almost nothing about heredity. While he knew phenotypes were inherited (i.e., that offspring resemble their parents), he had no knowledge of the mechanism by which this occurred. He acknowledged this missing link in his argument for evolution, and when pushed, devised a theory for the mechanism of inheritance...

    • V.1 Molecular Evolution
      (pp. 367-373)
      Charles F. Aquadro

      The molecules of life (DNA, RNA, and proteins) change over evolutionary time. Much can be learned about evolutionary process and biological function from the rates and patterns of change in these molecules. The study of these changes is the study of molecular evolution. This chapter discusses why these molecules change, what can be learned about pattern and process from these changes, and how the changes in the molecules of life can be used to infer important past evolutionary events....

    • V.2 Genome Evolution
      (pp. 374-379)
      Sara J. Hanson and John M. Logsdon Jr.

      The entirety of an organism’s DNA content—its genome—is a heritable storage system containing all information a cell needs to dictate the organism’s growth, development, and phenotypic characteristics. Throughout all forms of life, huge variation exists in the size and content of genomes, demonstrating the highly flexible, dynamic, and complex nature of their evolution. The frequently striking amounts of noncoding DNA present in eukaryotic genomes—largely absent in prokaryotic genomes—is particularly striking. This includes intragenic (introns and untranslated regions) and extragenic (regulatory sequences) as well as transposable elements: features that dominate eukaryotic genomes and usually make up the...

    • V.3 Comparative Genomics
      (pp. 380-386)
      Jason E. Stajich

      Genome sequencing now makes it possible to inventory the genetic material of most living and, in some cases, ancient organisms. To date hundreds of genomes have been sequenced from bacteria and single-cell eukaryotes, as well as animals, plants, and fungi. The vast majority of sequences have come from microbes, including Bacteria and Archaea from diverse environments including those living in hot springs, inside animal digestive tracts, in soil, and in disease-causing organisms. The fungi are the most sampled eukaryotes, but dozens of animals and plants, with their large genomes, have also been tackled. The pace of this sequencing is still...

    • V.4 Evolution of Sex Chromosomes
      (pp. 387-396)
      Doris Bachtrog

      Sex is universal among most groups of eukaryotes, yet a remarkable diversity of sex-determining (SD) mechanisms exist. The evolution of separate sexes has been accompanied by the acquisition of sex chromosomes many times across fungi, plants, and animals. Despite independent origins, sex chromosomes of many organisms share common features, reflecting similar evolutionary forces acting on them. Sex chromosomes are of particular interest to biologists for different reasons. First, sex chromosomes determine the gender of many species; thus they contain the gene ultimately responsible for sex determination. Second, Y or W chromosomes often lack recombination and undergo chromosome-wide degeneration. Finally, sex...

    • V.5 Gene Duplication
      (pp. 397-405)
      Jianzhi Zhang

      The number of genes in a genome varies by two orders of magnitude across cellular organisms. A primary mechanism underlying this variation is gene duplication, which provides raw genetic materials from which new genes and new gene functions arise. As with other types of genetic mutations, gene duplication first occurs in an individual organism, and its population genetic fate depends on its fitness effect. Even after a duplicate gene is fixed in a population, it will degenerate into a pseudo-gene unless its presence is beneficial to the organism. Stably retained duplicate genes are quite common in almost all eukaryotic genomes...

    • V.6 Evolution of New Genes
      (pp. 406-412)
      Manyuan Long

      Every gene has its first moment: this is its origination, when a new gene appears in a genome and evolves a distinct or new function(s) that did not previously exist. The genes in extant organisms are of different ages, from ancient to very young. To understand the origination of a gene is to understand the earliest stage of its evolution; however, the origination process cannot be directly observed for most genes because they are ancient. For these ancient genes, there were likely multiple evolutionary events, which may have obliterated the early signature of the gene’s origination process. An alternative is...

    • V.7 Evolution of Gene Expression
      (pp. 413-419)
      Patricia J. Wittkopp

      Genetic changes affecting either the function or regulation of a gene product can contribute to phenotypic evolution. Studies of evolutionary mechanisms have historically focused on changes inprotein-coding sequences, but during the last decade, multiple lines of evidence have shown that changes in gene expression are at least equally important. The last few years have brought great progress in understanding the genetic basis of expression differences within and between species. From a growing collection of single-gene case studies and comparative analyses of gene expression on a genomic scale, common themes and patterns in regulatory evolution have begun to emerge....

    • V.8 Epigenetics
      (pp. 420-427)
      Florian Maderspacher

      Although coined by Waddington more than 70 years ago, the term epigenetic has become widely used only in the past 15 years. A concept, rather than a discipline, epigenetics is being constantly redefined, often controversially. In its broadest sense, epigenetics refers to stable phenotypic changes without a change in genotype. As phenotypes are the result of gene activity, epigenetics is studied by molecular biologists mainly in the context of gene regulation during cellular differentiation. Of particular interest for evolution are epigenetic changes, often induced by the environment, that can be transmitted across generations. At present, it is unclear whether such...

    • V.9 Evolution of Molecular Networks
      (pp. 428-435)
      Mark L. Siegal

      The importance of interactions between genes has been evident to biologists since the rediscovery of Gregor Mendel’s work at the turn of the twentieth century. Indeed, William Bateson coined the term epistasis in 1907 to refer to the masking effect of a variant at one locus on a variant at another locus. Notably, this was two years before Wilhelm Johannsen coined the term gene. The study of genetic interactions remains central to many fields, from developmental biology to human genetics to evolution. No longer limited to a single pair of genes at a time, scientists are using new technologies to...

    • V.10 Evolution and Development: Organisms
      (pp. 436-443)
      Paul M. Brakefield

      The essence of evolution by natural selection is uncomplicated: phenotypic variation among individuals is generated from genetic variation via the processes of development, and this “fuel” is then screened for performance in the ecological and reproductive arena. This chapter examines the extent to which both the generation of fuel and its performance influence the paths of evolution. Paleontologist David Raup showed in the 1960s that the set of all theoretical shapes of snail shells fit a cube, with each axis reflecting a simple mathematical description of one component of shell growth (figure 1). He then observed that only a small...

    • V.11 Evolution and Development: Molecules
      (pp. 444-451)
      Antónia Monteiro

      In this chapter, major research themes and approaches in evolutionary developmental biology, commonly referred to as evo-devo, are presented from a molecular perspective. The field is concerned primarily with connecting changes at the DNA level to changes in developmental pathways and gene regulatory networks that lead to the evolution of morphology, physiology, and behavior. Researchers in the field are interested in identifying whether mutations in DNA are altering the regulation or the function of proteins, and describing how these changes alter the output of larger gene regulatory networks and ultimately the adult phenotype. In addition, interest is mounting in understanding...

    • V.12 Genetics of Phenotypic Evolution
      (pp. 452-457)
      Catherine L. Peichel

      The incredible diversity of life on earth is most easily evidenced at the level of the phenotype, which is any characteristic of an organism that can be observed or measured. Thus, the term phenotype encompasses morphological, behavioral, and physiological traits. For evolution of a phenotype to occur, it must have a genetic basis (i.e., be heritable). It is therefore necessary to understand the genetic underpinnings of phenotypic traits to understand the process of phenotypic evolution. This chapter will focus on the genetic and molecular basis of phenotypes that are adaptive; that is, phenotypes that contribute to fitness in a given environment. Although the genetics of adaptation has a long history of study, experimental progress was somewhat limited for much of the last...

    • V.13 Dissection of Complex Trait Evolution
      (pp. 458-465)
      Bret A. Payseur

      This chapter describes approaches that use naturally occurring variation to dissect the genetic basis of phenotypic evolution. Emphasis is given to complex traits—those phenotypes controlled by multiple genetic and environmental factors. The use of laboratory crosses to locate mutations that affect trait variation is briefly reviewed. Then the strategy of comparing phenotypes and genotypes in population samples of unrelated individuals is explained. The factors that affect success in association testing when conducted on the genome-wide scale are discussed, along with some lessons from studies in humans....

    • V.14 Searching for Adaptation in the Genome
      (pp. 466-474)
      Dmitri A. Petrov

      The study of adaptation lies at the heart of evolutionary biology; despite 150 years of intense study, however, many foundational questions about the mode and tempo of adaptation remain unanswered. The development of population genetics theory and the rise of genomics are bringing a promise of new types of data that are able to provide insight into these long-standing issues. This chapter discusses some of the key conceptual underpinnings of methods that use population and comparative genomics data to study adaptation, and it underscores some of the remaining difficulties and challenges....

    • V.15 Ancient DNA
      (pp. 475-482)
      Beth Shapiro

      Ancient DNA is a field of molecular evolutionary biology that uses DNA sequence data recovered from poorly preserved organisms, usually deceased for hundreds to hundreds of thousands of years. Ancient DNA data can provide unique snapshots in time to better understand how populations and species evolve. The field was born in the early 1980s, when the first ancient DNA sequences were recovered from preserved muscle of a quagga, a relative of the zebra, which had been extinct for nearly 100 years. Although the early days of ancient DNA were marked by a few spectacular but flawed results, the field has...

  10. Section VI Speciation and Macroevolution

    • [VI Introduction]
      (pp. 483-488)
      Dolph Schluter

      Since the Big Bang, not much has happened in the universe more interesting than the diversification of life on earth. Most of life’s current diversity is wrapped up in the genetic and phenotypic differences between species, between the communities of species they form, and between the higher taxonomic groups that species make up, such as families and phyla. For this reason the study of the origin of species—speciation—and its consequences tells us a great deal about how the extraordinary diversity of life arose, how it is distributed across the globe, how it is presently maintained, and how it...

    • VI.1 Species and Speciation
      (pp. 489-495)
      Richard G. Harrison

      Species are the fundamental units of biodiversity, but the definition of a species remains a subject of debate within evolutionary biology. One resolution of this debate views alternative species definitions as different stages in the process of speciation, in which conspecific populations diverge, accumulate intrinsic barriers to gene exchange, and ultimately become exclusive or reciprocally monophyletic groups. Most studies of speciation have focused on the evolution of reproductive isolation or intrinsic barriers to gene exchange. Such barriers may result from a variety of trait differences, some of which are simply a by-product of divergence in allopatry. Barriers may prevent individuals...

    • VI.2 Speciation Patterns
      (pp. 496-503)
      Timothy G. Barraclough

      Speciation refers to the splitting of a single ancestral species into two or more descendant species. The way in which speciation occurs can affect many aspects of biodiversity, such as phenotypic variation among organisms, the geographic distributions of related species, and the number of species in a geographic region or clade. All these aspects of biodiversity, if studied in relation to speciation, are referred to as speciation patterns. These patterns provide vital clues into the causes of speciation and their variation among different organisms. By studying patterns we can understand processes occurring over many human life spans and over large...

    • VI.3 Geography, Range Evolution, and Speciation
      (pp. 504-511)
      Albert Phillimore

      The distribution of biodiversity is very uneven across the earth, a testament to geographic variation in the net contribution made by speciation, shifting geographic ranges, and extinction. One of the most obvious diversity patterns on the planet is the tendency for species richness to be greatest close to the equator and to decline toward the poles. However, identifying the mechanisms whereby speciation, geographic range dynamics, and extinction contribute to this global latitudinal diversity gradient continues to confound ecologists and evolutionary biologists alike. Geography features prominently in speciation research—so much so, that until recently the geographic distributions of species undergoing...

    • VI.4 Speciation and Natural Selection
      (pp. 512-519)
      David B. Lowry and Robin Hopkins

      Natural selection is the process whereby heritable genetic variation changes in frequency as a result of its effect on survival and reproduction. The idea that natural selection plays an important role in speciation dates to Charles Darwin. Even so, major advancements in our understanding of how both ecological and reinforcing selection act to drive speciation have occurred since the mid-1990s. Extensive research investigating the role of selection in the process of speciation has revealed the importance of disruptive and directional selection in causing reproductive isolation between diverging groups of organisms. While the idea that ecological adaptation can cause reproductive isolation...

    • VI.5 Speciation and Sexual Selection
      (pp. 520-528)
      Janette W. Boughman

      How does the diversity of life arise? Many of the most striking differences among species occur in traits involved in mating—especially traits that males use to compete with other males or to attract females, or that females use to select mates. Big differences in these same traits also make mating between species unlikely, contributing to reproductive isolation. It seems fairly intuitive, then, that whatever process causes differences in mating traits is involved in the formation of new species. The most likely process is sexual selection, which is defined as variation in mating success among individuals varying in phenotype within...

    • VI.6 Gene Flow, Hybridization, and Speciation
      (pp. 529-534)
      C. Alex Buerkle

      The extent to which genetic material moves between divergent populations and species is a critical determinant of their evolutionary independence. High gene flow causes homogenization of populations and leads to their evolutionary cohesion, whereas low gene flow is more permissive of evolutionary divergence and independence. When divergent lineages mate or hybridize, there is the potential for genetic material to move between them. Gene flow through hybrids can erode evolved differences and can lead to stable hybrid zones, and to evolutionary novelty, including new species. The genetic, ecological, and evolutionary processes that affect the success of gene flow and hybrids are...

    • VI.7 Coevolution and Speciation
      (pp. 535-542)
      John N. Thompson

      The web of life constantly changes as species impose strong natural selection on one another. During the past century alone, there have been dozens of examples of rapidly evolving interactions between parasites and their hosts, predators and their prey, competitors, and mutualists. This process sometimes involves reciprocal evolutionary change in interacting species driven by natural selection, which is called coevolution. We know that the coevolutionary process is responsible for many of the adaptations found in species, and it may also be responsible for many instances of speciation and adaptive radiation. This chapter explores the current hypotheses and results regarding coevolution...

    • VI.8 Genetics of Speciation
      (pp. 543-548)
      H. Allen Orr and Daniel McNabney

      This chapter reviews current understanding of the genetic basis of speciation. Much progress has been made in the past several decades in uncovering how new species arise genetically. These recent studies analyze the barriers that prevent gene flow between closely related populations or species....

    • VI.9 Speciation and Genome Evolution
      (pp. 549-558)
      Jeffrey Feder, Scott P. Egan and Patrik Nosil

      Speciation involves the splitting of one group of interbreeding natural populations into two or more reproductively isolated groups. Therefore, to understand speciation one must understand how genetically based barriers to gene flow (i.e., reproductive isolation) evolve between populations. Progress has been made in discerning the importance of different factors, traits, and individual speciation genes in generating reproductive isolation. However, we are just beginning to understand how speciation genes are embedded and arrayed within the genome, and thus how genomes evolve collectively during population divergence. Although it is now clear that different regions of the genome often vary in their level...

    • VI.10 Adaptive Radiation
      (pp. 559-566)
      Peter R. Grant

      The world has millions of species, and they display an astonishing variety of size, color, and behavior. Adaptive radiations comprise groups of distinctive yet closely related species that have evolved from a common ancestor in a relatively short time. Studies of these radiations help reveal the causes of their evolution. As a result of natural selection during and after speciation, descendant species differ morphologically or physiologically in the way they exploit different environments. Adaptive differentiation also depends on the absence of constraints from competitor species. The guiding force of natural environments is revealed in the observation that the same evolutionary...

    • VI.11 Macroevolutionary Rates
      (pp. 567-572)
      Luke J. Harmon

      Rates of evolution—both the rate of trait evolution and the rate at which new species form and go extinct—vary tremendously through time and across lineages. Variations in these rates relate to a number of core theories of evolutionary change over long timescales....

    • VI.12 Macroevolutionary Trends
      (pp. 573-578)
      Gene Hunt

      Trend hypotheses suggest an underlying directionality to evolution in which some changes are more probable than others. Such trends can operate narrowly—within a single species—or so broadly as to encompass all life. By tracking the characteristics of species and clades over time, paleontologists have documented trends in many kinds of traits and across many types of organisms. Selected examples are used here to illustrate aspects of trend hypotheses, including their scope, evidence, and expression in the fossil record. Fundamentally, two kinds of mechanisms can generate trends: (1) biased microevolutionary changes within species and (2) differential proliferation of species...

    • VI.13 Causes and Consequences of Extinction
      (pp. 579-585)
      Michael J. Benton

      Species extinction is a normal part of evolution, but there have been many times in the earth’s history when higher-than-expected numbers of extinctions have occurred. During sudden extinction events, and especially during mass extinctions, major physical environmental crises have wiped out large portions of life. The fact that selectivity during extinction events differs from natural selection suggests that higher-level macroevolutionary processes have continually affected the evolution of life....

    • VI.14 Species Selection
      (pp. 586-591)
      Emma E. Goldberg

      The logic of Charles Darwin’s view of evolution by natural selection applies not only to individual organisms within populations but also to other levels of the evolutionary hierarchy. Entire species can differ from one another in traits that interact with the environment to affect speciation and extinction, and when those traits are inherited through lineage divergence, species selection occurs. This process has the potential to drive evolution on a large scale, making some clades more species rich than others and determining how commonly particular traits are possessed across groups of species. The precise scope of the definition of species selection...

    • VI.15 Key Evolutionary Innovations
      (pp. 592-598)
      Michael E. Alfaro

      Biologists have long suspected that evolution of traits with strong ecological significance fuels rapid diversification in both species formation and phenotypes. New tools and advances in macroevolutionary theory have helped clarify how key evolutionary changes are expected to affect diversification. Empirical studies often reveal that the relationship between key traits and evolutionary does not conform to simple expectations....

    • VI.16 Evolution of Communities
      (pp. 599-604)
      Mark A. McPeek

      Changes in abundances of species over time, combinations of species that can and cannot live together, and the number of species that can live together in one place at one time are all influenced by the abilities of each species to deal with the abiotic environment and to interact with the other species they encounter. These abilities are shaped by evolution, and so evolution is the foundational process shaping the properties of biological communities. The genetic diversity of one species can influence the outcomes of species interactions. Also, as species adapt to one another, they alter many aspects of the...

  11. Section VII Evolution of Behavior, Society, and Humans

    • [VII Introduction]
      (pp. 605-608)
      Allen J. Moore

      This section presents the current view of animal behavior and animal societies, and their application and relevance to human evolution, reflecting the return of researchers to the original integration of these themes promoted by Darwin in The Descent of Man and Selection in Relation to Sex. Darwin treated the evolution of behavior, society, and humans more extensively and exclusively in this follow-up to On the Origin of Species because these traits represented a particular challenge for the theory of natural selection. Why is there so much variation in behavior? How can apparently cognitively complex and advanced behavior (such as mate...

    • VII.1 Genes, Brains, and Behavior
      (pp. 609-615)
      Yehuda Ben-Shahar

      Behavior is defined as the directed action of an animal in response to a stimulus. In multicellular animals, behavior is the product of the nervous system. Behavioral phenotypes are often conserved across distant taxa and are heritable. Yet, the role of genetics and evolution in determining behavior has been controversial for much of the first half of the twentieth century, often paraphrased as the “nature versus nurture” debate. While heredity clearly plays a role in behavior, linking “behavioral” genes to behaviors has not been easy. Two primary approaches have been used over the years to identify causal loci: studies of...

    • VII.2 Evolution of Hormones and Behavior
      (pp. 616-623)
      Ellen D. Ketterson, Jonathan W. Atwell and Joel W. McGlothlin

      Early evolutionary biologists often focused on either genes or visible phenotypes while neglecting the myriad developmental and physiological mechanisms that link them. Recently, evolutionary biologists have become more interested in these mechanisms and have come to appreciate the role they play in the evolutionary process. This chapter focuses on a major class of physiological mechanisms—hormones—and discusses a few of the many ways that understanding hormonal mechanisms can enrich our understanding of evolution. Although the discussion is biased toward vertebrate animals and those mechanisms that mediate behavior, the same principles apply to other taxa and to other complex phenotypes....

    • VII.3 Game Theory and Behavior
      (pp. 624-631)
      John M. McNamara

      The two main motivating ideas of evolutionary game theory are described in this section. These ideas are, however, just the basics; other necessary ingredients are discussed in section 3.

      Suppose that the environment experienced by a species is constant over many generations. Then, natural selection can be envisaged as a hill-climbing process in which species members become fitter over evolutionary time. The end point of this process is that species members will behave so as to approximately maximize fitness within this constant environment. This idea of fitness maximization is useful, since it allows us to predict and understand end points...

    • VII.4 Sexual Selection and Its Impact on Mating Systems
      (pp. 632-640)
      Rhonda R. Snook

      In sexually reproducing animals, males and females interact for mating, and the way in which they interact defines an organism’s mating system. Mating systems reflect the action of sexual selection, including sexual conflict, and can be quantified. Mating systems also determine a population’s evolutionary potential and perhaps its ability to respond to anthropogenic changes....

    • VII.5 Sexual Selection: Male-Male Competition
      (pp. 641-646)
      Christine W. Miller

      Males commonly compete for access to potential mates. This chapter addresses these competitive interactions among males, including alternative mating strategies and sperm competition....

    • VII.6 Sexual Selection: Mate Choice
      (pp. 647-654)
      Michael D. Jennions and Hanna Kokko

      The evolution of many extravagant traits and bizarre behaviors is attributed to sexual selection arising from mate choice. Mate choice occurs when individuals’ traits or behaviors (preferences) make them less likely to produce offspring when they encounter certain individuals of the opposite sex. It involves either some form of rejection of mating or fertilization opportunities, or mating multiply and selectively using the gametes from these mating partners to produce offspring. Such behaviors are expected to increase the interval between successive breeding events. All else being equal, slowing down breeding is costly; thus one expects some compensatory benefits of being choosy...

    • VII.7 Evolution of Communication
      (pp. 655-662)
      Michael D. Greenfield

      The evolution of animal communication remains one of the more fascinating questions in evolutionary biology, but it is also presents us with some of the more complex problems. Owing to the diverse and often elaborate ways in which animals send, receive, and evaluate messages, animal communication attracts considerable attention from a wide range of professional scientists and the lay public. The conspicuousness of animal communication to the human observer and the expectation that an understanding of communication in nonhuman animals may shed light on our own behavior—the origin of human language in particular—are additional factors that draw our...

    • VII.8 Evolution of Parental Care
      (pp. 663-670)
      Mathias Kölliker, Per T. Smiseth and Nick J. Royle

      Across the animal kingdom there are many species in which parents enhance their offspring’s fitness by providing various forms of care. In some animal taxa, such as birds and mammals, almost all species have parental care, and parental care is complex and necessary for offspring survival. In other taxa, such as fish, reptiles, amphibians, or invertebrates, parental care occurs more sporadically, is more variable, is often less complex, and is not always obligate. The diversity in the forms of parental care is vast, ranging from the choice of oviposition sites to providing food, shelter, and protection to the young (table...

    • VII.9 Cooperation and Conflict: Microbes to Humans
      (pp. 671-676)
      Joan E. Strassmann and David C. Queller

      Cooperative interactions characterize all life, giving us spectacular multicellular organisms like kelp and kangaroos; complex societies like army ants, and hyenas; and extensive cooperative networks, like pollinators and their plants. Fraternal cooperation among related, like entities explains multicellularity and social insects. Egalitarian cooperation among different entities explains pollination, cleaning stations, and bacteria-insect symbioses. For cooperation to flourish, exploitation must be controlled; when it is, organismality results....

    • VII.10 Cooperative Breeding
      (pp. 677-682)
      Michael A. Cant

      Cooperative breeding is a relatively rare but taxonomically widespread social system in which adult helpers work to rear offspring that are not their own. Approximately 10 percent of birds and 2 percent of mammals are cooperative breeders; examples are also seen in insects, spiders, crustaceans, and some fish. These diverse systems present an opportunity to investigate how cooperation and helping can be favored in the face of natural selection, which is expected to work for self-interest. Cooperative breeding animals present concrete examples of altruism and helping, together with the possibility of measuring the lifetime fitness consequences of helping decisions. Research...

    • VII.11 Human Behavioral Ecology
      (pp. 683-689)
      Virpi Lummaa

      Human behavioral ecology applies the general theories and mathematical models developed for understanding variation in traits across species to test similar questions in humans. The focus is on studying the consequences of particular traits or behavioral strategies for an individual’s success at passing on its genes to the following generations, given the ecological and social environment of that individual. Humans experience a wide global range of living conditions and lifestyles, from traditional communities to extreme urbanization, and human behavioral ecologists today use a range of study designs and data sources to investigate all these populations from an evolutionary perspective. The...

    • VII.12 Evolutionary Psychology
      (pp. 690-696)
      Robert C. Richardson

      Evolutionary psychology is an approach to cognitive psychology that aims to inform work in psychology with evolutionary ideas and to reform cognitive science by placing it in an evolutionary context, that is, by focusing on how psychological traits such as aggression, mate selection, and social reasoning were adaptive in ancestral environments. This methodology involves a variety of psychological and behavioral evidence that is relatively independent but may be interpretable in evolutionary terms; in other cases, it involves psychological models that depend on evolutionary models. One such example is incest aversion, which can be interpreted in terms of kin selection or...

    • VII.13 Evolution of Eusociality
      (pp. 697-702)
      Laurent Keller and Michel Chapuisat

      Animal societies can reach very high levels of coordination and integration. In ants, bees, termites, and naked mole rats, hundreds of permanently nonreproducing workers help rear the offspring of a few fertile individuals, the queens and males. Societies with such a reproductive division of labor are called eusocial. The evolution of eusociality puzzled Darwin: How could workers pass on their characteristics to the next generation if they did not reproduce? W. D. Hamilton provided the answer in the 1960s with the concept of kin selection, the indirect transmission of genes through relatives, which occurs in stable associations of related individuals...

    • VII.14 Cognition: Phylogeny, Adaptation, and By-Products
      (pp. 703-709)
      Marc D. Hauser

      The mind consists of feelings, decisions, plans, and memories generated by the brain. To study how minds evolve, a comparative approach is necessary, one that seeks evidence of phylogenetic similarities and differences, together with evidence of adaptive function. This chapter describes a set of challenges associated with exploring mental evolution, together with a framework for exploring a corner of this problem, focused on the patterns and processes that led to the evolution of human minds. This is a story of phylogeny, adaptation, and by-products. The chapter examines the hypothesis that despite some similarities between human and nonhuman animal minds, there...

    • VII.15 Evolution of Apparently Nonadaptive Behavior
      (pp. 710-717)
      Nathan W. Bailey

      Behaviors appear to be nonadaptive when their costs, in terms of reproductive fitness, appear to outweigh their benefits. As long as there is genetic variation, selection should eliminate such behaviors under those conditions. However, apparently nonadaptive behaviors are much more common than might be expected. Examples are numerous and include counterintuitive responses to infection by pathogens or parasites, sexual cannibalism, and same-sex sexual behavior. This chapter explores how an evolutionary framework can be used to understand how and why such behaviors evolve, and what causes them to be maintained within populations despite what appear to be fitness disadvantages....

    • VII.16 Aging and Menopause
      (pp. 718-726)
      Jacob A. Moorad and Daniel E. L. Promislow

      Given enough time, organisms lose vigor as they age. Traits that may have once seemed optimized for survival and reproduction degrade, increasing the risk of death and reducing fertility. On the surface, it seems paradoxical that natural selection, which always favors increasing fitness, should permit aging to be nearly ubiquitous. However, evolutionary theory provides simple but powerful hypotheses to explain why humans senesce and die. At its heart, this theory states that fitness depends more on what happens early in life than what happens at old age. In other words, there is more natural selection for early-life function. A basic...

  12. Section VIII Evolution and Modern Society

    • [VIII Introduction]
      (pp. 727-732)
      Richard E. Lenski

      Many people think of evolution as a fascinating topic, but one with little relevance to modern society. After all, most people first encounter the idea of evolution in museums, where they see the fossilized remnants of organisms that lived long ago. Later exposure to evolution may come in courses that present the basic theory along with evidence from the tree of life and the genetic code shared by all life on earth. For those enamored of wildlife, evolution might also be discussed in shows about exotic organisms in faraway lands, often showing nature “red in tooth and claw.” So it...

    • VIII.1 Evolutionary Medicine
      (pp. 733-740)
      Paul E. Turner

      Whereas evolutionary biology concerns the ultimate origins of trait variation within and among populations, human medicine concerns the proximate consequences of individual variation for manifestation of health versus disease. Although knowing how disease symptoms arise is essential for practicing medicine, understanding why these symptoms appear is additionally crucial. The merger of these two disciplines is evolutionary medicine, defined as the use of modern evolutionary methods and theory to better understand human health, with the prospect of improving disease treatment. The central question in evolutionary medicine is, Why has natural selection left our bodies vulnerable to disease? Many possible answers exist,...

    • VIII.2 Evolution of Parasite Virulence
      (pp. 741-746)
      Dieter Ebert

      Diseases caused by parasite or pathogen infections impair normal functioning in organisms. These impairments can include very diverse symptoms leading to the organism’s morbidity and mortality. Studies of the evolution of the virulence of infectious diseases strive to understand the expression of these symptoms as the result of the evolutionary process. This approach is primarily focused on the evolution of parasites (here used to include pathogens), but it may also consider the coevolution of hosts and parasites.

      Until about 30 years ago, it was widely accepted that the harmful symptoms of infectious diseases were the side effects of poorly adapted...

    • VIII.3 Evolution of Antibiotic Resistance
      (pp. 747-753)
      Dan I. Andersson

      Antibiotics have revolutionized human and veterinary medicine, and over the last 60 years they have made it possible to treat efficiently most types of bacterial infections. Unfortunately, the extensive use—and frequent misuse—of antibiotics has resulted in the rapid evolution and spread of bacteria that are resistant to antibiotics. Arguably, the global use of antibiotics is one of the largest evolution experiments performed by humans, and the frightening consequence is that we are now at the brink of a postantibiotic era in which antibiotics have lost their miraculous power. This problem originates from the strong selection imposed by the...

    • VIII.4 Evolution and Microbial Forensics
      (pp. 754-759)
      Paul Keim and Talima Pearson

      The tools of molecular biology coupled with the evolutionary methods of phylogenetics have found powerful applications in tracking the origins and spread of infectious diseases. Microbial forensics is a new discipline focused on identifying the source of the infective material involved in a biological crime and it, too, increasingly depends on evolutionary analysis and molecular genetic tools....

    • VIII.5 Domestication and the Evolution of Agriculture
      (pp. 760-765)
      Amy Cavanaugh and Cameron R. Currie

      Agriculture is an ancient and important factor shaping life on earth. Through the cultivation of food, populations of agriculturalists are able to greatly expand and can even develop a division of labor. This chapter explores the evolution of agriculture, including domestication and selection under domestication, along with the evolutionary events and consequences of farming. It also describes how agricultural associations are perhaps best viewed in the framework of a coevolved mutualism....

    • VIII.6 Evolution and Conservation
      (pp. 766-773)
      H. Bradley Shaffer

      Traditionally, evolutionary biology has had a distant relationship to conservation compared with ecology and field-based natural history. However, this situation has changed dramatically in the last two decades, particularly as abundant molecular data have become available for at-risk species of conservation concern. As the availability of genome-level data for these species increases, the role of evolutionary biology in conservation management continues to grow to a far greater extent. The combination of these new data from microevolutionary analyses with more traditional input from phylogenetics and systematics has elevated evolutionary biology to a position of primary importance in conservation science....

    • VIII.7 Directed Evolution
      (pp. 774-779)
      Erik Quandt and Andrew D. Ellington

      Directed evolution is a process in which scientists perform experiments that use selection to push molecular or cellular systems toward some goal or outcome of interest. The objectives of this work include the production of substances of value and improved understanding of the evolutionary process. Elucidating the precise mechanisms by which improvements occur is often of particular interest. In general, directed evolution requires a genetic system in which information is encoded, heritable, and mutable; a means for selecting among variants based on differences in their functional capacities; and the ability to amplify those molecules or organisms that have been selected....

    • VIII.8 Evolution and Computing
      (pp. 780-785)
      Robert T. Pennock

      Shared principles between evolution and computing are opening up fruitful areas for research. This chapter discusses some unexpected connections between evolutionary biology and computer science, such as the core ideas of code, information, and function, and how these are leading to theoretical and practical ways in which each is benefiting the other. The chapter highlights the emerging field of evolutionary computation, giving a brief history and some examples of its utility not only in helping solve basic research problems in biology and computer science but also for generating novel designs in engineering....

    • VIII.9 Linguistics and the Evolution of Human Language
      (pp. 786-794)
      Mark Pagel

      This chapter discusses how human language differs from all other forms of animal communication, when and why it evolved, and how elements of language evolve over long periods of time. It closes with a brief account of how languages might evolve in an increasingly globalized world....

    • VIII.10 Cultural Evolution
      (pp. 795-800)
      Elizabeth Hannon and Tim Lewens

      For most of the twentieth century, evolutionary theory focused on phenotypic variation underpinned by inherited genetic variation. Any comprehensive account of the evolution of the human species, and some animal species, must acknowledge that this is at best a simplification of the forces affecting change and stasis in these lineages. Habits, know-how, and technology—what we might consider cultural traits—can also contribute to survival and reproduction. Moreover, these traits are often maintained, in our own species at the very least, by learning from others— that is, they are inherited nongenetically. Further, these traits often show patterns of cumulative improvement...

    • VIII.11 Evolution and Notions of Human Race
      (pp. 801-808)
      Alan R. Templeton

      Races exist in humans in a cultural sense, but it is essential to use biological concepts of race that are applied to other species to see whether human races exist in a manner that avoids cultural biases and anthropocentric thinking. Modern concepts of race can be implemented objectively with molecular genetic data, and genetic data sets are used to see whether biological races exist in humans and in our closest evolutionary relative, the chimpanzee....

    • VIII.12 The Future of Human Evolution
      (pp. 809-816)
      Alan R. Templeton

      How humans will evolve in the future is highly speculative because the process of evolution depends critically on random processes such as mutation, recombination, and genetic drift, and because adaptive evolution is strongly influenced by changing environments. Because the human environment includes culture, which can change quickly, it is difficult to predict future environments and hence future adaptive evolution. Nevertheless, some predictions can be made based on a basic understanding of evolutionary mechanisms....

    • VIII.13 Evolution and Religion
      (pp. 817-824)
      Francisco J. Ayala

      Theologians and other religious authors have over centuries sought to demonstrate the existence of God by the argument from design, which asserts that organisms have been designed and that only God could account for the design. Its most extensive formulation is William Paley’s Natural Theology (1802). Darwin’s (1859) theory of evolution by natural selection disposed of Paley’s arguments: the adaptations of organisms are outcomes of a natural process that causes the gradual accumulation of features beneficial to organisms. There is “design” in the living world, but the design is not intelligent, as expected from an engineer, but imperfect and worse:...

    • VIII.14 Creationism and Intelligent Design
      (pp. 825-831)
      Eugenie C. Scott

      Many are unaware that there are several kinds of creationisms, even within the tradition of Christianity. In that tradition, the various creationisms are a function of how the Bible is interpreted, and the differences reflect how much of modern science is accepted. Intelligent design is a more recent form of creationism, but in its particulars it reflects themes similar to other forms of Christian creationism. New forms of creationism may develop in the future, but it is likely that they will reflect the same ideas as their ancestors....

    • VIII.15 Evolution and the Media
      (pp. 832-836)
      Carl Zimmer

      On March 28, 1860, the New York Times ran a very long article on a newly published book called On the Origin of Species. The Times explained that the dominant explanation for life’s staggering diversity at the time was the independent creation of every species on earth. “Meanwhile,” the anonymous author wrote, “Mr. DARWIN, as the fruit of a quarter of a century of patient observation and experiment, throws out, in a book whose title has by this time become familiar to the reading public, a series of arguments and inferences so revolutionary as, if established, to necessitate a radical...

  13. Index
    (pp. 837-854)