Theories of Population Variation in Genes and Genomes

Theories of Population Variation in Genes and Genomes

Copyright Date: 2008
Pages: 432
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  • Book Info
    Theories of Population Variation in Genes and Genomes
    Book Description:

    This textbook provides an authoritative introduction to both classical and coalescent approaches to population genetics. Written for graduate students and advanced undergraduates by one of the world's leading authorities in the field, the book focuses on the theoretical background of population genetics, while emphasizing the close interplay between theory and empiricism. Traditional topics such as genetic and phenotypic variation, mutation, migration, and linkage are covered and advanced by contemporary coalescent theory, which describes the genealogy of genes in a population, ultimately connecting them to a single common ancestor. Effects of selection, particularly genomic effects, are discussed with reference to molecular genetic variation. The book is designed for students of population genetics, bioinformatics, evolutionary biology, molecular evolution, and theoretical biology--as well as biologists, molecular biologists, breeders, biomathematicians, and biostatisticians.

    Contains up-to-date treatment of key areas in classical and modern theoretical population geneticsProvides in-depth coverage of coalescent theoryDiscusses genomic effects of selectionGives examples from empirical population geneticsIncorporates figures, diagrams, and boxed features throughoutIncludes end-of-chapter exercisesSpeaks to a wide range of students in biology, bioinformatics, and biostatistics

    eISBN: 978-1-4008-6665-6
    Subjects: Ecology & Evolutionary Biology

Table of Contents

  1. Front Matter
    (pp. i-iv)
  2. Table of Contents
    (pp. v-viii)
  3. Preface and Acknowledgments
    (pp. ix-x)
  4. Introduction
    (pp. 1-4)

    Genomes and genomic variation entered into the study of genetic variation in natural populations in this century. The human genome sequencing projects led to increasingly affordable procedures for studying sequence variation, and by 2001¹ population genetic studies of genes were already dominated by analyses of sequence variation. During the work on the human sequence more than a million places in the genome were discovered to vary among 24 individuals representing the ethnic variation in the world.² This corresponds to one single nucleotide polymorphism for every 2000 base pairs in the DNA of the human genome, corresponding to a recombination distance...

  5. I Genetic Variation
    • Chapter 1 Genetics
      (pp. 7-20)

      Mendel based his description of heredity on experiments with the edible pea,Pisum sativum. Offspring of a cross between plants from a true-breeding line¹ of yellow peas (first parental line P1) and one of green peas (P2) gave yellow offspring (first filial generation F1) peas in the pods. Selfing plants grown from F1peas gave most pods with both yellow and green peas, the F2generation. These qualitative results were known among plant breeders, but Mendel contributed a quantitative analysis. The 258 plants grown from the F1peas yielded 8023 pea seeds (the F2generation), of which 6022 were yellow...

    • Chapter 2 Conservation of Variation
      (pp. 21-52)

      Mendel’s first law is fundamental to any discussion of inheritance in diploid individuals. Even in a well-executed study a deviation from the expected segregation does not warrant a rejection of the law, but rather suggests that assumptions about the experiment or the considered variation may be unfounded. Upon further analysis the unexpected result may lead to the discovery of a new phenomenon (see, e.g., Sturtevant and Morgan 1923). The corresponding rules of population genetics are in the same way unquestionable, and form the basis for interpretation of observations in nature or in the laboratory.

      Observations in Mendel’s experiments on plant...

    • Chapter 3 Diploid Populations
      (pp. 53-70)

      The gamete pool or Wright–Fisher model is simplified to allow description of the genetic dynamics entirely in terms of transmission of genes between generations. This corresponds to assuming a population of haploid organisms. Higher organisms with sexual reproduction have a life cycle that oscillates between haploid and diploid life stages, and in most animals and plants the diploid stage is the most conspicuous, while the haploid, or gametic, stage leads a more inconspicuous life. The gametes—in humans, eggs and sperm—unite to form the zygote that develops into the individual, which at maturity breeds and transmits its genetic...

    • Chapter 4 Mutation and Variation
      (pp. 71-107)

      The replication mechanism of the DNA molecule ensures conservative transmission of genetic information from the mother to the two daughter cells resulting after cell division. Errors do occur, however. An error in the transmission of genetic information is called amutation. Mutation is random. In a functional genetic element mutation occurs independently of its function and efficacy—an implementation of the central dogma of molecular biology.

      One of the assumptions in the law of gene frequency conservation is that the genes do not change, that is, mutation is absent. Mutation is in fact never absent, but the assumption is that...

    • Chapter 5 Migration
      (pp. 108-138)

      The genetic variation we find within a species is not necessarily present in local populations. Individuals in a local population tend to have more similar genotypes, and the remaining variation is manifested as differences in the genetic composition of the various populations of the species. An example of variation at different levels can be found in morphological characters in the fishZoarces viviparus, which was subject to one of the first population genetic investigations by Johannes Schmidt (1917). The number of vertebrae was counted in samples of individuals from locations along the coasts of northern Europe. The observed distributions of...

    • Chapter 6 Linkage
      (pp. 139-180)

      The fundamental rules of population genetics that describe the transmission of genes from a parent population to its offspring population are a consequence of Mendel’s first law. Mendel also studied the simultaneous inheritance of several characters that by themselves obeyed the law of inheritance. In one experiment he analyzed variants of pea color and form (Table 2.2 on page 23) and crossed plants grown from true-breeding yellow, round peas with plants grown from true-breeding green, wrinkled peas. As expected, all the F1peas were yellow and round, and in the 556 F2peas all four combinations of the traits were...

    • Chapter 7 Phenotypic Variation
      (pp. 181-212)

      The study of variation in genomes and changes in genetic composition of populations through time is a study of the record of evolution, the unbroken descent of genes through time. In any study of evolution inference is based on observations made today, and in terms of genetic observations we rely on the principle that extant genes trace an unbroken descent back through time to the first living organism. This states the axiom of evolution in terms of genetic material. For Charles Darwin and his predecessors Erasmus Darwin and Jean Baptiste de Lamarck this axiom was a simple expression of the...

  6. II Variation and Selection
    • [Part II Introduction]
      (pp. 213-215)

      The phenomena addressed in Chapters 2, 4, 5, and 6 are fundamental to population genetics because they describe the effects of the basic genetic processes of Mendelian segregation, mutation, and recombination on the distribution of genetic variation in populations. They describe and develop the theoretical basis of the neutral theory of molecular evolution. This theory stems from the observation of high levels of molecular genetic variation within and between populations and species. The recognition of systematic regularity in molecular differentiation among species had a special influence on the formulation of the neutral theory. These evolutionary regularities are known as molecular...

    • Chapter 8 Effects of Selection
      (pp. 216-263)

      In Darwin’s evolutionary theory natural selection seems formulated as exerting pressure on heritable variation. However, natural selection should rather be considered a consequence of variation in a character that influences the survival and reproduction of the individual. The variation in vertebra count ofZoarces viviparusis heritable, with a heritability of about 0.8 (Figure 7.1 on page 182). If the number of vertebrae affects, say, the survival of the individual, the distribution of vertebrae among parents of the next generation will deviate from that among their peers at birth and evolution will result. Selection of the parents of the next...

    • Chapter 9 Genomic Effects of Selection
      (pp. 264-308)

      Genes at different loci associate due to linkage in the transmission from parents to offspring—they interact in the formation of offspring populations (Chapter 6). In addition, genes may interact in their function, and if the variation in the corresponding phenotype is subject to natural selection, the effects of selection and the evolution of the phenotype cannot be understood by considering single loci. To get a full understanding of the effects of selection, we need to study selection on multiple loci, if not on whole genomes.

      Bateson, Saunders, and Punnett observed not only linkage in their experiments with sweet peas...

    • Chapter 10 Population Structure
      (pp. 309-344)

      Natural selection can vary with the local environment—the obvious example is selection on the morphs ofBiston betulariain polluted and undisturbed forest. As a first approximation the changes in polluted forest populations may be understood by neglecting exchange of individuals among different habitats, but as thecarbonariaallele becomes more common immigration may play a role. Surely, the incidence ofcarbonariaindividuals in pristine forest must be higher than expected by mutation alone, and we may inquire about the properties of such an immigration–selection balance, which should resemble mutation–selection balance when the immigration rate is low....

  7. Appendix A Probability Theory and Statistics
    (pp. 345-362)
  8. Appendix B Solutions to Exercises
    (pp. 363-382)
  9. Bibliography
    (pp. 383-412)
  10. Index
    (pp. 413-421)