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Homology, Genes, and Evolutionary Innovation

Homology, Genes, and Evolutionary Innovation

Günter P. Wagner
Copyright Date: 2014
Pages: 496
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  • Book Info
    Homology, Genes, and Evolutionary Innovation
    Book Description:

    Homology-a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird's wing-is one of the most fundamental yet challenging concepts in evolutionary biology. This groundbreaking book provides the first mechanistically based theory of what homology is and how it arises in evolution.

    Günter Wagner, one of the preeminent researchers in the field, argues that homology, or character identity, can be explained through the historical continuity of character identity networks-that is, the gene regulatory networks that enable differential gene expression. He shows how character identity is independent of the form and function of the character itself because the same network can activate different effector genes and thus control the development of different shapes, sizes, and qualities of the character. Demonstrating how this theoretical model can provide a foundation for understanding the evolutionary origin of novel characters, Wagner applies it to the origin and evolution of specific systems, such as cell types; skin, hair, and feathers; limbs and digits; and flowers.

    The first major synthesis of homology to be published in decades,Homology, Genes, and Evolutionary Innovationreveals how a mechanistically based theory can serve as a unifying concept for any branch of science concerned with the structure and development of organisms, and how it can help explain major transitions in evolution and broad patterns of biological diversity.

    eISBN: 978-1-4008-5146-1
    Subjects: Ecology & Evolutionary Biology, General Science, Biological Sciences

Table of Contents

  1. Front Matter
    (pp. i-vi)
  2. Table of Contents
    (pp. vii-x)
    (pp. xi-xvi)
    Günter P. Wagner
  4. Introduction: What This Book Aims to Do and What It Is Not
    (pp. 1-4)

    Homology, the correspondence of characters from different species or even within the same organism, is a fundamental concept in evolutionary biology and biology in general (Wake 1999). It is broadly recognized that homology is explained by derivation from a common ancestor that had the same character or trait. This explanation applies at least to characters from different species. Accordingly, this concept has applications in many fields of biology by referring to morphological characters, behaviors (Lorenz 1981; Prum 1990; Griffiths 1997; Scholes-III 2008), proteins and genes, as well as to gene regulatory networks (Abouheif 1999) and developmental mechanisms and processes (Bolker...

  5. Part I: Concepts and Mechanisms

    • [PART I Introduction]
      (pp. 5-6)

      This book is divided into two parts that assume different perspectives on the problem of homology and character identity. The first part begins with the conceptual issues that surround the idea of homology and attempts to sort out these complications so that mechanistic facts can be productively connected to the homology concept. Thus, the first part is a mix of highly conceptual chapters along with chapters on developmental, genetic, and evolutionary mechanisms in an attempt to build a bridge between these two areas. The integrity of this bridge will come under scrutiny in the second part of this book where...

    • 1 The Intellectual Challenge of Morphological Evolution: A Case for Variational Structuralism
      (pp. 7-38)

      Throughout the history of evolutionary biology, as well as many other sciences, there has been a conflict between two styles of thinking (Mayr 1982; Hughes and Lambert 1984; Ghiselin 1997; Amundson 2005). One is conventionally called functionalism, although in evolutionary biology the term “adaptationism” is more frequently used today because a trait’s “functional fit for its office” is produced through adaptation by natural selection (i.e., function is explained by adaptation through natural selection). The functionalist stance is one that explains organismal traits through their functional and adaptive values.

      The alternative style of thinking does not have a generic name in...

    • 2 A Conceptual Roadmap to Homology
      (pp. 39-81)

      In chapter 1 it was argued that the core idea of variational structuralism is that organisms and their parts play causal roles in shaping the patterns of phenotypic evolution. It was stated that homology is a problem for which structuralist thinking has to prove its value. It was also noted that explaining homology, the origin and maintenance of character identity over phylogenetic time, faces considerable obstacles. In particular, this is because the developmental processes underlying homologous characters change over time. In this chapter I want to begin working toward the goal of proposing a mechanistic account of character identity, its...

    • 3 A Genetic Theory of Homology
      (pp. 82-118)

      The concepts outlined in chapter 2 were intended to capture the major patterns of phenotypic variation: the existence of quasi-independent units of variation, of different character states, of different modes of variation, and of repeated body parts. These patterns have to be the product of both natural selection and the developmental mechanisms that engender the phenotype in each generation. Hence, the question arises, to what extent is there a mechanistic/developmental explanation for these patterns? Is the continuity of character identity subscribed by the continuity of genes? This is the point at which discussions regarding homology tended to become derailed in...

    • 4 Evolutionary Novelties: The Origin of Homologs
      (pp. 119-157)

      In chapter 2 the homology concept was introduced as reflecting a pattern of phenotypic evolution, one for which species that descend from a common ancestor tend to retain corresponding parts, like brains and limbs. The idea is that parts of organisms retain historical continuity and that they undergo (quasi-) independent modifications. It was also noted that historical continuity of parts has its limits in that tracing the history of a body part into deep evolutionary time always leads to a point where the traces of the body part disappear. It was concluded that homologs (i.e., body parts with historical continuity)...

    • 5 Developmental Mechanisms for Evolutionary Novelties
      (pp. 158-185)

      When analyzing the development of any body part, one is confronted by a canonical set of themes: many, if not all characters develop from an interaction with the environment; organ rudiments start to form in response to certain inductive signals that tell the embryo where and when to form a certain body part; once organ-specific development is initiated, the field of cells becomes spatially organized, often through the action of discrete signaling centers; and gene regulation is organized in a way that ensures character-specific execution of the developmental program. Given their role in the development of virtually all body parts,...

    • 6 The Genetics of Evolutionary Novelties
      (pp. 186-228)

      In chapter 3 the ChIN concept was introduced: a conserved gene regulatory network that translates positional information signals into the expression of those genes that result in a character’s phenotype. ChINs enable the differential gene expression that is necessary to develop individualized body parts. ChINs are the most conserved part of the gene regulatory network that underlies character development and, thus, are most consistently associated with manifest character identity. Here we want to discuss which molecular mechanisms might be involved in the origination of novel gene regulatory networks (and, thus, ChINs) and what these mechanisms imply for the origin of...

    • 7 The Long Shadow of Metaphysics on Research Programs
      (pp. 229-246)

      A chapter on “metaphysics” would seem to be out of place in a book on a scientific subject. The vast majority of these books can do without this, thank you very much, although the shadow of metaphysics hangs over all of them, even if often unrecognized. This is because science and philosophy have a two-way relationship with respect to their influence. On one side, scientific discoveries affect how we see the world and ourselves and, thus, also affect how our worldview is cast into concepts and categories, like matter and mind, causality and chance, or factual and theoretical ideas. On...

  6. Part II: Paradigms and Research Programs

    • [PART II Introduction]
      (pp. 247-249)

      The first part of this book was dedicated to the conceptual problems associated with the notions of homology and character identity. The objective was to clarify the concepts to a degree that would allow them to be connected to the mechanisms of development and evolution. In this first part, empirical facts were primarily used to exemplify conceptual ideas. The degree of detail explained in Part I was, by necessity, limited and certainly not sufficient to give a satisfactory account of biological reality.

      In the second part of this book, the relationships between conceptual ideas and biological facts are reversed. Each...

    • 8 Cell Types and Their Origins
      (pp. 250-293)

      One of the elementary facts of biology is that higher organisms consist of functionally specialized cells. There are muscle cells that aid the body in locomotion or with moving body fluids or gut contents, and aid in reproduction (e.g., birth in mammals). There are liver cells that detoxify the blood, sensory cells of all kinds that monitor signals from the environment, and many more. These cells have been classified according to their function and their phenotype into cell types, such as striped and smooth muscle cells, neurons and glial cells, to name but a few.

      In most cases,¹ all cells...

    • 9 Skin and a Few of Its Derivatives
      (pp. 294-326)

      Although less conspicuous than the endoskeleton or the brain and eyes, one of the key novelties of vertebrates is their skin. Vertebrate skin is unique among metazoans in at least two respects. For one, vertebrates are the only phylum for which the body is completely covered by a multilayered epidermal cover (figure 9.1).¹ This facilitated the evolution of many functional specializations, including the fully keratinized skin of amniotes (reptiles and mammals), also a key innovation for terrestrial life.

      The other peculiarity of the vertebrate skin is that it is a composite structure comprising the epidermis, which corresponds to the embryonic...

    • 10 Fins and Limbs
      (pp. 327-355)

      The origin and evolution of tetrapod limbs hold a particular fascination for us. Some of the most momentous periods in the history of the human lineage involved evolutionary changes to the paired appendages. Modifications of the hind limb and foot were key during the evolution of bipedal locomotion and the erect posture that is characteristic of humans by freeing our hands to perform more sophisticated functions than locomotion, like making and using tools, or playing the piano. The hand was predisposed to these new functional challenges because of previous adaptations for climbing in trees. This led to the evolution of...

    • 11 Digits and Digit Identity
      (pp. 356-384)

      Digits are the most distal appendages of the tetrapod limb. They are supported by a series of small long bones, are one of the defining features of the tetrapod limb, and are the locus of many adaptive modifications. For some authors, such as Neil Shubin at the University of Chicago, the origin of the tetrapod limb is synonymous with the origin of digits, while others like Denis Duboule from the University of Geneva, Switzerland think that the origin of the mesopodial joint is more important. Digits have been traced back to the radials of sarcopterygian fins, which raises the interesting...

    • 12 Flowers
      (pp. 385-415)

      All previous chapters on specific systems placed a heavy emphasis on vertebrates. This was mostly due to the author’s greater familiarity with vertebrate developmental evolution and did not do justice to the outstanding work done in invertebrate systems, in particular insects and other arthropods. The literature on arthropod devo-evo, however, is vast, and would be better synthesized by someone intimately familiar with this field. The current chapter on flower evolution in this book is an exception to the vertebrate bias.

      The motivation is that research on character identity and character origination is much more advanced in plant biology than in...

    • 13 Lessons and Challenges
      (pp. 416-426)

      The twelve preceding chapters provided a long argument for the reality of a class of biological entities that have a hard time finding their place in modern biology—that is, a place in a theory of evolution based on genetics and population biology. These entities are things like cell types, homologs, body plans, and so on—that is, entities that Amundson calls developmental types (Amundson 2005). At this point it is impossible to know whether this argument will be successful or not because success in science is historically post hoc. Rather, the question at hand is whether these ideas can...

    (pp. 427-466)
  8. INDEX
    (pp. 467-478)