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The role of mutational and other biases in variation

  • Introduction
  • Projects
  • Brief reference list on mutation biases and evolution

    • Introduction

    This area of research is based on a new view of a very old problem in evolutionary theory: the role of propensities of variation. The New Synthesis provides only a limited basis for understanding this influence: variation is either present as the abundant "raw materials" for selection, or its absence constitutes a "constraint". While mutation is ultimately necessary for evolution, it is assumed (in this view) that variation is normally so abundant that its properties simply play no role in the dynamics of evolution. In this view, there is no middle ground in which propensities of variation influence the course of evolution. To suggest such a principle would be to indulge in the heresy of orthogenesis, the view that there exist "internal" factors that can exert a directional influence on the course of evolution.

    The New Synthesis position, we suggest, was distorted by its opposition to mutationism and orthogenesis, and does not correspond to the kind of theory that we would construct today, if we were starting over again. The New Synthesis view treats mutation as a collection of "random" events that fill up a bounteous "gene pool" with variants that serve as the inert "raw material" for selection, which is the only "force" strong enough to impose order and direction on evolution. In reality, mutation is not random in any sense other than in respect of being logically prior to selection (which is not a reason to call it "random"), and the idea of a bounteous Dobzhanskian "gene pool"-- the magic hat from which selection can pull any trick-- died years ago.

    The third proposition, that patterns of variation are inert and incapable of influencing the course of evolution, is presently leading a double life.  On the one hand, Fisher's classic anti-othogeneticist argument of 1930, claiming to demonstrate that (by the laws of population genetics) the course of evolution can not be influenced by factors that merely influence the character of variation, is still held in high regard by evolutionary geneticists.  On the other hand, most modern "evo-devo" commentaries begin with the presumption that development somehow exerts a strong influence on the course of evolution by way of its effect on variation.  Let me highlight this contrast with some quotations that emphasize variation, first from an "evo-devo" article:

    The whole thrust of the developmentalist approach to evolution is to explore the possilibity that asymmetries in the introduction of variation at the focal level of individual phenotypes, arising from the inherent properties of developing systems, constitutes a powerful source of causation in evolutionary change (Thomson 1985, p. 222)
    and now from defenders of the New Synthesis (which Gould here calls "Darwinism",
    though it is but one school of Darwinism):
    It is most important to clear up first some misconceptions still held by a few, not familiar with modern genetics: (1) Evolution is not primarily a genetic event. Mutation merely supplies the gene pool with genetic variation; it is selection that induces evolutionary change. (Mayr 1963, p. 613)
    The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies the raw material only. Natural selection directs the course of evolutionary change. (Gould 1977, p. 44)

    Although recent commentaries give the impression that the differences between classic neo-Darwinism and "evo-devo" are being resolved, we do not believe that this is the case. One cannot integrate these two contradictory views. Either propensities of variation exert an important shaping influence on evolution, or they do not. By implying the former, the "evo-devo" heterodoxy strikes at the root of the New Synthesis: its case for the supremacy of selection and its case against any possible internal causes of directionality. Far from being resolved, the controversy has not even been clearly recognized yet.

    Our research addresses theoretical and empirical issues at the center of this budding controversy, which we suspect will define the course of evolutionary research for decades to come. The basis for further theoretical research is our initial work showing the lack of generality of Fisher's argument, and demonstrating an orienting influence of mutation bias in a simple model (Yampolsky & Stoltzfus, 2001). The key to exploring the possibility of such an influence is to include the introduction of novelty by discrete events of mutation as part of the evolutionary process. The focus of empirical work is two-fold. First, the spectrum of mutation rates is difficult to quantify. We wish to develop descriptive models of mutation spectra that are based on experimental studies of mutation (or pseudogene divergence) and that are useful in evolutionary modeling. Second, we wish to analyze specific cases in which propensities of variation may have influenced the course of evolution. A particular focus is protein

    Projects


    Several ongoing, planned or possible research areas have been identified that relate to the possibility that biases in the introduction of variants in a population are important determinants of the course of evolutionary change. The projects can be separated into four different types of activities:

    1. Statistical data analysis & descriptive modeling. The goals are to extract useful data on specific mutation biases, to build more general descriptive models of mutation spectra, and to explore cases in which evolutionary change has been influenced by known mutation biases.
      For a brief introduction to this topic, please refer to the list of references on mutation biases and evolution.
    2. Modeling (mainly with computer simulation). Models that relate to systems for which we have abundant empirical data are of particular interest. One of these will be the case of GC-bias in the context of amino acid sequence evolution. Other models will address the issue of interacting sites in protein evolution. See Yampolsky & Stoltzfus (2001) and Stoltzfus (1999) for simple examples.
    3. Evolutionary theory. The interest here is in developing an expanded view of evolutionary causes based on or work in modeling evolution (see Stoltzfus, 1999; Yampolsky and Stoltzfus, 2001). This work highlights the fact that there is considerably more to evolution than is reflected in the New Synthesis view. In particular, we are interested in exploring concepts that relate developmental causes to propensities of variation, and in general methodologies for exploring the influence of propensities of variation on classic cases of evolutionary parallelism.