Beneficial Mutations

6 Key excerpts on "Beneficial Mutations"

• 

  eBook - ePub

  New Thinking About Evolution

  • Britannica Educational Publishing, John P Rafferty(Authors)
  • 2010(Publication Date)
  • Britannica Educational Publishing

    (Publisher)

  Gene mutations can occur spontaneously—that is, without being intentionally caused by humans. They can also be induced by ultraviolet light, X-rays, and other high-frequency electromagnetic radiation, as well as by exposure to certain mutagenic chemicals, such as mustard gas. The consequences of gene mutations may range from negligible to lethal. Mutations that change one or even several amino acids may have a small or undetectable effect on the organism’s ability to survive and reproduce if the essential biological function of the coded protein is not hindered. But where an amino acid substitution affects the active site of an enzyme or modifies in some other way an essential function of a protein, the impact may be severe.

  Newly arisen mutations are more likely to be harmful than beneficial to their carriers, because mutations are random events with respect to adaptation—that is, their occurrence is independent of any possible consequences. The allelic variants present in an existing population have already been subject to natural selection. They are present in the population because they improve the adaptation of their carriers, and their alternative alleles have been eliminated or kept at low frequencies by natural selection. A newly arisen mutant is likely to have been preceded by an identical mutation in the previous history of a population. If the previous mutant no longer exists in the population, it is a sign that the new mutant is not beneficial to the organism and is likely also to be eliminated.

  This proposition can be illustrated with an analogy. Consider a sentence whose words have been chosen because together they express a certain idea. If single letters or words are replaced with others at random, most changes will be unlikely to improve the meaning of the sentence; very likely they will destroy it. The nucleotide sequence of a gene has been “edited” into its present form by natural selection because it “makes sense.” If the sequence is changed at random, the “meaning” rarely will be improved and often will be hampered or destroyed.

  Occasionally, however, a new mutation may increase the organism’s adaptation. The probability of such an event’s happening is greater when organisms colonize a new territory or when environmental changes confront a population with new challenges. In these cases the established adaptation of a population is less than optimal, and there is greater opportunity for new mutations to be better adaptive. The consequences of mutations depend on the environment. Increased melanin pigmentation may be advantageous to inhabitants of tropical Africa, where dark skin protects them from the Sun’s ultraviolet radiation, but it is not beneficial in Scandinavia, where the intensity of sunlight is low and light skin facilitates the synthesis of vitamin D.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Complex Systems

  Lecture Notes of the Les Houches Summer School 2006

  • (Author)
  • 2011(Publication Date)
  • Elsevier Science

    (Publisher)

  3.4.4. Depletion of Beneficial Mutations In a constant environment with only the simplest genome-independent competi-tion which does not change as the organisms evolve, one would expect there to be Evolutionary dynamics 433 locally optimal genomes whose fitness cannot be increased by single mutations — i.e., fitness peaks. If such a peak is reached, there will be no more Beneficial Mutations available — except more complicated processes with deleterious inter-mediaries such as the two-hit process discussed above. Before a peak is reached, the supply of Beneficial Mutations is likely to decrease and the rate of increase of the fitness slow down. If the effects of Beneficial Mutations are additive, they will simply be depleted, although how long this takes depends on whether there are a modest number of available Beneficial Mutations — or classes of such mu-tations — with relatively high rates, or many more available mutations but each with much lower rates. With interactions between mutations the situation is more complicated: if on average each beneficial mutation acquired enables one other to become available, the evolution can continue — unless an unlucky route that ends in a local fitness maximum is taken. And if two-hit processes with delete-rious intermediaries can occur, the chances of becoming stuck at a local fitness maximum is far lower. Understanding the possible behaviors even with a con-stant environment requires far more knowledge of local fitness landscapes. And these depend on many aspects of the biological architecture as well as particulars of the past history and the type of selective pressures in the current environment. 3.5. Experiments on the speed of asexual evolution To test the basic results of the theory outlined above for acquisition of multiple Beneficial Mutations, Michael Desai undertook experiments on asexual evolution of budding yeast in Andrew Murrray’s lab.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Advanced Molecular Biology

  A Concise Reference

  • Richard Twyman(Author)
  • 2018(Publication Date)
  • Garland Science

    (Publisher)

  Chapter 15

  Mutation and Selection

  Fundamental concepts and definitions

  • A mutation is a stable, heritable change in genotype caused by an alteration to the nucleotide sequence in a particular region of the genome (c.f. epimutation, paramatation). A gene, genome, cell or individual carrying a given mutation is a mutant.
  • Mutations can be localized (i.e. affecting a single nucleotide or a small cluster of nucleotides) or can involve large segments of the genome. In the former category, gene mutations occur within a gene and can affect the nature of the gene product or interfere with its expression, whereas extragenic mutations usually have no effect (unless they disrupt a regulatory element). Large-scale mutations involve tens to many thousands of nucleotides and affect whole genes or groups of genes. In eukaryotes, the largest mutations are visible at the cytogenetic level and are termed chromosome mutations (see Chromosome Mutation).
  • Gene mutations convert one allelic form of a gene into another. For many gene loci, there is a wild-type allele which predominates in the population because it confers the greatest fitness (ability to survive and reproduce). This generally encodes the normal, functional product associated with the gene, and the wild-type phenotype reflects this normal gene activity. Other, rare alleles are designated mutant alleles, and the quantity and/or structural properties of the encoded product may differ, generating distinct mutant phenotypes. Gene mutations away from the wild type are usually deleterious or selectively neutral; few are beneficial.
  • Instead of a single wild-type allele, several alleles conferring equal fitness may exist in equilibrium within the population, and the locus is described as polymorphic.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Quantitative Genetics

  • Armando Caballero(Author)
  • 2020(Publication Date)
  • Cambridge University Press

    (Publisher)

  Obviously, loci with effects on quantitative traits not only encode enzymes, but with this model it is possible to explain the tendency for large-effect mutations to be recessive without the need for modifiers of dominance. 7.1.4 Beneficial Mutations and Summary of Mutational Parameters for Fitness So far we have only considered the parameters corresponding to deleterious mutations. The rate and effects of beneficial mutation can only be estimated in organisms that reproduce sufficiently fast, such as viruses, bacteria and yeast, where mutation accumulation experi- ments can be performed with very high population sizes and durations of thousands of generations, as well as with clonal analyses. The results suggest beneficial mutation rates in E. coli and yeast on the order of U ≈ 2 × 10 −5 , with mean effects on the order of s ≈ 0.01 or lower (Sniegowski and Gerrish, 2010). Since the overall genomic mutation rate in E. coli and yeast has been estimated to be 3 × 10 −3 (Drake et al., 1998), this would indicate that Beneficial Mutations make up about 1% of all mutations. On the other hand, considering the deleterious mutation rates in these species obtained with the Bateman–Mukai method (Figure 7.3c), the deleterious mutation fraction would constitute 7% of all mutations. Considering humans, it has been estimated that between 1% and 10% of mutations can be deleterious (Keightley, 2012; Rands et al., 2014). It is difficult to draw conclusions about the distribution of beneficial mutation effects although some evidence suggests an approximately exponential distribution (Eyre-Walker and Keightley, 2007; Bataillon and Bailey, 2014). Figure 7.7 presents a general summary of the mutational parameters for fitness and its major components.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Quantitative Biosciences

  Dynamics across Cells, Organisms, and Populations

  • Joshua S. Weitz(Author)
  • 2024(Publication Date)
  • Princeton University Press

    (Publisher)

  Yet, as limited, it would also suggest that the timing of these jumps will vary across experiments and associated populations. One of the reasons why there can be variation in evolutionary dynamics is that, as we have shown, not all beneficial mutants fix. A beneficial mutant with fitness benefit s will invade a fraction s(s + 1) of the time in the infinite population limit. Moreover, there can be extended periods where the more fit mutant persists at relatively low frequencies. It is only once the number of mutants with a fitness advantage exceeds some critical level, usually on the order of 1s, that they increase exponentially. That is, if there is a fitness advantage of 10%, then it requires 10 individuals (irrespective of the large, final population size) to likely lead to fixation, whereas it would take 100 individuals if the fitness advan- tage is only 1%. Hence, even a selectively beneficial gene will predominantly experience the stochastic effects of drift until it reaches a critical subpopulation size. These insights lead to the open question of whether or not mutants with beneficial alleles (or genotypes) appear frequently or rarely. The use of such adjectives implies a time scale of reference. Hence, for reference, consider the time scale to be the fixation or “sweep” time—this should be on the order of  s = log Ns. In that event, the following operational definitions will be helpful: 108 Chapter 4 Limiting beneficial mutation regime: New Beneficial Mutations appear slowly (e.g., more slowly than the time over which such mutations can sweep). Overlapping beneficial mutation regime: New Beneficial Mutations appear rapidly (e.g., faster than the time over which such mutations can sweep).

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  The Princeton Guide to Evolution

  • David A. Baum, Douglas J. Futuyma, Hopi E. Hoekstra, Richard E. Lenski, Allen J. Moore, Catherine L. Peichel, Dolph Schluter, Michael C. Whitlock, David A. Baum, Douglas J. Futuyma, Hopi E. Hoekstra, Richard E. Lenski, Allen J. Moore, Catherine L. Peichel, Dolph Schluter, Michael C. Whitlock(Authors)
  • 2013(Publication Date)
  • Princeton University Press

    (Publisher)

  chapter V.12 ). Generally speaking, this is not borne out by laboratory experiments, in which adaptation can occur very rapidly through the substitution of a few alleles of large effect. It is true that most of the beneficial alleles that appear by mutation when a population first experiences stressful conditions have rather small effects on fitness. This can be demonstrated by isolating mutants resistant to an antibiotic and then measuring their fitness in the absence of the antibiotic. This provides the distribution of fitness of new mutations at the time when they first arise. A few of these mutants are fitter than their ancestor, but most are only slightly superior, and very few are much more fit. If such Beneficial Mutations are allowed to spread, however, and collected only when they have become fixed, a very different picture emerges: the bulk of these fixed Beneficial Mutations have large effects, often amounting to a doubling of fitness. The reason is that Beneficial Mutations that increase fitness only slightly, although they may be very numerous, are likely to be overtaken by the much faster spread of mutations that greatly increase fitness, despite their rarity. The rapid spread of large-effect Beneficial Mutations is often observed in laboratory experiments. This provides a concrete alternative to the gradualist interpretation of adaptation, especially when populations are severely stressed.

  5. WHAT IS THE LIMIT TO ADAPTATION?

  If conditions remain unchanged, the first few mutations to be fixed may well increase fitness substantially, but the supply of these large-effect mutations is sure to be limited, and as the supply is depleted, only those of more modest effect remain available for selection. Consequently, the rate of adaptation will tend to diminish over time. This pattern has been demonstrated by long-term serial-transfer experiments with E. coli

  Sign up to read

  Learn more about book