Selection Acting on Genomes

Methods Mol Biol. 2019:1910:373-397. doi: 10.1007/978-1-4939-9074-0_12.


Populations evolve as mutations arise in individual organisms and, through hereditary transmission, may become "fixed" (shared by all individuals) in the population. Most mutations are lethal or have negative fitness consequences for the organism. Others have essentially no effect on organismal fitness and can become fixed through the neutral stochastic process known as random drift. However, mutations may also produce a selective advantage that boosts their chances of reaching fixation. Regions of genomes where new mutations are beneficial, rather than neutral or deleterious, tend to evolve more rapidly due to positive selection. Genes involved in immunity and defense are a well-known example; rapid evolution in these genes presumably occurs because new mutations help organisms to prevail in evolutionary "arms races" with pathogens. In recent years genome-wide scans for selection have enlarged our understanding of the genome evolution of various species. In this chapter, we will focus on methods to detect selection on the genome. In particular, we will discuss probabilistic models and how they have changed with the advent of new genome-wide data now available.

Keywords: Codon models; Conserved and accelerated regions; Polymorphism-aware phylogenetic models; Positive selection scans; Selection-mutation models.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Codon
  • Computational Biology / methods
  • Evolution, Molecular*
  • Genome*
  • Genome-Wide Association Study
  • Genomics / methods
  • Genotype
  • Humans
  • Mammals / genetics
  • Models, Genetic
  • Models, Statistical
  • Mutation
  • Phylogeny
  • Polymorphism, Genetic
  • Selection, Genetic*
  • Software
  • Web Browser


  • Codon