6  Molecular Evolution

This is part of the UHH MSc Biology Course EvoSys 2023 (5/11)

6.1 Mutation

  • Genome mutation
  • Chromosome mutation
  • Indel = Insertion and/or Deletion
  • Inversion
  • Transition
  • Transversion

Suppressor mutation: a second mutation which alleviates or reverts the phenotypic effects of an already existing mutation - Intragenic suppression: suppressor mutation occured in the same gene as the original mutation. - Crick, et al. used this to establish the fundamental nature of the genetic code. - Intergenic suppresion (extragenic): the second mutation is not on the same gene as the original mutation. - Useful for identifying new genetic sites which affect a biological process of interest - Provides evidence between functionally interacting molecules and intersecting biological pathways

6.2 Nucleotide substitutions

  • synonymous (silent): no amino acid change
  • missense: amino acid changes to some else except stop codon
  • nonsense: amino acid changes to stop codon

All substitution on the second codon site and 96% of the substitutions on the first site are non-synonymous, while 70% of the substitutions on the third site are synonymous

6.3 Evolutionary dynamics

Transitions occurs more frequently than transversions, but many transitions can be “overwritten” by one transversion.

Mutation rate of non-synonymous substitution is usually lower than the rate of synonymous substitution

6.3.1 Models of nucleotide substitution

  • eg. JC69 (one parameter, assuming equal sequence frequencies), K80, HKY85, GTR (most complex w/ 7 parameters) etc.
  • The likelihood of a certain nucleotide in a given vertex is not based on the assumption that nucleotides appear equally, but on the frequency observed in the vertex itself (eg. different GC account in genomes from different species)

6.3.2 Models of amino acid substitution

  • JTT: based on a larger protein database
  • WAG: avoids need to use closely-related sequence pairs by obtaining ML estimate of Q matrix
  • LG: add rate heterogeneity to ML estimation of Q matrix
  • I: Invariable sites model
  • G: Discrete Gamma model
  • Test for best-fitting substitution models, calculate likelihood for each model, choose model with smallest BIC or AIC(AICc) score