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Molecular Evolution and Molecular Clocks Study Guide

This guide covers the fundamental principles of molecular evolution, including types of genetic changes, the molecular clock hypothesis, methods for calibrating evolutionary rates using fossil and biogeographic data, and the challenges posed by multiple hits and rate variation. It also discusses strict and relaxed clock models, including maximum likelihood and Bayesian approaches, for estimating evolutionary rates and divergence times.

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Molecular Evolution and Sequence Change

Models and Molecular Clocks of Evolution

This lecture explains types of changes in DNA and protein sequences, the neutral theory, and how models of sequence evolution and molecular clocks can be used to date divergences between species.

  • DNA substitutions
  • Transitions and transversions
  • Purines and pyrimidines
  • Synonymous and non-synonymous substitutions
  • Fourfold degenerate sites
  • Twofold degenerate sites
  • Nondegenerate sites
  • KA/Ks ratio
  • Positive selection
  • Negative purifying selection
  • Amino acid substitution classes
  • Neutral theory of molecular evolution
  • Random genetic drift
  • Models of sequence evolution
  • Molecular clocks
  • Multiple hits

Molecular Evolution Models and Multiple Hits

Molecular evolution models provide a mathematical description to correct for multiple hits where superimposed changes in DNA or protein sequences underestimate actual evolutionary change.

  • Multiple hits
  • Superimposed changes
  • Multiple substitution
  • Coincidental substitution
  • Parallel substitution
  • Convergent substitution
  • Back substitution
  • Homoplasious similarity
  • Models of sequence evolution
  • Nucleotide substitutions
  • Amino acid sequences

Models and Methods of Molecular Evolution

Molecular Evolution and Molecular Clocks

Molecular evolution models use molecular clocks to estimate species divergences by calculating rates of amino acid replacement and substitution.

  • molecular clocks
  • amino acid replacement
  • rate of molecular evolution
  • species divergences
  • calibration of molecular clocks
  • substitution rate
  • strict clock methods
  • relaxed clock methods
  • maximum likelihood techniques

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