title: Directional Darwinian Selection in proteins.
abstract: BACKGROUND
  Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins.
  
  
  METHODS
  Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test.
  
  
  RESULTS
  Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations.
  
  
  CONCLUSIONS
  Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.
authors.forename: David A
authors.initials: DA
authors.lastname: McClellan
mesh_terms: D016001:Confidence Intervals; D019143:Evolution, Molecular; D049810:Genetic Speciation; D054629:Genome, Mitochondrial; D006801:Humans; D012641:Selection, Genetic; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein