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Table 1 Models of codon substitution employed on the present analysis.

From: Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses

Levela Model Description Site classes Np Free parameters Datasets analyzede
Sites M7 Distribution of ω along sites follows a β distribution, no selection 7 2 p, q Alignments of DEF- and GLO-like genes without basal angiosperm outgroup.
  M8 β distribution where ω > 1. Implements BEBb. 8 4 p0, p, q, ωs, where s = number of site categories  
Branches M0 one ω value for all branches 0 1 ω Alignments of DEF- and GLO-like genes without basal angiosperm outgroup.
  M2 n different ω values on n specified branches 0 User-specified Different ω values corresponding to each of the user-specified groups of branches  
Clades and sites M1a nearly neutral evolution 1 2 Clades 1 and 2: 0 < ω0 < 1, ω1 = 1 Alignment of orchid DEF-like genes from clades 1 and 2.
      p 0  
  MC In site classes 2 and 3 selective pressure varies in different parts of the phylogeny. Implements BEBb. 2 5 Clade 1: 0 < ω0 < 1, ω1 = 1, ω2 Alignment of orchid DEF-like genes from clades 3 and 4.
      Clade 2: 0 < ω0 < 1, ω1 = 1, ω3 Alignment of Poales GLO-like genes from clades 1 and 2.
      Proportions: p0, p1 c  
  M3 Assumes several site classes with independently estimated ω. 3 5 ω0, ω1, ω2 Same datasets analyzed with M1a vs. MC.
      Proportions: p0, p1,  
  MD In site class 2, selective pressure is different on each clade. 3 6 Clade 1: ω0, ω1, ω2 Clade 1  
      Clade 2: ω0, ω1, ω2 Clade 2  
      Proportions: p0, p1 d  
Branches and sites MA1 Neutral or purifying selection on individual codons along specific clades. 4 3 Site class Background Foreground Alignments of DEF- and GLO-like genes without basal angiosperm outgroup. Specific branches of the phylogenies were tested in separate analyses.
      0 0 < ω0 < 1 0 < ω0 < 1  
      1 ω1 = 1 ω1 = 1  
      2a 0 < ω0 < 1 ω2 = 1  
      2b ω1 = 1 ω2 = 1  
      Proportions: p0, p1 d  
  MA Tests for positive selection on individual codons along specific clades. Implements BEBb. Only foreground clades experience positive selection. 4 4 Site class Background Foreground  
      0 0 < ω0 < 1 0 < ω0 < 1  
      1 ω1 = 1 ω1 = 1  
      2a 0 < ω0 < 1 ω2>1  
      2b ω1 = 1 ω2>1  
      Proportions: p0, p1 d  
  1. a. Refers to the kind of data where the process of codon substitution is analyzed
  2. b. Bayes Empirical Bayes calculation indicates the posterior probability a site belongs to a given class. This information in valuable to identify sites under positive selection.
  3. c. The values of p0 and p1 are also used to calculate p2 proportions of sites with ω2 and ω3
  4. d. The values of p0 and p1 are used to calculate the proportions of site classes 2a and 2b
  5. e. As previously explained, each dataset includes an un-rooted phylogeny reconstructed with Mr. Bayes using the most appropriate model identified by Modeltest.