Table 3 Comparison of alternative branch-class models (1, 2 and 3, Yang 1998[45]) and the branch-site model (4, Yang et al. 2005[46])
From: Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers
Model | LnL | Akaike Information Criterion | dN/dS ratios (± standard errors) |
|---|---|---|---|
1) ω1 = average dN/dS ratio across tree | −15025 | 30052 | 0.015±0.001 |
2) ω1 = dN/dS ratio within classes | −15000 | 30004 | 0.013 ±0.001 |
0.078±0.011 | |||
ω2 = dN/dS ratio between classes | |||
3) ω1 = dN/dS ratio within class 1 | −14989 | 29984 | 0.008±0.001 |
0.016±0.001 | |||
0.074±0.010 | |||
ω2 = dN/dS ratio within classes 2,3,4,5 | |||
ω3 = dN/dS ratio between classes | |||
4) site class 0, ω1 = dN/dS of codons under equivalent purifying selection on both between class and within class branches. p 1  = proportion of codons | −14945 | 29897 | ω1 = 0.013±0.001 |
p 1  = 0.76±0.053 | |||
ω2 = 1.00±0.011 | |||
site class 2a, ω2 = dN/dS of codons with higher dN/dS ratios on between class branches than on within class branches (with dN/dS ratio = ω1). p 2  = proportion of codons | p 2  = 0.24±0.053 | ||
(No codons were reconstructed to occupy site class 1 and 2b of model) |