Table 1. Sites under PDS in the A. thaliana MADS-box gene family: “Site-specific analyses”
Site-specific analyses (type I) n dN/dS (ω) under M0 Embedded Image M3 vs. M0 (df LRT 3) Embedded Image M2 vs. M1 (df 2) Embedded Image M8 vs. M7 (df 2) Parameter estimates (β and ω) under M8 β (p,q) Positively selected sites under M3 Positively selected sites under M2 Positively selected sites under M8
Node AG 7 0.22 28.76*** 10.10* 10.57* P1 = 0.98, ω = 8.44 β (0.87, 3,82) 123 No rate classes with dN/dS > 1 123
Node AH 7 0.26 59.09*** 11.75** 7.36* P1 = 0.81, ω = 1.96 β (0.87, 3.48) 73 7461 72 82 107 63 73 747261 82 63 107 73 72 7461 82 10763 48 58 81 110
Node AL 9 0.25 90.35*** 18.39*** 4.55 P1 = 0.93, ω = 1.24 β (0.80, 2.28) 61 72 73 82 107 110 48 74 8658 64 6663 65 109 72 73 827461 107 48 110 7273 8248 61 74 107 110 58
Node AP 12 0.25 130.47*** 21.26*** 7.59* P1 = 0.75, ω = 1.18 β (0.56, 3.46) 58 58 48 57 78 8972 12373 81 48 57 58 72 73 78 89 123 59 65 8147 6066 92 74 100
Node AQ 14 0.22 116.71*** 14.97*** 7.73* P1 = 0.97, ω = 4.67 β (0.47, 1.52) 58 89 58 58
Node AR 20 0.15 102.65*** 30.18*** 8.22* P1 = 0.96, ω = 1.12 β (1.64, 8.94) No rate classes with dN/dS > 1. 73 82 72 82 73
  • Each comparison has n sequences, dN/dS is average ratio over sites under a codon model with one ω. Proportion of the component of positively selected sites (P1) and parameters p and q of the beta distribution β(p,q) are given under M8. *, P < 0.5; **, P < 0.005; ***, P < 0.001; bold underlined, PP ≥ 0.99 of being under positive selection; bold, 0.99 > PP ≥ 0.95; italics, 0.95 > PP ≥ 0.90; underlined, 0.90 > PP ≥ 0.70; normal, 0.70 > PP ≥ 0.50.