Skip to main content

Advertisement

Table 5 Parameter estimates and LRT of MA1 vs. MA in DEF-like genes from Poales.

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

Clade Model Estimate of parameters Positive selection L
Poales
(P1)
A ω0 = 0.08303, f0 = 0.89319
ω1 = 1.00000, f1 = 0.03486
ω2a fore =936.29115, ω2a back =0.08303, f2a = 0.06925
ω2b fore =936.29115, ω2b back =1.00000, f2b = 0.00270
45 L 0.612
50 S 0.703
54 L 0.531
55 S 0.996**
77 I 0.556
82 A 0.588
86 K 0.583
89 N 0.991**
92 N 0.517
103 K 0.689
116 I 0.573
117 K 0.976*
126 L 0.625
132 L 0.993**
152 V 0.604
159 H 0.535
164 R 0.899←
167 E 0.742
170 N 0.931←
175 E 0.639
177 Y 0.996**
181 L 0.610
-9975.021057
  A1 ω0 = 0.08196, f0 = 0.78512
ω1 = 1.00000, f1 = 0.03088
ω2a fore =1.00000, ω2a back =0.08196, f2a = 0.17704
ω2b fore =1.00000, ω2b back =1.00000, f2b = 0.00696
  -9979.237754
LRT 2δ = 8.433394 df = 1 P = 0.0037    
Poales
(P2)
A ω0 = 0.08281, f0 = 0.86235
ω1 = 1.00000, f1 = 0.03283
ω2a fore =4.43236, ω2a back =0.08281, f2a = 0.10097
ω2b fore =4.43236, ω2b back =1.00000, f2b = 0.00384
14 S 0.813
42 E 0.747
44 S 0.846
50 S 0.993**
54 L 0.571
57 F 0.799
64 T 0.787
75 S 0.992**
78 N 0.706
81 S 0.788
103 K 0.893
128 E 0.892
142 N 0.821
154 N 0.736
171 Y 0.801
-9983.412368
  A1 ω0 = 0.08278, f0 = 0.76740
ω1 = 1.00000, f1 = 0.02922
ω2a fore =1.00000, ω2a back =0.08278, f2a = 0.19592
ω2b fore =1.00000, ω2b back =1.00000, f2b = 0.00746
  -9984.514801
LRT 2δ = 2.204866 df = 1 P = 0.1376    
Poales
(P3)
A ω0 = 0.08393, f0 = 0.95687
ω1 = 1.00000, f1 = 0.03593
ω2a fore =8.40943, ω2a back =0.08393, f2a = 0.00694
ω2b fore =8.40943, ω2b back =1.00000, f2b = 0.00026
33 T 0.517
183 L 0.954*
-9987.927062
  A1 ω0 = 0.08401, f0 = 0.95276
ω1 = 1.00000, f1 = 0.03571
ω2a fore =1.00000, ω2a back =0.08401, f2a = 0.01111
ω2b fore =1.00000, ω2b back =1.00000, f2b = 0.00042
  -9988.396587
LRT 2δ = 0.93905 df = 1 P = 0.3325    
  1. The branches tested are those labeled with cursive fonts in Figure 3.