Table 2 Tests of positive selection on Lepidopteran α-glucosidase family with site-specific, branch-specific and branch-site models.
From: Molecular evolutionary mechanisms driving functional diversification of α-glucosidase in Lepidoptera
Model | Foreground branch | -lnL | 2lnL | P level | Parameter Estimates | Positive sites |
|---|---|---|---|---|---|---|
Site Model | ||||||
M7 | 39876.24 | 20621.34 | <0.01 | p=0.67039, q=12.21042 | not allowed | |
M8 | 50195.31 | p0=0.99999, p=0.36811, q=1.82680 (p1=0.00001), ω=2.06636 | 97E**, 154I**, 158A**, 159R*, 180G**, 181V**, 202K**, 212A**, 213I**, 224A**, 234K**, 251Y**, 263R**, 272L**, 275F**, 277S**, 280L**, 281G**, 283T**, 284I**, 291L**, 309N**, 310K*, 311N**, 326N**, 327V**, 328S**, 332L**, 340A**, 341I**, 350D*, 355L*, 357S**, 358K**, 362R**, 366Y**, 367I**, 370R**, 377Y**, 379G**, 380I**, 391N*, 399H**, 400D**, 409N**, 411L**, 427R*, 429G, 466N**, 467S**, 468T**, 476T**, 477N**,484E**, 487Q**, 488E**, 489I**, 495K**, 496E**, 497T**, 499R**,507A**,510K**,513K**,585E**, 587T**, 588S**, 589S**, 590Q**, 591L** | |||
Branch-specific model | ||||||
M0 | 41427.55 | 499.04 | <0.01 | ω=0.04 | not allowed | |
Free-ratio model | 41178.03 | ωsuh=17.14, ωsuh1=0.10, ωsuh2=4.94, ωLMal1=0, ωLMal2=0.14, ωLMal3=0.18, ωLMal4=0.88, ωLMal=9.01, ωLMal234=15.49, ωLMal34=0.39 | not allowed | |||
Branch-site model | ||||||
Ma0 | SUH1 | 41314.68 | 4.24 | <0.05 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41312.56 | ω0=0.04, ω1=1.00, ω2=999.00 | none | |||
Ma0 | SUH2 | 41320.28 | 17.24 | <0.01 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41311.66 | ω0=0.04, ω1=1.00, ω2=21.51 | 184 P**, 195 S*, 222 N*, 288 T* | |||
Ma0 | Ancestral SUH | 41305.76 | 0.96 | >0.05 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41305.28 | ω0=0.04, ω1=1.00, ω2=2.51 | 108S**, 150S**, 152Y**, 158A*, 181V*, 186S**, 191Q**, 279Q*, 280L*, 283T**, 292I**, 294L**, 357S*, 369L*, 407I**, 409N* | |||
Ma0 | Ancestral SUH and Mal | 41313.43 | 13.67 | <0.01 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41306.60 | ω0=0.04, ω1=1.00, ω2=999.00 | 162G**, 483A* | |||
Ma0 | Ancestral LMal | 41320.28 | 36.48 | <0.01 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41302.04 | ω0=0.04, ω1=1.00, ω2=999.00 | 199W* | |||
Ma0 | LMal1 | 41306.11 | 6.40 | <0.05 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41302.91 | ω0=0.04, ω1=1.00, ω2=10.07 | 181V*, 191Q*, 224A*, 226K*, 251Y**, 276E*, 366Y*, 588S* | |||
Ma0 | LMal2 | 41313.39 | 0.96 | >0.05 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41312.91 | ω0=0.04, ω1=1.00, ω2=2.14 | 341I* | |||
Ma0 | LMal3 | 41311.50 | 9.46 | <0.01 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41306.77 | ω0=0.04, ω1=1.00, ω2=999.00 | None | |||
Ma0 | LMal4 | 41300.05 | 14.14 | <0.01 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41292.98 | ω0=0.04, ω1=1.00, ω2=999.00 | 147S**, 191Q*, 279Q*, 366Y*, 400D*, 585E* | |||
Ma0 | Ancestral LMal2, LMal3 and LMal4 | 41320.28 | 16.50 | <0.01 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41312.03 | ω0=0.04, ω1=1.00, ω2=119.75 | 161P*, 420Q*, 479S* | |||
Ma0 | Ancestral LMal3 LMal4 | 41320.05 | 9.56 | <0.01 | ω0=0.04, ω1=1.00, ω2=1.00 | not allowed |
Ma | 41315.27 | ω0=0.04, ω1=1.00, ω2=54.58 | 156S*, 203R**, 362R*, 371W** | |||
