TABLE 2

Overview of the results modeling selection on type III effector families obtained with CODEML

Proportion of sites
 under positive
 selection detectedParameters in the ω-distribution
FamilyNo. of
 sequences
 in the
 analysisAverage
 dN/dSTree length
 (CODEML)P-value
 M3:M0P-value
 M3:M1P-value
 M8:M7With M3
 (%)With M8
 (%)Model
 best
 fitting
 the dataln L for
 the
 model
 fitting
 the bestM3 modelM8 model
avrA 30.2348 3.334061.09E-054.2E-067.94E-01NPNPM3−2749.29p0 = 0.34653
 p1 = 0.23706
 (p2 = 0.41641)
 ω0 = 0.05365
 ω1 = 0.05365
 ω2 = 0.48857p0 = 0.59405
 p = 6.07760
 q = 99.00000
 (p1 = 0.40595)
 ω = 0.49497
avrB 50.175829.932231.62E-233.6E-444.49E-02NPNPM8−3573.96p0 = 0.31227
 p1 = 0.39459
 (p2 = 0.29314)
 ω0 = 0.00834
 ω1 = 0.06173
 ω2 = 0.50765p0 = 0.69727
 p = 0.32013
 q = 0.95376
 (p1 = 0.30273)
 ω = 0.03425
avrD100.5905 0.42266NA9.4E-017.43E-01 0.400.40M0−2109.60p0 = 0.25498
 p1 = 0.74069
 (p2 = 0.00432)
 ω0 = 0.00001
 ω1 = 0.80099
 ω2 = 20.31307p0 = 0.99594
 p = 0.42952
 q = 0.28467
 (p1 = 0.00406)
 ω = 20.39960
avrF 70.16179.14276.64E-107.0E-216.34E-01NPNPM3−1696.30p0 = 0.34049
 p1 = 0.54809
 (p2 = 0.11142)
 ω0 = 0.01238
 ω1 = 0.16599
 ω2 = 0.59723p0 = 0.65160
 p = 0.31952
 q = 1.61894
 (p1 = 0.34840)
 ω = 0.15917
avrPphD 60.3591 1.697371.29E-182.5E-025.96E-01NPNPM3−5494.22p0 = 0.30676
 p1 = 0.3637
 (p2 = 0.32954)
 ω0 = 0.05915
 ω1 = 0.05915
 ω2 = 0.96926p0 = 0.67219
 p = 6.42498
 q = 99.00000
 (p1 = 0.32781)
 ω = 0.97081
avrPphE150.2248 3.600383.02E-113.8E-207.37E-01NPNPM3−3453.96p0 = 0.31937
 p1 = 0.59722
 (p2 = 0.08341)
 ω0 = 0.00001
 ω1 = 0.23083
 ω2 = 1.04236p0 = 0.44450
 p = 0.01294
 q = 0.03997
 (p1 = 0.55550)
 ω = 0.21628
avrPpiA 40.342 3.126415.04E-118.0E-019.08E-01NPNPM3−1590.64p0 = 0.28033
 p1 = 0.28447
 (p2 = 0.43521)
 ω0 = 0.00993
 ω1 = 0.00993
 ω2 = 0.77284p0 = 0.56549
 p = 1.07220
 q = 99.00000
 (p1 = 0.43451)
 ω = 0.77351
avrPpiG 60.031175.405032.48E-58NA9.9E-01NPNPM3−7405.67p0 = 0.21592
 p1 = 0.40989
 (p2 = 0.37419)
 ω0 = 0.00259
 ω1 = 0.01926
 ω2 = 0.06065p0 = 0.98934
 p = 0.93298
 q = 27.26896
 (p1 = 0.01066)
 ω = 6.22186
holPtoN 30.610950.620561.22E-768.3E-844.1E-78 4.503.50M8−2347.01p0 = 0.34136
 p1 = 0.6133
 (p2 = 0.04534)
 ω0 = 0.01089
 ω1 = 0.29653
 ω2 = 8.20972p0 = 0.96412
 p = 0.42451
 q = 1.41097
 (p1 = 0.03588)
 ω = 8.84753
holPtoQ 40.274125.897761.38E-361.2E-500.0741497211.109.30M3−4716.92p0 = 0.42576
 p1 = 0.46246
 (p2 = 0.11178)
 ω0 = 0.00539
 ω1 = 0.05947
 ω2 = 2.18535p0 = 0.90709
 p = 0.67503
 q = 13.51907
 (p1 = 0.09291)
 ω = 8.43318
holPtoW 30.134310.58151.85E-21NANANPNPM3−4886.02p0 = 0.30963
 p1 = 0.61712
 (p2 = 0.07325)
 ω0 = 0.00308
 ω1 = 0.10674
 ω2 = 0.92158p0 = 0.40787
 p = 0.05149
 q = 0.22848
 (p1 = 0.59213)
 ω = 0.09956
hopPmaB 40.478410.957193.13E-149.3E-024.1E-01 83.50M3−3354.29p0 = 0.39762
 p1 = 0.5168
 (p2 = 0.08558)
 ω0 = 0.00001
 ω1 = 0.56004
 ω2 = 2.20767p0 = 0.96484
 p = 0.24336
 q = 0.38236
 (p1 = 0.03516)
 ω = 3.04737
hopPmaG 60.1338 8.214252.21E-457.3E-731.1E-01NPNPM3−5526.22p0 = 0.2444
 p1 = 0.34908
 (p2 = 0.40652)
 ω0 = 0.00001
 ω1 = 0.06712
 ω2 = 0.2715p0 = 0.74314
 p = 0.42775
 q = 3.85984
 (p1 = 0.25686)
 ω = 0.24394
hopPmaI 30.42282.33279.07E-128.5E-047.4E-01 8.505M3−3704.37p0 = 0.35997
 p1 = 0.55466
 (p2 = 0.08537)
 ω0 = 0.00001
 ω1 = 0.41804
 ω2 = 2.23638p0 = 0.94869
 p = 0.40628
 q = 0.92608
 (p1 = 0.05131)
 ω = 2.51152
hopPmaJ 30.1659 0.803910.999031.6E-039.7E-01NPNPM3−1002.55p0 = 0.0513
 p1 = 0.93801
 (p2 = 0.01069)
 ω0 = 0.15336
 ω1 = 0.15336
 ω2 = 1.3276p0 = 0.01487
 p = 2.54205
 q = 0.00100
 (p1 = 0.98513)
 ω = 0.15215
hopPmaL 80.9709 3.620743.55E-174.0E-041.8E-03 6.808.20M3−6003.88p0 = 0.39724
 p1 = 0.54094
 (p2 = 0.06182)
 ω0 = 0.13304
 ω1 = 0.91632
 ω2 = 6.83261p0 = 0.93207
 p = 0.45587
 q = 0.34351
 (p1 = 0.06793)
 ω = 6.26811
hopPtoA 40.1998 2.600538.39E-187.0E-22NANPNPM3−4736.63p0 = 0.71581
 p1 = 0.00000
 (p2 = 0.28419)
 ω0 = 0.05406
 ω1 = 0.35487
 ω2 = 0.56702p0 = 1.00000
 p = 0.37860
 q = 1.50673
 (p1 = 0.00000)
 ω = 0.35156
hrpW 50.287316.528121.46E-371.7E-395.6E-0212.501.50M3−5321.77p0 = 0.28823
 p1 = 0.58613
 (p2 = 0.12565)
 ω0 = 0.00489
 ω1 = 0.186
 ω2 = 1.4079p0 = 0.98450
 p = 0.43715
 q = 1.53500
 (p1 = 0.01550)
 ω = 9.53042
hrpZ110.21052.878816.9E-091.1E-194.2E-01NPNPM3−3538.67p0 = 0.49306
 p1 = 0.20477
 (p2 = 0.30217)
 ω0 = 0.06795
 ω1 = 0.06796
 ω2 = 0.53965p0 = 0.30370
 p = 99.00000
 q = 84.99636
 (p1 = 0.69630)
 ω = 0.06776
  • NP, no positive selection could be detected using this test; NA, the P-value could not be calculated.