Table 1

Phylogenetic Tests of Positive Selection

Sites under positive selection identified by different methods a


Gene

No. of species

lnL M7

lnL M8

-2lnΔL

PAML M8

SLACb

FELc

RELd

Total no. of sites

%. of sites


TLR1

17

-14643.639

-14633.663

20.00

    174
, 318

    174
,
    293

4,15,27,46, 61, 186, 231, 275, 289,

    293
, 317, 339, 352, 366, 378, 386, 417, 447, 458, 463, 477, 536, 539, 555, 590, 597, 599, 602, 606

-

2

0.25


TLR2

23

-21078.575

-21069.646

17.86

296, 453

    3
,
    161
,
    182
,
    302
,
    602
,
    636

    3
, 63, 93, 111, 133,
    161
,
    182
, 215, 220, 261, 266,
    302
, 303, 321,
    602
,
    636
, 770

    302
,
    602
,
    636

6

0.77


TLR3

20

-18074.201

-18060.466

27.47

    4
, 269, 506,
    749

    4
,
    12
,
    712

    4
, 7, 11,
    12
,
    25
, 69,
    79
, 139, 167,
    258
,
    285
, 326, 406, 432, 456, 616, 693,
    712
, 715, 741,
    780
, 782, 854

    4
,
    12
,
    25
,
    79
,
    258
,
    285
, 473, 558, 588,
    712
,
    749
,
    780

9

0.99


TLR4

19

-20735.203

-20658.940

152.53

5, 271,

    276
,
    295
, 298, 321, 322, 325, 349, 351, 364, 368,
    370
, 371,
    394
, 400, 437, 460,
    468
,
    471
, 505, 520,
    542

    204
,
    300
,
    301
,
    317
,
    363
,
    382
,
    394
,
    468
,
    471
,
    487
,
    542
,
    604
,
    673

9, 56, 58, 120, 189, 193, 203,

    204
,
    240
, 250,
    270
,
    276
, 290,
    295
,
    300
,
    301
,
    317
,
    319
, 323, 324, 329, 336, 342,
    356
, 357,
    363
,
    370
,
    382
,
    394
, 396, 447,
    468
,
    471
    ,
    487
, 493,
    500
,
    542
,
    604
, 622,
    639
,
    673
, 822

4, 161, 204,

    240
,
    270
,
    276
,
    295
,
    300
,
    301
,
    317
,
    319
, 329, 338,
    356
, 360,
    363
,
    370
, 447,
    468
,
    471
, 474,
    487
, 493,
    500
, 537,
    542
, 613, 616,
    639
, 648

22

2.65


TLR5

17

-23742.766

-23737.519

10.49

305, 466, 592

    674
,
    742

    14
, 71,
    128
, 154, 170,
    207
, 340, 382,
    400
, 408, 420,
    674
,
    721
,
    742

    14
,
    128
,
    207
,
    400
,
    721

7

0.81


TLR6

20

-17602.606

-17594.945

15.32

293, 471

    604
,
    607
,
    796

2, 20, 32, 56, 72, 89, 149, 219, 315, 412, 428, 463, 482, 501, 541, 544, 595, 602,

    604
,
    607
, 611, 626, 740, 743,
    796

-

3

0.38


TLR7

21

-15564.048

-15551.690

24.72

    697

    359
,
    667

19, 89, 103, 113, 125, 151, 162,

    283
, 357,
    359
,
    386
, 398, 413, 425, 487, 496, 530, 566,
    599
,
    667
,
    697
, 719,
    776
, 885, 1017

39, 111,

    283
,
    359
,
    386
, 388, 528,
    599
,
    667
, 693,
    697
, 737,
    776

7

0.67


TLR8

18

-23527.219

-23483.262

87.91

1, 100, 109, 110, 138,

    146
,
    160
,
    174
, 186, 188,
    191
,
    214
, 235,
    249
, 268, 288,
    338
,
    349
, 361, 367, 392,
    416
,
    441
,
    459
,
    472
,
    481
,
    498
, 603, 608, 637,
    639
, 675, 691, 699, 739,
    761
, 770

    174
,
    388
,
    418
,
    459
,
    472
,
    712
,
    766

22, 24,

    39
, 101,
    160
,
    214
,
    236
, 238,
    249
, 290, 331,
    388
, 413,
    416
,
    418
,
    441
, 442,
    459
,
    472
,
    481
,
    498
, 508, 593,
    606
,
    629
,
    633
, 677,
    712
,
    766
, 826, 833, 840

5,

    39
, 102,
    146
,
    174
,
    191
,
    214
,
    236
, 246,
    249
, 285, 312,
    338
,
    349
, 350, 371,
    388
, 413,
    416
,
    418,
    441
, 451, 470,
    472
,
    481
,
    498
,
    606
,
    629
,
    633
,
    639
,
    761
,
    766

26

2.50


TLR9

21

-18708.518

-18689.712

37.61

91, 185,

    217
, 302, 355, 449, 674

    71
,
    161
,
    217
,
    332
, 702

8, 42,

    71
,
    161
,
    332
, 625

    71
,
    161
, 397, 728

4

0.39


TLR10

13

-11931.949

-11928.377

7.14

-

    91
,
    392
,
    469
,
    545

34, 71, 76, 89,

    91
,
    238
, 246, 273, 369,
    392
, 395, 396, 423,
    469
,
    492
,
    545
, 552, 600, 679, 775, 799,
    803

110, 235,

    238
, 261, 345,
    392
, 400,
    492
,
    803

7

0.86


a Codons identified by more than one ML method are underlined. The identified codons that are in agreement with Wlasiuk and Nachman (2010) are in bold.

b, c Codons with P values <0.1

d Codons with Bayes factor >50

Areal et al. BMC Evolutionary Biology 2011 11:368   doi:10.1186/1471-2148-11-368

Open Data