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

SLAC^b

FEL^c

REL^d

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