Table 1 Phylogenetic Tests of Positive Selection
From: Signatures of positive selection in Toll-like receptor (TLR) genes in mammals
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 |