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Table 4 Identification of positively selected sites in Atlantic cod tlr22 paralogues by maximum likelihood analysis

From: Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua

Models Parameter estimates Ln likelihood Model comparison Positively Selected sites
M0: neutral ω = 1.12 −10057.27   None
M1: nearly neutral ω0 = 0.081, ω1 = 1 −9946.92   Not allowed
p0 = 0.39, p1 = 0.61
M2: positive selection ω0 = 0.05, p0 = 0.28 −9850.74 M2 vs M1 4, 6, 30, 41, 73, 126, 170, 224, 250, 274, 279, 318, 326, 333, 369, 371, 427, 443, 452, 455, 458, 478, 484, 501, 503, 505, 507, 509, 528, 531, 553, 577, 674
ω1 = 1, p1 = 0.54 2ΔlnL = 192.35,
ω 2 = 4.08, p2 = 0.18 df = 2, p = 0
M3: discrete ω0 = 0.18, p0 = 0.35 −9850.56 M3 vs M0 1, 3, 4, 6, 9, 11, 12, 13, 16, 18, 23, 25, 27, 28, 30, 33, 37, 40, 41, 43, 44, 49, 51, 52, 54, 56, 57, 59, 68, 70, 71, 73, 75, 76, 78, 80, 81, 82, 83, 94, 95, 97, 108, 110, 112, 115, 116, 122, 124, 126, 127, 129, 132, 134, 147, 152, 154, 156, 157, 159, 163, 169, 170, 172, 174, 175, 177, 178, 179, 180, 181, 189, 194, 196, 197, 210, 211, 212, 215, 224, 227, 230, 231, 233, 234, 236, 237, 240, 241, 245, 246, 247, 250, 251, 252, 253, 257, 260, 262, 267, 268, 271, 273, 274, 276, 277, 279, 281, 284, 287, 288, 294, 295, 297, 298, 301, 302, 303, 305, 307, 311, 313, 315, 316, 318, 320, 326, 330, 331, 333, 334, 335, 336, 338, 339, 340, 341, 342, 344, 345, 347, 349, 350, 352, 354, 355, 357, 358, 368, 369, 371, 375, 376, 378, 379, 382, 383, 387, 388, 392, 393, 395, 397, 400, 402, 403, 406, 410, 413, 414, 416, 417, 419, 421, 426, 427, 428, 429, 430, 432, 434, 438, 440, 441, 443, 445, 448, 452, 453, 455, 457, 458, 460, 471, 472, 474, 475, 476, 478, 480, 481, 484, 493, 495, 498, 499, 501, 503, 504, 505, 506, 507, 508, 509, 510, 517, 524, 526, 528, 529, 530, 531, 532, 533, 535, 538, 539, 548, 549, 550, 551, 552, 553, 555, 556, 557, 572, 574, 577, 578, 579, 595, 596, 598, 600, 601, 603, 613, 616, 619, 620, 622, 624, 639, 642, 643, 645, 650, 662, 666, 670, 673, 674, 680, 681, 691, 702, 712, 719
ω1 = 1.19 , p1 = 0.49 2ΔlnL = 413.43,
ω 2 = 4.36, p2 = 0.16 df = 4, p = 0
M7: β p = 0.02, q = 0.01 −9951.60   Not allowed
M8: β + ωS>1 p = 0.1, q = 0.05 −9850.86 M8 vs M7 1, 4, 6, 30, 41, 56, 73, 126, 170, 174, 224, 245, 250, 274, 279, 287, 295, 318, 326, 333, 342, 344, 355, 369, 371, 378, 393, 400, 427, 443, 452, 455, 457, 458, 460, 471, 474, 478, 484, 501, 503, 505, 506, 507, 509, 528, 529, 530, 531, 553, 577, 619, 674
ω = 4.06 2ΔlnL = 201.48,
p0 = 0.81, p1 = 0.19 df = 2, p = 0
REL     4, 6, 30, 41, 49, 73, 76, 126, 147, 157, 170, 224, 246, 274, 279, 295, 318, 320, 326, 333, 342, 369, 371, 397, 400, 427, 452, 455, 478, 484, 501, 503, 507, 509, 553, 578, 613
  1. Only positively selected sites with Bayesian posterior probabilities above 95% are indicated and the ones greater than 99% are highlighted in bold.
  2. In the REL analysis, positively selected sites with a Bayes factor greater than 50 are highlighted in bold.