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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

Ļ‰ = 1.12

āˆ’10057.27

Ā 

None

M1: nearly neutral

Ļ‰0 = 0.081, Ļ‰1 = 1

āˆ’9946.92

Ā 

Not allowed

p0 = 0.39, p1 = 0.61

M2: positive selection

Ļ‰0 = 0.05, p0 = 0.28

āˆ’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

Ļ‰1 = 1, p1 = 0.54

2Ī”lnL = 192.35,

Ļ‰ 2 = 4.08, p2 = 0.18

df = 2, p = 0

M3: discrete

Ļ‰0 = 0.18, p0 = 0.35

āˆ’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

Ļ‰1 = 1.19 , p1 = 0.49

2Ī”lnL = 413.43,

Ļ‰ 2 = 4.36, p2 = 0.16

df = 4, p = 0

M7: Ī²

p = 0.02, q = 0.01

āˆ’9951.60

Ā 

Not allowed

M8: Ī² + Ļ‰S>1

p = 0.1, q = 0.05

āˆ’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

Ļ‰ = 4.06

2Ī”lnL = 201.48,

p0 = 0.81, p1 = 0.19

df = 2, p = 0

REL

Ā Ā Ā 

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.