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Table 5 Selected sites in P. rapae NSP domains 2 and 3 identified by at least two of the methods

From: Microevolutionary dynamics of a macroevolutionary key innovation in a Lepidopteran herbivore

    Analysis Method
Codon Domain Sel. SLAC FEL IFEL REL
276 2, exon 4   -37.08 (0.246) -24.60 (0.236) -24.60 (0.328) -5.28 (3348.03; 0.001)
277 2, exon 4 N -136.86 (0.004) -120.18 (0.002) -120.18 (0.010) -17.83 (1,207,160,000.00; < 0.001)
284 2, exon 5   -30.24 (0.302) -22.12 (0.195) -22.12 (0.280) -1.36 (95.85; 0.029)
287 2, exon 5 N -27.37 (0.333) -59.18 (0.071) -59.17 (0.115) -13.32 (31,730.30; 0.001)
299 2, exon 5   12.69 (0.745) 13.36 (0.358) 23.00 (0.257) 8.57 (260.85; 0.0013)
303 2, exon 5   -37.08 (0.246) -26.42 (0.224) -26.41 (0.313) -6.12 (3,645.68; 0.001)
316 2, exon 5 N -93.32 (0.109) -340.07 (0.020) -340.07 (0.035) -17.06 (49,267.90; 0.001)
329 2, exon 5 N -46.91 (0.242) -81.89 (0.070) -81.89 (0.136) -8.79 (2,163.10; 0.002)
334 2, exon 5 N -111.25 (0.015) -85.83 (0.006) -85.82 (0.019) -17.82 (55,812,800.00; < 0.001)
338 2, exon 5   -27.37 (0.333) -20.84 (0.181) -20.83 (0.263) -1.31 (93.12; 0.03)
355 2, exon 5   22.27 (0.672) 29.94 (0.259) 50.70 (0.163) 8.53 (114.69; 0.0031)
379 2, exon 5 P 28.03 (0.488) 63.06 (0.108) 201 (0.021) 8.64 (2,410.59; < 0.001)
389 2, exon 5   -29.36 (0.333) -33.44 (0.161) -33.44 (0.300) -1.31 (93.37; 0.03)
390 2, exon 5 N -29.36 (0.333) -92.94 (0.087) -92.95 (0.186) -3.76 (143.98; 0.02)
393 2, exon 5   -16.89 (0.579) -35.67 (0.201) -35.68 (0.355) -1.30 (93.64; 0.03)
395 2, exon 5   -29.36 (0.333) -32.64 (0.181) -32.64 (0.329) -1.30 (92.46; 0.03)
405 2, exon 5   -29.36 (0.333) -32.54 (0.213) -32.54 (0.369) -1.30 (92.02; 0.031)
430 3, exon 5 N -39.78 (0.246) -40.08 (0.123) -40.08 (0.244) -1.55 (103.69; 0.027)
434 3, exon 5   -32.44 (0.302) -35.73 (0.192) -35.73 (0.342) -1.38 (96.44; 0.029)
437 3, exon 5 N -102.62 (0.109) -585.52 (0.019) -585.52 (0.046) -11.21 (344.05; 0.009)
441 3, exon 5 N -119.35 (0.015) -161.93 (0.021) -161.93 (0.086) -17.73 (830,226.00; 0.001)
467 3, exon 5   22.31 (0.508) 30.17 (0.245) 36.57 (0.244) 3.11 (333.06; <0.001)
480 3, exon 5 N -96.13 (0.004) -124.06 (0.001) -124.08 (0.0114) -37.22 (30,456.40; 0.0001)
483 3, exon 6 N -19.22 (0.333) -22.54 (0.132) -22.54 (0.2689) -2.80 (174.20; 0.032)
493 3, exon 6 N -38.45 (0.111) -54.50 (0.026) -54.50 (0.0975) -6.97 (194.36; 0.028)
505 3, exon 7   19.00 (0.455) 19.49 (0.204) 24.46 (0.203) 3.19 (845.98; <0.001)
508 3, exon 7 N -38.45 (0.111) -56.79 (0.023) -56.79 (0.0909) -7.59 (201.55; 0.027)
523 3, exon 7 P 28.57 (0.306) 28.63 (0.122) n/a 3.20 (12725.90; <0.001)
532 3, exon 7 N -19.22 (0.333) -26.85 (0.114) -26.85 (0.2402) -3.05 (174.17; 0.032)
548 3, exon 7   16.83 (0.635) 24.43 (0.372) 63.24 (0.181) 3.05 (114.56; 0.001)
573 3, exon 7   16.84 (0.636) 24.32 (0.388) 30.54 (0.363) 3.04 (98.82; 0.001)
580 3, exon 7 N -184.42 (0.000) -239.57 (< 0.001) -239.57 (0.0021) -37.41 (1,829,600.00; <0.001)
594 3, exon 7 N -19.22 (0.333) -27.67 (0.110) -27.67 (0.2337) -3.06 (175.61; 0.031)
  1. Note. - For every method, first value is scaled dN - dS and number in parentheses shows P value, except for the REL method, where first value is Bayes factor value followed by P value based on the Bayes factor posterior probability). Significant values (P < 0.15) shown in bold and when 2 of the four methods are significant, the Selection column indicates "N" for negative or "P" for positive selection. Codon numbering is relative to start codon of the signal peptide.