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Table 4 Tests of overall selection and selection by domain

From: Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids

Domain Alleles length (AAs) dN dN Number dS dS Number dN/dS P- value (purifying) P- value (positive)
LP, β1 & β2 Group I-IV and ungrouped (N69) 228 0.221 (0.024) 44.488 (4.998) 0.327 (0.053) 18.525 (2.234) 0.676 0.021 1.000
β1 Group I-IV and ungrouped (N69) 91 0.254 (0.032) 37.703 (3.988) 0.301 (0.059) 12.807 (1.679) 0.844 0.219 1.000
β2 Group I-IV and ungrouped (N60) 93 0.129 (0.029) 8.502 (2.154) 0.459 (0.101) 7.238 (1.585) 0.282 <0.001 1.000
β1 & β2 Group I (N20) 113 0.008 (0.003) 1.616 (0.521) 0.000 (0.000) 0.000 (0.000) - - -
LP, β1 & β2 Group II-IV and ungrouped (N49) 229 0.193 (0.022) 41.637 (4.845) 0.306 (0.044) 18.101 (2.142) 0.633 0.005 1.000
β1 Group II-IV and ungrouped (N49) 91 0.216 (0.028) 33.987 (3.776) 0.270 (0.049) 11.568 (1.579) 0.800 0.131 1.000
β2 Group II-IV and ungrouped (N40) 94 0.138 (0.034) 9.378 (2.293) 0.463 (0.114) 8.030 (1.679) 0.298 0.001 1.000
  1. Tests of overall selection on the entire length of sequences, and on the different domains were performed. The leading peptide LP, and the two domains β1 and β2, comprise the entire known sequence, despite not all alleles have full coverage of both domains and the LP. The amino acid lengths for each test are given as the number of sites that were included in the test. Three alleles (0005, 0006 and 0012) from Group I, and six alleles (0203, 040103, 0406, 05, 25, 27) from Groups II-IV were excluded for the test of selection on the β2 domain, as they lack sequence information for this domain. dN, number of non-synonymous substitution per non-synonymous site; dS, number of synonymous substitutions per synonymous site; standard error (SE). Significant p-values (at 99% confidence level) are shown bold