Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications

Table 2 Variation in amino acid sequence and rates of synonymous and nonsynonymous mutations across antigen and non-antigen binding MHC-DRB sites

Region of MHC-DRB	Total AA	Variable AA [%]	dAA ± S.E.	dN ± S.E.	dS ± S.E.	Z [p]
All sites	57	21 [36.8 %]	8.857 ± 2.65	0.090 ± 0.03	0.018 ± 0.02	3.985 [0.000*]
non-ABS sites	42	10 [23.8 %]	4.142 ± 1.88	0.051 ± 0.02	0.001 ± 0.00	2.745 [0.003*]
ABS sites	15	11 [73.3 %]	4.715 ± 1.66	0.217 ± 0.10	0.068 ± 0.07	2.767 [0.003*]

Note. This table shows the total number of amino acid codons [AA] as well as the number and percentage of variable amino acid codons [Variable AA] in the MHC-DRB second exon, the average [± S.E.] pairwise AA differences [dAA] between alleles, the average [± S.E.] rates of nonsynonymous [dN] and synonymous [dS] substitutions per site, and the one-tailed test of positive selection [Z] with p-values [p]. All standard errors were obtained from 1000 bootstrap replicates [83]

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