Table 2.

Testing simultaneously for consistent within-species and within-lineage variations in nucleotide substitution rates (N: non-synonymous, S: synonymous) of the MHC-DRB molecule at different regions (ABS: contact residues, non-ABS: non-contact residues).

All lineages	Species-specific effects	Lineage-specific effects
dN, ABS	F42,91 = 2.311, P < 0.001	F59,89 = 1.875, P = 0.004
dS, ABS	F42,91 = 1.809, P = 0.010	F59,89 = 1.572, P = 0.026
dN, non-ABS	F42,91 = 1.491, P = 0.058	F59,89 = 1.490, P = 0.044
dS, non-ABS	F42,91 = 1.690, P = 0.019	F59,89 = 2.628, P < 0.001
dN, all sites	F42,91 = 2.120, P = 0.002	F59,89 = 1.694, P = 0.012
dS, all sites	F42,91 = 1.908, P = 0.005	F59,89 = 2.135, P < 0.001
Only HLA orthologous	Species-specific effects	Lineage-specific effects
dN, ABS	F20,18 = 3.152, P = 0.009	F16,18 = 1.155, P = 0.381
dS, ABS	F20,18 = 1.632, P = 0.150	F16,18 = 0.356, P = 0.979
dN, non-ABS	F20,18 = 2.253, P = 0.044	F16,18 = 1.104, P = 0.417
dS, non-ABS	F20,18 = 3.058, P = 0.010	F16,18 = 0.878, P = 0.601
dN, all sites	F20,18 = 3.347, P = 0.006	F16,18 = 0.986, P = 0.507
dS, all sites	F20,18 = 2.842, P = 0.015	F16,18 = 0.645, P = 0.809

GLM results, when including all lineages and only human orthologues (i.e. after excluding W lineages)