Table 1.

Dependent variables used in the comparative analysis representing MHC diversity and indicators of selection

Dependent variable	Indicates	Interpretation	Prediction
dN/dS at ABS	Historic balancing selection	High dN/dS indicates positive selection at sites that recognize pathogens	Reduced in species with non-functional duplicated loci; reduced in species with lower effective population sizeand stronger genetic drift
dS-dN at non-ABS	Purifying selection	High dS–dN indicates greater rates of silent substitutions that preserve amino acid configurations at sites surrounding ABS	Higher in species with duplicated loci to preserve allelic divergence; reduced in species with lower effective population size and stronger genetic drift
Average nucleotide divergence (π)	Genetic diversity	Extent of variation between sequences	Higher in species with duplicated loci; higher in species with larger effective population size
Number of alleles	Genetic diversity	Number of unique sequences	Higher in species with duplicated loci; higher in species with larger effective population size