Standard intra-population genetic diversity indices at neutral and ELA loci.

Genetic diversity estimates are reported for microsatellites (μsats), the β-Fibr intron, and ELA loci (DRA, DQA). Indices include allelic richness (A), rarefaction-corrected allelic richness (ACORR), expected heterozygosity (HE), number of segregating sites (S), insertion/deletion mutations (indels) in base pairs (bp), average pair-wise difference between sequences (k), haplotype diversity (HD), and nucleotide diversity (π). The number of individuals (N) used in calculating diversity estimates are reported. Standard deviation (SD) or standard error (± SE) for estimates shown in parentheses. Diversity estimates for the DQA locus are reported both excluding (DQA) and including (DQAALL) individuals with multi-locus genotypes.1 Mean (± SE) estimates reported, averaged over 13 loci.2 A and HE incorporate indel mutations in allele identification.