Genetic diversity

GenAlEx v. 6.503⁷⁷ (Peakall and Smouse 2012) was used to generate allelic frequencies, and to calculate a range of population genetic parameters⁷⁴ including the mean number of alleles per locus (A), observed and expected heterozygosity (H_O and H_E), and the fixation index (F) as an estimate of past inbreeding. Allelic richness (A_R) and private allelic richness (P_AR) per population were calculated in HP-RARE⁸⁰, using rarefaction to account for unequal sample size. Differences between the diversity and inbreeding measures for the K’gari and mainland populations were analysed using independent sample T-tests (normal data) or Mann–Whitney U-tests (skewed data) using SPSS software (SPSS Inc. Chicago).

To detect the likelihood of recent bottlenecks, the program BOTTLENECK was used to test for mutation-drift equilibrium⁸¹. The observed level of heterozygosity was compared to the expected HetEQ using the intermediate two-phased model (TPM), due to its suitability for microsatellite data^81,82. The TPM was applied with 95% of the mutations following a two-phase mutation pattern and a variance among multiple steps of 12⁸³, with deviations from equilibrium determined using Wilcoxon’s Sign Rank tests, which are most suitable in instances where less than 20 loci are used⁸¹. Effective population size (N_e) was estimated assuming a closed population with discrete generations and random variance in reproductive success using the program NeEstimator v2.01⁸⁴. The linkage disequilibrium method (LD) was used with the random mating model and results were reported for P_crit 0.02 which is recommended for greater precision with microsatellite markers^84,85.