Modelling SNP frequency distributions
The distributions of expected Hardy-Weinberg (HW) equilibrium genotype frequencies were simulated using a custom R script (Chivers, 2011) for three population sizes of the SNP profiles from single larval samples (number of larvae in each population, n = 34, 19, 15). A null distribution of allele frequencies in a population that is not evolving follows HW proportions. SNP profiles were constructed from single larval samples for all families as well as bioinformatically pooled by geographic source of parental corals (WW, WC, CW). Parameters included were number of parents, total population sizes, number of genotypes, and number of generations to simulate in randomly mated populations. Expected HW genotype frequencies were statistically compared to the experimentally observed genotype frequencies from the families and a multidimensional, distribution-free Kolmogorov-Smirnov Two-Sample test was used to assess statistical significance of differences between paired continuous two-dimensional distributions using the package ‘Peacock.test’ (Fasano & Franceschini, 1987).