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).