Simulations
Theoretical results were obtained using forward individual-based simulations run over 104 non-overlapping generations to reach quasi-stationary distributions of both genotypic and genetic diversity. In the initial generations, alleles at all neutral loci were randomly drawn from a uniform distribution (i.e. , maximum genetic diversity merged at random within individuals). In these simulations, all diploid individuals lived in constant finite-sized populations.
Each population produced the next generation using clonal or panmictic sexual reproduction following a fixed rate of clonality. All hermaphrodite individuals in each generation had identical probabilities of being parents, in both clonal and sexual events. The probability of an individual parent being drawn i) to birth a clonal descendant and ii) to sire half a sexual descendant followed a Bernoulli scheme, with respective probabilities \(P(clonal\ parent)=\frac{c}{N}\) and\(P(sexual\ parent)=\frac{1-c}{2N}\), where N is the population size. In clonal reproduction, new independent individuals were produced as full genetic copies of their only parent, with somatic mutations occurring at a fixed rate of 10-6 mutations per generation per locus. This choice was driven by the high end of estimates of DNA polymerase mutations ranging between 10-8 and 10-9 bp/generation (McCulloch & Kunkel, 2008), which for a locus of 100 to 1000 base pairs would imply a mutation rate of 10-5 to 10-7. In panmictic sexual reproduction, new independent individuals descended from two parents chosen at random within the previous generation, from which the individuals inherited half their genomes and mutated at a rate of 10-3mutations per generation per locus, following estimated mutation rates for sexual eukaryotes ranging from 10-4 to 10-7 and 10-2 to 10-5 across generations for single-nucleotide polymorphisms (SNPs) and microsatellites, respectively (Payseur & Cutter, 2006). Genomes were coded as 100 independent loci. Alleles mutated following a K-allele mutation (KAM) model (Putman & Carbone, 2014; Weir & Cockerham, 1984), which has the advantage of simulating the behaviour of both microsatellites and SNPs well and which best approximates the “disturbing factor of gene frequencies” (in the sense of Wright, 1931) in finite-sized populations. Mutating alleles in both clonal and sexual reproduction were drawn at random from the respective pools of clonal and sexual offspring. In simulations, the clonality rate, genetic drift and mutation rate were applied homogeneously across generations and loci.
To understand the effect of clonality on population genetics indices, we ran simulations with varying population sizes (N = 103, 104 and 105, to be studied with arbitrarily fixed mutation rates), rates of clonality (c =0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.99 and 1), and numbers of generations elapsed since the initial population (generations=10, 100, 500, 1000, 5000, and 10000). At each time step, indices were examined for the whole population (all N genotypes considered) as well as for subsamples without replacement of different sizes (n =10, 20, 30, 50, 100, 200, 500, and 1000 and when population sizes allowed, n =5000, 10000, 50000, and 100000).
Each scenario was run 100 times and characterised by a set of parameters (N , c ). When subsampling populations, we performed 10 independent resamplings of each generation and sample size, resulting in 1000 independent data points per set of parameters for each sample size.