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.