Evolution of the genetic composition of populations under an increasing rate of clonality
In contrast to the genotypic results but in agreement with previous studies on populations at equilibrium with a realistic low mutation rate (Balloux et al., 2003; Navascués et al., 2010; Stoeckel & Masson, 2014), all mean genetic indices are nearly unaffected until the rate of clonality reaches 0.95 (Figures 1 and S1). In fact, only a slightly larger variance, exemplified at smaller population sizes, can be observed at c =0.9 for F IS and its moments and for \({\overset{\overline{}}{r}}_{d}\). The effects of c on genetic parameters are thus limited to extreme c values.
When the rate of clonality reaches 0.99, values ofF IS are slightly negative, a situation perceptible mostly in a small population (N =1000, Figure S1a). The three deeper moments of F IS distributions, however, show values strongly departing from zero. At this highly elevated rate of clonality, LD very slightly departs from 0 for large population sizes (N ≥10000) and then shows extreme values atc =1 (\({\overset{\overline{}}{r}}_{d}\) of approximately 0.8 and 0.6 for N =10000 and 100000, respectively). Interestingly, very small populations show a modest (mean value of approximately 0.06) but noticeable departure from 0 as well as large variance at c =0.99, whereas \({\overset{\overline{}}{r}}_{d}\) returns to zero (in fact to a very slightly negative value) at c =1, with a more limited variance. This unexpected behaviour occurs because clonality, by increasing the number of generations to reach the genotype frequencies expected under Hardy-Weinberg assumptions, allows genetic drift to control the dynamics of genetic diversity (Reichel et al., 2016; Rouger, Reichel, Malrieu, Masson, & Stoeckel, 2016). In strictly clonal small populations containing 1000 individuals, the number of genets ranges from a minimum of 91 to a maximum of 102, with a median of 97. These populations are dominated by one main multi-locus genotype (MLG), and the remaining MLGs are scarcely represented (two or three copies each), appearing as derived from the main one only through somatic mutations. These populations thus consist of the same multi-locus lineage (MLL) characterising the genet, i.e. , the ensemble of ramets issued from the same event of sexual reproduction (Arnaud-Haond et al., 2007). MLGs mostly diverge from each other by 1 to a maximum of 16 alleles (median=2) over a total of 200 alleles per MLG. The\({\overset{\overline{}}{r}}_{d}\) values are thus driven by the random association of the few alleles recently appearing by mutation in an overdominant clonal lineage fixed by genetic drift. MLGs differing by very few loci imply that \(V_{D}\) tends to zero and that\(\text{var}_{j}\) tends to non-zero positive values at each locus\(j\).