The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates

Abstract

Partial clonality is widespread across the tree of life, but most population genetic models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetic data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their relationships with genotypic (clonal richness, R, and distribution of clonal sizes, Pareto β) and genetic (FIS and linkage disequilibrium) indices, and tested predictions of c from population genetic data through supervised machine learning. Two complementary behaviours emerged from the probability distributions of genotypic and genetic indices with increasing c. While the impact of c on R and Pareto β was easily described by simple mathematical equations, its effects on genetic indices were noticeable only at the highest levels (c > 0.95). Consequently, genotypic indices allowed reliable estimates of c, while genetic descriptors led to poorer performances when c < 0.95. These results provide clear baseline expectations for genotypic and genetic diversity and dynamics under partial clonality. Worryingly, however, the use of realistic sample sizes to acquire empirical data systematically led to gross underestimates (often of one to two orders of magnitude) of c, suggesting that many interpretations hitherto proposed in the literature, mostly based on genotypic richness, should be reappraised. We propose future avenues to derive realistic confidence intervals for c and show that, although still approximate, a supervised learning method would greatly improve the estimation of c from population genetic data.

Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader

“…Thus, our simulated 100% clonal reproduction probably overestimates true clonal rates. Clonality may have modified the consequences of a bottleneck, but it did not primarily drive observed patterns (see also Navascués et al, 2010;Stoeckel et al, 2021).…”

Genomic consequences and selection efficacy in sympatric sexual versus asexual kelps

“…Significance of F IS from 0 was tested by applying 9999 permutations and calculating the 99% confidence interval. As variance of F IS and distribution patterns of F IS values across loci are thought to be slightly more informative in cases of partial clonality than average F IS (Reynes et al, 2021;Stoeckel et al, 2021), these metrics were also calculated. Linkage disequilibrium was assessed by calculating the standard index of association (r̄d) as implemented in poppr v2.8.3 (Kamvar et al, 2014).…”

Genetic variation and clonal diversity in floating aquatic plants: Comparative genomic analysis of water hyacinth species in their native range

“…Commonly used indices of clonal diversity have included the ratio of genotypes ( G ) to the number of individuals ( N ) sampled G/N or ( G ‐1)/( N ‐1) and the Shannon and Simpson index D * (Arnaud‐Haond et al, 2005, 2007; Dorken & Eckert, 2001; Ellstrand & Roose, 1987; Silvertown, 2008). More recent approaches include: (1) using genetic distance to identify multilocus lineages (MLLs) and calculating Pareto β, the slope of the size distribution of lineages (Arnaud‐Haond et al, 2007; Krueger‐Hadfield et al, 2021; Stoeckel et al, 2021), and (2) using the distribution of F IS to make inferences on the amounts of sexual reproduction in populations (Arnaud‐Haond et al, 2007, 2020; Hernández‐García et al, 2006; Reynes et al, 2021; Rozenfeld et al, 2007).…”

“…Theoretical studies indicate that the genetic consequences of clonality depend on the relative amounts of sexual versus asexual reproduction in populations (Balloux et al, 2003;Bengtsson, 2003;Ceplitis, 2003;de Meeûs & Balloux, 2004a;Hartfield, 2016aHartfield, , 2016bOrive, 1993;Stoeckel et al, 2021;Yonezawa et al, 2004). At the individual level, predominant clonality produces strong associations between alleles at different loci (linkage disequilibrium) as they share a common history in a clonal lineage, with sex breaking up these associations and generating new genetic combinations (de Meeûs & Balloux, 2004a& Balloux, , 2004bGlémin et al, 2001;Navascués et al, 2010).…”

“…(1) using genetic distance to identify multilocus lineages (MLLs) and calculating Pareto β, the slope of the size distribution of lineages (Arnaud-Haond et al, 2007;Krueger-Hadfield et al, 2021;Stoeckel et al, 2021), and (2) using the distribution of F IS to make inferences on the amounts of sexual reproduction in populations (Arnaud-Haond et al, 2007Hernández-García et al, 2006;Reynes et al, 2021;Rozenfeld et al, 2007).…”