Detecting clonality under realistic conditions
Based on our results, clonal richness (R ) and clonal evenness
(Pareto \(\beta\)) are highly sensitive to sampling. Even using
relatively large sample sizes (from 100 to 500 individuals) leads to
deeply biased estimates of the true R and \(\beta\) and thusc values. R is always greatly overestimated, by some
orders of magnitude more than previously demonstrated with empirical
datasets for which the rates of clonality remained unknown (Arnaud-Haond
et al., 2007; Gorospe et al., 2015), and except in nearly strictly
sexual populations, \(\beta\) was also greatly overestimated (for\(c\geq 0.1\)). Genotypic descriptors computed from realistic sample
sizes may be informative only for rare cases of small population sizes
(N ≤1000 individuals in the case of our simulations). For most
situations where population sizes are large, genotypic descriptors
computed with realistic sample sizes result in extreme underestimation
of the rates of clonality (see below) or even in overlooking the
occurrence of PC (i.e. , considering the species as strictly
sexual). These results raise questions regarding the conclusions derived
in the literature from studies assessing the occurrence or even
sometimes the extent of clonality based only on genotypic indices.
In contrast, the distribution moments of F IS and
mean LD for common sample sizes (more than 20 individuals) produced
values consistent with those obtained from genotyping the whole
population, yet they previously could be interpreted only for extreme
rates of clonality (c≥0.95). Consequently, when analysing samples from
populations with more than 1000 individuals, most genetic descriptors
should remain informative and sometimes, together with any Rvalues lower than 1, should be interpreted as a likely signature of a
high prevalence of clonality (c≥0.95)
This worrying limitation recalls, for example, the results recently
reported by Dia et al. (2014) for a unicellular phytoplankton species
involved in harmful algal blooms (HABs), Alexandrium minutum .
This species, which causes paralytic shellfish poisoning (PSP), shows an
alternation between clonal (during the bloom) and sexual phases. Dia et
al. (2004) sampled populations throughout the bloom (clonal) events,
during which they grew from being nearly undetectable to exhibiting a
concentration of 104 to 105 cells
per litre. Of the more than 1000 strains cultivated, 265 were fully
genotyped, among which no replicated genotypes were found, driving the
estimate of clonal diversity to R =1. Without extensive knowledge
of the biology of this species, clonality would not have been diagnosed
on the basis of this sampling, which raises questions regarding the
occurrence of clonality. Unfortunately, no F ISvalues could be reported in this study because only the haploid phase
could be sampled, and the LD detected suggested the occurrence of
recombination. However, according to these results, genetic descriptors
allow the detection or estimation of clonality when its prevalence is
extreme: the results by Dia et al. (2014) thus mainly suggest that the
clonal rate during the bloom event did not exceed 0.95 in the few
previous generations, still leaving great uncertainty as to the
prevalence of sexual or clonal reproduction in this species.
Most target species in the literature, including clonal plants and
invasive and pathogenic species, exhibit extremely large population
sizes, thus raising serious questions regarding our ability to detect
clonality based on realistic sample sizes, let alone infer its
importance. The importance of sample size is reflected in the guidelines
provided by the pioneering work of Tibayrenc et al. (1991), who listed 8
criteria to detect clonality, among which fixed heterozygosity,
deviation from HWE and LD were expected to be important in the ability
to diagnose clonality. Nevertheless, these criteria would apply only to
diploid species with extreme rates of clonality, excluding haploid
lineages and diploid species with c <0.95.
One may consider the clonal mechanisms and the way clonal replicates
spatially disperse to better estimate the effect of the joint incidence
of the sampling density and scale of dispersal of clones (driving the
scale of spatial autocorrelation of genotypes compared to the grain size
of sampling) on the ability of a given strategy to detect clonal
replicates and therefore on the conclusions derived from population
genetics data as to the incidence of sexual versus clonal reproduction.
Along a continuum of dispersal from microorganisms such as unicellular
algae and flying aphids to clonal plants with strong rhizomatic
connections and ramets more often clumped than dispersed, the spatial
autocorrelation of clones increases, as does the ability of a given
sampling strategy to reveal clonal replicates at equal sampling
densities. As a consequence, at the first end of this continuum, where
spatial dispersal is not limited (as is the case for A. minutum ),
genotypic parameters alone may not be informative on the existence or
extent of clonality except for nearly strictly clonal organisms such as
the human pathogen Trypanosoma cruzi . Such power would be gained
as the spatial distance of clonal dispersal becomes lower than the
sampling mesh size (for an example
of the influence of sampling strategy in corals, see Gorospe et al.,
2015; see Riginos, 2015) for a comment), and clonal replicates would
become decreasingly randomly diluted at large population sizes and
across vast spatial scales.