
Bailleul, D., Stoeckel, S., & ArnaudHaond, S. (2016). RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in r. Methods Ecol. Evol., 7(8), 966–970.
Résumé: Partially, clonal species are common in the Tree of Life. And yet, population genetic models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here, we present an R package built upon genclone software including new functions and several improvements. The RClone package includes functions to handle clonal data sets, allowing (i) checking for data set reliability to discriminate multilocus genotypes (MLGs), (ii) ascertainment of MLG and semiautomatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs and (iv) describing several spatial components of clonality. RClone allows the oneshot analysis of multipopulation data sets without size limitation, suitable for data sets now increasingly produced through nextgeneration sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin. RClone is provided with two vignettes to handle analysis on one (RClonequickmanual) or several populations (RCloneqmsevpops).



Reichel, K., Masson, J.  P., Malrieu, F., ArnaudHaond, S., & Stoeckel, S. (2016). Rare sex or out of reach equilibrium? The dynamics of FIS in partially clonal organisms. BMC Genet., 17, 76.
Résumé: Background: Partially clonal organisms are very common in nature, yet the influence of partial asexuality on the temporal dynamics of genetic diversity remains poorly understood. Mathematical models accounting for clonality predict deviations only for extremely rare sex and only towards mean inbreeding coefficient (FIS) over bar < 0. Yet in partially clonal species, both FIS < 0 and FIS > 0 are frequently observed also in populations where there is evidence for a significant amount of sexual reproduction. Here, we studied the joint effects of partial clonality, mutation and genetic drift with a stateandtime discrete Markov chain model to describe the dynamics of FIS over time under increasing rates of clonality. Results: Results of the mathematical model and simulations show that partial clonality slows down the asymptotic convergence to FIS = 0. Thus, although clonality alone does not lead to departures from HardyWeinberg expectations once reached the final equilibrium state, both negative and positive FIS values can arise transiently even at intermediate rates of clonality. More importantly, such “transient” departures from Hardy Weinberg proportions may last long as clonality tunes up the temporal variation of FIS and reduces its rate of change over time, leading to a hyperbolic increase of the maximal time needed to reach the final mean (FIS,Finfinity) over bar value expected at equilibrium. Conclusion: Our results argue for a dynamical interpretation of FIS in clonal populations. Negative values cannot be interpreted as unequivocal evidence for extremely scarce sex but also as intermediate rates of clonality in finite populations. Complementary observations (e.g. frequency distribution of multiloci genotypes, population history) or time series data may help to discriminate between different possible conclusions on the extent of clonality when mean (FIS) over bar values deviating from zero and/or a large variation of FIS over loci are observed.

