FN Archimer Export Format PT J TI The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal rates BT AF Stoeckel, Solenn Porro, Barbara Arnaud‐Haond, Sophie AS 1:1;2:2,3;3:3; FF 1:;2:;3:PDG-RBE-MARBEC-LHM; C1 Institute for Genetics, Environment and Plant Protection INRA, UMR1349 Le Rheu ,France Institute for Research on Cancer and Aging (IRCAN) CNRS UMR 7284, INSERM U1081, Université de Nice‐Sophia‐Antipolis Nice 06107 ,France MARBEC – Marine biodiversity exploitation and conservation Univ Montpellier, CNRS, Ifremer, IRD, MARBEC F‐34200 Sète, France C2 INRAE, FRANCE UNIV NICE, FRANCE IFREMER, FRANCE SI SETE SE PDG-RBE-MARBEC-LHM UM MARBEC IN WOS Ifremer UMR copubli-france copubli-p187 copubli-univ-france IF 8.678 TC 13 UR https://archimer.ifremer.fr/doc/00668/77993/80210.pdf LA English DT Article DE ;F-statistics;genotypic diversity;population genetics;rates of clonality;sampling AB 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. PY 2021 PD MAY SO Molecular Ecology Resources SN 1755-098X PU Wiley VL 21 IS 4 UT 000610842200001 BP 1068 EP 1084 DI 10.1111/1755-0998.13316 ID 77993 ER EF