Hengchi Chen

Summary Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole‐genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building K S ‐age distributions and applying substitution rate corrections and by conducting statistical gene tree–species tree reconciliation analyses. Our integrative analyses not only identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree–species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often‐overlooked issues.