Fig. 2. Orthologous K_s distributions and WGD events identified based on K_s distributions for the whole paranomes of different fern species.

(a-c) One-to-one orthologous K_s distributions between Lygodium japonicum and species from Cyatheales (a), Salviniales (b), and Polypodiales (c). (d) WGD events identified based on K_s distributions for the whole paranome of species in the phylogeny. On the left, a species phylogram is shown with branch lengths in K_s units, while WGD events are depicted as dots (calculated as half the K_s peak value of each species starting from the corresponding tip). Solid dots denote significant K_s peaks in the SiZer analysis, whereas hollow dots denote K_s peaks only identified by GMM but not SiZer (see Materials and Methods and Fig. S3, S4). On the right, a species cladogram is shown, where WGD events are depicted as rhombs according to the analyses of ksrates (Sensalari et al. 2021). Note that when a WGD and a speciation event overlap in the ksrates analysis, the WGD event is placed at the speciation event in the cladogram.