Decoding the Evolutionary Transitions and Distribution of Basal and Keystone Lineages of Polycladida (Rhabditophora)

The evolutionary history of ancient marine lineages is often obscured by geological change, long-term isolation, and morphological conservatism. Here, we investigate whether population genetic patterns can reveal deep-time evolutionary processes by integrating haplotype structure and differentiation, molecular dating, and ancestral-range reconstruction in two early-diverging genera of Polycladida, Boninia and Pericelis. Time-calibrated phylogenies and ancestral-range reconstructions place the origins of both genera in tropical marine regions during the Miocene, with the most recent common ancestor of Boninia dated to 8.3 Ma and that of Pericelis to 14–17 Ma. Despite this shared origin, they followed contrasting evolutionary trajectories. Boninia diversified primarily through vicariant fragmentation, followed by founder-event dispersal and regional radiations, whereas Pericelis preserves evidence of a formerly widespread tropical distribution through reciprocal relict species linking the Atlantic and Indo-Pacific, followed by independent regional diversification. Both genera exhibit pronounced geographic genetic structure, indicating long-term evolutionary persistence rather than recent cosmopolitan dispersal. These results demonstrate the value of integrating regional genetic diversity, molecular dating, and ancestral-range reconstruction to resolve the historical biogeography of early-diverging marine lineages.