Adaptive introgression facilitates tropical plant evolution: Pandanus as a case study

Hybridization and adaptive introgression are increasingly recognized as important components of how natural selection shapes plant speciation and ecological diversification, yet their roles in tropical clades remain poorly understood. We investigated these processes in Pandanus Parkinson (Pandanaceae), a palaeotropical tree genus of high ecological significance and the tenth-most diverse tree genus worldwide. Although morphological evidence suggested hybridization across the Indian Ocean, its genomic basis remained untested. Using 398 total samples (331 nuclear ones for Pandanus), we assessed hybridization and adaptive phenotypes by: (i) testing for broad and morphology-specific transoceanic gene flow through genome-wide conflict, gene conflict, and admixture analyses from Angiosperms353 data; (ii) evaluating whether gene flow occurred via long-distance dispersal or through a bridge clade; and (iii) testing directly and indirectly for adaptive introgression. We found strong, statistically significant evidence of bidirectional transoceanic gene flow, with nuclear clade Ba acting as a critical genetic and biogeographical bridge between Asian and Afro-Malagasy lineages. Contrary to predictions, the striking morphological similarity between geographically disjunct "swamp" lineages reflects convergent evolution rather than shared introgressive history, likely shaped by similarly distinct macroclimatic regimes. Support for adaptive introgression in the bridge clade rested on a consilience of independent evidence: inferred chloroplast capture, differential purifying selection on plastome clades, correlated distribution of a novel foliar water-storage trait, and ecological niche overlap, all coinciding with Miocene forest contraction, Tethys Sea closure, and increasing climatic seasonality. These results highlight hybridization's central role in shaping tropical tree diversity and facilitating ecological adaptation under environmental change.