Long-distance dispersal (LDD) of seeds plays an important role in the plant migration to a new habitat and maintaining gene flow among populations. Pantropical plants with sea-drifted seeds have achieved their global distribution by LDD. However, the spatiotemporal processes to achieve the wide distribution and the role of LDD in it have not yet been investigated.

In this study, we conducted phylogenomic analyses on the plastome, genome-wide nuclear SNP, and low-copy gene data of Hibiscus tiliaceus and its relatives. We conducted shotgun sequencing for extracting plasome sequence and MIG-seq for a genome-wide SNPs genotyping.

The dated phylogeny showed that global expansion started approximately four million years ago (MYA), and species diversification occurred 1 MYA. Plastome phylogeny suggested the non-monophyly of the haplotypes in the two widely distributed coastal species, H. tiliaceus and H. pernambucensis. In contrast, genome-wide nuclear SNP phylogenies clearly illustrated genetic segregation among species and/or geographical regions. Ancestral polymorphisms in chloroplast genomes shared among distinct species have remained below the range of rapid expansion and speciation of marginal populations. This study demonstrated that the LDD of sea-drifted seeds contributed to the rapid expansion and pantropical distribution of sea hibiscus, and adaptation to local environment or isolation by regional effect after LDD promoted speciation, suppressing gene flow.

plastome_dating.fas: Assembled and aligned from NGS short reads.

plastome_Hibiscus_tiliaceus_complex.fas: Assembled and aligned from NGS short reads and DNA database.

MIG-seq_cXXmXX.nexus: SNPs calling by ipyrad from MIG-seq data in BioSamples PRJDB14856.

MIG-seq_ABBABABA_c85m24.loci: SNPs calling by ipyrad from the MIG-seq in BioSamples PRJDB14856.

GBSSI.nexus: Assembled and aligned from Sangar sequencing data.