Data matrix for phylogeography of sea hibiscus (Hibiscus tiliaceus) group

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 gene..., 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., , # Data matrix files for: Spatiotemporal process of long-distance seed dispersal of a pantropically distributed sea hibiscus group

**plastome_dating.fas** A fasta file including the sequence matrix of plastome CDSs used for molecular dating analysis by BEAST

**plastome_Hibiscus_tiliaceus_complex.fas** A fasta file including the sequence matrix of whole plastome used for phylogenetic analyses by BEAST, PAUP, and RAxML

**MIG-seq_cXXmXX.nexus** 21 nexus files containing the SNPs matrix used for phylogenetic analyses by PAUP and RAxML, the values in XX corresponds to the parameters of the populations module in ipyrad: c (clust) = 0.80, 0.85, and 0.90 and m (min) = 4, 8, 16, 24, 32, 40, and 48. 

**MIG-seq_ABBABABA_c85m24.loci** SNPs matrix used for ipyrad-analysis toolkit: abba-baba

**GBSSI.nexus** Sequence matrix of GBSSI gene used for phylogentic analyses by PAUP and RAxML

## Usage Notes

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