DOI: 10.5061/dryad.jq2bvq8d4
title: Data matrix for phylogeography of sea hibiscus (Hibiscus tiliaceus) group

description: 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.
description: 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.
description: # 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 All data files can
 be viewed in a standard text editor. Recommended software for interacting
 with these data: plastome_dating.fas: BEAST
 plastome_Hibiscus_tiliaceus_complex.fas: BEAST, PAUP, and RAxML
 MIG-seq_cXXmXX.nexus: PAUP and RAxML MIG-seq_ABBABABA_c85m24.loci:
 ipyrad-analysis toolkit: abba-baba GBSSI.nexus: PAUP and RAxML