DOI: 10.5061/dryad.b5mkkwhpf
title: Data from: Genetic admixture and novel host shifts in a parasitic plant, Orobanche boninsimae (Orobanchaceae), endemic to the Ogasawara Islands

description: Parasitic plants depend on other plants for nutrients and water and have
 undergone evolutionary processes tightly linked to their host range. As
 parasitic adaptations specialize host range, host shifts between parasite
 lineages are considered essential events that can lead to genetic
 differentiation and speciation. A thorough examination of population
 genealogy covering the entire host range is imperative to comprehend the
 impact of host-shift evolution on parasitic plant species diversity.
 Therefore, we investigated the population genetic structure of Orobanche
 boninsimae (Orobanchaceae), an endemic parasitic plant in the Bonin
 (Ogasawara) Islands. The host species of O. boninsimae are entirely
 distinct from those of other Orobanche species and show differences
 between geographically isolated islands, even though the host species
 coexist in some localities. Genetic differentiation was observed among
 populations from different islands, corresponding to variations in the
 host range of O. boninsimae. Demographic analysis supported a scenario in
 which populations on southern island emerged through the admixture of
 populations parasitic on the different host species from the northern
 islands. This suggests a progressive colonization process, wherein
 continental ancestors established in the northern islands underwent a host
 shift, followed by the migration of a lineage to the southern island.
 Notably, host shift across islands may have occurred through the admixture
 of populations. These findings provide a foundation for elucidating the
 roles of host plants and geographical isolation in the speciation of
 parasitic plants and enhance our understanding of the mechanisms driving
 parasitic plant diversification.
description: # Data from: Genetic admixture and novel host shifts in a parasitic plant,
 Orobanche boninsimae (Orobanchaceae), endemic to the Ogasawara Islands
 [https://doi.org/10.5061/dryad.b5mkkwhpf](https://doi.org/10.5061/dryad.b5mkkwhpf) ## Description of the data and file structure Data matrix files for a paper titled "Genetic Admixture and Novel Host Shifts in a Parasitic Plant, Orobanche boninsimae (Orobanchaceae), Endemic to the Ogasawara Islands" by Akihiro Nishimura and Koji Takayama ### Files and variables #### File: Haplotype_network_whole_plastome.nex **Description:** An alignment of plastome sequences for haplotype network made by MAFFT. #### File: MIGseq_DIYABC.snp **Description:** Input data of SNPs for DIYABC-RF made from MIGseq_populations.snps.vcf. #### File: MIGseq_PCA.plink.map **Description:** Input data of SNPs for PCA made by Stacks. #### File: MIGseq_Fst.str **Description:** Input data of poppr for FST calculation made from MIGseq_STRUCTURE.structure. #### File: MIGseq_STRUCTURE.structure **Description:** Input data of STRUCTURE for population genetic structure estimation made by Stacks. #### File: MIGseq_TreeMix.treemix **Description:** Input data of TreeMix for population divergence made by Stacks. #### File: Phylogeny_ITS.phy **Description:** An alignment of ITS sequences for Maximum likelihood (ML) phylogenetic tree construction made by MAFFT. #### File: Phylogeny_plastome_16CDS.phy **Description:** An alignment of 16 protein-coding genes of plastomes for Maximum likelihood (ML) phylogenetic tree construction made by MAFFT. #### File: MIGseq_PCA.plink.ped **Description:** Input data of SNPs for PCA made by Stacks. #### File: Phylogeny_whole_plastome.phy **Description:** An alignment of plastome sequences for haplotype network made by MAFFT. #### File: Sample_information.tsv **Description:** Information on the populations and individuals for plastome, ITS and MIG-seq. #### File: MIGseq_populations.snps.vcf **Description:** Data on all variations made by Stacks. #### File: MIGseq_SplitsTree.nex **Description:** Input data of SNPs for SplitsTree made from MIGseq_populations.snps.vcf. ## Code/software Phylogeny_ITS.phy: MEGA, RAxML-NG, Figtree. Phylogeny_plastome_16CDS.phy: MEGA, RAxML-NG, Figtree. Phylogeny_whole_plastome.phy: MEGA, RAxML-NG, Figtree. Haplotype_network_whole_plastome.nex: PopART. MIGseq_SplitsTree.nex: SplitsTree. MIGseq_STRUCTURE.structure: STRUCTURE. MIGseq_TreeMix.treemix: TreeMix. MIGseq_DIYABC.snp: DIYABC-RF. MIGseq_Fst.str: poppr. MIGseq_PCA.plink.ped: PLINK. MIGseq_PCA.plink.map: PLINK. ## Access information Other publicly accessible locations of the data: * n/a Data was derived from the following sources: * n/a