DOI: 10.5061/dryad.xd2547dhw
title: Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

description: Understanding biological diversity and the mechanisms of the Sino-Japanese
 disjunctions are major challenges in eastern Asia biogeography. The
 Sino-Japanese flora has been broadly studied as an ideal model for plant
 phylogeography. Diabelia (Caprifoliaceae) is an East Asian genus, with a
 disjunctive distribution across the Sino-Japanese region. However,
 relationships within Diabelia remain elusive. In this study, we
 reconstructed the phylogeny of Diabelia and inferred historical
 biogeography and evolutionary patterns based on nuclear and plastid
 sequences from target enrichment and genome skimming approaches,
 respectively. We found that the main clades within Diabelia were
 discordant between nuclear and plastid trees. Both nuclear and plastid
 phylogenetic analyses supported five main clades: D. serrata, D.
 tetrasepala, D. sanguinea, D. spathulata var. stenophylla and D.
 spathulata var. spathulata. Species network analyses revealed that
 Diabelia tetrasepala is likely the result of a hybridization event.
 Divergence time estimation and ancestral area reconstructions showed that
 Diabelia originated in Japan during the early Miocene, with subsequent
 vicariance and dispersal events between Japan and Korea, and between Japan
 and China. Overall, our results support the division of Diabelia into five
 main clades and the recognition of five species in the genus. This
 research provides new insights in the species delimitation and speciation
 processes of taxonomically complex lineages such as Diabelia.
description: DATA PACKAGE FROM KE ET AL (Journal of Systematics and
 Evolution) Nuclear and plastid phylogenomic analyses
 provide insights into the reticulate evolution, species delimitation and
 biogeography of the Sino-Japanese disjunctive Diabelia
 (Caprifoliaceae) This package contains the data and
 software outputs (i.e. fasta filtes, alignments, trees, etc).
 Part 1. File called. Data_part_1.tar.gz
 1_alignments. Unaligned fasta files (*.fa), MAFFT aligned fasta
 files (*.aln), and Cleaned alignments with Phyx (*.aln-cln)<br>
 2_trees. RAxML bipartition labeled trees (*.tre).<br>
 3_masked_mono_para_tips. Trees from 2_trees with masked monophyletic and
 grades of the same species.<br> 4_masked_spurious_tips. Trees from
 3_masked_mono_para_tips with spurious tips removed with TreeShrink. Some
 *.txt files represent the tips removed byTreeShrink. Empty *.txt means
 that TreeShrink did not remove any tip from that tree.<br>
 5_orthologs<br>     1_final_orthologs. MO orthologs pruned from
 trees of 4_masked_spurious_tips.<br>   
  2_fasta_files_from_orthologs. Individual fasta file from the MO orthologs
 (*.fa)<br>     3_fasta_to_tree. MAFFT aligned fasta files (*.aln),
 and Cleaned alignments with Phyx (*.aln-cln), RAxML bipartition labeled
 trees (*.tre), and boostrapt trees (*.trees) from each of MO fasta
 file.<br>     4_concatenated_alignments. Concatenated alignments of
 the individual clean alignments of 3_fasta_to_tree<br>
 6_Analyses ASTRAL. ASTRAL species trees from all trees
 from 5_orthologs/3_fasta_to_tree.<br> Phylonet<br>   
  1_fasta_to_tree. Alignments and RAxML trees from the 15-taxa reduced data
 set.<br>     2_rooted_trees. Rooted trees from
 1_fasta_to_tree.<br>     3_Phylonet. Phylonet results from MPL
 analyses from 1-5 hybridization events.<br> RAxML. RAxML tree from
 the alignment of 4_concatenated_alignments.<br> QS<br>   
  QS_Diabelia_Astral. QuartetSampling results fo the ASTRAL tree.<br>
     QS_Diabelia_Raxml. QuartetSampling results fo the RAxML
 tree.<br>     QS_Diabelia_cpDNA_IQtree. QuartetSampling results fo
 the cpDNA tree.<br> cpDNA. Chloroplast alignment and inferred tree
 with Iqtree.<br> phyparts. Phyparts result from the ASTRAL and RAxML
 trees.<br>     <br> If you have any question about data in
 Data_part_1.tar.gz, please do not hesitate to contact Diego F.
 Morales-Briones at dfmoralesb@gmail.com Part 2. File
 called. Data_part_2.tar.gz divertime_nuclear. This
 folder contains the XML input and result files output of the divergence
 time estimation with BEAST for the nuclear data.<br>
 ancestral_area_reconstructions. This folder contain the tre input of the
 ancestral area reconstructions for the nuclear data. If
 you have any question about data in Data_part_2.tar.gz, please do not
 hesitate to contact Xiu-Rong Ke at 1310474618@qq.com or Hua-Feng Wang at
 hfwang@hainanu.edu.cn