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Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

Citation

Ke, Xiu-Rong et al. (2021), Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae), Dryad, Dataset, https://doi.org/10.5061/dryad.xd2547dhw

Abstract

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.

Usage Notes

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)
2_trees. RAxML bipartition labeled trees (*.tre).
3_masked_mono_para_tips. Trees from 2_trees with masked monophyletic and grades of the same species.
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.
5_orthologs
    1_final_orthologs. MO orthologs pruned from trees of 4_masked_spurious_tips.
    2_fasta_files_from_orthologs. Individual fasta file from the MO orthologs (*.fa)
    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.
    4_concatenated_alignments. Concatenated alignments of the individual clean alignments of 3_fasta_to_tree
6_Analyses

ASTRAL. ASTRAL species trees from all trees from 5_orthologs/3_fasta_to_tree.
Phylonet
    1_fasta_to_tree. Alignments and RAxML trees from the 15-taxa reduced data set.
    2_rooted_trees. Rooted trees from 1_fasta_to_tree.
    3_Phylonet. Phylonet results from MPL analyses from 1-5 hybridization events.
RAxML. RAxML tree from the alignment of 4_concatenated_alignments.
QS
    QS_Diabelia_Astral. QuartetSampling results fo the ASTRAL tree.
    QS_Diabelia_Raxml. QuartetSampling results fo the RAxML tree.
    QS_Diabelia_cpDNA_IQtree. QuartetSampling results fo the cpDNA tree.
cpDNA. Chloroplast alignment and inferred tree with Iqtree.
phyparts. Phyparts result from the ASTRAL and RAxML trees.
    
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.
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