10.5061/DRYAD.XD2547DHW
Ke, Xiu-Rong
Hainan University
Morales-Briones, Diego F.
0000-0003-1535-5739
Ludwig Maximilian University of Munich
Wang, Hong-Xin
Hainan University
Sun, Qing-Hui
Hainan University
Landis, Jacob B.
Cornell University
Wen, Jun
Smithsonian Institution
Wang, Hua-Feng
Hainan University
Nuclear and plastid phylogenomic analyses provide insights into the
reticulate evolution, species delimitation and biogeography of the
Sino-Japanese disjunctive Diabelia (Caprifoliaceae)
Dryad
dataset
2021
2021-11-18T00:00:00Z
2021-11-18T00:00:00Z
en
https://doi.org/10.1101/2021.05.31.446416
695142603 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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