DOI: 10.5061/dryad.v6wwpzgx8
title: Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization

description: • Background and Aims Abelia (Caprifoliaceae) is a small genus with five
 species, including one man-made hybrid and several natural hybrids. The
 genus has a discontinuous distribution in Mainland China, the Taiwan
 Island, and the Ryukyu Islands, providing a model system to explore
 mechanisms of species dispersal in the East Asian flora. However, the
 current phylogenetic relationships within Abelia remain uncertain. •
 Methods In this study, we reconstructed the phylogenetic relationships
 within Abelia using nuclear loci generated by target enrichment and
 plastomes from genome skimming. Divergence time estimation, ancestral area
 reconstruction, and ecological niche modelling (ENM) were used to examine
 the diversification history of Abelia. • Key Results We found extensive
 cytonuclear discordance across the genus. By integrating lines of evidence
 from molecular phylogenies, divergence times, and morphology, we propose
 to merge A. macrotera var. zabelioides into A. uniflora. Network analyses
 suggested that there have been widespread and multiple hybridization
 events among Abelia species. These hybridization events may have
 contributed to the speciation mechanism and resulted in a high observed
 morphological diversity. The diversification of Abelia began in the early
 Eocene, followed by A. chinensis var. ionandra colonizing the Taiwan
 Island in the Middle Miocene. The ENM results suggested an expansion of
 climatically suitable areas during the Last Glacial Maximum and range
 contraction during the Last Interglacial. Disjunction between the
 Himalayan-Hengduan Mountain region (HHM) and the Taiwan Island is most
 likely the consequence of topographic isolation and postglacial
 contraction. • Conclusions We used genomic data to reconstruct the
 phylogeny of Abelia and found a clear pattern of reticulate evolution in
 the group. In addition, our results support shrinkage of postglacial range
 and the heterogeneity of the terrain have led to the disjunction of the
 Mainland China-Taiwan Island. This study provides important new insights
 into the speciation process and taxonomy of Abelia.
description: DATA PACKAGE FROM SUN ET AL (ANNALS OF BOTANY)
 Phylogenomic analyses of the East Asian endemic Abelia
 (Caprifoliaceae) shed insights into the temporal and spatial
 diversification history with widespread hybridization
 This package contains the data and software outputs (i.e. fasta
 filtes, alignments, trees, etc). Part 1. File called.
 Data_part_1.tar.gz <br> 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), and boostrapt trees (*.trees) from each of the
 alignments of 1_alignments.<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>  <br> 5_orthologs<br>  <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 <br> ASTRAL. ASTRAL species trees from
 all trees from 5_orthologs/3_fasta_to_tree.<br> Iqtree. IQ-TREE tree
 from the alignment of 4_concatenated_alignments.<br>
 Phylonet<br>     12_taxa_E48<br>         1_fasta_to_tree.
 Alignments and RAxML trees from the 12-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>     15_taxa<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> QS<br>     QS_Abelia_Astral. QuartetSampling
 results fo the ASTRAL tree.<br>     QS_Abelia_IQtree.
 QuartetSampling results fo the cpDNA tree<br>     QS_Abelia_cpDNA.
 QuartetSampling results fo the RAxML tree cpDNA.
 Chloroplast alignment and inferred tree with Iqtree.
 <br> If you have any questions about data in
 Data_part_1.tar.gz, please do not hesitate to contact Diego F.
 Morales-Briones at dfmoralesb@gmail.com  
 <br> Part 2. File called. Data_part_2.tar.gz
 divertime_chroloplast. This folder contains the XML input and
 nexus files output of the divergence time estimation with BEAST for the
 cpDNA data.<br> divertime_nuclear. This folder contains the XML
 input and nexus files output of the divergence time estimation with BEAST
 for the nuclear data.<br> ancestral_area_reconstructions. This
 folder contains the tre input of the ancestral area reconstructions for
 the nuclear data.<br> Ecological_niche_modelling. This folder
 contains the csv input and asc files output of the ecological niche
 modelling. If you have any questions about data in
 Data_part_2.tar.gz, please do not hesitate to contact Qing-Hui Sun at
 378618006@qq.com or Huafeng Wang at hfwang@hainanu.edu.cn