• 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.

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

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), and boostrapt trees (*.trees) from each of the alignments of 1_alignments.
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.
Iqtree. IQ-TREE tree from the alignment of 4_concatenated_alignments.
Phylonet
    12_taxa_E48
        1_fasta_to_tree. Alignments and RAxML trees from the 12-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.
    15_taxa
        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.
QS
    QS_Abelia_Astral. QuartetSampling results fo the ASTRAL tree.
    QS_Abelia_IQtree. QuartetSampling results fo the cpDNA tree
    QS_Abelia_cpDNA. QuartetSampling results fo the RAxML tree

cpDNA. Chloroplast alignment and inferred tree with Iqtree.

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

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.
divertime_nuclear. This folder contains the XML input and nexus files output of the divergence time estimation with BEAST for the nuclear data.
ancestral_area_reconstructions. This folder contains the tre input of the ancestral area reconstructions for the nuclear data.
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