DOI: 10.5061/dryad.tx95x69xj
title: A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

description: The use of diverse datasets in phylogenetic studies aiming for
 understanding evolutionary histories of species can yield conflicting
 inference. Phylogenetic conflicts observed in animal and plant systems
 have often been explained by hybridization, incomplete lineage sorting
 (ILS), or horizontal gene transfer. Here, we employed target enrichment
 data and species tree and species network approaches to infer the backbone
 phylogeny of the family Caprifoliaceae, while distinguishing among sources
 of incongruence. We used 713 nuclear loci and 46 protein-coding sequences
 of plastome data from 43 samples representing 38 species from all major
 clades to reconstruct the phylogeny of the group using concatenation and
 coalescence approaches. We found significant nuclear gene tree conflict as
 well as cytonuclear discordance. Additionally, coalescent simulations and
 phylogenetic species network analyses suggest putative ancient
 hybridization among subfamilies of Caprifoliaceae, which seems to be the
 main source of phylogenetic discordance. Ancestral state reconstruction of
 six morphological characters revealed some homoplasy for each character
 examined. By dating the branching events, we inferred the origin of
 Caprifoliaceae at approximately 69.38 Ma in the late Cretaceous. By
 integrating evidence from molecular phylogeny, divergence times, and
 morphology, we herein recognize Zabelioideae as a new subfamily in
 Caprifoliaceae. This work shows the necessity to use a combination of
 multiple approaches to identify the sources of gene tree discordance. Our
 study also highlights the importance of using data from both nuclear and
 chloroplast genomes to reconstruct deep and shallow phylogenies of plants.
description: DATA PACKAGE FROM Wang ET AL (JOURNAL OF SYSTEMATICS AND
 EVOLUTION) A phylogenomic perspective on gene tree
 conflict 1 and character evolution in Caprifoliaceae using target
 enrichment data, with Zabelioideae recognized as a new subfamily
 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), 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>  5_orthologs<br>      1_final_orthologs.
 MO orthologs pruned from trees of 4_masked_spurious_tips.<br>     
 2_fasta_files_from_orthologs. Clean alignments (MAFFT and Phyx) from
 1_final_orthologs.<br>      3_concatenated_alignments. Concatenated
 alignments of the individual clean alignments of
 3_concatenated_alignments.<br>      4_gene_trees. RAxML trees from
 alignments of 3_concatenated_alignments.<br>     
 5_rooted_trees.<br>         all_rooted. Rooted trees from
 4_gene_trees<br>         no_root. Trees without root.<br>     
 6_analyses<br>          ASTRAL. ASTRAL species trees from all trees
 from 4_gene_trees<br>          Phylonet<br>            
 11_taxa<br>                1_fasta_to_tree. Alignments and RAxML
 trees from the 11-taxa reduced data set.<br>               
 2_rooted_trees. Rooted trees from 1_fasta_to_tree<br>               
 3_analyses. Phylonet results from MPL analyses from 1-5 hybridization
 events.<br>             7_taxa<br>               
 1_taxa_to_tree. Alignments and RAxML trees from the 7-taxa reduced data
 set.<br>                2_rooted_trees. Rooted trees from
 1_fasta_to_tree<br>                3_analyses. Phylonet results from
 MPL analyses from 1-5 hybridization events.<br>            
 9_taxa<br>                 1_fasta_to_tree. Alignments and RAxML
 trees from the 9-taxa reduced data set.<br>                
 2_rooted_trees. Rooted trees from 1_fasta_to_tree<br>        
         3_analyses. Phylonet results from MPL analyses from 1-5
 hybridization events.<br>          Phyparts. Phyparts result from
 the ASTRAL, RAxML, cpDNA tree.<br>         
 QuartetSampling.<br>             QS_ASTRAL. QuartetSampling results
 fo the ASTRAL tree.<br>             QS_cpDNA. QuartetSampling
 results fo the cpDNA tree<br>             QS_RAxML. QuartetSampling
 results fo the RAxML tree<br>          RAxML. RAxML tree from the
 alignment of 3_concatenated_alignments. 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
 baits-Moderate-RM25pc-17056.fas. This file contains the baits
 designed for Dipsacales.<br> character_chroloplast_and_nuclear. This
 folder contains the morphological character coding matrix, and the output
 of Mesquite for the nuclear and cpDNA data.<br> cpDNA. This folder
 contains the cpDNA alignment and the inferred tree with RAxML.<br>
 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> If you have any question about
 data in Data_part_2.tar.gz, please do not hesitate to contact Hong-Xin
 Wang at 854616397@qq.com or Huafeng Wang at
 hfwang@hainanu.edu.cn