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A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

Citation

Wang, Hong-xin et al. (2021), A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily, Dryad, Dataset, https://doi.org/10.5061/dryad.tx95x69xj

Abstract

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.

Usage Notes

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)  
 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. Clean alignments (MAFFT and Phyx) from 1_final_orthologs.
     3_concatenated_alignments. Concatenated alignments of the individual clean alignments of 3_concatenated_alignments.
     4_gene_trees. RAxML trees from alignments of 3_concatenated_alignments.
     5_rooted_trees.
        all_rooted. Rooted trees from 4_gene_trees
        no_root. Trees without root.
     6_analyses
         ASTRAL. ASTRAL species trees from all trees from 4_gene_trees
         Phylonet
            11_taxa
               1_fasta_to_tree. Alignments and RAxML trees from the 11-taxa reduced data set.
               2_rooted_trees. Rooted trees from 1_fasta_to_tree
               3_analyses. Phylonet results from MPL analyses from 1-5 hybridization events.
            7_taxa
               1_taxa_to_tree. Alignments and RAxML trees from the 7-taxa reduced data set.
               2_rooted_trees. Rooted trees from 1_fasta_to_tree
               3_analyses. Phylonet results from MPL analyses from 1-5 hybridization events.
            9_taxa
                1_fasta_to_tree. Alignments and RAxML trees from the 9-taxa reduced data set.
                2_rooted_trees. Rooted trees from 1_fasta_to_tree
                3_analyses. Phylonet results from MPL analyses from 1-5 hybridization events.
         Phyparts. Phyparts result from the ASTRAL, RAxML, cpDNA tree.
         QuartetSampling.
            QS_ASTRAL. QuartetSampling results fo the ASTRAL tree.
            QS_cpDNA. QuartetSampling results fo the cpDNA tree
            QS_RAxML. QuartetSampling results fo the RAxML tree
         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.
character_chroloplast_and_nuclear. This folder contains the morphological character coding matrix, and the output of Mesquite for the nuclear and cpDNA data.
cpDNA. This folder contains the cpDNA alignment and the inferred tree with RAxML.
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.


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