DOI: 10.5061/dryad.wstqjq2wm
title: Data for: Phylogenetic resolution and conflict in the species-rich flowering plant family Leguminosae

description: The Tree of Life is central to evolutionary biology, yet resolving deep,
 recalcitrant phylogenetic relationships remains challenging due to complex
 processes such as incomplete lineage sorting (ILS), hybridization, and
 polyploidization. Although previous phylogenetic studies have advanced our
 understanding of Leguminosae (Fabaceae), a species-rich and ecologically
 diverse family, many deep relationships at the tribal and higher levels
 remain unresolved. Integrating newly generated genome skimming data for
 231 species with previously issued plastid genomic, mitochondrial genomic
 and transcriptomic data, we reconstructed a phylogeny of the family using
 whole plastome, 39 mitochondrial genes, and 1559 low-copy nuclear genes,
 achieving dense taxonomic sampling across almost all recognized tribes and
 major unplaced lineages. Our results supported the monophyly of the six
 subfamilies and 49 recognized tribes, resolved ten clades worthy of
 recognition as new tribes in subfamily Papilionoideae, and clarified many
 contentious relationships. However, nuclear-nuclear and cytonuclear
 conflicts persists at multiple nodes among trees inferred from different
 datasets and analytical methods. We propose the most probable resolution
 for 22 contentious nodes by applying nuclear gene-tree quartet analysis
 and corroboration from support of nuclear Maximum Likelihood (ML) and
 ASTRAL trees. Our results indicate ILS significantly contributes to
 observed phylogenetic conflicts, while gene flow represents an additional
 and previously underappreciated factor that mainly contributes to
 cytonuclear conflicts, particularly along the branches of the
 Angylocalyceae + Dipterygeae + Amburaneae (ADA) clade and Wisterieae. Both
 processes likely underlie recalcitrant phylogenetic relationships, such as
 those within the 50-kb inversion clade of Papilionoideae. Our study uses
 multiple data partitions and analytical methods to resolve contentious
 phylogenetic relationships in Leguminosae, resulting in a robust
 phylogenomic framework to guide further investigations in this
 economically important and exceptionally diverse family.
description: All these files were produced during the sampling, designing, and
 analyzing processes.
description: # Data for: Phylogenetic resolution and conflict in the species-rich
 flowering plant family Leguminosae
 [https://doi.org/10.5061/dryad.wstqjq2wm](https://doi.org/10.5061/dryad.wstqjq2wm) ## Description of the data and file structure All these files were produced during the sampling, designing, and analyzing processes. ### Files and variables #### Mito-39CDSs-aln.zip This folder contains multiple sequence alignments used for phylogenetic analyses. Files are in FASTA format. File names indicate 39 mitochondrial protein coding sequences' alignments These alignments was aligned using MAFFT v7.475. #### Mito-39genes-aln.zip This folder contains multiple sequence alignments used for phylogenetic analyses. Files are in FASTA format. File names indicate 39 mitochondrial protein coding gene' alignments These alignments are different to the above alignments because they include introns. These alignments were aligned using MAFFT v7.475. #### Mito-9introns.aln.zip This folder contains multiple sequence alignments used for phylogenetic analyses. Files are in FASTA format. File names indicate 9 mitochondrial intron sequences' alignments. These alignments was aligned using MAFFT v7.475. #### MG39.fas.reduced.fas This file contains a dataset concatenated from 39 mitochondrial genes's alignments, is used  to construct the maximum likelihood phylogentic tree of 459 samples. This file is provided in FASTA format. #### MG39-pf.txt.reduced This file provides the gene partition information for the "MG39.fas.reduced.fas" dataset. #### PCN203_696-2.nogap.fa This file contains the PCN203 dataset of plastomes, including all 203 plastid loci––both coding and noncoding, which is used to construct the PCN203 ML tree. Files are in FASTA format. #### PCN203_696-2.parts This file provides the gene partition information for the "PCN203_696-2.nogap.fa" dataset. #### Platstome.122intergenes.aln.zip This folder contains 122 plastomic noncoding alignments, which was used to construct the PN122 ML tree. Files are in FASTA format. #### Platstome.81genes.aln.zip This folder contains 81 plastomic gene's alignments, which was used to construct the PC81 ML tree. #### Supplemental_file_1_newicktrees.zip This folder contains inferred 17 phylogenetic trees in Newick format in this study. Trees were inferred using maximum likelihood or coalescent-based methods. *X1_PCN203.ML.concord.cf.tre* was constructed by 203 coding and noncoding sequences using RAxML v8.1.2 and evaluated gene concordance (gCF) in IQ-Tree v1.6.6. *X2_PCN203.ASTRAL.concord.cf.tre* was constructed by 203 coding and noncoding gene trees using ASTRAL-III v5.1.170 and evaluated gene concordance (gCF) in IQ-Tree v1.6.6. *X3_Nucl1559.ML.concord.cf.tre* was constructed by 1559 nuclear orthologs (this dataset was procuded in Zhao et al, 2021) using RAxML v8.1.2 and evaluated gene concordance (gCF) in IQ-Tree v1.6.6. *X4_Nucl1559.ASTRAL.concord.cf.tre* was constructed by 1559 gene trees of nuclear orthologs (this dataset was procuded in Zhao et al, 2021) using ASTRAL-III v5.1.170 and evaluated gene concordance (gCF) in IQ-Tree v1.6.6. *X5_PCN203.ASTRAL.MLBScutoff10.tre* was constructed by 203 coding and noncoding gene trees (cutoff boostrap support=10%) using ASTRAL-III v5.1.170 and evaluated gene concordance (gCF) in IQ-Tree v1.6.6. *X6_PC81.ML.tre* was constructed by the 81 genes' concatenated aligment using RAxML v8.1.2. *X7_PN122.ML.tre* was constructed by the 122 noncoding sequences' concatenated aligment using RAxML v8.1.2. *X8_PCN203-trimAl.ML.tre* was constructed by the 203 coding and noncoding sequences' concatenated aligment using RAxML v8.1.2. These gene alignments were trimed by trimAl using default parameters. *X9_PC81-trimAl.ML.tre* was constructed by the 81 genes' concatenated aligment using RAxML v8.1.2. These gene alignments were trimed by trimAl using default parameters. *X10_PN122-trimAl.ML.tre* was constructed by the 122 noncoding sequences' concatenated aligment using RAxML v8.1.2. These gene alignments were trimed by trimAl using default parameters. *X11_Nucl1559.ASTRAL.MLBScutoff10.tre* was constructed by the 1559 nuclear gene trees (cutoff boostrap support = 10%) using ASTRAL-III v5.1.170 and evaluated gene concordance (gCF) in IQ-Tree v1.6.6. *X12_MG39.ML.tre* was constructed by the 39 mitochondrial genes' concatenated aligment using RAxML v8.1.2. *X13_MG39-trimAl.ML.tre* was constructed by the 39 mitochondrial genes' concatenated aligment using RAxML v8.1.2. These gene alignments were trimed by trimAl using default parameters. *X14_MC39.ML.tre* was constructed by the 39 mitochondrial genes' concatenated aligment using RAxML v8.1.2. *X15_MC39-trimAl.ML.tre* was constructed by the 39 mitochondrial coding regions' concatenated aligment using RAxML v8.1.2. These alignments were trimed by trimAl using default parameters. *X16_MI9.ML.tre* was constructed by the 9 mitochondrial introns' concatenated aligment using RAxML v8.1.2. *X17_MI9-trimAl.ML.tre* was constructed by the 9 mitochondrial introns' concatenated aligment using RAxML v8.1.2. These alignments were trimed by trimAl using default parameters. #### sub-51plastomes.gb.zip This folder includes 51 plastomes' gb files, which are incomplete plastomes assembled from genome skimming data using GetOrganelle v1.6.3. All plastome information were available in the supplemental Table S1 of the journal website. #### scripts.zip This folder contains scripts used to generate figures or summary statistics. Scripts are provided for reference but may require external R software and packages. ## Access information Our new sequencing data will be uploaded to a public database following the manuscript review process. Other data in this study are sourced from the following databases and articles. Other publicly accessible locations of the data: * [https://doi.org/10.5061/dryad.1vhhmgqpb](https://doi.org/10.5061/dryad.1vhhmgqpb). * GenBank ([https://www.ncbi.nlm.nih.gov/genbank/](https://www.ncbi.nlm.nih.gov/genbank/)): accession numbers are found in supplemental Table S1.