Data for: Phylogenetic resolution and conflict in the species-rich flowering plant family Leguminosae

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,..., All these files were produced during the sampling, designing, and analyzing processes., , # 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 mul...,

生命之树（Tree of Life）是进化生物学的核心研究主题，然而受限于不完全谱系分选（incomplete lineage sorting, ILS）、杂交及多倍化等复杂演化过程，解析深层、顽固的系统发育关系仍极具挑战。尽管此前的系统发育研究已推进了我们对物种丰富、生态多样的豆科（Leguminosae/Fabaceae）的认知，但该科在族级及以上高阶元的诸多深层系统发育关系仍未得到解析。
本研究整合了231个物种的全新基因组浅层测序数据（genome skimming data），以及已公开发布的质体基因组（plastid genome）、线粒体基因组（mitochondrial genome）与转录组数据（transcriptomic data），通过全质体基因组（whole plastome）、39个线粒体基因以及1559个低拷贝核基因（low-copy nuclear genes）重构了该科的系统发育树，在几乎所有已确认的族与主要未归类支系上实现了高密度的类群采样。研究结果支持6个亚科及49个已确认族的单系性（monophyly），解析出10个可被认定为蝶形花亚科（Papilionoideae）新族的支系……所有文件均产生于采样、实验设计与数据分析流程中。
# 数据关联研究：物种丰富的显花植物豆科的系统发育解析与系统冲突
[https://doi.org/10.5061/dryad.wstqjq2wm]

## 数据与文件结构说明
所有文件均产生于采样、实验设计与数据分析流程中。

### 文件与变量说明
#### Mito-39CDSs-aln.zip
该压缩包包含用于系统发育分析（phylogenetic analyses）的多序列比对文件，文件格式为FASTA格式。文件名对应39个线粒体蛋白编码序列的比对结果，比对使用MAFFT v7.475完成。

#### Mito-39genes-aln.zip
该压缩包包含用于系统发育分析（phylogenetic analyses）的多序列比对文件，文件格式为FASTA格式。文件名对应39个线粒体蛋白编码基因的比对结果。与上述比对文件不同，该组比对包含内含子区域，比对使用MAFFT v7.475完成。

#### Mito-9introns.aln.zip
该压缩包包含多……