Supplementary Material: Are the Heteromyidae paraphyletic? Molecular phylogenetics of extant geomyoid rodents

Description of the data and file structureAre the Heteromyidae paraphyletic? Molecular phylogenetics of extant geomyoid rodentsEnrique P. Lessa* and Andrés ParadaDepartamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República. Iguá 4225, Montevideo 11400, Uruguay. E-mail: [e-mail] (EPL); [e-mail] (AP).*Corresponding author: Enrique P. LessaFilesSupplementary Table 1Table containing accession number for the mitochondrial data, mitochondrial dataset stats, partition scheme and substitution model for each loci, UCE dataset stats, partition scheme and substitution model for each loci and Summary stats for each datasetMitochondrial DatasetFile: Mitochondrial.zipDescription: The analysis of 2 mitochondrial dataset was conducted as follows:Mitochondrial dataset: the 13 protein-coding mitochondrial DNA genes (for 13 species).Mitochondrial dataset: matrix of 12s, 16s, and COX1 loci (for 43 species).Mitochondrial.zip contains the following files:Archives with the extension .fas, .part and .tree denote the alignment, the partition file and the best tree with support for this datasetsUltraconserved ElementsFile: IQ-TREE.zipDescription: The analysis of 2 ultraconserved elements dataset was conducted as follows:Ultraconserved dataset: a matrix of 3991 loci, allowing for up to 2 taxa missing per locus (for 9 species).Ultraconserved dataset: a matrix of 1750 loci (no missing data).The IQ-TREE.zip file contains the results of the concatenated approach.Archives with the extension .fas, .part and .tree denote the alignment, the partition file and the best tree with support for this datasetsThe ASTRAL.zip file contains the results of the coalescent approach.Archives with the extension .trees contain the topologies searched.File: ASTRAL.zipDescription:The topology of either the 1750 or 3991 dataset are identical. ASTRAL_3991_SCORED.tree is the species tree recovered with ASTRAL and the associated node support.Individual AlignmentsEach alignment can be reconstructed splitting the .fas file with a tool such as AMAS and omitting the first column of the partition file e.g.awk '{ print $2" "$3" "$4}' mito13x13.part > AMAS-mito13x13.partconda create -n amas python=3 pipconda activate amaspip install amasgh repo clone marekborowiec/AMASpython ./AMAS/amas/AMAS.py split -f fasta -d dna -i mito13x13.fas -l AMAS-mito13x13.part -u fasta

数据与文件结构说明：异鼠科是否为并系群？现存衣囊鼠类啮齿动物的分子系统发育研究
Enrique P. Lessa* 与 Andrés Parada
乌拉圭共和国大学理学院生态与进化系，蒙得维的亚11400，乌拉圭伊瓜大道4225号。
电子邮箱：[e-mail]（EPL）；[e-mail]（AP）。
*通讯作者：Enrique P. Lessa

## 文件说明
### 补充表1
该表格包含线粒体数据登录号、线粒体数据集统计信息、每个基因座的分区方案与替换模型、超保守元件（Ultraconserved Elements, UCE）数据集统计信息、每个基因座的分区方案与替换模型，以及各数据集的汇总统计信息。

### 线粒体数据集
文件：Mitochondrial.zip
说明：本研究针对2组线粒体数据集开展分析，具体如下：
1. 线粒体数据集1：涵盖13个蛋白编码线粒体DNA基因（涉及13个物种）。
2. 线粒体数据集2：包含12S、16S及COX1基因座的序列矩阵（涉及43个物种）。
Mitochondrial.zip 包含以下文件：扩展名为.fas、.part和.tree的归档文件分别对应序列联配文件、分区文件以及带支持度信息的最优拓扑树。

### 超保守元件数据集
文件：IQ-TREE.zip
说明：本研究针对2组超保守元件数据集开展分析，具体如下：
1. 超保守元件数据集1：包含3991个基因座的序列矩阵，每个基因座允许最多2个类群存在缺失数据（涉及9个物种）。
2. 超保守元件数据集2：包含1750个基因座的序列矩阵（无缺失数据）。
IQ-TREE.zip 文件包含串联法分析的结果。扩展名为.fas、.part和.tree的归档文件分别对应序列联配文件、分区文件以及带支持度信息的最优拓扑树。

ASTRAL.zip 文件包含溯祖法分析的结果，扩展名为.trees的归档文件包含所搜索到的拓扑结构。

#### ASTRAL.zip 文件说明
1750与3991数据集的拓扑结构完全一致。ASTRAL_3991_SCORED.tree为通过ASTRAL重建得到的物种树及其对应的节点支持度信息。

### 独立联配文件
各联配文件可通过如下方式重构：使用AMAS等工具拆分.fas格式文件，并省略分区文件的第一列，示例命令如下：
awk '{ print $2" "$3" "$4}' mito13x13.part > AMAS-mito13x13.part
conda create -n amas python=3 pip
conda activate amas
pip install amas
gh repo clone marekborowiec/AMAS
python ./AMAS/amas/AMAS.py split -f fasta -d dna -i mito13x13.fas -l AMAS-mito13x13.part -u fasta