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 Parada
Departamento 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. Lessa
FilesSupplementary 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 dataset

Mitochondrial 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 datasets
Ultraconserved ElementsFile: IQ-TREE.zip
Description: 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 datasets
The 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.part
conda create -n amas python=3 pipconda 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