This repository contains data and trees associated with the article: Rincon-Sandoval M, Betancur-R R, Maldonado-Ocampo J.A. Comparative Phylogeography of Trans-Andean Freshwater Fishes Based on Genome-Wide Nuclear and Mitochondrial Markers The file library_samples_otophysi.csv contains sample information including: locality, associated specimen and tissues number, and data availability information. The file target_capture.csv contains target capture information showing total length of the alignments by individuals, number of loci and locus length. The file mitogenomes.csv contains mitogenome information by individuals with the respective sequence length in base pairs. Additionally, there are four directories, containing data and trees 1. Master Reference: contains a fasta file with the master references of Danio rerio 2. Alignments: contains two nexus files with the concatenated datasets including partitions for exon loci and mitochondrial DNA. 3. BPP: contains information about 70 random loci utilized in each analysis and seven libraries (a library by species) containing information about every random analysis 4. SNPs: contains three libraries SNAPP contains SNPs alignment in fasta file and a xml file by species STRUCTURE contains structure project data and a joblist file by species SVD contains nexus files of unlinked SNPs with the taxpartitions 5. Trees: contains three libraries BI contains bayesian trees inferred from mitogenomic DNA PCF contains species trees inferred with *BEAST and SNAPP used as input data for PCF analyses RAxML contains maximum likelihood trees inferred from concatenated nuclear loci and mitogenomic DNA.