Genomic blueprints of marine-freshwater transitions: How South American silversides (Odontesthes) conquered the salinity gradient

This repository contains the processed data and custom analysis scripts supporting the results of the study on marine-freshwater divergence in the genus Odontesthes. The archive includes: Genome QC metrics (BUSCO summaries). ddRAD-seq data: ipyrad parameter files, filtered VCF files for four evolutionary contrasts, and R scripts for population genomic scans (pcadapt, BayPass) and shared outlier detection. RNA-seq data: Gene count matrices, variant calling outputs, and R scripts for differential expression analysis (PCA, Volcano plots) and functional enrichment visualization. Machine-readable versions (.csv) of all Supplementary Tables. A detailed README.txt file is included in the archive, providing instructions on software dependencies, file descriptions, and workflow reproduction. All raw sequencing data are available in the NCBI SRA under the following BioProject accession numbers: PRJNA546013 (Hughes et al., 2020), PRJNA796799 (González-Castro et al., 2022), PRJNA1135156 (Briñoccoli et al., 2025), PRJNA1359383 (Briñoccoli et al., 2026) and PRJNA311227 (Hughes et al., 2017, previously published RNA-seq data reanalyzed in this study).