Data and analysis scripts for "Neutral processes shape genome-wide homogeneity in the deep-shelf shrimp Heterocarpus"

This repository contains the processed genotype datasets, metadata, spatial data, and analysis scripts associated with the manuscript “Neutral processes shape genome-wide homogeneity in the deep-shelf shrimp Heterocarpus.” The principal neutral dataset used for the manuscript conclusions comprises 127 individuals and 91,064 LD-pruned SNPs. A reduced noLowDiff dataset comprising 40,456 LD-pruned SNPs was used as ssensitivity dataset specifically for DAPC, STRUCTURE, and ADMIXTURE to prevent the large number of low-differentiation loci from masking population-structure patterns. The original filtered VCF containing 117,656 variants and 127 individuals is provided as the common starting point for the analyses. The repository includes scripts for outlier detection, dataset preparation, population structure, genetic differentiation, discriminant analysis of principal components, genetic diversity, distance-based analyses, depth correlations, redundancy analysis, and sequencing-quality assessment. Scripts are numbered according to their intended execution order. The README provides software requirements, dependencies, input descriptions, and detailed execution instructions. Raw sequencing reads are deposited separately in the NCBI Sequence Read Archive under the accession reported in the manuscript.