Scripts for genomic insights on conservation priorities for global snow leopards.
Read alignment and preprocessing of raw sequencing data, including quality control, mapping to the reference genome, sorting, and duplicate removal.
Variant calling pipeline, including individual GVCF generation and joint genotyping to produce a unified variant dataset across all samples.
Principal Component Analysis (PCA) to infer population structure based on genome-wide SNP data.
Phylogenetic tree construction using genome-wide variants to infer evolutionary relationships among individuals or populations.
Population structure analysis using ADMIXTURE, including estimation of ancestry proportions and cross-validation to determine optimal K.
Genome-wide heterozygosity estimation for each individual.
Detection of runs of homozygosity (ROH) to assess inbreeding levels and demographic history.
Estimation of mutational load, including annotation and classification of deleterious variants.
Inference of population splits and gene flow using TreeMix.
D-statistics (ABBA-BABA related tests) using Dsuite to detect introgression signals.
Additional ABBA-BABA analyses to quantify gene flow among populations.
Demographic history inference using MSMC2, including effective population size changes over time.
Approximate Bayesian Computation (ABC)-based estimation of population size history.
Admixture graph modeling using qpGraph to test complex evolutionary scenarios.
Demographic modeling using fastsimcoal to infer population parameters under different evolutionary models.
Forward simulations using SLiM to model evolutionary processes and validate demographic scenarios.
Analysis of climate adaptation signals, including environmental association and genomic offset estimation.
All scripts are designed to reproduce the analyses described in the manuscript. Users should adapt file paths and parameters according to their own datasets.