Supplementary Notebooks
Filtering 131,048 SNPs to 110,353 high-quality markers using PLINK: missingness, HWE, MAF, and LD pruning.
View Notebook →Genome-wide FST-based outlier detection identifying loci under divergent selection.
View Notebook →Latent factor mixed model approach to detecting selection using population structure.
View Notebook →LDna (v2.15) identifies Single-Outlier Clusters of SNPs in high LD on chromosomes 1, 2, and 3.
View Notebook →Overlap between 158 selection scan outliers and 793 differentially expressed genes from RNAseq.
View Notebook →Predicted functional effects of outlier SNPs using a custom SnpEff database (AalbF3 genome).
View Notebook →Allele and genotype frequency distributions across AUTO, NON-AUTO, and NON-AUTO-FIELD populations.
View Notebook →Pairwise FST between populations and sliding-window FST across all three chromosomes.
View Notebook →CLI Analysis Pipeline
Run the full analysis from the command line — no notebooks needed. Each step maps to its supplementary notebook. See scripts/README.md for details.
bash scripts/run_pipeline.sh --dry-run
# Run all steps (skips completed)
bash scripts/run_pipeline.sh
| Step | Script | Output | Notebook |
|---|---|---|---|
| 01 | 01_qc/run_qc.sh |
output/quality_control/file7.* | File S1 |
| 02 | 02_selection_scans/run_selection_scans.sh |
output/selection_scans/ | Files S2, S3 |
| 03 | 05_ldna/run_ldna.sh |
output/ldna/ ~45 min, 32 GB RAM | Files S4a–S4e |
| 04 | 03_annotation/run_snpeff.sh |
output/snpeff/ | File S6 |
| 05 | 07_gene_expression/run_gene_expression.sh |
output/gene_expression/ | File S5 |
| 06 | 04_diversity/run_diversity.sh |
output/diversity/, output/fst/ | Files S7, S8 |