Accompanying data files for "Ancient DNA reveals that natural selection has upregulated the immune system over the last 10,000 years"

This repository contains: 

1. LMM selection summary statistics, including versions restricted to HapMap3 SNPs (we also provide deflated GLMM selection Z-scores, used for locus discovery). 
2. Per-chromosome fine-mapping results using LMM selection statistics (including 95% credible sets), performed as described in the Materials and Methods. 
3. GWAS summary statistics analyzed in this study, other than the ones generated by the FinnGen consortium, which can be accessed at https://www.finngen.fi/en/access_results. 
4. gsMap results for LMM selection statistics analyzed with the human-gut single-cell, spatial transcriptomics dataset by (Hickey et al. 2023, Nature), as described in the Materials and Methods. We provide:
   1. Raw gsMap output for each sample, when annotating cells by 1 of 4 increasingly fine-grained annotations.
   2. Annotation-level enrichment p-values across all intestinal regions, or across all samples for a given intestinal region, obtained by the gsMap Cauchy aggregation test. We include plots for annotation-level p-values (subfolder per-annotation_enrichment_pval_plots).