Mesopotamian ancient DNA reveals Iron Age integration of heterogeneous Bronze Age genetic ancestries following resettlement

# BakrAwa_aDNACustom scripts to perform downstream analyses of qpWave and outgroup f3-statistic tests. ## Analysis Scripts This repository contains the R code used to generate the statistical results and figures. ### File Descriptions * **`qpWave_Permutation_Enrichment_Test.R`**: * **Purpose:** Tests for significant clade enrichment between the target individual and individuals from the surrounding meta-regions. * **Input:** Processed qpWave RDS files and metadata maps. * **Output:** Enrichment statistics tables for ChL-EBA, EBA-LBA, and IA-Hist periods. * **`Bayesian_GLM_PopStruct_Correction.R`**: * **Purpose:** Runs a Bayesian GLM (MCMCglmm) to predict significant connections to the surrounding meta-regions while controlling for genetic structure. * **Usage:** Designed to be run via command line (e.g., `Rscript Bayesian_GLM_Kinship_Correction.R `). * **Output:** Diagnostic plots (Trace, PPC, ROC) and summary tables of Log-Odds and genetic variance. * **`Within_Region_F3_Diversity_Analysis.R`**: * **Purpose:** Assesses genetic homogeneity within meta-regions. * **Method:** Uses `1 - F3` as a dissimilarity metric and performs `betadisper` analysis (multivariate homogeneity of groups dispersions). * **Output:** Violin plots, heatmaps, and statistical test results (ANOVA/Permutation).