Multiple local expansions of PfDHFR I164L drive evolution of antifolate resistance in Plasmodium falciparum in Uganda

This repository contains datasets supporting the evolution of antifolate resistance in Plasmodium falciparum isolates collected in Uganda. The files include sample metadata, pairwise identity-by-descent (IBD) estimates, network cluster summaries, and drug-resistance genotypes used to investigate parasite-relatedness and selection. Files 1. Network cluster summary: Characteristics of IBD network clusters, including cluster size, average degree, dominant sampling site and genotype, and Shannon diversity indices for site and genotype composition. 2. Pairwise IBD estimates: Pairwise comparisons between parasite isolates with sample identifiers, geographic indicator, and the fraction of the genome shared identical by descent (IBD). 3. Sample metadata: Sample identifier, complexity of infection (COI), sampling site, collection year, and geographic region. 4. Drug-resistance genotypes: Genotypes at codons 164 and 581, including combined genotype classifications (WT-WT, WT-MT, MT-WT, MT-MT). 5. Pairwise IBD with genotype annotations: Integrated dataset containing pairwise IBD values, sampling sites, genotypes for each sample in a pair, and combined genotype comparisons. Dataset relationships Sample identifiers link all datasets. Sample metadata and genotype data describe individual isolates, pairwise IBD estimates quantify genetic relatedness, the integrated pairwise dataset combines relatedness with genotype information, and the network cluster summary provides cluster-level characteristics derived from the IBD network. Keywords: Plasmodium falciparum, malaria, Uganda, identity by descent, IBD, genomic epidemiology, population genomics, drug resistance, molecular surveillance, network analysis.