ArticleNature communications2024
Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Global-scale population genetic analysis of Plasmodium falciparum identifies region-specific patterns of malaria parasite adaptation.Nature communications · 2026Article
- PvGTSeq and PvCRiSP: Two amplicon-based targeted sequencing panels for Plasmodium vivax.PLoS neglected tropical diseases · 2026Article
- Multiple-testing corrections in case-control studies using identity-by-descent segments.American journal of human genetics · 2026Article
- hmmibd-rs: an enhanced hmmIBD implementation for parallelizable identity-by-descent detection from large-scale Plasmodium genomic data.Malaria journal · 2026Article
- Article
- TS-IBD: An efficient ancestral recombination graph-based identity by descent segment detection method.Human population genetics and genomics · 2026Article
- Towards an evolutionary baseline model ofbioRxiv : the preprint server for biology · 2025Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.American journal of human genetics · 2025Article
- Inference of complex demographic history using composite likelihood based on whole-genome genealogies.bioRxiv : the preprint server for biology · 2025Article
- Identity-by-descent segments in large samples.Theoretical population biology · 2025Article
- Benchmarking and optimization of methods for the detection of identity-by-descent in high-recombiningeLife · 2025Article
- Multiple-testing corrections in case-control studies using identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
- Article
- Cryptic absence and genetic variation of Plasmodium falciparum PfHRP2 and PfHRP3 from isolates in Papua, Indonesia.Scientific reports · 2025Article
- Fast simulation of identity-by-descent segments.Bulletin of mathematical biology · 2025Article
- Systematic bias in malaria parasite relatedness estimation.G3 (Bethesda, Md.) · 2025Article
- Potential and pitfalls of using identity-by-descent for malaria genomic surveillance.Trends in parasitology · 2025Review
- MalKinID: A classification model for identifying malaria parasite genealogical relationships using identity-by-descent.Genetics · 2025Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
- Fast simulation of identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
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Abstract
Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD), yet strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we use simulations, a true IBD inference algorithm, and empirical data sets from different malaria transmission settings to investigate the extent of this bias and explore potential correction strategies. We analyze whole genome sequence data generated from 640 new and 3089 publicly available Plasmodium falciparum clinical isolates. We demonstrate that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discover that the removal of IBD peak regions partially restores the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness and extent of inbreeding. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.
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