ArticlePLoS genetics2019
Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56 citing papers in PubMed.
- Recovering the precolonial population structure of Khoe-San descendant populations.Science advances · 2026Article
- Single Nucleotide Polymorphisms in Distant Kinship Inference and Forensic Genetic Genealogy.International journal of molecular sciences · 2026Review
- The rights and wrongs of rescaling in population genetics simulations.PLoS genetics · 2026Review
- Comparing the genomic inbreeding of an isolated rhesus macaque study population to wild populations.bioRxiv : the preprint server for biology · 2026Article
- From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference.bioRxiv : the preprint server for biology · 2026Article
- Ancient genomes reveal an extensive kinship network and endogamy in a Three-Kingdoms period society in Korea.Science advances · 2026Article
- The rate of identical-by-descent segment sharing between close and distant relatives.HGG advances · 2026Article
- A large mass grave from the Early Iron Age indicates selective violence towards women and children in the Carpathian Basin.Nature human behaviour · 2026Article
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- Evaluating the performance of ancient DNA genetic relatedness estimation methods using high-fidelity pedigree simulations.Genome biology · 2026Article
- Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Ancient genomes from eastern Kazakhstan reveal dynamic genetic legacy of Inner Eurasian hunter-gatherers.Science advances · 2025Article
- Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses.HGG advances · 2025Article
- Recovering the pre-colonial population structure of Khoe-San descendant populations.bioRxiv : the preprint server for biology · 2025Article
- Ancient DNA reveals the population interactions and a Neolithic patrilineal community in Northern Yangtze Region.Nature communications · 2025Article
- Slab Grave expansion disrupted long co-existence of distinct Bronze Age herders in central Mongolia.Nature communications · 2025Article
- Article
- Phase-free local ancestry inference mitigates the impact of switch errors on phase-based methods.G3 (Bethesda, Md.) · 2025Article
- clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.Genomics, proteomics & bioinformatics · 2025Article
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11 authors.
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Abstract
Simulations of close relatives and identical by descent (IBD) segments are common in genetic studies, yet most past efforts have utilized sex averaged genetic maps and ignored crossover interference, thus omitting features known to affect the breakpoints of IBD segments. We developed Ped-sim, a method for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either a model of crossover interference or the traditional Poisson model for inter-crossover distances. To characterize the impact of previously ignored mechanisms, we simulated data for all four combinations of these factors. We found that modeling crossover interference decreases the standard deviation of pairwise IBD proportions by 10.4% on average in full siblings through second cousins. By contrast, sex-specific maps increase this standard deviation by 4.2% on average, and also impact the number of segments relatives share. Most notably, using sex-specific maps, the number of segments half-siblings share is bimodal; and when combined with interference modeling, the probability that sixth cousins have non-zero IBD sharing ranges from 9.0 to 13.1%, depending on the sexes of the individuals through which they are related. We present new analytical results for the distributions of IBD segments under these models and show they match results from simulations. Finally, we compared IBD sharing rates between simulated and real relatives and find that the combination of sex-specific maps and interference modeling most accurately captures IBD rates in real data. Ped-sim is open source and available from https://github.com/williamslab/ped-sim.
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