ArticleG3 (Bethesda, Md.)2016
Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution.
Article in G3 (Bethesda, Md.), 2016. 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.
- TS-IBD: An efficient ancestral recombination graph-based identity by descent segment detection method.Human population genetics and genomics · 2026Article
- Runs of Homozygosity and Inferences in Wild Populations.Molecular ecology · 2025Review
- Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Estimating evolutionary and demographic parameters via ARG-derived IBD.PLoS genetics · 2025Article
- Estimating evolutionary and demographic parameters via ARG-derived IBD.bioRxiv : the preprint server for biology · 2024Article
- Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques.bioRxiv : the preprint server for biology · 2024Article
- Accurate detection of identity-by-descent segments in human ancient DNA.Nature genetics · 2024Article
- Recombination map tailored to Native Hawaiians may improve robustness of genomic scans for positive selection.Human genetics · 2024Article
- Methods for Assessing Population Relationships and History Using Genomic Data.Annual review of genomics and human genetics · 2023Review
- Demographic inference for spatially heterogeneous populations using long shared haplotypes.bioRxiv : the preprint server for biology · 2023Article
- Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt.Molecular biology and evolution · 2022Article
- A genealogical estimate of genetic relationships.American journal of human genetics · 2022Article
- Parental relatedness through time revealed by runs of homozygosity in ancient DNA.Nature communications · 2021Article
- Fast and Robust Identity-by-Descent Inference with the Templated Positional Burrows-Wheeler Transform.Molecular biology and evolution · 2021Article
- Genetic substructure and complex demographic history of South African Bantu speakers.Nature communications · 2021Article
- Population collapse in Congo rainforest from 400 CE urges reassessment of the Bantu Expansion.Science advances · 2021Article
- Current Developments in Detection of Identity-by-Descent Methods and Applications.Frontiers in genetics · 2021Review
- Probabilistic Estimation of Identity by Descent Segment Endpoints and Detection of Recent Selection.American journal of human genetics · 2020Article
- Population-Specific Recombination Maps from Segments of Identity by Descent.American journal of human genetics · 2020Article
- A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data.American journal of human genetics · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Identity-by-descent (IBD) is a fundamental concept in genetics with many applications. In a common definition, two haplotypes are said to share an IBD segment if that segment is inherited from a recent shared common ancestor without intervening recombination. Segments several cM long can be efficiently detected by a number of algorithms using high-density SNP array data from a population sample, and there are currently efforts to detect shorter segments from sequencing. Here, we study a problem of identifiability: because existing approaches detect IBD based on contiguous segments of identity-by-state, inferred long segments of IBD may arise from the conflation of smaller, nearby IBD segments. We quantified this effect using coalescent simulations, finding that significant proportions of inferred segments 1-2 cM long are results of conflations of two or more shorter segments, each at least 0.2 cM or longer, under demographic scenarios typical for modern humans for all programs tested. The impact of such conflation is much smaller for longer (> 2 cM) segments. This biases the inferred IBD segment length distribution, and so can affect downstream inferences that depend on the assumption that each segment of IBD derives from a single common ancestor. As an example, we present and analyze an estimator of the de novo mutation rate using IBD segments, and demonstrate that unmodeled conflation leads to underestimates of the ages of the common ancestors on these segments, and hence a significant overestimate of the mutation rate. Understanding the conflation effect in detail will make its correction in future methods more tractable.
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