ArticleMolecular biology and evolution2020
Unbiased Estimation of Linkage Disequilibrium from Unphased Data.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A curated genome-scale nucleotide diversity panel of non-human primates.Genome biology · 2026Article
- Inferring hominin history with recurrent gene flow from single unphased genomes and a two-locus statistic.bioRxiv : the preprint server for biology · 2026Article
- Genomic insights intoFrontiers in plant science · 2026Article
- GHIST 2024: The First Genomic History Inference Strategies Tournament.Molecular biology and evolution · 2025Article
- Effective Population Size Estimation in Large Marine Populations: Considering Current Challenges and Opportunities When Simulating Large Data Sets With High-Density Genomic Information.Evolutionary applications · 2025Review
- Missing genotype imputation in non-model species using self-organizing maps.Molecular ecology resources · 2025Article
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- Background Selection From Unlinked Sites Causes Nonindependent Evolution of Deleterious Mutations.Genome biology and evolution · 2024Article
- Demographic modeling of admixed Latin American populations from whole genomes.American journal of human genetics · 2023Article
- Article
- Review
- A Pipeline for Phasing and Genotype Imputation on Mixed Human Data (Parents-Offspring Trios and Unrelated Subjects) by Reviewing Current Methods and Software.Life (Basel, Switzerland) · 2022Review
- The Linkage-Disequilibrium and Recombinational Landscape in Daphnia pulex.Genome biology and evolution · 2022Article
- Local fitness and epistatic effects lead to distinct patterns of linkage disequilibrium in protein-coding genes.Genetics · 2022Article
- Genetic diversity and marker trait association for phytophthora resistance in chilli.Molecular biology reports · 2022Article
- Linkage disequilibrium between rare mutations.Genetics · 2022Article
- Scalable bias-corrected linkage disequilibrium estimation under genotype uncertainty.Heredity · 2021Article
- Brassica rapa Domestication: Untangling Wild and Feral Forms and Convergence of Crop Morphotypes.Molecular biology and evolution · 2021Article
- Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa.Genome biology and evolution · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Linkage disequilibrium (LD) is used to infer evolutionary history, to identify genomic regions under selection, and to dissect the relationship between genotype and phenotype. In each case, we require accurate estimates of LD statistics from sequencing data. Unphased data present a challenge because multilocus haplotypes cannot be inferred exactly. Widely used estimators for the common statistics r2 and D2 exhibit large and variable upward biases that complicate interpretation and comparison across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, including D2, for both single and multiple randomly mating populations. These unbiased statistics are particularly well suited to estimate effective population sizes from unlinked loci in small populations. We develop a simple inference pipeline and use it to refine estimates of recent effective population sizes of the threatened Channel Island Fox populations.
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