ArticleGenetics2016
Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Historical introgression from commercial meat-type ducks constitutes the common genetic basis of white plumage in egg-type duck breeds.Poultry science · 2026Article
- Understanding Genomic Landscapes of Differentiation in Round-Tailed Horned Lizards (Phrynosoma modestum).Genome biology and evolution · 2026Article
- Differential introgression of mutations reveals selection in spruce.BMC biology · 2026Article
- The genomic architecture of local adaptation in two connected populations of three-spined stickleback.G3 (Bethesda, Md.) · 2026Article
- GENERAL MOMENT CLOSURE FOR THE NEUTRAL TWO-LOCUS WRIGHT-FISHER DYNAMICS.bioRxiv : the preprint server for biology · 2026Article
- Fine-scale recombination rates inferred using the canFam4 assembly are strongly correlated with previous maps of dog recombination.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress.Nature communications · 2025Article
- Recombination Rate and Recurrent Linked Selection Shape Correlated Genomic Landscapes Across a Continuum of Divergence in Swallows.Molecular ecology · 2025Article
- Leveraging Whole Genomes, Mitochondrial DNA and Haploblocks to Decipher Complex Demographic Histories: An Example From a Broadly Admixed Arctic Fish.Molecular ecology · 2025Article
- High-recombining genomic regions affect demography inference based on ancestral recombination graphs.Genetics · 2025Article
- A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation.bioRxiv : the preprint server for biology · 2025Article
- Diversity in Recombination Hotspot Characteristics and Gene Structure Shape Fine-Scale Recombination Patterns in Plant Genomes.Molecular biology and evolution · 2024Article
- On the estimation of genome-average recombination rates.Genetics · 2024Article
- Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques.bioRxiv : the preprint server for biology · 2024Article
- Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap.Genome biology and evolution · 2024Article
- Recombination map tailored to Native Hawaiians may improve robustness of genomic scans for positive selection.Human genetics · 2024Article
- Article
- The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons.Scientific reports · 2023Article
- Scaling the Discrete-time Wright Fisher model to biobank-scale datasets.bioRxiv : the preprint server for biology · 2023Article
- The fine-scale recombination rate variation and associations with genomic features in a butterfly.Genome research · 2023Article
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4 authors.
Funding
Abstract
Two-locus sampling probabilities have played a central role in devising an efficient composite-likelihood method for estimating fine-scale recombination rates. Due to mathematical and computational challenges, these sampling probabilities are typically computed under the unrealistic assumption of a constant population size, and simulation studies have shown that resulting recombination rate estimates can be severely biased in certain cases of historical population size changes. To alleviate this problem, we develop here new methods to compute the sampling probability for variable population size functions that are piecewise constant. Our main theoretical result, implemented in a new software package called LDpop, is a novel formula for the sampling probability that can be evaluated by numerically exponentiating a large but sparse matrix. This formula can handle moderate sample sizes ([Formula: see text]) and demographic size histories with a large number of epochs ([Formula: see text]). In addition, LDpop implements an approximate formula for the sampling probability that is reasonably accurate and scales to hundreds in sample size ([Formula: see text]). Finally, LDpop includes an importance sampler for the posterior distribution of two-locus genealogies, based on a new result for the optimal proposal distribution in the variable-size setting. Using our methods, we study how a sharp population bottleneck followed by rapid growth affects the correlation between partially linked sites. Then, through an extensive simulation study, we show that accounting for population size changes under such a demographic model leads to substantial improvements in fine-scale recombination rate estimation.
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