ArticlePLoS genetics2020
Accounting for long-range correlations in genome-wide simulations of large cohorts.
Article in PLoS genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- The rights and wrongs of rescaling in population genetics simulations.PLoS genetics · 2026Review
- ARGscape: a modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.Bioinformatics (Oxford, England) · 2026Article
- Limited Selection on Neanderthal DNA in 30,780 Recently Admixed Genomes with African-like Ancestry.Molecular biology and evolution · 2026Article
- The Effects of Post-Divergence Gene Flow on Simultaneous Divergence Time Testing.Molecular ecology resources · 2026Article
- From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference.bioRxiv : the preprint server for biology · 2026Article
- Recent population history in Swedish cattle breeds.Genetics, selection, evolution : GSE · 2026Article
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- Likelihoods for a general class of ARGs under the SMC.Genetics · 2026Article
- TS-IBD: An efficient ancestral recombination graph-based identity by descent segment detection method.Human population genetics and genomics · 2026Article
- Human ancestries simulation and inference: a review of ancestral recombination graph-based approaches.Frontiers in bioinformatics · 2026Review
- ARGscape: A modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.ArXiv · 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
- Admixed and single-continental genome segments of the same ancestry have distinct linkage disequilibrium patterns.Genome biology · 2025Article
- Performance of qpAdm-based screens for genetic admixture on graph-shaped histories and stepping stone landscapes.Genetics · 2025Article
- Estimating effective population size trajectories from time-series identity-by-descent segments.Genetics · 2025Article
- Likelihoods for a general class of ARGs under the SMC.bioRxiv : the preprint server for biology · 2025Article
- Understanding admixture fractions: theory and estimation of gene-flow.Journal of mathematical biology · 2024Article
- Article
- Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA.Genetics · 2024Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Coalescent simulations are widely used to examine the effects of evolution and demographic history on the genetic makeup of populations. Thanks to recent progress in algorithms and data structures, simulators such as the widely-used msprime now provide genome-wide simulations for millions of individuals. However, this software relies on classic coalescent theory and its assumptions that sample sizes are small and that the region being simulated is short. Here we show that coalescent simulations of long regions of the genome exhibit large biases in identity-by-descent (IBD), long-range linkage disequilibrium (LD), and ancestry patterns, particularly when the sample size is large. We present a Wright-Fisher extension to msprime, and show that it produces more realistic distributions of IBD, LD, and ancestry proportions, while also addressing more subtle biases of the coalescent. Further, these extensions are more computationally efficient than state-of-the-art coalescent simulations when simulating long regions, including whole-genome data. For shorter regions, efficiency can be maintained via a hybrid model which simulates the recent past under the Wright-Fisher model and uses coalescent simulations in the distant past.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.