ArticleProceedings of the National Academy of Sciences of the United States of America2014
Distortion of genealogical properties when the sample is very large.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- The rights and wrongs of rescaling in population genetics simulations.PLoS genetics · 2026Review
- Likelihoods for a general class of ARGs under the SMC.Genetics · 2026Article
- Estimation of demography and mutation rates from one million haploid genomes.American journal of human genetics · 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
- Fast simulation of identity-by-descent segments.Bulletin of mathematical biology · 2025Article
- Likelihoods for a general class of ARGs under the SMC.bioRxiv : the preprint server for biology · 2025Article
- Labelled histories with multifurcation and simultaneity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Fast simulation of identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
- The Promise of Inferring the Past Using the Ancestral Recombination Graph.Genome biology and evolution · 2024Article
- Article
- Scaling the Discrete-time Wright Fisher model to biobank-scale datasets.bioRxiv : the preprint server for biology · 2023Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- Pseudoreplication in genomic-scale data sets.Molecular ecology resources · 2022Article
- Article
- Accounting for long-range correlations in genome-wide simulations of large cohorts.PLoS genetics · 2020Article
- The multifurcating skyline plot.Virus evolution · 2019Article
- Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes.Molecular ecology resources · 2019Article
- Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions.Genetics · 2019Article
- Efficient pedigree recording for fast population genetics simulation.PLoS computational biology · 2018Article
- Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography.Genetics · 2018Article
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3 authors.
Funding
Abstract
Study sample sizes in human genetics are growing rapidly, and in due course it will become routine to analyze samples with hundreds of thousands, if not millions, of individuals. In addition to posing computational challenges, such large sample sizes call for carefully reexamining the theoretical foundation underlying commonly used analytical tools. Here, we study the accuracy of the coalescent, a central model for studying the ancestry of a sample of individuals. The coalescent arises as a limit of a large class of random mating models, and it is an accurate approximation to the original model provided that the population size is sufficiently larger than the sample size. We develop a method for performing exact computation in the discrete-time Wright-Fisher (DTWF) model and compare several key genealogical quantities of interest with the coalescent predictions. For recently inferred demographic scenarios, we find that there are a significant number of multiple- and simultaneous-merger events under the DTWF model, which are absent in the coalescent by construction. Furthermore, for large sample sizes, there are noticeable differences in the expected number of rare variants between the coalescent and the DTWF model. To balance the trade-off between accuracy and computational efficiency, we propose a hybrid algorithm that uses the DTWF model for the recent past and the coalescent for the more distant past. Our results demonstrate that the hybrid method with only a handful of generations of the DTWF model leads to a frequency spectrum that is quite close to the prediction of the full DTWF model.
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