ArticleGenome research2015
Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Faster inference of complex demographic models from large allele frequency spectra.Bioinformatics (Oxford, England) · 2026Article
- Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence.Molecular biology and evolution · 2026Article
- The TMRCA of general genealogies in populations with deterministically varying size.Theoretical population biology · 2025Article
- Accelerated Bayesian inference of population size history from recombining sequence data.Nature genetics · 2025Article
- Estimation of demography and mutation rates from one million haploid genomes.American journal of human genetics · 2025Article
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- Isolating selective from non-selective forces using site frequency ratios.PLoS genetics · 2025Article
- A structured coalescent model reveals deep ancestral structure shared by all modern humans.Nature genetics · 2025Article
- A likelihood-based framework for demographic inference from genealogical trees.Nature genetics · 2025Article
- Estimating evolutionary and demographic parameters via ARG-derived IBD.PLoS genetics · 2025Article
- Population Genomic Scans for Natural Selection and Demography.Annual review of genetics · 2024Review
- Conditional frequency spectra as a tool for studying selection on complex traits in biobanks.bioRxiv : the preprint server for biology · 2024Article
- Exact Decoding of a Sequentially Markov Coalescent Model in Genetics.Journal of the American Statistical Association · 2024Article
- Haplotype-based inference of recent effective population size in modern and ancient DNA samples.Nature communications · 2023Article
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- Scaling the Discrete-time Wright Fisher model to biobank-scale datasets.bioRxiv : the preprint server for biology · 2023Article
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- Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data.Methods in ecology and evolution · 2022Article
- Robust inference of population size histories from genomic sequencing data.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
3 authors.
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Abstract
With the recent increase in study sample sizes in human genetics, there has been growing interest in inferring historical population demography from genomic variation data. Here, we present an efficient inference method that can scale up to very large samples, with tens or hundreds of thousands of individuals. Specifically, by utilizing analytic results on the expected frequency spectrum under the coalescent and by leveraging the technique of automatic differentiation, which allows us to compute gradients exactly, we develop a very efficient algorithm to infer piecewise-exponential models of the historical effective population size from the distribution of sample allele frequencies. Our method is orders of magnitude faster than previous demographic inference methods based on the frequency spectrum. In addition to inferring demography, our method can also accurately estimate locus-specific mutation rates. We perform extensive validation of our method on simulated data and show that it can accurately infer multiple recent epochs of rapid exponential growth, a signal that is difficult to pick up with small sample sizes. Lastly, we use our method to analyze data from recent sequencing studies, including a large-sample exome-sequencing data set of tens of thousands of individuals assayed at a few hundred genic regions.
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