ArticleGenetics2012
Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- GENERAL MOMENT CLOSURE FOR THE NEUTRAL TWO-LOCUS WRIGHT-FISHER DYNAMICS.bioRxiv : the preprint server for biology · 2026Article
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- Conditional frequency spectra as a tool for studying selection on complex traits in biobanks.bioRxiv : the preprint server for biology · 2024Article
- Computationally Efficient Demographic History Inference from Allele Frequencies with Supervised Machine Learning.Molecular biology and evolution · 2024Article
- Computationally efficient demographic history inference from allele frequencies with supervised machine learning.bioRxiv : the preprint server for biology · 2024Article
- Self-contained Beta-with-Spikes approximation for inference under a Wright-Fisher model.Genetics · 2023Article
- Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data.Methods in ecology and evolution · 2022Article
- The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects.Molecular biology and evolution · 2021Article
- Article
- The impact of purifying and background selection on the inference of population history: problems and prospects.bioRxiv : the preprint server for biology · 2021Article
- A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data.Molecular biology and evolution · 2020Article
- Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data.Molecular biology and evolution · 2020Article
- Efficiently inferring the demographic history of many populations with allele count data.Journal of the American Statistical Association · 2020Article
- Inference of complex population histories using whole-genome sequences from multiple populations.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania.Nature communications · 2019Article
- Article
- multi-dice: r package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes.Molecular ecology resources · 2017Article
- Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models.Genetics · 2017Article
- Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation.Genetics · 2017Article
- Statistical Inference in the Wright-Fisher Model Using Allele Frequency Data.Systematic biology · 2017Review
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2 authors.
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Abstract
We present an implementation of a recently introduced method for estimating the allele-frequency spectrum under the diffusion approximation. For single-nucleotide polymorphism (SNP) frequency data from multiple populations, the method computes numerical solutions to the allele-frequency spectrum (AFS) under a complex model that includes population splitting events, migration, population expansion, and admixture. The solution to the diffusion partial differential equation (PDE) that mimics the evolutionary process is found by means of truncated polynomial expansions. In the absence of gene flow, our computation of frequency spectra yields exact results. The results are compared to those that use a finite-difference method and to forward diffusion simulations. In general, all the methods yield comparable results, although the polynomial-based approach is the most accurate in the weak-migration limit. Also, the economical use of memory attained by the polynomial expansions makes the study of models with four populations possible for the first time. The method was applied to a four-population model of the human expansion out of Africa and the peopling of the Americas, using the Environmental Genome Project (EGP) SNP database. Although our confidence intervals largely overlapped previous analyses of these data, some were significantly different. In particular, estimates of migration among African, European, and Asian populations were considerably lower than those in a previous study and the estimated time of migration out of Africa was earlier. The estimated time of founding of a human population outside of Africa was 52,000 years (95% confidence interval: 36,000-80,800 years).
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