ArticleGenetics2017
Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models.
Article in Genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence.Molecular biology and evolution · 2026Article
- Article
- 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
- Recurrent mutation in the ancestry of a rare variant.Genetics · 2023Article
- Patterns of Population Structure and Introgression Among Recently Differentiated Drosophila melanogaster Populations.Molecular biology and evolution · 2022Article
- Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow.National science review · 2021Article
- Article
- Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History.Molecular biology and evolution · 2020Article
- Wild African Drosophila melanogaster Are Seasonal Specialists on Marula Fruit.Current biology : CB · 2018Article
- Article
- Impacts of Recurrent Hitchhiking on Divergence and Demographic Inference in Drosophila.Genome biology and evolution · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Population genomic datasets collected over the past decade have spurred interest in developing methods that can utilize massive numbers of loci for inference of demographic and selective histories of populations. The allele frequency spectrum (AFS) provides a convenient statistic for such analysis, and, accordingly, much attention has been paid to predicting theoretical expectations of the AFS under a number of different models. However, to date, exact solutions for the joint AFS of two or more populations under models of migration and divergence have not been found. Here, we present a novel Markov chain representation of the coalescent on the state space of the joint AFS that allows for rapid, exact calculation of the joint AFS under isolation with migration (IM) models. In turn, we show how our Markov chain method, in the context of composite likelihood estimation, can be used for accurate inference of parameters of the IM model using SNP data. Lastly, we apply our method to recent whole genome datasets from African
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