ArticleGenetics2016
The Site Frequency Spectrum for General Coalescents.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- The TMRCA of general genealogies in populations with deterministically varying size.Theoretical population biology · 2025Article
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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
- Long-term evolution of Streptococcus mitis and Streptococcus pneumoniae leads to higher genetic diversity within rather than between human populations.PLoS genetics · 2024Article
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- Scaling the Discrete-time Wright Fisher model to biobank-scale datasets.bioRxiv : the preprint server for biology · 2023Article
- Interpreting the pervasive observation of U-shaped Site Frequency Spectra.PLoS genetics · 2023Article
- Article
- Nonparametric coalescent inference of mutation spectrum history and demography.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Cannings models, population size changes and multiple-merger coalescents.Journal of mathematical biology · 2020Article
- The multifurcating skyline plot.Virus evolution · 2019Article
- Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography.Genetics · 2018Article
- Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation.Genetics · 2017Article
- Current hypotheses to explain genetic chaos under the sea.Current zoology · 2016Article
- Explosive genetic evidence for explosive human population growth.Current opinion in genetics & development · 2016Review
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3 authors.
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Abstract
General genealogical processes such as Λ- and Ξ-coalescents, which respectively model multiple and simultaneous mergers, have important applications in studying marine species, strong positive selection, recurrent selective sweeps, strong bottlenecks, large sample sizes, and so on. Recently, there has been significant progress in developing useful inference tools for such general models. In particular, inference methods based on the site frequency spectrum (SFS) have received noticeable attention. Here, we derive a new formula for the expected SFS for general Λ- and Ξ-coalescents, which leads to an efficient algorithm. For time-homogeneous coalescents, the runtime of our algorithm for computing the expected SFS is O(n2) where n is the sample size. This is a factor of[Formula: see text]faster than the state-of-the-art method. Furthermore, in contrast to existing methods, our method generalizes to time-inhomogeneous Λ- and Ξ-coalescents with measures that factorize as[Formula: see text] and [Formula: see text]respectively, where ζ denotes a strictly positive function of time. The runtime of our algorithm in this setting is[Formula: see text]We also obtain general theoretical results for the identifiability of the Λ measure when ζ is a constant function, as well as for the identifiability of the function ζ under a fixed Ξ measure.
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