ArticleGenetics2013
Statistical properties of the site-frequency spectrum associated with lambda-coalescents.
Article in Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Rare variation in malaria parasites biases population-genetic inference.bioRxiv : the preprint server for biology · 2026Article
- PhaseGen: exact solutions for time-inhomogeneous multivariate coalescent distributions under diverse demographies.Genetics · 2026Article
- Inference of Multiple Mergers while Dating a Pathogen Phylogeny.Systematic biology · 2025Article
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- Deep-pelagic fishes: Demographic instability in a stable environment.Ecology and evolution · 2024Article
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- How Can We Resolve Lewontin's Paradox?Genome biology and evolution · 2022Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution.Evolution; international journal of organic evolution · 2020Article
- The multifurcating skyline plot.Virus evolution · 2019Article
- Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions.Genetics · 2019Article
- Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography.Genetics · 2018Article
- The Site Frequency Spectrum for General Coalescents.Genetics · 2016Article
- Can the site-frequency spectrum distinguish exponential population growth from multiple-merger coalescents?Genetics · 2015Article
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3 authors.
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Abstract
Statistical properties of the site-frequency spectrum associated with Λ-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estimating coalescent parameters introduced by certain Λ-coalescents for data sets too large for full-likelihood methods is our focus. The recursions for the expected values we obtain can be used to find the parameter values that give the best fit to the observed frequency spectrum. The expected values are also used to approximate the probability a (derived) mutation arises on a branch subtending a given number of leaves (DNA sequences), allowing us to apply a pseudolikelihood inference to estimate coalescence parameters associated with certain subclasses of Λ-coalescents. The properties of the pseudolikelihood approach are investigated on simulated as well as real mtDNA data sets for the high-fecundity Atlantic cod (Gadus morhua). Our results for two subclasses of Λ-coalescents show that one can distinguish these subclasses from the Kingman coalescent, as well as between the Λ-subclasses, even for a moderate (maybe a few hundred) sample size.
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