Affiliation:
1. Institut für Mathematik, Johannes-Gutenberg-Universität, 55099 Mainz, Germany
2. Institut für Mathematik, Technische Universität Berlin, 10623 Berlin, Germany
Abstract
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.
Publisher
Oxford University Press (OUP)
Reference62 articles.
1. Testing for neutrality in samples with sequencing errors.;Achaz;Genetics,2008
2. Frequency spectrum neutrality tests: one for all and all for one.;Achaz;Genetics,2009
3. Current vs. historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations.;Avise;Mol. Biol. Evol.,1988
4. Mitochondrial cytochrome b variation in the high-fecundity Atlantic cod: trans-Atlantic clines and shallow gene genealogy.;Árnason;Genetics,2004
Cited by
44 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献