Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

Genetics
Sebastian MatuszewskiJeffrey D Jensen

Abstract

Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale-analogous to the Kingman coalescent-we find that the ancestral process can be rescaled to its time-homogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, ...Continue Reading

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Citations

Apr 2, 2020·Evolution; International Journal of Organic Evolution·Ana Y Morales-ArceJeffrey D Jensen
May 13, 2020·Genome Biology and Evolution·Rebecca B Harris, Jeffrey D Jensen
Feb 3, 2020·Journal of Mathematical Biology·Fabian Freund
Jul 16, 2020·Molecular Biology and Evolution·F MenardoFabian Freund
Sep 2, 2020·Annual Review of Genetics·Bjarki Eldon
Oct 14, 2020·Evolution; International Journal of Organic Evolution·Jeffrey D JensenMichael Lynch

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