Efficient strategies for calculating blockwise likelihoods under the coalescent

Lohse, Konrad and Chmelík, Martin and Martin, Simon H and Barton, Nicholas H (2016) Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics, 202 (2). pp. 775-786. ISSN 1943-2361

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Official URL: http://www.genetics.org/content/202/2/775

Abstract

The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno.

Item Type: Article
DOI: 10.1534/genetics.115.183814
Additional Information: "This is the peer reviewed version of the following article: Lohse, Konrad and Chmelík, Martin and Martin, Simon H and Barton, Nicholas H (2016) Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics, 202 (2). pp. 775-786., which has been published in final form at http://dx.doi.org/10.1534/genetics.115.183814. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."
Uncontrolled Keywords: Gene Flow, generating function, Maximum likelihood, Population divergence, structured coalescent
Subjects: 500 Science > 570 Life sciences; biology
Research Group: Barton Group
SWORD Depositor: Sword Import User
Depositing User: Nicholas Barton
Date Deposited: 11 May 2016 11:31
Last Modified: 30 Aug 2017 07:54
URI: https://repository.ist.ac.at/id/eprint/561

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