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2019 | OriginalPaper | Chapter

Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks

Authors : Peng Du, Huw A. Ogilvie, Luay Nakhleh

Published in: Bioinformatics Research and Applications

Publisher: Springer International Publishing

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Abstract

Statistical methods were recently introduced for inferring phylogenetic networks under the multispecies network coalescent, thus accounting for both reticulation and incomplete lineage sorting. Two evolutionary processes that are ubiquitous across all three domains of life, but are not accounted for by those methods, are gene duplication and loss (GDL).

In this work, we devise a three-piece model—phylogenetic network, locus network, and gene tree—that unifies all the aforementioned processes into a single model of how genes evolve in the presence of ILS, GDL, and introgression within the branches of a phylogenetic network. To illustrate the power of this model, we develop an algorithm for estimating the parameters of a phylogenetic network topology under this unified model.

We demonstrate the application of the model and the accuracy of the algorithm on simulated as well as biological data.

Our work adds to the biologist’s toolbox of methods for phylogenomic inference by accounting for more complex evolutionary processes.

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previous chapter Sorting by Reversals, Transpositions, and Indels on Both Gene Order and Intergenic Sizes

next chapter The Cluster Affinity Distance for Phylogenies

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Title: Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks
Authors: Peng Du
Huw A. Ogilvie
Luay Nakhleh
Publisher: Springer International Publishing
Book: Bioinformatics Research and Applications
Print ISBN: 978-3-030-20241-5

Electronic ISBN: 978-3-030-20242-2

Copyright Year: 2019
DOI: https://doi.org/10.1007/978-3-030-20242-2_4

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