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Genes 2018, 9(3), 132; https://doi.org/10.3390/genes9030132

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Received: 1 December 2017 / Revised: 30 January 2018 / Accepted: 16 February 2018 / Published: 28 February 2018
(This article belongs to the Special Issue Estimating Phylogenies from Large Genomic Datasets)
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Abstract

Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest. View Full-Text
Keywords: incomplete lineage sorting; multi-species coalescent model; summary methods; phylogenomics; polytomy; multifurcation; statistical test incomplete lineage sorting; multi-species coalescent model; summary methods; phylogenomics; polytomy; multifurcation; statistical test
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Sayyari, E.; Mirarab, S. Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies. Genes 2018, 9, 132.

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