Empirical Analysis of Phylogenetic Quasi-Terraces

Empirical Analysis of Phylogenetic Quasi-Terraces

Abstract

Terraces in phylogenetic tree space are, among other things, important for the design of tree space search strategies. While the phenomenon of phylogenetic terraces is already known for unlinked partition models on partitioned phylogenomic data sets, it has not yet been studied if an analogous structure is present under linked and scaled partition models. To this end, we analyze aspects such as the log-likelihood distributions, likelihood-based significance tests, and nearest neighborhood interchanges on the trees residing on a terrace and compare their distributions among unlinked, linked, and scaled partition models. Our study shows that there exists a terrace-like structure under linked and scaled partition models as well. We denote this phenomenon as quasi-terrace. Therefore quasi-terraces should be taken into account in the design of tree search algorithms as well as when reporting results on ‘the’ final tree topology in empirical phylogenetic studies.

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Authors
  • Breitling, Paula
  • Stamatakis, Alexandros
  • Chernomor, Olga
  • Bettisworth, Ben
  • Reszczynski, Lukasz
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Shortfacts
Category
Journal Paper
Divisions
Bioinformatics and Computational Biology
Journal or Publication Title
bioRxiv
ISSN
none
Publisher
Cold Spring Harbor Laborat
Number
810309
Date
18 October 2019
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