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Empirical Analysis of Phylogenetic Quasi-Terraces

Paula Breitling, Alexandros Stamatakis, Olga Chernomor, Ben Bettisworth, Lukasz Reszczynski
doi: https://doi.org/10.1101/810309
Paula Breitling
Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
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Alexandros Stamatakis
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  • For correspondence: alexandros.stamatakis@h-its.org
Olga Chernomor
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Ben Bettisworth
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Lukasz Reszczynski
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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.

Footnotes

  • paula.breitling{at}kit.edu, olga.chernomor{at}univie.ac.at, Ben.Bettisworth{at}h-its.org, lukasz.reszczynski{at}univie.ac.at

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 18, 2019.
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Empirical Analysis of Phylogenetic Quasi-Terraces
Paula Breitling, Alexandros Stamatakis, Olga Chernomor, Ben Bettisworth, Lukasz Reszczynski
bioRxiv 810309; doi: https://doi.org/10.1101/810309
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Empirical Analysis of Phylogenetic Quasi-Terraces
Paula Breitling, Alexandros Stamatakis, Olga Chernomor, Ben Bettisworth, Lukasz Reszczynski
bioRxiv 810309; doi: https://doi.org/10.1101/810309

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