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Quantifying the risk of hemiplasy in phylogenetic inference

View ORCID ProfileRafael F. Guerrero, Matthew W. Hahn
doi: https://doi.org/10.1101/391391
Rafael F. Guerrero
aDepartment of Biology and Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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  • For correspondence: rafguerr@indiana.edu
Matthew W. Hahn
aDepartment of Biology and Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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Abstract

Convergent evolution is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely— or more likely—than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a new method to calculate the ratio of these two probabilities (the “hemiplasy risk factor”) along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree in order to identify when and where incongruent traits may be more likely to be due to hemiplasy than homoplasy.

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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 August 14, 2018.
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Quantifying the risk of hemiplasy in phylogenetic inference
Rafael F. Guerrero, Matthew W. Hahn
bioRxiv 391391; doi: https://doi.org/10.1101/391391
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Quantifying the risk of hemiplasy in phylogenetic inference
Rafael F. Guerrero, Matthew W. Hahn
bioRxiv 391391; doi: https://doi.org/10.1101/391391

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