Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
The incongruence of character states with phylogenetic relationships is often interpreted as evidence of convergent evolution. However, trait evolution along discordant gene trees can also generate these incongruences – a phenomenon known as hemiplasy. Classic comparative methods do not account for discordance, resulting in incorrect inferences about the number, timing, and direction of trait transitions. Biological sources of discordance include incomplete lineage sorting (ILS) and introgression, but only ILS has received theoretical consideration in the context of hemiplasy. Here, we present a model that shows introgression makes hemiplasy more likely, such that methods that account for ILS alone will be conservative. We also present a method and software (HeIST) for making statistical inferences about the probability of hemiplasy and homoplasy in large datasets that contain both ILS and introgression. We apply our methods to two empirical datasets, finding that hemiplasy is likely to contribute to the observed trait incongruences in both.
Availability of the lizard genomic data and Heliconius phylogenetic network is detailed in the Acknowledgements section of the source manuscript. Source code and test cases for our software HeIST are freely available from the GitHub repository. Source data files have been provided for Figures 1, 4, 5, and 6. The Appendix details all the mutation rate parameters of our mathematical model.
Raw sequencing reads from ultraconserved elements of Australasian skinksNCBI Sequence Read Archive, BioProject PRJNA420910.
Data from: Genomic architecture and introgression shape a butterfly radiationDryad Digital Repository, doi:10.5061/dryad.b7bj832.
Article and author information
National Science Foundation (DEB-1936187)
- Matthew W Hahn
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Antonis Rokas, Vanderbilt University, United States
- Received: October 6, 2020
- Accepted: December 18, 2020
- Accepted Manuscript published: December 21, 2020 (version 1)
- Version of Record published: January 11, 2021 (version 2)
- Version of Record updated: November 19, 2021 (version 3)
© 2020, Hibbins et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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