Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

Abstract
Data availability
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Abstract

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.

Data availability

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.

The following previously published data sets were used

(2018) Raw sequencing reads from ultraconserved elements of Australasian skinks
NCBI Sequence Read Archive, BioProject PRJNA420910.

https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA420910
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22. Jiggins CD
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(2019) Data from: Genomic architecture and introgression shape a butterfly radiation
Dryad Digital Repository, doi:10.5061/dryad.b7bj832.

http://dx.doi.org/10.5061/dryad.b7bj832

Article and author information

Author details

Mark S Hibbins

Department of Biology, Indiana University, Bloomington, United States

For correspondence
mhibbins@iu.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4651-3704
Matthew JS Gibson

Department of Biology, Indiana University, Bloomington, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7855-1628
Matthew W Hahn

Department of Biology, Indiana University, Bloomington, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5731-8808

Funding

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.

Copyright

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.