1. Evolutionary Biology
Download icon

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

  1. Mark S Hibbins  Is a corresponding author
  2. Matthew JS Gibson
  3. Matthew W Hahn
  1. Indiana University, United States
Research Article
  • Cited 3
  • Views 944
  • Annotations
Cite this article as: eLife 2020;9:e63753 doi: 10.7554/eLife.63753


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

Article and author information

Author details

  1. Mark S Hibbins

    Department of Biology, Indiana University, Bloomington, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4651-3704
  2. Matthew JS Gibson

    Department of Biology, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7855-1628
  3. Matthew W Hahn

    Department of Biology, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5731-8808


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.

Reviewing Editor

  1. Antonis Rokas, Vanderbilt University, United States

Publication history

  1. Received: October 6, 2020
  2. Accepted: December 18, 2020
  3. Accepted Manuscript published: December 21, 2020 (version 1)
  4. Version of Record published: January 11, 2021 (version 2)
  5. 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.


  • 944
    Page views
  • 86
  • 3

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Evolutionary Biology
    2. Neuroscience
    Jan Clemens et al.
    Research Article Updated

    How neural networks evolved to generate the diversity of species-specific communication signals is unknown. For receivers of the signals, one hypothesis is that novel recognition phenotypes arise from parameter variation in computationally flexible feature detection networks. We test this hypothesis in crickets, where males generate and females recognize the mating songs with a species-specific pulse pattern, by investigating whether the song recognition network in the cricket brain has the computational flexibility to recognize different temporal features. Using electrophysiological recordings from the network that recognizes crucial properties of the pulse pattern on the short timescale in the cricket Gryllus bimaculatus, we built a computational model that reproduces the neuronal and behavioral tuning of that species. An analysis of the model’s parameter space reveals that the network can provide all recognition phenotypes for pulse duration and pause known in crickets and even other insects. Phenotypic diversity in the model is consistent with known preference types in crickets and other insects, and arises from computations that likely evolved to increase energy efficiency and robustness of pattern recognition. The model’s parameter to phenotype mapping is degenerate – different network parameters can create similar changes in the phenotype – which likely supports evolutionary plasticity. Our study suggests that computationally flexible networks underlie the diverse pattern recognition phenotypes, and we reveal network properties that constrain and support behavioral diversity.

    1. Evolutionary Biology
    Lu Chen et al.
    Research Article

    A high portion of the earliest known insect fauna is composed of the so-called ‘lobeattid insects’, whose systematic affinities and role as foliage feeders remain debated. We investigated hundreds of samples of a new lobeattid species from the Xiaheyan locality using a combination of photographic techniques, including reflectance transforming imaging, geometric morphometrics, and biomechanics to document its morphology, and infer its phylogenetic position and ecological role. Ctenoptilus frequens sp. nov. possessed a sword-shaped ovipositor with valves interlocked by two ball-and-socket mechanisms, lacked jumping hind-legs, and certain wing venation features. This combination of characters unambiguously supports lobeattids as stem relatives of all living Orthoptera (crickets, grasshoppers, katydids). Given the herein presented and other remains, it follows that this group experienced an early diversification and, additionally, occurred in high individual numbers. The ovipositor shape indicates that ground was the preferred substrate for eggs. Visible mouthparts made it possible to assess the efficiency of the mandibular food uptake system in comparison to a wide array of extant species. The new species was likely omnivorous which explains the paucity of external damage on contemporaneous plant foliage.