TY - JOUR TI - Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression AU - Hibbins, Mark S AU - Gibson, Matthew JS AU - Hahn, Matthew W A2 - Rokas, Antonis A2 - Wittkopp, Patricia J VL - 9 PY - 2020 DA - 2020/12/21 SP - e63753 C1 - eLife 2020;9:e63753 DO - 10.7554/eLife.63753 UR - https://doi.org/10.7554/eLife.63753 AB - 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. KW - introgression KW - convergent evolution KW - phylogenetics KW - comparative methods KW - gene tree discordance JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -