<p>(A) Illustration of all the RE presence/absence patterns that are theoretically possible after ILS across two to four speciation events (extension of the examples shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.g001" target="_blank">Fig 1C–1E</a>). This permitted us to calculate the amounts of possible character distributions that are incongruent or congruent with the species tree under the observed durations of ILS across up to 17 speciation events (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s011" target="_blank">S5 Table</a>). Note that conflict-free patterns parsimoniously correspond to ILS across one or fewer speciation events. (B) The amount of species tree-congruent patterns increases linearly (2<i>n</i>) with ILS duration. (C) The amount of hemiplasy (i.e., species tree-incongruent patterns) increases exponentially (2<sup><i>n</i></sup><i>–</i> 2<i>n</i>) with ILS duration. (D) The probability for the occurrence of hemiplasy in a biallelic polymorphism reaches 50% after ILS across three speciation events and 99% after ILS across eleven speciation events (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s011" target="_blank">S5 Table</a>).</p
