Figure 2

(a) Three evolutionary histories, each involving the same underlying tree (black lines) and a single reticulation edge from the set of three reticulation edges 1, 2, and 3. The diameters of the three reticulation edges 1, 2, 3 are 0.5, 1.0, and 1.5, respectively. (b,c) The performance of ML for estimating the inheritance probabilities on data simulated with a single reticulation event. The genome size corresponds to the number of gene data sets used in the inference. Each panel contains three segments, corresponding to three different values of true inheritance probabilities: 0.1, 0.3, and 0.5. The inheritance probabilities γ _e were estimated using Eq. (4). The two diameters of d = 0.5 (b) and d = 1.5 (c) correspond to the two networks of (a), with HGT edges 1 and 3, respectively; results for the third network are omitted due to space limitations. See text for more details.