# Improved Duplication-Transfer-Loss Reconciliation with
## 4 Results
### Results on Simulated Datasets  
We used simulated datasets to systematically evaluate the accuracy of DTLx reconciliations and to compare its accuracy and functionality against eeceTERA, the only other parsimony-based reconciliation model that handles \(\mathbb{TL}\) and \(\mathbb{TX}\) events. Our implementation is built upon the open-source RANGER-DTL software package [17] and we refer to the new software implementation as RANGER-DTLx. We used the recently developed phylogenetic tree simulation software ZOMBI [29] to evolve simulated gene trees with known ground-truth evolutionary histories containing explicit transfers from extinct lineages. ZOMBI tracks species lineages that eventually go extinct and allows for such lineages to participate in horizontal gene transfer events before going extinct. In our analysis, we simulated two datasets, each consisting of 500 gene tree/species tree pairs. Note that each of these 500 pairs consist of a unique (i.e., different) species tree and gene tree, where each of the species trees has exactly 50 taxa. The specific parameters used to generate the datasets are shown in Table 1. Notably, Dataset-2 has a higher rate of transfers and more \(\mathbb{TX}\) events in the gene trees due to a higher extinction rate. For increased realism, the transfer rate was split evenly between additive and replacing transfers. The final gene trees, obtained after pruning out all gene lineages with no surviving gene descendants, had, on average, 152.5 leaves, 11.6 duplications, 18.1 transfers, 3.0 \(\mathbb{TX}\) events, and 121.7 speciations for Dataset-1, and 180.3 leaves, 10.5 duplications, 26.7 transfers, 5.7 \(\mathbb{TX}\) events, and 142 speciations for Dataset-2. For reference, the unpruned gene trees showed on average, for Dataset-1, 16.1 losses and 42 extinctions, and for Dataset-2, 24.2 \begin{table}
\begin{tabular}{c c c c c c c} \hline  & \multicolumn{3}{c}{**Gene Tree Parameters**} & \multicolumn{3}{c}{**Species Tree Parameters**} \\ \hline
**Dataset** & **Duplication Rate** & **Transfer Rate** & **Loss Rate** & **Birth Rate** & **Extinction Rate** & **\# Taxa (Leaves)** \\ \hline
1 & 0.022 & 0.04 & 0.01 & 0.1 & 0.025 & 50 \\
2 & 0.020 & 0.06 & 0.008 & 0.1 & 0.032 & 50 \\ \hline \end{tabular}
\end{table} 
Table 1: Parameter settings used to generate simulated datasets using Zombi. losses and 67.4 extinctions. Thus, Datasets 1 and 2 correspond to low and moderate rates, respectively, of the relevant evolutionary events. We used these two simulated datasets to address the following three questions: (i) Does using DTLx reconciliation, i.e., RANGER-DTLx, improve upon the overall accuracy of DTL reconciliation in the presence of \(\mathbb{TX}\) events? (ii) How well do RANGER-DTLx and eceTERA detect \(\mathbb{TX}\) events? Furthermore, (iii) How do RANGER-DTLx and eceTERA compare in their ability to detect the phylogenetic location of the extinct donor of a \(\mathbb{TX}\) event? _Comparing accuracies of DTL and DTLx reconciliation_. Since both RANGER-DTLx and eceTERA can account for additional evolutionary scenarios that cannot be correctly handled in traditional DTL reconciliation, it is reasonable to expect that both RANGER-DTLx and eceTERA should result in greater overall reconciliation accuracy than traditional DTL reconciliation. We therefore applied RANGER-DTLx, eceTERA, and RANGER-DTL (which implements the traditional DTL reconciliation framework) to both simulated datasets and evaluated the overall accuracies of the resulting reconciliations. Note that, for a fair comparison, we only compared reconciliation accuracy across the nodes present on the input gene trees, without inclusion of any hidden nodes inferred by RANGER-DTLx. For an inferred reconciliation \(\alpha\), let \(\Sigma_{\alpha}\), \(\Delta_{\alpha}\), \(\Theta_{\alpha}\), \(\mathcal{M}_{\alpha}\), and \(\tau_{\alpha}\) denote the sets of speciation nodes, duplication nodes, standard transfer nodes, mappings for internal nodes of \(G\), and transfer recipients for standard transfers, respectively.