Synergizing Bayesian and heuristic approaches: D-BPP uncovers ghost introgression in <em>Panthera</em> and <em>Thuja</em>

Hybridization involving extinct or unsampled (“ghost”) lineages profoundly influences species’ evolutionary histories, but detecting such introgression remains methodologically challenging. We introduce D-BPP, a framework that integrates the heuristic D-statistic (or ABBA-BABA test) with Bayesian phylogenomic inference (implemented in BPP) to efficiently infer phylogenetic networks. In D-BPP, we first employ the D-statistic to rapidly identify candidate introgression events on a predefined bifurcating species tree; then we leverage the Bayesian test in BPP to rigorously validate these can- didates and sequentially add them to the species tree, retaining only those events with strong statistical support. When the species tree is ambiguous, D-BPP identifies the most probable topology by comparing introgression models in a Bayesian framework. Through dedicated simulation analyses, we show that the D-BPP workflow has high power: the D-statistic reli- ably detects the presence of introgressi..., , # Data from: Synergizing Bayesian and heuristic approaches: D-BPP uncovers ghost introgression in *Panthera* and *Thuja* Dataset DOI: 10.5061/dryad.47d7wm3sr #### Description This dataset contains input files and simulation data necessary to replicate the D-BPP phylogenetic network analyses presented in Synergizing Bayesian and Heuristic Approaches: D-BPP Uncovers Ghost Introgression in *Panthera* and *Thuja*. The D-BPP framework is designed to detect and quantify ghost introgression—gene flow from unsampled or extinct lineages—by integrating heuristic screening with rigorous Bayesian model testing. The dataset is organized by empirical study systems (*Panthera* and *Thuja*) and includes simulated data used for method validation. #### Data Files and Directory Structure The data are contained within the `dataset.zip` archive. Upon extraction, the following directory structure is created: ``` dataset.zip ├── Panthera/ │ ├── data.even.nocat.txt │ ├── ..., ,