Ortho2Web: A workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae

Phylogenetic networks, rather than simple bifurcating trees, more accurately depict the intricate evolutionary dynamics of organisms. Darwin’s Tree of Life (ToL) model has been increasingly challenged by the Web of Life (WoL) model due to the growing recognition of extensive reticulation events. However, most existing workflows examine evolutionary mechanisms such as hybridization and allopolyploidization separately, leaving integrated analyses of these processes underexplored. To address this gap, we developed Ortho2Web, a new workflow incorporating orthologs into a web-like phylogenetic framework to analyze the combined effects of hybridization and polyploidization. Ortho2Web employs multiple strategies to reduce the impact of non-biological factors, including integrating multi-source genomic data to minimize sampling gaps, generating distinct datasets to quantify phylogenetic signals, and using tree-based orthology inference methods to mitigate the effects of paralogs. In addition, t..., , , # Data from: Ortho2Web: A workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae

[https://doi.org/10.5061/dryad.7sqv9s531](https://doi.org/10.5061/dryad.7sqv9s531)

## Description of the data and file structure

Data from: Ortho2Web: A workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae

### Files and variables

**Trees:**

Campanuleae_MO_ASTRAL = the phylogenetic tree estimated using ASTRAL-III based on the MO dataset

Campanuleae_MO_IQTREE = the phylogenetic tree estimated using IQ-TREE2 based on the MO dataset

Campanuleae_MO_RAxML = the phylogenetic tree estimated using RAxML based on the MO dataset

Campanuleae_MO_MrBayes = the phylogenetic tree estimated using MrBayes based on the MO dataset

Campanuleae_MI_ASTRAL = the phylogenetic tree estimated using ASTRAL-III based on the MI dataset

Campanuleae_MI_IQTREE = the phylogenetic tree estimated using IQ-TREE...,