DOI: 10.5061/dryad.7sqv9s531
title: Data from: Ortho2Web: A workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae

description: 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, the
 workflow combines various complementary methods to clarify the roles of
 incomplete lineage sorting, hybridization/gene flow, and polyploidization
 in species diversification. Here, to elucidate the broad applicability of
 this workflow, we applied Ortho2Web to reconstruct the WoL of the
 bellflower tribe Campanuleae, which is characterized by extensive
 reticulation. Our results show that hybridization and allopolyploidization
 were key drivers of diversity in the tribe, particularly during the early
 diversification of clade α. Ortho2Web’s flexibility and scalability offer
 a solid platform for inferring web-like phylogenies, making it a valuable
 tool for researchers interested in exploring mechanisms of reticulation in
 complex biological systems with greater depth and precision. The Ortho2Web
 workflow is available at: https://github.com/PhyloAI/Ortho2Web.
description: # 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-TREE2 based on the MI dataset Campanuleae_MI_RAxML = the phylogenetic tree estimated using RAxML based on the MI dataset Campanuleae_MI_MrBayes = the phylogenetic tree estimated using MrBayes based on the MI dataset Campanuleae_RT_ASTRAL = the phylogenetic tree estimated using ASTRAL-III based on the RT dataset Campanuleae_RT_IQTREE = the phylogenetic tree estimated using IQ-TREE2 based on the RT dataset Campanuleae_RT_RAxML = the phylogenetic tree estimated using RAxML based on the RT dataset Campanuleae_RT_MrBayes = the phylogenetic tree estimated using MrBayes based on the RT dataset Campanuleae_1to1_ASTRAL = the phylogenetic tree estimated using ASTRAL-III based on the 1to1 dataset Campanuleae_1to1_IQTREE = the phylogenetic tree estimated using IQ-TREE2 based on the 1to1 dataset Campanuleae_1to1_RAxML = the phylogenetic tree estimated using RAxML based on the 1to1 dataset Campanuleae_1to1_MrBayes = the phylogenetic tree estimated using MrBayes based on the 1to1 dataset Campanuleae_CDS_ASTRAL = the phylogenetic tree estimated using ASTRAL-III based on the plastid CDS dataset Campanuleae_CDS_IQTREE = the phylogenetic tree estimated using IQ-TREE2 based on the plastid CDS dataset Campanuleae_CDS_RAxML = the phylogenetic tree estimated using RAxML based on the plastid CDS dataset Campanuleae_CDS_MrBayes = the phylogenetic tree estimated using MrBayes based on the CDS dataset **Log files:** Campanuleae_MO_ASTRAL = the log file of phylogenetic tree estimated using ASTRAL-III based on the MO dataset Campanuleae_MO_IQTREE = the log file of phylogenetic tree estimated using IQ-TREE2 based on the MO dataset Campanuleae_MO_RAxML = the log file of phylogenetic tree estimated using RAxML based on the MO dataset Campanuleae_MO_MrBayes = the log file of phylogenetic tree estimated using MrBayes based on the MO dataset Campanuleae_MI_ASTRAL = the log file of phylogenetic tree estimated using ASTRAL-III based on the MI dataset Campanuleae_MI_IQTREE = the log file of phylogenetic tree estimated using IQ-TREE2 based on the MI dataset Campanuleae_MI_RAxML = the log file of phylogenetic tree estimated using RAxML based on the MI dataset Campanuleae_MI_MrBayes = the log file of phylogenetic tree estimated using MrBayes based on the MI dataset Campanuleae_RT_ASTRAL = the log file of phylogenetic tree estimated using ASTRAL-III based on the RT dataset Campanuleae_RT_IQTREE = the log file of phylogenetic tree estimated using IQ-TREE2 based on the RT dataset Campanuleae_RT_RAxML = the log file of phylogenetic tree estimated using RAxML based on the RT dataset Campanuleae_RT_MrBayes = the log file of phylogenetic tree estimated using MrBayes based on the RT dataset Campanuleae_1to1_ASTRAL = the log file of phylogenetic tree estimated using ASTRAL-III based on the 1to1 dataset Campanuleae_1to1_IQTREE = the log file of phylogenetic tree estimated using IQ-TREE2 based on the 1to1 dataset Campanuleae_1to1_RAxML = the log file of phylogenetic tree estimated using RAxML based on the 1to1 dataset Campanuleae_1to1_MrBayes = the log file of phylogenetic tree estimated using MrBayes based on the 1to1 dataset ## Code/software The Ortho2Web workflow is available at: [https://github.com/PhyloAI/Ortho2Web](https://github.com/PhyloAI/Ortho2Web). ## Access information Other publicly accessible locations of the data: * All raw reads (130 accessions) sequenced for this study have been deposited in the NCBI SRA under the BioProject PRJNA895940.