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

Chao, Xu12; Jin, Ze-Tao123; Xie, Si-Yu124; Wang, Hui12; Lin, Xiao-Hua124; Ma, Dai-Kun125; Zhang, Yu124; Liu, Bin-Bin12

Published Aug 27, 2025 on Dryad. https://doi.org/10.5061/dryad.7sqv9s531

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Aug 27, 2025 version files 37.84 MB

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Abstract

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.