DOI: 10.5061/dryad.9zw3r22s2
title: Data from: Phylogenomic insights into Adenophora and its allies (Campanulaceae): Revisiting generic delimitation and hybridization dynamics

description: Hybridization and introgression have long obscured relationships within
 Adenophora and its relatives, complicating generic delimitation.
 Leveraging deep genome skimming (DGS) data, we generated a large dataset,
 including thousands of single-copy nuclear (SCN) genes and plastomes, to
 untangle this reticulate history. Specifically, 9.89 TB of DGS data from
 165 samples—representing 48 species and 13 subspecies
 of Adenophora (out of ca. 72 species) plus 24 outgroup
 species—yielded 1,506 SCN genes and 77 plastid coding sequences. Tree-like
 phylogenies inferred with both coalescent- and concatenation-based methods
 revealed pronounced gene tree heterogeneity. Subsequent analysis showed
 that incomplete lineage sorting contributed minimally to this discordance;
 instead, hybridization and introgression were the primary drivers of early
 diversification. Integrating phylogenomic, morphological, and geographic
 evidence, we propose a revised generic framework for this group.
 Adenophora is expanded to include Campanula delavayi and the Korean
 Peninsula endemic genus Hanabusaya. We also recommend reinstating Hyssaria
 as a distinct Central Asian genus and introducing two new genera,
 Boreoasia and Rosomala.
description: # Data from: Phylogenomic insights into Adenophora and its allies
 (Campanulaceae): Revisiting generic delimitation and hybridization
 dynamics
 [https://doi.org/10.5061/dryad.9zw3r22s2](https://doi.org/10.5061/dryad.9zw3r22s2) ## Description of the data and file structure ### Files and variables #### File: 1to1_astral.tre **Description:** ASTRAL-III Species tree of *Adenophora* within tribe Campanuleae inferred from 1to1 dataset. #### File: 1to1_iq.tre **Description:** Maximum likelihood phylogeny of *Adenophora* within tribe Campanuleae inferred from IQ-TREE2 using 1to1 dataset. #### File: cds_raxml.tre **Description:** Maximum likelihood phylogeny of *Adenophora* within tribe Campanuleae inferred from RAxML using plastid CDS dataset. #### File: cds_iq.tre **Description:** Maximum likelihood phylogeny of *Adenophora* within tribe Campanuleae inferred from IQ-TREE2 using plastid CDS dataset. #### File: mo_iq.tre **Description:** Maximum likelihood phylogeny of *Adenophora* within tribe Campanuleae inferred from IQ-TREE2 using MO dataset. #### File: mo_astral.tre **Description:** ASTRAL-III Species tree of *Adenophora* within tribe Campanuleae inferred from MO dataset. #### File: rt_iq.tre **Description:** Maximum likelihood phylogeny of *Adenophora* within tribe Campanuleae inferred from IQ-TREE2 using RT dataset. #### File: rt_astral.tre **Description:** ASTRAL-III species tree of *Adenophora* within tribe Campanuleae inferred from RT dataset. #### File: cds.phy **Description:** Alignment of *Adenophora* and and its allies (Campanulaceae) based on plastid CDS dataset #### File: 1to1.phy **Description:** Alignment of *Adenophora* and and its allies (Campanulaceae) based on 1to1 dataset #### File: mo.phy **Description:** Alignment of *Adenophora* and and its allies (Campanulaceae) based on MO dataset #### File: rt.phy **Description:** Alignment of *Adenophora* and and its allies (Campanulaceae) based on RT dataset