Unraveling evolutionary pathways: Allopolyploidization and introgression in polyploid Prunus (Rosaceae)

Allopolyploidization, resulting from hybridization and subsequent whole‐genome duplication (WGD), is a fundamental mechanism driving evolutionary diversification across various lineages within the Tree of Life. The polyploid Prunus (Rosaceae), significant for its economic and agricultural value, provides an ideal model for investigating the evolutionary dynamics associated with allopolyploidy. In this study, we utilized deep genome skimming (DGS) data to demonstrate a comprehensive analytical framework for elucidating the underlying allopolyploidy that includes a newly adapted tool (DGS‐Tree2GD) tailored explicitly for accurately detecting WGD events. Additionally, we introduced two methods to evaluate the contribution of incomplete lineage sorting (ILS) to lineage diversification. Phylogenomic discordance analyses revealed that allopolyploidization, rather than ILS, played a dominant role in the origin and dynamics of polyploid Prunus. Moreover, we inferred that the uplift of the Himal..., Taxon sampling, DNA extraction, and sequencing 
Based on the recently proposed phylogenetic backbone of Prunus s.l. (Hodel et al., 2023), we performed comprehensive sampling across all major clades to investigate the evolutionary origins and diversification patterns of the polyploid Prunus. The Maddenia group, in particular, was extensively sampled due to its suitability as a model system for investigating rapid radiation involving allopolyploidization and hybridization. We collected a total of 41 samples representing five morphologically delineated Maddenia species: Prunus fujianensis and P. gongshanensis (seven individuals), P. himalayana and P. hypoxantha (five), and P. hypoleuca (17). This targeted sampling strategy enabled us to capture the comprehensive morphological, genetic, and geographic diversity observed within this group (Su et al., 2021). To address the lack of fossil records in Prunus s.l., we expanded our phylogenetic analysis to include 30 additional species from t..., , # README: Unraveling evolutionary pathways: Allopolyploidization and introgression in polyploid Prunus (Rosaceae)

[https://doi.org/10.5061/dryad.fbg79cp46](https://doi.org/10.5061/dryad.fbg79cp46)

The package contains the datasets and analysis output files.

## Description of the data and file structure

**Alignments:**

Data 1. 1_Prunus_SCN1806_ref.fasta = 1806 single copy nuclear reference genes filtered from three genomes (*P. dulcis*, *P. armeniaca*, and *P. persica*)

Data 2. 2_Prunus_SCN_MO.phy = concatenated alignments of 1622 SCN genes from “Monophyletic Outgroup” (MO) dataset

Data 3. 3_Prunus_SCN_RT.phy = concatenated alignments of 2268 SCN genes from “RooTed ingroup” (RT) dataset

Data 4. 4_CDS77_ref.fasta = plastid coding genes reference genes

Data 5. 5_Prunus_CDS.phy = concatenated alignments of plastid coding genes (CDSs)

Data 6. 6_Maddenia_cp.phy = concatenated alignments of the *Maddenia*-plastome dataset

**Trees:**

Prunus_MO_ASTRAL.tre = the phylogenetic tree esti...,