Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in slipper orchid genus Cypripedium L.

Background and Aims: Cypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time.
Methods:  We used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny of Cypripedium based on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events.
Key Results: All sections were recovered as monophyletic, contrary to the two subsections within sect. Cypripedium. The two sub..., , , # Data from: Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid Genus Cypripedium L.

[https://doi.org/10.5061/dryad.tmpg4f57d](https://doi.org/10.5061/dryad.tmpg4f57d)

## Description of the data and file structure

#### 1\_nuclear\_analyses:

```
1_original_nuclear_fasta_files: Unaligned fasta files (*.fna) of nuclear loci
2_raw_nuclear_homologs: Raw nuclear homolog trees. Cleaned alignments with Phyx (*.aln-cln) and ML trees with IQ-TREE 2 without bootstrap support (*.treefile)
3_final_nuclear_homologs:
1_all_taxa: Filtered homolog trees containing all taxa in the original dataset (*.treefile; monophyletic clades and paraphyletic grades of same species masked, spurious tips removed with TreeShrink)
2_reduced_taxa: Filtered homolog trees (*.tm) with taxa C_calceolus_50, C_himalaicum_66, C_calceolus_var_par_54, C_guttatum_64, C_calceolus_51, C_tibeticum_72, C_cordigerum_60, C_tibeticum_73 removed d...,