Hybridization and polyploidy shaped the evolutionary history of a complex of cryptic species in European woodrushes (<em>Luzula</em> sect. <em>Luzula</em>)

Luzula sect. Luzula (Juncaceae) is a taxonomically intricate group characterized by widespread polyploidy, agmatoploidy, and high morphological similarity. Focusing on the Eastern Alps, a key center of its diversity, we collected 1,002 samples of nine species and applied an integrative framework combining ddRADseq, plastid sequencing, relative genome size estimation, and chromosome counting to disentangle its evolutionary history. We first reconstructed phylogenetic relationships and assessed gene flow among diploids (dataset 01.Diploids), establishing a baseline for investigating the origin of polyploids. By analyzing patterns of genotype frequencies (dataset 03.Tetraploids) and genetic affinities to diploids (dataset 02.MixedPloidy), we inferred the most likely parental species of polyploids and identified key hybridization events shaping the current taxonomic and karyotypic diversity within this group. Our results reveal weak genetic differentiation among some diploid lineages, likel..., , # Hybridization and polyploidy shaped the evolutionary history of a complex of cryptic species in European woodrushes (*Luzula* sect. *Luzula*) --- Data archive for: **Hybridization and Polyploidy shaped the Evolutionary History of a Complex of Cryptic Species in European Woodrushes (*Luzula* sect. *Luzula*)** Authors: Valentin Heimer, Pau Carnicero, Carolina Carrizo García, Andreas Hilpold, Jasna Dolenc Koce, J. Luis Leal, Mingai Li, Claudio Varotto, Peter Schönswetter, Božo Frajman\ Year: 2025 Contact: Valentin Heimer, [[e-mail]](mailto:[e-mail]) This data archive contains genomic data derived from ddRADseq and Sanger sequencing of plastid regions. For each analysis, the most relevant input and results files that should allow replication of the workflow are included. Scripts used for these analyses are organized in a corresponding structure available on Zenodo ([https://doi.org/10.5281/zenodo.15719018](https://doi.org/10.5281/zenodo.15719018))...,