Abstract
Polyploidization has played a central role in the evolutionary history of most plant lineages, yet it poses significant challenges for phylogenetic inference, particularly in allopolyploid complexes with reticulate species relationships. Luzula sect. Luzula (Juncaceae) is a taxonomically intricate group characterized by widespread polyploidy, agmatoploidy, and high morphological uniformity. 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 extended previously inferred phylogenetic relationships and assessed gene flow among diploids, establishing a baseline for investigating the origin of polyploids. By analyzing patterns of genotype frequencies and genetic affinities to diploids, 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, likely reflecting gene flow and incomplete lineage sorting. We propose a common allopolyploid origin of two tetraploids, which subsequently gave rise to a third tetraploid and a hexaploid species through interploidy hybridization. Although the parental species of some polyploids remain obscure, our genomic data highlight polyploidy and hybridization as major drivers of speciation in this poorly understood lineage. This study underscores the value of integrative approaches in resolving reticulate plant phylogenies and advances our understanding of polyploid speciation.