Abstract
Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris, but their cytological and evolutionary consequences remain poorly understood. Here, we investigated chromosome numbers and genome sizes in 64 accessions representing the morphological diversity across the genus. Chromosome numbers ranged from 12 to 33, with seven accessions newly identified, including L. chunxiaoensis (2n = 33), two putative L. guangxiensis (2n = 19), and five natural hybrids (2n = 16, 18, 29, 33). Genome sizes varied from 18.03 Gb (L. wulingensis) to 32.62 Gb (L. caldwellii). Although no significant correlation was found between genome size and chromosome number across all accessions, a strong correlation within ploidy-level groups (i.e., diploid or aneuploid) suggested roles for post-polyploid diploidization, aneuploidy, and dysploidy in speciation. Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significant discordance, indicating a complex reticulate evolution and historical hybridization, which may complicate morphological classification. Chromosome number aligned more closely with morphological groups, underscoring the necessity of integrating cytological, molecular, and morphological data for accurate taxonomy, particularly in large-genome taxa. Based on this evidence, we propose a putative speciation pathway involving multiple hybridization and polyploidization events, with allopolyploidy playing a predominant role. Furthermore, our results indicate that the species L. insularis and L. longifolia are geographic populations of L. sprengeri and L. aurea, respectively, and confirmed the distribution of L. traubii and L. albiflora in mainland China. These findings offer new insights into the mechanisms underlying speciation, interspecific relationships, and the evolutionary history of Lycoris.