Clarifying the Taxonomic Relationships of <i>Tulipa iliensis</i> and <i>T. thianschanica</i> Based on Multiple Evidences of Phenotypic, Karyotype, Molecular, and Chloroplast Genomes

In China, the genus <i>Tulipa</i> L. has been identified as a national second-class protected plant. Due to the complex evolutionary and genetic backgrounds of tulips, the taxonomy of the genus <i>Tulipa</i> and its species remains a matter of dispute. The current study is dedicated to clarifying the taxonomic relationship between two closely related species, <i>T. iliensis</i> and <i>Tulipa thianschanica</i>, by integrating morphological, karyotypic, and molecular evidence—a novel framework for resolving taxonomic ambiguities in closely related species. Morphological analyses showed significant differences in filament shape, pistil length, overall plant height, presence or absence of stem hairs, and perianth length and width, which supports the conclusion that they are distinct species (<i>p</i> < 0.001). Karyotype analysis further verified disparities in their chromosome morphology, and distinct karyotype indices and scatter plot distributions suggest differences between the two species. Molecular phylogenetic analyses using Internal Transcribed Spacer sequences (ITSs) and chloroplast genomes confirmed the genetic differences between <i>T. iliensis</i> and <i>T. thianschanica</i>, and there is evidence indicating the possible occurrence of hybridization events. The research findings demonstrate that <i>T. thianschanica</i> and <i>T. iliensis</i> are independent species, thereby providing valuable insights into the taxonomy of wild tulips and contributing to the conservation of these protected species.