Phylogenomic insights into the genus <i>Tulipa</i> (Liliaceae): Taxonomy, evolution, and biogeography

PREMISE: Tulips are one of the best-known geophytes, but their taxonomy remains convoluted and their evolutionary history poorly understood. Here, we used plastid genomes to identify some issues with current classification, understand the diversification history of the genus, and identify potential species linked to historical cultivation. METHODS: We gathered a large number of tulip specimens from living collections, herbaria, and online sources and through extensive fieldwork to infer maximum likelihood phylogenies of the plastid genomes of Tulipa (Liliaceae), representing ~86% of accepted species alongside a range of occasionally accepted synonyms. We used BEAST and secondary calibration points to date the tree, before assessing the biogeographical history of the genus using BioGeoBEARS. RESULTS: Based on our results, we described a fifth subgenus, Eduardoregelia, and identified a range of species where our results do not align with current taxonomy. Our data suggests the genus diverged from a clade containing Amana and Erythronium around 32.5 million years ago (Mya), with the most recent common ancestor existing around 22.8 Mya in the broader Central Asia region, a period that saw rapid uplift of mountain ranges and associated aridification in the region. The genus primarily diversified in Central Asia with rapid radiations within the last 10 My, possibly as a response to further orogenesis. Several migrations outside of the ancestral region have occurred, primarily via the steppes of Kazakhstan and Russia and along the Caucasus and Iranian and Anatolian Mountains to the eastern Mediterranean region. We also provide evidence that the maternal lineage of the garden tulip involved several species including T. scardica and T. suaveolens. CONCLUSIONS: Many tulip species present limited diagnostic characters, making their taxonomy difficult, compounded by their long use in horticulture and widespread hybridization, especially in gardens. We provide an up-to-date phylogenetic framework for this genus that may help resolve many taxonomic issues in the future, while highlighting further work to be done. We reinforce the importance of Central Asia in the evolutionary history of this genus and provide an important foundation for further study of Tulipa and more effective conservation of wild tulip species.

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