| Summary: | Tulipa (Tulips; Liliaceae) is a genus of horticulturally important flowering bulbs (geophytes) comprising approximately 76 species. The taxonomy of the genus has long been confused. The most recent revision of supra-specific taxa has used DNA sequence data to inform taxonomy for the first time. This study sampled 25 species, so there is scope for better sampling to increase understanding of the evolutionary history of the genus and to contribute to a more robust taxonomy. The current study sampled 74 plants representing 61 species. Two nuclear gene regions were used for phylogeny reconstruction, and for both regions a complete survey of the extent of intraindividual polymorphism was made. The study using the first region, the internal transcribed spacer (ITS), included 347 sequences in total. Phylogeny was reconstructed using Bayesian and Maximum Likelihood and network methods. Significant intra-individual polymorphism was revealed, with only 18 species with all clones comprising a monophyletic group. One of the four subgenera were monophyletic, but core subgenera were recovered. Similarly, well-supported clades corresponded to the core species of several sections, though none was monophyletic. A second nuclear gene region was identified for phylogeny reconstruction by scrutinising published EST data from T. gesneriana. The nuclear gene region was a candidate single copy nuclear region (conserved orthologous sequence; COS). The final alignment included 240 sequences and the same plants as the ITS study. As for the ITS region, significant intra-individual polymorphism was revealed, and existing supra-specific taxa were not monophyletic. The extent of intra-individual polymorphism precluded concatenation of the two alignments for total evidence analysis. However, inspecting trees for common patterns revealed some core groupings. Subgenus Tulipa does not appear to be monophyletic, as has been previously proposed. Several sections could be re-circumscribed. In this study we do not make taxonomic changes, because the study highlights problems with using few or single plants to represent species, especially when the plants are not wild collected. A detailed study of wild-collected Tulipa kurdica included phylogenetic and morphometric analyses. Plants in trade as T. kurdica do not correspond to the wild-collected plants or to plants used in previous phylogenetic studies to represent T. kurdica, though these studies have been used to justify placing T. kurdica in synonymy with T. humilis. T. kurdica may be more closely related to T. pulchelta than to T. humilis.
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