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We studied hybrid interactions of  Lilium meleagrinum ,  Lilium gongshanense , and  Lilium saluenense  using an integrative approach combining population genetics, fieldwork, and phenological research. These three species occur along an elevational gradient, with  L. meleagrinum  occurring at lower elevations,  L. saluenense  at higher elevations, and  L. gongshanense  between them. The species show strong morphological differentiation despite there being no clear environmental barriers to gene flow among them.  Lilium gongshanense  is likely to have a hybrid origin based on our prior work, but its progenitors remain uncertain. We sought to determine whether gene flow occurs among these three parapatric species, and, if so, whether  L. gongshanense  is a hybrid of  L. meleagrinum  and/or  L. saluenense . We analyzed data from multiple chloroplast genes and spacers, nuclear internal transcribed spacer (ITS), and 18 nuclear Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) microsatellites for accessions of the three species representing dense population-level sampling. We also inferred phenology by examining species in the field and using herbarium specimens. We found that there are only two types of chloroplast genomes shared among the three species and that  L. gongshanense  forms two distinct groups with closest links to other species of  Lilium  based on ITS. Taken together,  L. gongshanense  is unlikely to be a hybrid species resulting from a cross between  L. meleagrinum  and  L. saluenense , but gene flow is occurring among the three species. The gene flow is likely to be rare according to evidence from all molecular datasets, and this is corroborated by detection of only one putative hybrid individual in the field and asynchronous phenology. We suspect that the rarity of hybridization events among the species facilitates their continued genetic separation.

frontiers in plant science

Hybrid Speciation and Introgression Both Underlie the Genetic Structures and Evolutionary Relationships of Three Morphologically Distinct Species of Lilium (Liliaceae) Forming a Hybrid Zone Along an Elevational Gradient