Table 1.
Information of the investigated Lilium samples.
Table 2.
Primers applied in this study.
Fig 1.
Bayesian inference phylogram reconstructed using the concatenation of eight cpDNA genes with MrBayes.
The tree was rooted at Cardiocrinum cordatum. Sections are coded as follows: section Archelirion, solid square, section Daurolirion, blank diamond, section Leucolirion, blank square, section Liriotypus, blank triangle, section Pseudolirium, blank circle, section Sinomartagon, solid circle, and section Martagon, solid diamond. Posterior probabilities are shown below the branches.
Fig 2.
Bayesian inference phylogram reconstructed based on nrITS with MrBayes.
The tree was rooted at Cardiocrinum cordatum. Posterior probabilities are shown below the branches. The sections are coded the same as they are in Fig 1.
Fig 3.
The phylogeny reconstructed based on the combined data of nrITS and cpDNA genes with the BEAST analysis.
The tree was rooted at the outgroups of Fritillaria taipaiensis and Cardiocrinum cordatum. The sections are coded as they are in Fig 1. The scale bar denotes 2 million years ago (Ma). Posterior probabilities are shown below the branches. (A) All sampled taxa were analyzed. (B) L. bulbiferum, L. davidii var. willmotiae, L. ‘Casa Blanca’ were removed from the analysis due to their possible hybrid origins. The tree was deemed the hypothetical species tree. Numbers on the branches represent estimated divergence times.
Table 3.
Recombination rates and nucleotide diversities of the 20 Lilium species.
Fig 4.
Gene flow among the three clusters suggested by the hypothetical species tree.
Numbers denote the extent of the gene flow estimated by the IMa2 analysis. The thick arrow indicates significant gene flow as suggested by the likelihood ratio tests.