Biosystematic studies on Lilium (Liliaceae) II. Evolutionary history and taxon recognition in the L. maculatum–L. pensylvanicum complex in Japan

To clarify the evolutionary history of the Lilium maculatum–L. pensylvanicum complex in Japan and to improve the circumscription of its component taxa, we conducted phylogenetic analyses based on chloroplast and nuclear internal and external transcribed spacer (ITS, ETS) DNA sequences, a genome-wide analysis of single-nucleotide polymorphisms (SNPs) using multiplexed ISSR genotyping by sequencing (MIG-seq), and morphological observations. Topological differences between the chloroplast and nuclear ITS + ETS phylogenies indicate that ancient hybridization or incomplete lineage sorting were involved in the origin of “maculatum”, but the relatively long length of relevant branches indicates that incomplete lineage sorting is implausible. The results of STRUCTURE analysis (K = 3, the highest delta K value) using MIG-seq indicate that “maculatum” has already developed its own cluster and can be considered a species (L. maculatum) that originated through the hybridization of L. pacificum (sp. nov.) and L. pensylvanicum. MIG-seq Neighbor-Net and STRUCTURE analyses (K = 3), as well as chloroplast DNA phylogeny, reveal that populations in disjunct limestone areas (L. maculatum var. bukosanense) originated via the hybridization of L. maculatum and L. pacificum, whereas populations in the Sado-Tobishima Islands (L. maculatum var. sadoense, var. nov.) originated via hybridization between L. maculatum and L. pensylvanicum. These taxa appear to be more or less genetically isolated from other populations based on the STRUCTURE analysis (K = 5), although we do not know whether this isolation resulted from geographic distance or reproductive barriers. Based on available MIG-seq and morphological data, respectively, we consider the two hybrid-origin populations to be independent varieties. Furthermore, the morphology of seaside populations of L. maculatum in East Tohoku District appears to have deviated slightly from that of mountain populations (L. maculatum f. monticola); as such, coastal populations merit recognition as a form of L. maculatum (L. maculatum f. spontaneum, comb. & stat. nov.). Other seaside populations of L. maculatum in the West Tohoku District appear to have originated from populations of L. pacificum, but have been successively taken over by L. maculatum through introgression, and have consequently evolved into a form of L. maculatum (L. maculatum f. maculatum). In addition, we found putative extant hybrid populations of L. maculatum × L. pensylvanicum. We recognize three species, two varieties, two forms, and one hybrid in the L. maculatum–L. pensylvanicum complex in Japan.