Allotetraploid Origin and Putative Ancient Introgression in (Plantaginaceae).

(2 = 4 = 24) is an endangered endemic species that occurs in subalpine zones in Japan. To clarify the unresolved phylogenetic position of within subgenus , we constructed a phylogenetic tree based on the nuclear-encoded single-copy gene sucrose-proton symporter 1 () using 60 previously reported alleles from 24 taxa in subgenus . We found that was closely related to var. . The phylogenetic relationships between and var. were further examined by analyses of the nuclear regions and the internal transcribed spacer (ITS) of rDNA, genome-wide single-nucleotide polymorphism genotyping (via multiplexed inter-simple sequence repeat genotyping by sequencing), as well as by additional analyses of three chloroplast (cp) regions (, , and ) in 25 individuals of and 53 individuals of var. covering the species' geographical distribution. Monophyly of was suggested by the nuclear marker analyses, whereas the cp haplotypes of were shared with var. and in China. The disparity between the nuclear and cp data may be explained by the introgression of the cp genome (cp capture). This research provides a phylogenetic tree showing the position of within subgenus and molecular evidence that implies complicated introgressions between and var. .