Allotetraploid Origin and Putative Ancient Introgression in <i>Plantago hakusanensis</i> (Plantaginaceae)

<i>Plantago hakusanensis</i> (2<i>n</i> = 4<i>x</i> = 24) is an endangered endemic species that occurs in subalpine zones in Japan. To clarify the unresolved phylogenetic position of <i>P. hakusanensis</i> within subgenus <i>Plantago</i>, we constructed a phylogenetic tree based on the nuclear-encoded single-copy gene sucrose-proton symporter 1 (<i>SUC1</i>) using 60 previously reported alleles from 24 taxa in subgenus <i>Plantago</i>. We found that <i>P. hakusanensis</i> was closely related to <i>Plantago asiatica</i> var. <i>densiuscula</i>. The phylogenetic relationships between <i>P. hakusanensis</i> and <i>P. asiatica</i> var. <i>densiuscula</i> were further examined by analyses of the <i>SUC1</i> 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 (<i>trnL-F</i>, <i>ndhF-rpl32</i>, and <i>rpl32-trnL</i>) in 25 individuals of <i>P. hakusanensis</i> and 53 individuals of <i>P. asiatica</i> var. <i>densiuscula</i> covering the species' geographical distribution. Monophyly of <i>P. hakusanensis</i> was suggested by the nuclear marker analyses, whereas the cp haplotypes of <i>P. hakusanensis</i> were shared with <i>P. asiatica</i> var. <i>densiuscula</i> and <i>P. asiatica</i> 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 <i>P. hakusanensis</i> within subgenus <i>Plantago</i> and molecular evidence that implies complicated introgressions between <i>P. hakusanensis</i> and <i>P. asiatica</i> var. <i>densiuscula</i>.