To understand the relationships among species of Carex sect. Rarae in Japan, we conducted molecular phylogenetic analyses based on a combined dataset of DNA sequences of plastid (atpB–rbcL, rpl16– rpl16–rps3, rps16, trnT–trnL, trnL–trnL–trnF) and nuclear (ITS) regions. All species and varieties of C. sect. Rarae in Japan were included. The resulting phylogenetic tree consisted of two major clades: Clade I with distinctly veined perigynia, and Clade II with indistinctly veined perigynia. Clade I further consisted of two subclades A and B. Subclade A comprised C. biwensis and C. capillacea, while subclade B included the Japanese endemics C. fulta, C. koyaensis, C. noguchii, and C. ruralis. Clade II comprised C. hakonensis, C. onoei, C. semihyalofructa, and C. uda. Clade II and subclade A corresponded to Carex subsect. Capitellatae (excluding C. fulta) and Carex subsect. Rarae circumscribed by Egorova, respectively. We propose a new subsection, Fultae, for subclade B, which is characterized by distinctly veined perigynia that lack rusty dots. We suggest that Carex koyaensis var. yakushimensis be treated as C. yakushimensis. Carex inagawaensis is described as a new species from Hyogo Prefecture. A diagnostic key to subsections and species of Carex sect. Rarae in Japan is presented.

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Clerodendrum trichotomum s. lat., under which many infraspecific taxa have been recognized, includes both tetraploid and diploid individuals, although chromosome numbers and geographic variation in ploidy levels have not been investigated in the Japanese archipelago. The geographic distribution of ploidy levels and chloroplast haplotypes of four Japanese taxa of C. trichotomum s. lat., based on chromosome counts, flow cytometry, and genotyping of five microsatellite loci is reported. It was determined that Japanese C. trichotomum var. trichotomum and var. yakusimense are tetraploid (2n = 104), while var. esculentum and C. izuinsulare are diploid (2n = 52). The diploid taxa are distributed only on the southern edge of the Japanese archipelago, while tetraploid C. trichotomum is distributed widely. Such distribution patterns may be formed by temperate forest shrinkage during, and tetraploid expansion after, glacial periods. Thirteen haplotypes were detected, and were divided into the following three clades: (1) Japanese C. trichotomum var. trichotomum and C. izuinsulare, (2) C. trichotomum var. yakusimense and var. esculentum, and (3) Chinese C. trichotomum. Two haplotypes were shared between diploid and tetraploid lineages, suggesting multiple polyploidization events in C. trichotomum s. lat.. Inconsistency between nuclear and chloroplast phylogenetic trees suggests a past inter-lineage hybridization event in C. trichotomum s. lat.

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To classify the species of Pedicularis ser. Verticillatae Maxim. (Orobanchaceae) in Taiwan, phylogeographic analyses using internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA) and trnK (partial) regions of chloroplast DNA (cpDNA) were performed. It was determined that the Taiwanese populations formed a single strongly-supported clade with P. refracta (Maxim.) Maxim., an endemic of Kyushu, Japan. Little genetic variation between the Taiwanese populations and P. refracta was detected. Morphological analyses showed that the Taiwanese populations and P. refracta differed in three key characteristics: corolla length, distance between the rachis and the sinuses of the pinnae, and plant height. It was concluded that the Taiwanese populations should be treated as a variety of P. refracta (Kyushu populations); P. refracta var. transmorrisonensis (Hayata) Hurus. (lectotypified here). In addition, the phylogeographic analyses suggested that the disjunct distribution pattern between Taiwan and Kyushu was due to Quaternary vicariance events rather than to long distance dispersal of seeds.

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Recently, we found two species of Crassula newly introduced into central Japan. Based on their morphology, we identified them as Crassula peduncularis and C. saginoides, native to the New World. They closely resemble C. aquatica, which is indigenous to Japan. Here, we describe the morphological distinctions among the three species in detail. In addition, we examined genetic differences among the three species based on sequence variations in the nuclear ribosomal ITS region and three chloroplast intergenic regions. Although C. saginoides was considered to be an inland form of C. aquatica and had been treated as a synonym of C. aquatica, the degree of genetic differentiation was relatively large, suggesting that these two taxa should be considered to be independent species.

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An alien member of the Utricularia (Lentibulariaceae) discovered in Japan is currently assigned to U. inflata, a native of North America. However, some morphological traits differ between the plants in Japan and U. inflata, including the apex of the floral spur and filament of the stamens. The alien plants are completely sterile, while U. inflata is capable of seed production. DNA analysis revealed that the chloroplast DNA sequences of the alien also differ from those of U. inflata in four regions. We provisionally determine the alien plants to be U. cf. platensis, a South American species with which it shares many traits.

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A new peloric form of Cephalanthera longifolia (L.) Fritsch., C. longifolia f. conformis Suetsugu & Hiros. Hayak. (Orchidaceae), from Hokkaido, Japan, and Punakha District, Bhutan, discovered during recent field and herbarium studies, is described and named.

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