Atsuko Takano

Abstract Digital extraction of label data from natural history specimens along with more efficient procedures of data entry and processing is essential for improving documentation and global information availability. Herbaria have made great advances in this direction lately. In this study, using optical character recognition (OCR) and named entity recognition (NER) techniques, we have been able to make further advancements towards fully automatic extraction of label data from herbarium specimen images. This system can be developed and run on a consumer grade desktop computer with standard specifications, and can also be applied to extracting label data from diverse kinds of natural history specimens, such as those in entomological collections. This system can facilitate the digitization and publication of natural history museum specimens around the world.

Abstract Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as ”East Asian tulips” has a number of cryptic species and a huge genome size (1C = 21.48–57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within Amana are challenging. Here we included all species and 84 populations of Amana, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in Amana. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA‐BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, Amana polymorpha, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.

Abstract Herbarium specimens are dried plants mounted onto paper. They are used by a limited number of researchers, such as plant taxonomists, as a source of information on morphology and distribution. Recently, digitised herbarium specimens have begun to be used in comprehensive research to address broader issues. However, some specimens have been misidentified, and if used, there is a risk of drawing incorrect conclusions. In this study, we successfully developed a system for identifying taxon names with high accuracy using an image recognition system. We developed a system with an accuracy of 96.4% using 500,554 specimen images of 2171 plant taxa (2064 species, 9 subspecies, 88 varieties, and 10 forms in 192 families) that grow in Japan. We clarified where the artificial intelligence is looking to make decisions, and which taxa is being misidentified. As the system can be applied to digitalised images worldwide, it is useful for selecting and correcting misidentified herbarium specimens.

Meehania montis-koyae Ohwi (Lamiaceae), which has been considered a narrow endemic and endangered species in Japan, was found in eastern China in 2011. China and Japan belong to the same floristic region and share many plant species, but it is very rare that Japanese narrow endemic species are newly found outside of the country. We examined herbarium specimens of both countries, and conducted analyses of molecular phylogenetics, population genetics, and divergence time estimation using two nuclear (ITS and ETS) gene regions and MIG-seq data. Chinese plants tend to become larger than Japanese, and they are different in leaf shape and floral features. Molecular phylogenetic analysis shows Chinese and Japanese M. montis-koyae are the closest relatives to each other. Population genetic analysis indicates no current gene flow between the Chinese and Japanese populations, and divergence time analysis shows they were separated during the late Miocene. We reach the conclusion that Chinese and Japanese M. montis-koyae have already become distinct biological entities, and a new taxon name Meehania zheminensis A. Takano, Pan Li, G.-H.Xia is proposed for the Chinese plants. A key to Asian Meehania species is provided.

Major international herbaria, natural history museums and universities have recently begun to digitise their collections to facilitate studies and improve access to collections. In Japan, more than 10 million herbarium specimens are housed in various universities/museums; however, only 1% of these have been digitised. In this paper, we describe a new method for imaging herbarium specimens that is applicable to local/small herbaria. It is safe, fast, simple and inexpensive, but also satisfies usage guidelines for minimum image quality and can produce digital files suitable for long-term storage and future post production. During an eight-month trial at the Museum of Nature and Human Activities, Hyogo, with three part-time workers using a custom-made copy stand and a mirrorless interchangeable lens camera with a large LED light bank system, we were able to image 73,180 herbarium specimens (571 per day on average), obtaining two RAW and two JPEG files for each specimen.

Both Salvia akiensis and S. lutescens (Lamiaceae) are endemic to Japan. Salvia akiensis was recently described in 2014 in the Chugoku (= SW Honshu) region, and each four varieties of S.lutescens distributed allopatrically. Among varieties in S.lutescens, var. intermedia show a disjunctive distribution in the Kanto (=E Honshu) and Kinki (= W Honshu) regions. Recent field studies of S.lutescens var. intermedia revealed several morphological differences between the Kanto and Kinki populations. Here, I evaluated these differences among Salvia lutescens var. intermedia and its allies with morphological analysis and molecular phylogenetic analyses of nuclear ribosomal DNA (internal and external transcribed spacer regions) and plastid DNA (ycf1-rps15 spacer, rbcL, and trnL-F) sequences. Both morphological analysis and molecular phylogenetic analyses showed that S. lutescens var. intermedia from the Kinki region and var. lutescens were closely related to each other. However, var. intermedia from the Kanto region exhibited an association with S. lutescens var. crenata and var. stolonifera, which also grew in eastern Japan, rather than var. intermedia in the Kinki region. These results indicated that S. lutescens var. intermedia is not a taxon with a disjunctive distribution, but a combination of two or more allopatric taxa. Present study also suggested that S. akiensis was most closely related to S. omerocalyx.

Here we report newly found alien herb in Japan, Moenchia erecta (L.) G., M. et Sch. (Caryophylla-ceae). The species is native to Europe and has been naturalized in Australia, Canada and United States. Since 2008, the species has been known its existence in Hyogo Prefecture, and also found from Mie Prefecture in 2014. Its small habit and short life cycle may prevent them find out from the other part of Japan, but the species may spread out throughout this country.

Mating system of Meehania montis-koyae, a rare and endangered perennial herb, was studied by crossing experiments for multiple years and study sites. We conclude this species is self-fertile since both selfed and bagged flowers produced considerable fruits. Compare with other treatments (=selfing, crossing, and control), seed set of bagged flowers were significantly low. During the period of the observation the flowers of M. montis-koyae, visits of syrphus flies and small carpenter bees were confirmed but less frequently. Therefore, M. montis-koyae needs pollen vectors for seed production, however, there may be pollen limitation because of insufficient pollinator visits.

A novel species, Salvia akiensis A.Takano, Sera & Kurosaki, from western Honshu, Japan, is described. Salvia akiensis occurs in Hiroshima and Shimane prefectures and flowers in May and June. Salvia akiensis is similar to S. isensis, S. lutescens sensu lato and S. omerocalyx in having long exerted stamens. However, the species can be distinguished from S. isensis by having much larger flowers, and from S. omerocalyx by having one pair of cauline leaves, long pilose hairs on the inside upper half of the calyx tube, multicellular hairs 1-2 mm long on the outside of the dorsal calyx lobe, and pale bluish-purple corollas. It can be distinguished from S. lutescens sensu lato by its smaller flowering shoots, the leaf apex roundish, flowering shoot with a single pair of cauline leaves and larger calyx and corolla.

Gynodioecy and floral dimorphism in Salvia omerocalyx Hayata, an endangered species endemic to central Japan, is here reported for the first time. In three populations of flowering individuals, one population had approximately equal numbers of hermaphrodites (= individuals only with perfect flowers) and male sterile individuals, another population was composed entirely of hermaphrodites, and the third was hermaphroditic except for two individuals with perfect- and male sterile flowers. Examination of herbarium specimens suggested two other localities with male sterile individuals. Male sterile flowers are significantly smaller than hermaphroditic flowers, but there was no difference in seed set between the two floral morphs. Additional field surveys are needed to determine the exact sex expression of the species.

Floral size dimorphism, pollination, and genetic variation of Alpinia nieuwenhuizii (Zingiberaceae), a flexitylous ginger, were studied. This study revealed that floral size differed among habitats (i. e., roadsides/riversides vs. forest floors). The effective pollinators of small-flowered populations of the species on a forest floor were different from those of large-flowered populations along roadsides/riversides. Using inter-simple sequence repeat (ISSR) PCR, considerable genetic differentiation was detected between small- and large-flowered populations. These results indicate that reproductive isolation in A. nieuwenhuizii owing to the differentiation of pollen vectors between two floral size morphs may lead to genetic differentiation between the two morphs. © 2013 Springer-Verlag Wien.

To determine evolutionary relationships among all Japanese members of the genus Salvia (Lamiaceae), we conducted molecular phylogenetic analyses of two chloroplast DNA (cpDNA) regions (rbcL and the intergenic spacer region of trnL-trnF: trnL-trnF) and one nuclear DNA (nrDNA) region (internal transcribed spacer, ITS). In cpDNA, nrDNA, and cpDNA+nrDNA trees, we found evidence that all Japanese and two Taiwanese Salvia species are included in a clade with other Asian Salvia, and Japanese Salvia species were distributed among three subclades: (1) S. plebeia (subgenus Sclarea), (2) species belonging to subg. Salvia, and (3) species belonging to subg. Allagospadonopsis. At the specific level our findings suggest: a close relationship between S. nipponica and S. glabrescens, no support for monophyly of S. lutescens and its varieties in cpDNA, nrDNA and cpDNA+nrDNA trees, and that S. pygmaea var. simplicior may be more closely related to S. japonica than to other varieties of S. pygmaea.

Five new species of the genus Plagiostachys (Zingiberaceae) from Borneo, P. brevicalcarata, P. longicaudata, P. megacarpa, P. roseiflora, and P. viridisepala are described and illustrated. Of these, P. brevicalcarata, P. longicaudata, and P. viridisepala have mucilaginous inflorescences, while the inflorescences of the other two species are non-mucilaginous. A key to the Bornean species of Plagiostachys is also provided.

A new genus and species, Myxochlamys mullerensis (Zingiberaceae) from Central Kalimantan, Borneo is described. This new species is characterized by indistinct pseudostems; congested inflorescences with spirally arranged bracts; copious, highly viscous, axillary-pooled mucus secreted from glands on imbricate bracts; and flowers with a concave labellum, versatile anthers, and a groove formed by the inner surface of the corolla tube to envelope and hold the style. Parallel orientation of the plane of distichy of the leafy shoots, well-developed staminodes, and labellum not connate with the filament suggest that Myxochlamys belongs to the tribe Zingibereae. Among the genera in Zingibereae, Myxochlamys is similar to Scaphochlamys in that it lacks a distinct pseudostem and spiral inflorescence; it is distinct from Scaphochlamys, however, in that it has a groove within the corolla tube, concave labellum and versatile anthers. Phylogenetic analyses based on DNA sequences of the nuclear internal transcribed spacer (ITS) and maturase K (matK) of the chloroplast DNA show similarity with Distichochlamys, Myxochlamys, and Scaphochlamys. The similarities and differences between Myxochlamys and related genera are discussed.

A new species of ginger, Etlingera palangkensis (Zingiberaceae) is described from Borneo. Though similar to E. nasuta, the new species is clearly distinguished by the color of flowers and shape of labellum.

Trapa L. (Trapaceae) is one of the most common aquatic plants in Japan. However, its taxonomic treatment has differed among authors. As a step toward a revision of Japanese Trapa, we analyzed allozymes in plant samples collected from 55 populations and tentatively classified into 6 taxa. Allozyme analysis indicated three distinct groups corresponding to the size class of the fruits: T. incisa (small), T. japonica group (medium), and T. natans group (large). The development of lower protuberances or spines and the presence or absence of tubercles had no correspondence to allozymic differentiation and thus are to be considered as variants within taxa. Fixed heterozygosity found in the T. japonica group indicates that the group might be of hybrid origin between T. incisa and plants of the T. natans group. (c) 2005 Published by Elsevier B.V.

Flexistyly is a unique floral mechanism involving extreme curving of the style. It was first described in Chinese ginger (Amomum, Zingiberaceae). This is a pioneer report on flexistylous gingers of Malesia, where most species of this family grow. We observed the floral behaviour and flower visitors in Alpinia nieuwenhuizii Val., a Bornean endemic. Although the floral behaviour and effective pollinators (carpenter bees, Xylocopa) were similar between the Bornean species and the previously reported flexistylous Alpinia, the pollinator behaviour between them strikingly differed with regard to the visit frequency of the pollinators showing a bimodal pattern during the day. This was a better match for the floral behaviour of the flexistylous Alpinia. Some gender differentiation observed between the two types of morphs is also discussed in the present study.

All published information on Globba (Zingiberaceae) in Sumatra is summarized and augmented by our own data obtained by revision of herbarium materials and observations in the field. Sixteen species and five varieties of Globba are reported from Sumatra, including one new species, which belongs to sect. Globba, G. multifolia sp. nov. The difference between G. multifolia and allied species is discussed. A key to the species of Globba in Sumatra is provided.

Molecular phylogenetic analyses of the genus Globba, Zingiberaceae, using the trnK gene (including the matK.,gene) of chloroplast DNA and the internal transcribed spacers of nuclear ribosomal DNA (ITS) sequence data, were carried out in order to understand whether triploid formation was a rare event in Globba. The topologies of both the trnK gene and the ITS trees were almost identical except the position of G. patens var. costulata. Triploids were scattered into several clades. These results suggest that multiple triploid formations had taken place and that such formations may be one of the most important force for speciation of Globba. The monophyly of both sects. Ceratanthera and Globba was not positively supported.

A new variety of Globba atrosanguinea, var. sumatrana is described and illustrated. The difference from var. atrosanguinea is discussed. A key to varieties of G. atrosanguinea is provided.

Somatic chromosome numbers in 19 taxa of sects. Ceratanthera and Globba in Globba (Zingiberaceae) were determined to be 32 or 48. Pollen fertility of some species was also studied. Pollen fertility of plants with 2n=32 was relatively high, while fertility of taxa with 2n=48 was relatively low. Results of this and former cytological studies indicate that the basic chromosome number of sects. Ceratanthera and Globba is 16.

Four new Sumatran Globba species, G. fecunda, G. talangensis, G. flavibracteata and G. acehensis are described, and illustrated. Their relationships with allied species are discussed.

Karyomorphology of four taxa of Trapa native to Japan were studied for the first time using meristematic cells of young leaves. Chromosome numbers reported are 2n=48 in T. incisa, 2n=96 in T. japonica, 2n=48 in T. natans var. japonica, and 2n=ca. 96 in T. natans var. pumila. 2n=96 in T. japonica and 2n=ca. 96 in T. natans var. pumila are numbers unknown elsewhere in the genus so far. Features common to all the taxa investigated are : (1) interphase nucleus has the simple chromocenter type ; (2) chromosomes at metaphase mostly small(0, 3-1.2μm long by our methods) ; (3) χ=24(or 12). Evidence available suggests that 2n=96 in T. japonica and 2n=ca. 96 in T. natans var. pumila are amphiploids hybridized between T. incisa and T. natans var. japonica with 2n=48.