Atsuko Takano

HERBARIUM PLANT SPECIMENS AND THEIR HERBARIUM HOLDINGS Natural history collections around the globe represent a dormant source of taxonomic and biogeographic information, as it is estimated that one to three billion specimens are included in such collections (Soberon 1999; Ariño 2010). In the case of botanical collections, the worldwide distribution of specimens across herbaria is often uneven and biased by colonialism, with most specimens housed in the global North, and in many cases resulting in a reverse latitudinal relationship between plant diversity present in nature and the location of the herbaria housing it (Park et al. 2023). As an example, Yong (2013) reviewed holdings of common and type specimens and concluded that the type specimens’ accumulation in China is less than the world average. The number of type specimens is an important reflection of botanical accumulation in a country, and the number of specimens and their origins are therefore very important in a globalized framework. Accordingly, efforts to catalogue and digitize collections, and to make them globally accessible, are important tasks for herbaria. HERBARIA IN JAPAN AND THE UNIVERSITY OF TOKYO (TI) HERBARIUM In Japan, 74 herbaria are registered in Index Herbariorum (Thiers 2024), accounting for more than 13 million plant specimens. Herbaria in Japan date from the 19th century, with the first herbarium founded in Japan being the University of Tokyo’s (TI) herbarium (Herbarium of the University of Tokyo 2021) established in 1877. The herbarium holds a collection of more than 1,800,000 specimens of vascular plants, corresponding to ca. 14% of the total botanical collection of Japan. Although there is no complete survey of the number of specimens in the collection, it is estimated that the TI herbarium holds 20,000 type specimens, corresponding to 1% of the total number in the collection. Within the type specimens, only a fraction of the collection is digitized and available online, including 3,793 type specimens of angiosperms (and 1,743+ type specimens from other groups newly photographed in the last year). Regarding the ferns and lycophytes, the TI herbarium holds 35 families, including more than 300,000 specimens, comprising 1068+ type specimens (with 321 confirmed holotypes, 127 isotypes, and 510 syntypes), which are now being databased. The TI herbarium fern and lycophyte type collection includes plants from Japan, and important collections from Korea, Manchuria, Taiwan, and many Southeast Asian countries. Collections from outside Japan were mainly gathered by Japanese botanists that were assigned to expeditions in those countries, as Japan’s national power increased rapidly after the Meiji restoration (1869–1889). For example, Takiya Kawakami, originally from the Hokkaido University, actively worked on collecting plants from Taiwan; Hiroshi Hara worked on the Himalayan flora; Takenoshin Nakai worked on the Korean flora and collected medicinal plants from Indonesia and Ceylon (Sri Lanka); and Bunzo Hayata made a huge contribution to Taiwan’s flora. The specimens collected hold not only information on the taxonomic diversity, but also reflect historic events between Japan and these adjacent countries, thus proper curation of these materials is of great importance. The TI herbarium also holds unique collections, including many fern specimens collected from Seram Island (Indonesia), South America’s Andes collections by Fumio Maekawa, and Brazil’s Amazon collections by Masayuki Takeuchi. THE HIDDEN POTENTIAL OF THE TI HERBARIUM AND FUTURE PROSPECTS The TI herbarium collection is an important resource of natural history information, but its potential is still hindered by its incomplete databasing. In the Global Biodiversity Information Facility (GBIF) database, the Tracheophyta data from Japan currently consists of 3,503,623 herbarium specimens (GBIF.org 2024). Most of the data is from the TNS herbarium (500,060 specimens, National Museum of Nature and Science 2024), Kanagawa Prefectural Museum of Natural History (318,574 specimens, Kanagawa Prefectural Museum of Natural History 2024) and Nagano Environmental Conservation Research Institute (170,889 specimens, Nagano Prefecture 2023). The University of Tokyo's TI herbarium data only contains 40,382 specimens, not including any ferns or lycophytes, restricting access to the collection for researchers abroad. The TI herbarium mission now is to properly catalogue and make that information available, especially to those based in regions from where the plants were originally collected. Since 1981, many scientists have contributed to the cataloguing of the type specimens in the TI herbarium, with some of this data made available online. However, it is estimated that this database covers less than 10% of the collection, and does yet not include the ferns or lycophytes. We see the development of an open-access database for the TI herbarium as of utmost importance, as the herbarium represents an important historical and biodiversity account for East Asia.

The new collection building named Collectionarium*1 (CN) of the Museum of Nature and Human Activities, Hyogo, (HYO), Hitohaku*2 Japan, which opened in October 2022, contains ca. 600,000 vascular plant specimens, including 10% that were not mounted. Here, we describe the process of specimen moving to the CN, including integration with ca. 250,000 herbarium specimens of Shoei Junior College (known as SHO). At the same time, the collection sequence has been updated from the new Engler system (Melchior 1964) to the Angiosperm Phylogeny Group (APG) III system. The storage rooms of natural history museums are full everywhere across the world, and extensions are necessary. When collections spaces are enlarged, it creates opportunities to relocate specimens. We hope that our experiences will be useful to other institutions. The Status of the HYO Collection in 2020 When the construction of the CN started in early 2020, we had 600,000 plant specimens: ca. 350,000 on 220 shelves and the other 250,000 in ca. 1,500 cardboard boxes. The 250,000 specimens, donated by the SHO in 2012, were kept in boxes as existing shelves were too short to house them. Based on an estimated capacity of 1,000–2,000 specimens per shelf, the new storage consisting of 525 shelves would not have the capacity to store all the specimens. Therefore, it was necessary to estimate the total volume of specimens more accurately. The classification system also needed updating. Change From Engler to APG At the time of its opening in 1992, HYO specimens were arranged according to the new Engler system. However, the APG system began to be adopted more recently. The new Engler and APG systems are quite distinct, treating dicots in a different way, and some families have disappeared and new ones arisen. The plant picture books published recently in Japan all adopt the APG system. The younger generation studying plants never learned the new Engler system, making it impossible for them to find specimens arranged in this way. Therefore, we decided to change the arrangement of the specimens to the APG III system whilst relocating the herbarium. For pteridophytes, we decided to adopt the Pteridophyte Phylogeny Group (PPG) I system (PPG I 2016). In order to plan the placement of specimens, it was necessary to know the number of specimens at the genus level and to investigate how much space each family would need. We measured the thickness of all genus covers containing specimens, regardless of whether they were in shelves or boxes. Based on these results, we planned the layout. Next we packed the specimens into cardboard boxes following the APG system, and two surfaces of each box was labeled with the room number (=1 or 2) in the CN with locations in the room. All the boxes were moved to the Holonpia Hall (the Hall) from December 2021 to January 2022. Then, 220 empty specimen shelves were transported to the CN in February 2022. After the shelves were moved, ca. 4,000 boxes stored in the Hall were carried back into old repository in March 2022 to wait for moving. Moving to the new storage Gases, e.g., ammonia, are released from concrete buildings for a while after construction. Since these gases are harmful to specimens, it is necessary to wait until the gas concentration decreases to a safe level, before storing the specimens there. Beginning in April 2022, the ammonia concentration was measured once a month in the two new storage rooms at the CN. Rooms were ventilated nearly every day. In November 2022, the concentration of ammonia in both rooms fell to 30 ppb or less and it was finally safe to move the specimens in. Moving was carried out during the regular maintenance closure in January 2023. First, we carried the boxes to the exhibition area on the first floor of the CN because we needed enough space for unpacking and sorting. We opened boxes one by one for each family to combine the HYO and SHO specimens, sorted them in alphabetical order, re-packed them into boxes, brought the boxes up to the storage rooms on the second floor, and placed them onto the shelves. Two teams of people, three or four for each storage room, worked with this system for six days until all the specimens were placed, properly arranged, and on the shelves by late January. Specimens are now arranged according to the APG system, and ready to be examined. Please contact the authors for herbarium study requests.

We would like to introduce our recently developed systems for taking images of herbarium specimens and for the automatic extraction of data from specimen labels at the Herbarium of the Museum of Nature and Human Activities, Hyogo, Japan (HYO). Firstly, we designed a low-cost, but high-quality specimen imaging system for non-professional photographers to obtain images rapidly (Takano et al. 2019). Our system uses a mass-produced, mirrorless single-lens reflex (SLR) camera (SONY ILCE6300) with a zoom lens (Samyang Optics SYIO35AF-E35 mm F/2.8). We made a photo stand by ourselves to reduce costs. In addition, we have adopted an LED (light-emitting diode) lighting system with high color rendering. This imaging system has been introduced, with some improvements or adjustments for available space, to various herbaria in Japan (e.g., University of Tokyo (TI), Kyoto University (KYO)), contributing to the digitization of herbarium specimens across Japan. Next, we developed a system to extract label information from specimen images. The specimen image was uploaded to Google OCR and data were extracted in the form of text. Uploading the whole specimen image decreased the reading accuracy of the software because the plant images behaved as OCR (Optical Character Reader) noise. Therefore, the label part was cut out from the whole specimen image by using D-Lib*1 and uploaded to tesseract OCR*2 for OCR extraction of the label information (Aoki 2019, Takano et al. 2020). When installing this system for HYO, we designed it as an application accessible externally via the internet, which proved very useful during the coronavirus pandemic: part-time workers checked and conducted label data input from home. Finally, we decided to develop a system that would automatically label the text data extracted by OCR and input them into the appropriate cells of the database. Even though the text data could be extracted from specimen images, it needed a human to input them into the database. Therefore, we adopted Named Entity Recognition (NER), a system that extracts named entities such as place names, identifying proper nouns from unstructured text data. It enables information recorded in herbarium specimens to be tagged as named entities. We tried text matching at first, but the result was not satisfactory, so we started to use machine learning instead. We compared three natural language libraries for Japanese: BERT (Bidirectional Encoder Representations from Transformers), Albert (A Lite version of BERT), and SpaCy. Despite BERT and SpaCy returning similarly high f-scores (indicating good performance), we decided to use SpaCy because it runs better on ordinary PCs or servers. With sufficient machine learning after the creation of a text corpus (a specialised dataset) specific to labels on herbarium specimens, we successfully developed the application. The project files are available on GitHub*3 (Takano et al. 2024). We then examined whether this system could be applied to non-plant specimen images, i.e., fishes or birds, and found that it could efficiently extract data. Therefore, we decided to publicize this system on the cloud server and share it with other natural history museums in Japan*4. Curators can obtain a unique ID and password and upload specimen images from their collection to extract label data. The digitization of natural history collections in Japan has been long behind other countries, and this system will help to accelerate it. The system mentioned above is specialized for the natural history collections of Japan, but we believe it is possible to build similar programs in other countries, and we hope our experience will contribute to the mobilization of the world’s natural history collections.

Abstract Reproductive interference, an interspecific interaction in reproductive process that exerts an adverse effect, has gained attention as a contributing factor in promoting exclusive distributions between closely related species. However, detailed studies on the possibility of reproductive interference between native plants are still lacking, presumably because strong reproductive interference can rapidly realize exclusive distributions, leaving the two species apparently independent. Salvia japonica and S. lutescens are found in separate localities at a small scale, although their distributions overlap at a large scale. We investigated the possibility of reproductive interference between them through field surveys, hand-pollination experiments, evaluation of hybrid fertility, cpDNA and nrDNA genotyping, and genome-wide DNA analysis. The field survey results did not reveal apparent negative interaction in competition for pollinator services. Mixed pollination with conspecific pollen and counterpart pollen reduced seed set in S. japonica, and hybrid progeny produced by mixed pollination were less than 20% as fertile compared to the pure species. The DNA genotyping results suggested the possibility of hybridization where their distributions overlap, and the genome-wide DNA analysis results showed clear genetic differentiation between the two species as well as the existence of hybrids. These results suggest that bi-directional reproductive interference between S. japonica and S. lutescens may have led to their present separated distributions at a small scale.

Abstract Paraphlomideae (Lamioideae, Lamiaceae) is a recently established tribe endemic to East and Southeast Asia. It comprises three herbaceous genera: Paraphlomis, Matsumurella, and Ajugoides. Phylogenetic relationships among these genera have not yet been satisfactorily resolved and the monophyly of Paraphlomis was challenged in previous molecular phylogenetic studies. In this study, we performed maximum likelihood and Bayesian inference analyses on complete plastomes and nuclear ribosomal internal and external transcribed spacer sequences to further resolve the generic relationships within Paraphlomideae. All phylogenetic analyses support the monophyly of Paraphlomideae. Contrary to traditional classifications, both Ajugoides and Matsumurella were deeply nested within Paraphlomis, indicating the need to expand Paraphlomis to include Ajugoides and Matsumurella. Hence, six new combinations and one replacement name are proposed. Morphologically, species of the newly defined Paraphlomis share a rhizomatous or stoloniferous habit, plants with simple hairs, nutlets with a truncate apex, and actinomorphic calyces. In addition, widespread incongruence between nuclear and plastid trees may have been caused by hybridization and incomplete lineage sorting after rapid diversification in the re‐circumscribed Paraphlomis.

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.

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.

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.