Atsuko Takano

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.