Biodiversity Data Journal最新文献

The digitization of herbarium specimens is crucial for advancing biodiversity research and data sharing. However, this process is often hindered by the inefficiency of manual transcription and the technical challenges posed by the massive volume of specimens, heterogeneous label layouts, and the prevalence of handwritten texts. To overcome these bottlenecks, this study proposed an automated pipeline that integrates the PadddleOCR engine with the DeepSeek large language model (LLM) for structured information extraction from specimen labels. The pipeline is designed to extract 16 key metadata fields from both printed and handwritten labels. Evaluated on a benchmark dataset, it achieved a high field-level accuracy of 95.4% for printed labels, demonstrating strong reliability. For handwritten labels, the system maintained functionality while correctly identifying its limitations through a confidence-based quality control mechanism. A key finding was the compensatory role of the LLM, which effectively corrected upstream OCR errors, as evidenced by a weak correlation (r = 0.32) between OCR (Optical Character Recognition) confidence and final extraction accuracy. This hybrid architecture ensures data security through local image processing and cost-efficiency via text-only LLM parsing. This work provides a robust, scalable, and practical solution for accelerating the digitization of botanical collections. The method is directly applicable to real-world digitization workflows and promises to significantly enhance the efficiency of biodiversity data creation and sharing.

Background: Natural history collections serve as invaluable records of biological complexity across time and space. However, only a small fraction of these collections has been digitised globally, leaving the majority of specimen data inaccessible for research and digital analysis. Hog Island Audubon Camp, located in Bremen, Maine, United States, is a nature and birding education centre operated by the National Audubon Society's Seabird Institute. It houses a small, but historically valuable natural history collection, primarily used for science education and outreach programmes. By digitising these data, we have increased the research value and accessibility of the collection by enabling scientists to use these records in support of ecological, evolutionary and conservation goals.

New information: Between 2022 and 2024, we digitised all specimens in the collection with available occurrence data using Darwin Core (DwC) as our digital standard. In total, 764 records were captured, representing 417 unique scientific names across animal, plant, fungal and chromista specimens. Most specimens originate from the New England region and the tri-state areas of the United States. Notably, over 300 specimens were collected during the 1960s and 1970s, a period when the harmful effects of DDT (dichlorodiphenyltrichloroethane) on humans and wildlife were becoming increasingly recognised. The oldest specimens in the collection are five New World warblers collected between 1872 and 1897.

Background: The genus Allostoma von Beneden, 1861 (Pseudostomidae Graff, 1904) consists of generally small, often conspicuously colored species. These organisms are typically found on hard bottoms, in gravel, or among algae in marine and brackish-water environments. The Pseudostomid taxon encompasses approximately 55 known species globally, spanning regions across Europe, Asia, and North and South America. In Japan, however, only three species of this taxon have been reported to date: Allostoma durum (Fuhrmann, 1896), Allostoma densissimabursa (Omi, 2020) comb. nov., and Cylindrostoma monotrochum (Graff, 1882).

New information: Samples of seaweed and sand were collected from the coast of Shimane Prefecture in western Japan. Turbellarians were subsequently isolated and examined both in their live state and in histological sections. This investigation led to the description of a new species, Allostoma matsueensis sp. nov., characterized by a pear-shaped granular vesicle, non-sclerotized retractile penis, a narrow rigidly sclerotized conical spermatic duct, a supraterminal female pore, and a thin membraned bursa. The species further exhibits a yellow-to-pale brown body. This discovery constitutes the first record of the genus Allostoma from the western marine coast of Japan.

Background: The Tam Dao Mountain Stream Keelback, Opisthotropis tamdaoensis Ziegler, David & Vu, 2008, was previously described, based on one single holotype and subsequently expanded according to four newly-collected specimens from the type locality. Information on this species is extremely limited.

New information: On the basis of newly-collected Opisthotropis specimens from Hekou, Yunnan, China, this study reports the first country record of Opisthotropis tamdaoensis from China. The Chinese Opisthotropis tamdaoensis population totally agrees with the original description of this species and revealed only a minor genetic distance (lower than 2.9%) in the mitochondrial gene fragment of the cytochrome b (Cytb) compared with the topotypic population. Based upon the our newly-collected specimens and published data, we revised the diagnosis of Opisthotropis tamdaoensis: nasal not divided below nostril;loreal usually 1, not in contact with internasals;pre-oculars 1-2, postoculars 2 subocular, usually 1;anterior temporals 1-2, posterior temporals 2-4;supralabials usually 9, only the fifth or fifth to sixth supralabial (rarely none) in contact with the orbit;infralabials usually 9-10;first pair of chin shields longer than the second pair;dorsal scales smooth anteriorly, keeled posteriorly, in (17-19)-17-17 rows;tails relatively short, TaL/TL 0.143-0.161;pre ventrals 0-4, ventrals 160-176, precloacal divided; 48-56 divided subcaudals;uniform olive-grey dorsum, with a dark longitudinal lateral stripe within the dark flank colouration, ventral side pale or light yellow, without sharp transition towards the dark dorsal colouration, subcaudal region may bear dark mottling. This finding broadly extends our understanding of this poorly-known snake species and raises the total known Opisthotropis number in China to 14. Moreover, this study reports the second Opisthotropis species in Yunnan Province, China.

The Grey-headed woodpecker (Picus canus) inhabiting South Korea is an insectivorous bird species that favours ants. However, during winter, most insects enter a dormant stage, reducing their availability as food sources. This may prompt P. canus to change its primary food sources. To verify this hypothesis, we fabricated and installed 91 nest boxes in forests in Seocheon-gun, Chungnam Province, considering the body size of P. canus. From these, we collected faeces samples totalling 94 conical tubes of 1.5 ml each, obtained from 17 nest boxes used by P. canus as roosting sites. The collected faeces samples were examined under a microscope and their relative frequencies were calculated at the family or order level. Formicidae exceeded 70%, confirming it as the primary food source for P. canus during the breeding season and also in winter. Anacardiaceae fruits accounted for approximately 16%, significantly lower than Formicidae, but still considered a major winter food source for P. canus.

Background: During fieldwork conducted in the Bac Yen District of Son La Province, near the Ta Xua Nature Reserve, a representative of a previously never registered genus and species of rodent in Vietnam, the Yunnan field mouse (A. ilex O. Thomas, 1922), was discovered.

New information: This finding significantly expands our knowledge of the distribution of Apodemus species in northeastern Indochina. Morphological and genetic analysis of the specimen ruled out accidental introduction and established that the Vietnamese population is natural and belongs to the eastern phylogenetic branch of this species, which also inhabits the southern Yunnan-Guizhou Plateau, as well as the upper reaches of the Mekong, Hong Ha, and Da Rivers. Thus, the list of rodent species and genera in Vietnam has been expanded with a new species. Data on the species' geographic distribution across its range are also provided.

Background: The genus Drapetisca comprises 7 species distributed in Canada, Central Asia, China, Caucasus, Europe, Japan, Russia (Europe to the Far East), and the USA, out of which five species have been recorded in China (World Spider Catalog 2025). The males and females of Drapetisca can be distinguished from all other Linyphiidae genera by the palpal distal arm of the paracymbium anchor-shaped in the retrolateral view and the protruding epigyne without a scape.

New information: While examining Linyphiidae Blackwall, 1859 specimens from Gele Mountain in Chongqing, we discovered a new species of the genus Drapetisca, D. dentata sp. nov. Detailed descriptions, photographs of copulatory organs and somatic features, and a distribution map are provided.

Background: Species functional traits provide critical insights into how organisms interact with and respond to their environment. Key characteristics, such as body size, dispersal ability and trophic specialisation influence species' survival, reproduction and adaptability. Island ecosystems, particularly oceanic archipelagos like the Azores, serve as ideal natural laboratories for studying these traits due to their unique biogeographic history and high endemism. Arthropods, as dominant colonisers and ecosystem engineers, exhibit rapid adaptation and trait diversification in these isolated settings. However, island arthropods face escalating threats from habitat loss, climate change and invasive species, which disrupt ecological functions and increase extinction risks. Under the scope of BALA (Biodiversity of Arthropods from the Laurisilva of Azores) project (1999-2021) and SLAM (Long Term Ecological Study of the Impacts of Climate Change in the natural forest of Azores) project (2012-2025), we obtained a comprehensive and standardised dataset of arthropods functional traits currently known to occur in the Azores Archipelago.

New information: We present a standardised functional trait database for Azorean arthropods, building on 25 years of research on 602 species and subspecies across seven classes and 27 orders. The dataset includes endemic, native non-endemic and exotic species, with traits selected for their relevance to disturbance responses (e.g. body size, dispersal, verticality) and ecological interactions (e.g. trophic level, feeding behaviour). By synthesising these data, we aim to support predictive modelling of biodiversity responses to environmental change and provide information for conservation strategies. This resource provides a foundation for global comparisons and advances in trait-based ecology in island systems.

Background: The genus Coelotes Blackwall, 1841, comprises 156 species, primarily distributed in East Asia, including Japan (64 species), China (56 species) and Korea (1 species). Currently, only two species of this genus have been recorded in Guangxi, China.

New information: A new coelotine species, Coelotes fani Zhou, sp. nov. (♂♀), is described from the Guangxi Zhuang Autonomous Region, China. This includes a detailed description, diagnosis, illustrations and a distribution map of this species.

The combined pressures of overharvesting for ornamental and medicinal markets, along with pervasive habitat degradation, have precipitated a critical threat to wild populations of the jewel orchid, Ludisia discolor, within the biodiversity hotspots of Vietnam. The development of robust molecular tools is therefore essential to inform effective conservation strategies. This study established a suite of polymorphic Expressed Sequence Tag-derived Simple Sequence Repeat (EST-SSR) markers for L. discolor and applied them to assess genetic diversity and population structure. Transcriptome sequencing on the Illumina HiSeq™ 4000 platform yielded 44,764,702 high-quality reads. De novo assembly generated 26,271 unigenes (N50 = 2,160 bp; Q30 = 96.3%), which were comprehensively annotated against public databases (Nr, Swiss-Prot) and classified into Gene Ontology, KOG, and KEGG pathways. From 9,495 identified EST-SSR loci, 15 highly polymorphic markers were validated. Analysis of Vietnamese populations revealed moderate genetic diversity (Na = 3.17; He = 0.54; PIC = 0.59). Analysis of molecular variance (AMOVA) indicated significant genetic differentiation, with 23% of variation partitioned among populations. Bayesian clustering, Principal Coordinates Analysis (PCoA), and Neighbor-Joining (NJ) tree reconstruction consistently identified two distinct genetic clusters correlated with geography, suggesting restricted gene flow. These transcriptome-derived EST-SSR markers have proven effective for population genetic studies in L. discolor. The genomic resources and findings presented here provide a critical foundation for genetic monitoring and support the integration of molecular data into conservation and restoration programs for this ecologically and culturally significant orchid.