Biodiversity Data Journal最新文献

{"title":"Multiple graphical views for automatically generating SQL for the MycoDiversity DB; making fungal biodiversity studies accessible.","authors":"Irene Martorelli, Aram Pooryousefi, Haike van Thiel, Floris J Sicking, Guus J Ramackers, Vincent Merckx, Fons J Verbeek","doi":"10.3897/BDJ.12.e119660","DOIUrl":"10.3897/BDJ.12.e119660","url":null,"abstract":"<p><p>Fungi is a highly diverse group of eukaryotic organisms that live under an extremely wide range of environmental conditions. Nowadays, there is a fundamental focus on observing how biodiversity varies on different spatial scales, in addition to understanding the environmental factors which drive fungal biodiversity. Metabarcoding is a high-throughput DNA sequencing technology that has positively contributed to observing fungal communities in environments. While the DNA sequencing data generated from metabarcoding studies are available in public archives, this valuable data resource is not directly usable for fungal biodiversity investigation. Additionally, due to its fragmented storage and distributed nature, it is not immediately accessible through a single user interface. We developed the MycoDiversity DataBase User Interface (https://mycodiversity.liacs.nl) to provide direct access and retrieval of fungal data that was previously inaccessible in the public domain. The user interface provides multiple graphical views of the data components used to reveal fungal biodiversity. These components include reliable geo-location terms, the reference taxonomic scientific names associated with fungal species and the standard features describing the environment where they occur. Direct observation of the public DNA sequencing data in association with fungi is accessible through SQL search queries created by interactively manipulating topological maps and dynamic hierarchical tree views. The search results are presented in configurable data table views that can be downloaded for further use. With the MycoDiversity DataBase User Interface, we make fungal biodiversity data accessible, assisting researchers and other stakeholders in using metabarcoding studies for assessing fungal biodiversity.</p>","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11199959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New evidence on the identity of the European <i>Helorus</i> species (Hymenoptera, Proctotrupoidea, Heloridae).","authors":"Jonathan Vogel, Jerome Sauren, Ralph S Peters","doi":"10.3897/BDJ.12.e122523","DOIUrl":"10.3897/BDJ.12.e122523","url":null,"abstract":"<p><strong>Background: </strong>Species of <i>Helorus</i> Latreille 1802 are rarely collected endoparasitoids of Chrysopidae larvae (Neuroptera). Previous work on the limits between the European species of this species-poor genus, based on morphology only, has left some uncertainties. Here, we approach these cases and revisit previous taxonomic decisions using freshly collected and museum material.</p><p><strong>New information: </strong>We generated the first large-scale Heloridae DNA barcode dataset, combined these with morphological data in an integrative taxonomic approach, and added information from studying all relevant type material. We found five species, <i>Helorusanomalipes</i> (Panzer, 1798), <i>H.coruscus</i> Haliday, 1857 stat. rev., <i>H.nigripes</i> Förster, 1856, <i>H.ruficornis</i> Förster, 1856, and <i>H.striolatus</i> Cameron, 1906, for which we provide an updated identification key. DNA barcode data are added to publicly available DNA barcode reference databases, for all species, except <i>H.nigripes</i>.</p>","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11196891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterisation of the <i>Cinnamomumparthenoxylon</i> (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics.","authors":"Mai-Phuong Pham, Dinh Duy Vu, Cui Bei, Thi Tuyet Xuan Bui, Dinh Giap Vu, Syed Noor Muhammad Shah","doi":"10.3897/BDJ.12.e123405","DOIUrl":"10.3897/BDJ.12.e123405","url":null,"abstract":"<p><p><i>Cinnamomumparthenoxylon</i> is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of <i>C.parthenoxylon</i>, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (<i>C.parthenoxylon</i>) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of <i>C.parthenoxylon</i> were analyzed via an Illumina HiSeq^TM 4000 sequencing system. A total of 27,363,199 bases were generated for <i>C.parthenoxylon</i>. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. <i>COG, GO, KEGG, KOG, Pfam, Swiss-Prot</i>, and <i>NR</i> for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of <i>C.parthenoxylon</i>. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, H<i>o</i> = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of <i>C.parthenoxylon</i> was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in <i>C.parthenoxylon</i>. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of <i>C.parthenoxylon</i>.</p>","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11196892/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The number of Estonian black fungus gnats (Diptera, Sciaridae) doubled: the first records of 64 species","authors":"Ina Gorban, Kai Heller, O. Kurina","doi":"10.3897/bdj.12.e123368","DOIUrl":"https://doi.org/10.3897/bdj.12.e123368","url":null,"abstract":"Adult sciarid flies are small to medium-sized, delicate insects, typically black in colour and belonging to the superfamily Sciaroidea within the order Diptera. They exhibit a uniform appearance. Distinguishing them from other families of Sciaroidea is primarily achieved through their typical wing venation. Sciaridae are common in both natural and semi-natural ecosystems, where they play a significant role in decomposition during their larval stage. Prior to the current study, only one specific research project had been conducted on Sciaridae in Estonia. The number of sciarid species identified in Estonia was set at 67.\u0000 This research, conducted in north-eastern Estonia during 2015 and 2016, presents a comprehensive overview of Sciaridae diversity, shedding light on previously understudied aspects of Estonia's biodiversity. A total of 1038 specimens were identified, representing 91 species, amongst which 64 were previously unknown to Estonia. Notably, Corynoptera winnertzi (Mohrig, 1993) emerged as the most abundant species, followed by Corynoptera irmgardis (Lengersdorf, 1930), Corynoptera crassistylata (Frey, 1948) and Bradysia trivittata (Staeger, 1840). The genus Corynoptera Winnertz, 1867 exhibited the highest diversity, consistent with findings from broader European studies. This study underscores the importance of ongoing surveys for better understanding the distribution and composition of Sciaridae species in Estonia, emphasising the need for further research to delve into the intricate ecology and biology of these insects.","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141339461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards computable taxonomic knowledge: Leveraging nanopublications for sharing new synonyms in the Madagascan genus Helictopleurus (Coleoptera, Scarabaeinae)","authors":"M. Rossini, G. Montanaro, O. Montreuil, Sergei Tarasov","doi":"10.3897/bdj.12.e120304","DOIUrl":"https://doi.org/10.3897/bdj.12.e120304","url":null,"abstract":"Numerous taxonomic studies have focused on the dung beetle genus Helictopleurus d’Orbigny, 1915, endemic to Madagascar. However, this genus stilll needs a thorough revision. Semantic technologies, such as nanopublications, hold the potential to enhance taxonomy by transforming how data are published and analysed. This paper evaluates the effectiveness of nanopublications in establishing synonyms within the genus Helictopleurus.\u0000 In this study, we identify four new synonyms within Helictopleurus: H. rudicollis (Fairmaire, 1898) = H. hypocrita Balthasar, 1941 syn. nov.; H. vadoni Lebis, 1960 = H. perpunctatus Balthasar, 1963 syn. nov.; H. halffteri Balthasar, 1964 = H. dorbignyi Montreuil, 2005 syn. nov.; H. clouei (Harold, 1869) = H. gibbicollis (Fairmaire, 1895) syn. nov. Helictopleurus may have a significantly larger number of synonyms than currently known, indicating potentially inaccurate estimates about its recent extinction.\u0000 We also publish the newly-established synonyms as nanopublications, which are machine-readable data snippets accessible online. Additionally, we explore the utility of nanopublications in taxonomy and demonstrate their practical use with an example query for data extraction.","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141340753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomic inventory and distributions of Chenopodiaceae (Amaranthaceae s.l.) in Orenburg Region, Russia","authors":"A. Sukhorukov, M. Kushunina, Nina Stepanova, Olga Kalmykova, Yaroslav M. Golovanov, A. Sennikov","doi":"10.3897/bdj.12.e121541","DOIUrl":"https://doi.org/10.3897/bdj.12.e121541","url":null,"abstract":"Orenburg Region is located in the South Urals, mostly in the steppe zone and is characterised by various landscapes suitable for many Chenopodiaceae. The species of Chenopodiaceae are present in all major plant communities (saline vegetation, steppes, on limestone, chalk and sand, and as degraded or ruderal communities). In the steppe zone, many native subshrubby species (Atriplex cana, Caroxylon laricinum, Suaeda physophora) playing a crucial role in semi-deserts (known as southern steppes in the recent Russian literature) located southwards of Orenburg Region are locally found, and several annuals (Salicornia perennans, Suaeda spp.) are most common dominants in plant communities. Some typical semi-desert species (Kalidium foliatum, Bassia hyssopifolia, Soda foliosa, Spirobassia hirsuta) are found in the easternmost part of the region.\u0000 We compiled a checklist of Chenopodiaceae in Orenburg Region, with two new records (Chenopodium virgatum, Corispermum laxiflorum), based on our critical revision, comprehensive inventory of herbarium specimens and documented observations and field research. In total, we report 76 species in the Region, which is the third-highest number of the Chenopodiaceae species compared with other administrative territories of European Russia, North Caucasus and West Siberia. Alien and native taxa are distinguished. Zonal patterns of species distributions are confirmed. A preliminary conservation status is proposed for each native species. Three species are recommended for exclusion from the Red Data Book of Orenburg Region: Petrosimonia triandra (because of its extensive distribution), Kalidium foliatum and Anabasis salsa (because of the lack of actual threat to their populations). Arthrophytum lehmannianum and Salsola rosacea are considered threatened (Vulnerable) because of their restricted occurrence and population size and because their localities are under anthropogenic pressure. Atriplex hortensis, Atriplex rosea, Chenopodium acuminatum, C. karoi, C. praetericola, C. vulvaria, Climacoptera affinis, C. crassa, Halimocnemis karelinii, Salsola paulsenii and Xylosalsola arbuscula are excluded from the checklist, based on various reasons as discussed in the paper. Point distribution maps are provided for each species. Agriophyllum pungens (Vahl) Link is accepted as the correct authorship instead of \"M.Bieb. ex C.A.Mey.\"","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141344938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Five new species of the genus Paratemnoides Harvey, 1991 (Pseudoscorpiones, Atemnidae) from China","authors":"Yanmeng Hou, Lingchen Zhao, Feng Zhang","doi":"10.3897/bdj.12.e124585","DOIUrl":"https://doi.org/10.3897/bdj.12.e124585","url":null,"abstract":"Paratemnoides Harvey, 1991 is currently represented by 28 species and two subspecies, which are widespread in the world, except for Europe and Antarctica. Paratemnoides sinensis (Beier, 1932) represents the only species of this genus currently recorded from China.\u0000 Five new Paratemnoides species collected from China are described, including detailed diagnoses and illustrations: P. guangdongensis sp. nov. from Guangdong, P. parvus sp. nov., P. politus sp. nov. and P. yunnanensis sp. nov. from Yunnan and P. trisulcus sp. nov. from Guangxi. An identification key to all known Paratemnoides species from China and a distribution map are also provided.","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141342357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species diversity of fish at the Wuzhizhou Island, South China Sea, based on environmental DNA","authors":"Chongzhao Wang, Zhenhua Ma, Kun Cao, Xin Wang, Rui Xi, Ting Jiang, Rui Yang, Yingchun Xing","doi":"10.3897/bdj.12.e127120","DOIUrl":"https://doi.org/10.3897/bdj.12.e127120","url":null,"abstract":"Wuzhizhou Island (WZZ) is located in Haitang Bay in the northern region of Sanya, Hainan Island. The sea area surrounding WZZ represents a typical tropical marine ecosystem, characterised by diverse and complex habitats. Therefore, there is a rich variety of marine fish species at WZZ. The marine ecosystem of WZZ was seriously destroyed initially in the 1970s-1980s and recovered in the 1990s, then constructed as the first national tropical marine ranch demonstration area of China in 2019. As fish is an important high trophic vertebrate in the marine ecosystem, understanding the composition and distribution of fish species could help us to recognise the status of the ecosystem of WZZ and supply scientific data for construction of the national marine ranch demonstration area. This study used eDNA technology to investigate the composition of fish community surrounding WZZ and provided a scientific basis for realising and protecting the marine ecosystem of the South China Sea.\u0000 The WZZ is an offshore island in the South China Sea, harbouring abundant marine fish resources. Although previous research investigated fish species of WZZ, the data were, however, still incomplete due to limitation of sampling methods and survey seasons. In this study, we intended to take advantage of eDNA and supplement data of fish species at WZZ as much as possible. Based on eDNA, this study provided the data on 188 fish species (including nine undetermined species denoted by genus sp.) belonging to 17 orders, 63 families and 124 genera and they were the more comprehensive records of fish species surrounding WZZ. In addition, the information on Molecular Operational Taxonomic Units (MOTUs) for taxon identification was also provided, aiming to contribute to the establishment of a specific eDNA taxon database for fish of the South China Sea. This study included two datasets, which were occurrences of fish taxa at WZZ, as well as MOTUs sequences and geographical coordinate information of sampling sites. The “fish taxon occurrences” dataset presented records on taxonomic, distribution and habitat conditions of 188 fish species detected using eDNA, as well as the latitude and longitude information of the sampling sites, the \"MOTUs information\" dataset provided the MOTUs sequences, source of sequences, abundance of sequences for 188 fish species, also included the species matched in NCBI and the best NCBI BLAST sequence similarity.","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141342324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Otacilia khezu sp. nov., a new troglobitic spider (Araneae, Phrurolithidae) from Guangxi, China","authors":"Yejie Lin, Haifeng Chen, Xihao Wang, Shuqiang Li","doi":"10.3897/bdj.12.e126716","DOIUrl":"https://doi.org/10.3897/bdj.12.e126716","url":null,"abstract":"Only two Otacilia Thorell, 1897 species with troglobitic characteristics have been recorded from Laos and no records of troglobitic Otacilia species from China.\u0000 A new troglobitic species is reported from Guangxi, China: Otacilia khezu Lin & Li, sp. nov. (♂♀). Photos and morphological descriptions of the new species are presented; the type specimens of the new species are deposited in the Institute of Zoology, Chinese Academy of Sciences (IZCAS), Beijing.","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141347864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae)","authors":"G. Montanaro, James Balhoff, Jennifer C Girón, Max Söderholm, Sergei Tarasov","doi":"10.3897/bdj.12.e121562","DOIUrl":"https://doi.org/10.3897/bdj.12.e121562","url":null,"abstract":"Taxonomy has long struggled with analysing vast amounts of phenotypic data due to computational and accessibility challenges. Ontology-based technologies provide a framework for modelling semantic phenotypes that are understandable by computers and compliant with FAIR principles. In this paper, we explore the use of Phenoscript, an emerging language designed for creating semantic phenotypes, to produce computable species descriptions. Our case study centers on the application of this approach to dung beetles (Coleoptera, Scarabaeinae).\u0000 We illustrate the effectiveness of Phenoscript for creating semantic phenotypes. We also demonstrate the ability of the Phenospy python package to automatically translate Phenoscript descriptions into natural language (NL), which eliminates the need for writing traditional NL descriptions. We introduce a computational pipeline that streamlines the generation of semantic descriptions and their conversion to NL. To demonstrate the power of the semantic approach, we apply simple semantic queries to the generated phenotypic descriptions. This paper addresses the current challenges in crafting semantic species descriptions and outlines the path towards future improvements. Furthermore, we discuss the promising integration of semantic phenotypes and nanopublications, as emerging methods for sharing scientific information. Overall, our study highlights the pivotal role of ontology-based technologies in modernising taxonomy and aligning it with the evolving landscape of big data analysis and FAIR principles.","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141347820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}