Natural History Institutions Research Articles

Description of Rhipicephalus hibericus sp. nov. (Ixodoidea: Ixodidae), a species of the Rhipicephalus sanguineus group in southwestern Europe

We describe all the life stages of Rhipicephalus hibericus n. sp., provide the types, and present molecular support for a new species of the Rhipicephalus sanguineus sensu lato group, present in southwestern Europe, that has been historically confused with Rhipicephalus turanicus Pomerantzev, 1940. A new name is proposed for this taxon because it was impossible to ascribe to types of already described species in the group, deposited for more than 100 years in natural history institutions. The males have a dorsum showing deep and coarse punctations (absent in Rhipicephalus sanguineus sensu stricto) and adanal plates with large punctations (absent in R. sanguineus s.s.); the tail of the spiracular plate is as wide as the closest festoon (half the width in R. sanguineus s.s.). Females have large punctations in dorsal fields, a wide spiracular plate, and a “V” shaped genital opening; such a combination of characters cannot be found in other species of the group. Immatures are described from specimens collected on hosts (Rodentia and Eulipotyphla). Both larvae and nymphs are markedly smaller than R. sanguineus s.s. Nymphs display long, backward-projected auriculae; larvae are almost half the size of R. sanguineus s.s. The new species can hybridize with R. sanguineus s.s. in laboratory colonies producing an unfertile F2, laying brown and dry eggs that did not hatch. Phylogenetic analysis of partial coxI gene sequences placed R. hibericus in a well-supported clade with other sequences of R. sanguineus s.l. from Portugal, as a sister clade of R. sanguineus s.s. The new species does not belong to the R. turanicus group of species. Both 12S and 16S partial gene sequences were not as precise in the correct phylogenetic placement of R. hibericus, in part probably due to the existence of erroneously identified sequences in GenBank©. This description, together with the previous reinstatement of Rhipicephalus secundus and Rhipicephalus rutilus, and the description of the neotypes of R. sanguineus s.s. should help researchers to adequately identify their collections. Our findings demonstrate that R. turanicus is absent in southwestern Europe. Old collections should be re-examined to provide the actual range of the new species.

Tortoise Traffic

The paper examines local and global logistics involved in the transfer of animals to and from zoos in the twentieth century. The key contexts discussed here are, on the one hand, the relationship between the Museum für Naturkunde Berlin (Museum of Natural History) and Berlin Zoo, and on the other hand, trade in and the market of exotic animals, a market that both exceeds and constitutes the institutions of the museum and the zoo. Taking the accidental death of a giant tortoise in the zoo in 1969 as its starting point, the paper studies the movement of animals, dead and alive. It traces the acquisition history of two new Galápagos giant tortoises by following the animals’ trajectory from Ecuador to West Berlin during the Cold War. At the same time, it reconstructs the itineraries of the dead animals’ remains through different natural history institutions, leading into the shared history of trade and traffic between zoos and natural history museums and into the political geographies of the Cold War. To put these episodes into a broader historical context, the article looks back on the expansion of global networks in animal trade through the lens of transport infrastructures, trading networks, and the accompanying red tape, tracing this back to the period around 1900 in order to reveal genealogies, thereby historicizing current logistical practices, policies, and problems. Taking logistics as a critical analytical category for natural history and thus examining natural history as logistics allows us to gain new insights into how logistics not only enabled but also shaped and reshaped natural history’s material, economic, and epistemic frameworks.

Looking back to move forward – Impact of historical moss specimens on modern systematics

Natural history collections reflect our desire to understand the living world. Each collection is unique based on how it was composed, who composed it, where the specimens originated from, and how it has been enriched. Natural history institutions preserve, curate and enhance their collections on an ongoing basis and they serve as a powerful scientific resource. Collections provide a window into past, present and future biodiversity via the information contained on and in specimens. They play a crucial role in the documentation,description and understanding of species themselves, with the specimens held in global collections forming the foundation for all taxonomic endeavours.

Planning the Migration to a New Database: Implications for the Collections of Meise Botanic Garden

Established in 1796, the Meise Botanic Garden has undergone multiple changes in nationality, name, focus, and locations. These changes have impacted its herbarium, living collections, and associated data. The way specimens are filed in the herbarium varies according to specimen type, taxonomic group and historical importance. Pragmatic solutions were used in the past for dealing with the divergent collections and their users' specific needs. There are at least 15 filing systems used at the Botanic Garden at present. In 2015, funding facilitated the digitization of 1.2 million herbarium specimens. A follow-on project in 2018 digitzed another 1.4 million specimens. Together with other initiatives, like the Global Plants Initiative, we have more than 2.7 million imaged specimens, representing about 77% of our herbarium collections. Of the imaged specimens, 89% have minimal data (barcode, species name, collector(s), collector number, collection date, country and locality), while the remaining 11% still need the metadata captured from the scanned images (mostly being done through the crowdsourcing project DoeDat). In 2023, a call to tender was started for a new Collection Management System (CMS) as part of the Distributed System of Scientific Collections (DiSSCo) Flanders*1 project. This call for tender was compiled in consultation with various natural history institutions, botanic gardens and museums in Belgium. At present, we are in the process of evaluating the various tenders. As part of the preparation to migrate the data from our present database to the new database, data gaps are being filled and data is being cleaned where possible. This will facilitate the migration from one system to another. This is particularly important for fields relating to taxonomy, countries and collectors, as these have implications for the physical location of specimens in the herbarium. In the past months, much time has been dedicated to linking specimens to the taxon table. At present fewer than 0.6% of specimens with a filing name (the scientific name under which the specimen is filed in the herbarium cupboards) remain to be linked to the taxon table. The use of the Taxonomic Name Resolution Service helped to resolve some of the issues associated with unlinked names. Many of the remaining unlinked names are names of infraspecific taxa (which are not yet in the taxon table), orthographic variations, or names of commercial cultivars or hybrids. However, this does not include the 11% of the specimens without data mentioned above. The number of specimens lacking a country code is 7%. The African Herbarium, which represents about a third of the specimens at the Botanic Garden, is sorted according to species, country and collector. Resolving missing country codes would facilitate the curatorial process for this collection. Likewise, 6% of specimen data only have collectors as free-text that still needs to be linked to the standardised collectors table. Atomizing and linking these collector strings would also ease the migration to a new CMS. In 2015, a master plan was also drawn up for the physical renovation of the Garden, including the herbarium's infrastructure. Work on the herbarium is planned for 2025, but is contingent on funding. The CMS will form a crucial part of this move as specimens will be reclassified. As is mentioned above, there are several classification systems used at the Botanic Garden. The African and Belgian collections currently follow Mabberley (1997) for angiosperms. This system is no longer up-to-date, and we are considering moving to APG IV (Angiosperm Phylogeny Group) system for flowering plants. For example, the 213 genera present at the Botanic Garden for the family Liliaceae sensu lato (Mabberley 1997) would resolve to 24 families in APG IV. As the specimens are arranged alphabetically by family and genus, this would mean a significant physical reorganization of specimens. The CMS will also be used to track the movement of the various collections. Once the new CMS has been chosen, we will have a better idea of what needs to be done in order to facilitate data migration. For example, linking our taxonomic names to external sources using their permanent identifiers (e.g., World Flora Online, International Plant Names Index, Global Biodiversity Information Facility, Index Fungorum, MycoBank, World Register of Marine Species) would allow us to track and maintain taxonomic changes more easily in the future. Importing the various permanent identifiers into our current database would be prone to inconsistencies as the existing fields are not fit for the purpose. A possible solution would be to manage this data externally and import them into the new CMS. A similar approach could be followed with collectors and Wikidata permanent identifiers. We hope to develop a pragmatic approach with practical solutions.

The Ecosystem of Linked Biodiversity Publications: General Picture of Tools and Services Created by Plazi, Pensoft, MNHN, CETAF, Zenodo, and SIBiLS

A goal of natural history institutions is to contribute to the understanding of biodiversity and disseminate this knowledge through scholarly publications and other public activities. In today’s world, it is expected that this knowledge, imprisoned in separated silos of millions of publications scattered through ca. 500 million published pages, is readily available for exploring and reusing by humans and artificial intelligence tools. The goal of the BiCIKL project and its key product, the Biodiversity Knowledge Hub (BKH), is to put together novel tools and services to publish and extract data from publications to create findable, accessible, interoperable and reusable (FAIR) corpus of digital data, and establish explicit links between the data in publications and cited data types (taxonomic names, gene sequences, occurrences, images). This corpus of data is made available to the researchers and practitioners through the Biodiversity Literature Repository (BLR), the “Biodiversity PMC” digital library, Synospecies, and the OpenBiodiv knowledge graph through analytic tools, including artificial intelligence, and to a large extend through the re-use by the Global Biodiversity Information Facility (GBIF) and ChecklistBank (CLB). This presentation will focus on the entire ecosystem of interlinked services created by Plazi, Pensoft, the Muséum national d'Histoire naturelle, Paris (Science Press), the Consortium of European Taxonomic Facilities (CETAF) e-publishing working group, the Zenodo repository at the European Center for Nuclear Research (CERN) and the Literature Services of the Swiss Insitute of Bioinformatics (SIBiLS) to enforce both novel methods for prospective semantic publishing and text and data mining of legacy literature. In the end, all knowledge, published in various journals by many publishers in different parts of the world, comes together into a standardized and re-usable open and linked FAIR data pool for the benefit of the researchers and society.

Didactic proposal to discover Paleontology at the Museu de Ciències Naturals de Barcelona

Society’s fascination for fossils and the methodology followed for palaeontological work allows to raise awareness about the scientific labour of Palaeontology, and regarding the importance of Geoconservation. Outreach, along with Didactics, are efficient tools to transmit to society knowledge concerning the History of Earth and Life, and about the relevance of Natural Heritage conservation. allowing a meaningful learning towards these topics. An ideal environment to undertake palaeontological didactic and outreach activities for children and adults is the Museu de Ciències Naturals de Barcelona (MCNB), that disposes of a growing Palaeontological Didactic Collection, which includes fossils and replicas. In this work various didactic workshops have been proposed, regarding different Natural Science disciplines, and including activities presented as file cards in which the recommended age of participants, needed resources, explanations of the development of the activity, and observations to adapt them to different educational needs or levels are specified. In addition, an evaluation method for these workshops is also proposed, in order to adapt them in the future. Therefore, this proposal has the main objective of widening the offer of didact activities at the MCNB, in addition of being an example for other Natural History institutions which would like to incorporate meaningful learning experiences to their main scientific communication tasks.

Mobilizing and Enhancing Legacy Biodiversity Data: The case of Karl Wilhelm Verhoeff's correspondence

A considerable amount of biological data is preserved as physical documents, the legacy of former explorers, collectors, researchers, and others. Mobilizing data from handwritten documents has been considered particularly challenging, with well-known cases such as the manual transcription of specimen labels and herbarium sheets by museum staff, or crowdsourced transcription of data card collections through online platforms. Here we present a pipeline of open-source software that can be used to automatically transcribe handwritten text, make it publicly available, annotate it with e.g., scientific names, extract names in Darwin Core Archive (DwC-A) for third-party reuse, and automatically recognize named entities in the machine-readable text. automatically transcribe handwritten text, make it publicly available, annotate it with e.g., scientific names, extract names in Darwin Core Archive (DwC-A) for third-party reuse, and automatically recognize named entities in the machine-readable text. We based our use case on the correspondence of the German zoologist Karl Wilhelm Verhoeff, related to the Myriapoda collection held at the Musée Zoologique de Strasbourg. The documents were processed with Transkribus (Muehlberger et al. 2019), a mostly open-source virtual research environment (OS VRE), which allows text in images to be converted into machine-readable text amenable to semantic enrichment. We achieved a character error rate as low as 5%, a remarkable result for handwritten material, as an accuracy higher than 95% for printed material is acceptable (Deutsche Forschungsgemeinschaft 2016). We then used Myriatrix (Martínez-Muñoz 2019), an instance of the Scratchpads OS VRE (Smith et al. 2011), to create bibliographic references, publish the full text, and annotate the correspondence with scientific names of myriapods. During the process, we added new scientific name spellings and combinations to the taxonomic backbone of Myriatrix and exported the full taxon classification in DwC-A via the Global Biodiversity Information Facility (GBIF) for reuse by the Global Names Architecture and its open-source tools (Patterson et al. 2016, Mozzherin et al. 2017). As a next step we are planning to subject the corrected text from Transkribus to a specific text-preprocessing workflow combining natural language processing (NLP) and machine learning (ML) techniques (Lücking et al. 2021). This includes, inter alia, a multiple annotation approach for general and bioscientific term classification in order to detect the respective entities automatically. The workflow has been developed in the framework of the Specialized Information Service Biodiversity Research (Koch et al. 2017) to make biodiversity information available via a customized and (bio-)ontology-based semantic search engine (Pachzelt et al. 2021). We recommend our comprehensive approach to natural history institutions seeking to efficiently digitize and mobilize the rich biological data present in their archival documents.

Science, commerce, and politics: China’s giant pandas going global (1869-1948)

ABSTRACT The rise of modern natural history has changed the way Westerners see nature, and the generation and popularity of biological knowledge of species have caused transnational chain effects of commercial, ecological, and political nature. Giant pandas, a new species “reconstructed” after the rise of natural history, have attracted the attention of the Western public, and natural history institutions’ demand for exhibition has led to the commercialization of giant pandas. When large-scale hunting of giant pandas impacted the species, the Nationalist government shifted its focus from regulating foreigners to protecting a species: it became illegal for foreigners to hunt giant pandas in China. When the buying and selling of giant pandas was prohibited, European and US-American zoos requested that the Chinese government send giant pandas as gifts; hence the Nationalist government recognized the special role of giant pandas, and “panda diplomacy” began to emerge. Controlled species exchange also helped protect this species. Since natural history became a popular subject in the world, China’s wild animals became globally known as important “messengers” in China’s communication exchanges with the rest of the world.

Algorithms for connecting scientific names with literature in the Biodiversity Heritage Library via the Global Names Project and Catalogue of Life

Being able to quickly find and access original species descriptions is essential for efficiently conducting taxonomic research. Linking scientific name queries to the original species description is challenging and requires taxonomic intelligence because on average there are an estimated three scientific names associated with each currently accepted species, and many historical scientific names have fallen into disuse from being synonymized or forgotten. Additionally, non-standard usage of journal abbreviations can make it difficult to automatically disambiguate bibliographic citations and ascribe them to the correct publication. The largest open access resource for biodiversity literature is the Biodiversity Heritage Library (BHL), which was built by a consortium of natural history institutions and contains over 200,000 digitized volumes of natural history publications spanning hundreds of years of biological research. Catalogue of Life (CoL) is the largest aggregator of scientific names globally, publishing an annual checklist of currently accepted scientific names and their historical synonyms. TaxonWorks is an integrative web-based workbench that facilitates collaboration on biodiversity informatics research between scientists and developers. The Global Names project has been collaborating with BHL, TaxonWorks, and CoL to develop a Global Names Index that links all of these services together by finding scientific names in BHL and using the taxonomic intelligence provided by CoL to conveniently link directly to the page referenced in BHL. The Global Names Index is continuously updated as metadata is improved and digitization technologies advance to provide more accurate optical character recognition (OCR) of scanned texts. We developed an open source tool, “BHLnames,” and launched a restful application programming interface (API) service with a freely available Javascript widget that can be embedded on any website to link scientific names to literature citations in BHL. If no bibliographic citation is provided, the widget will link to the oldest name usage in BHL, which often is the original species description. The BHLnames widget can also be used to browse all mentions of a scientific name and its synonyms in BHL, which could make the tool more broadly useful for studying the natural history of any species.

Pomegranates, Peccaries, and Love

As a participant in the Natural History Institute's confluence on Reciprocal Healing, I was impressed by inconsistencies among nature lovers regarding human relationships with our environments. Her...

BOOK REVIEW: ORCHIDS OF PALAU: A FIELD GUIDE

Orchids of Palau: A field guide by Ann Hillmann Kitalong and Makoto Uesugi. Middletown, DE: The Environment, Inc., 2017. 112 pp. Soft Cover. ISBN 978-982-98016-5-4. £19.00 Micronesian orchid communities are gaining attention from researchers and enthusiasts alike (see, e.g., Raulerson & Rinehart, 1992; GPEPP, 2017; Crain, 2018), however, readily accessible field guides for many of the individual islands or archipelagos are limited in availability. Moreover, 30 to 100 years have passed since much of the literature on Micronesian orchids has been published (e.g., Schlechter, 1921; Tuyama, 1939; Fosberg & Sachet, 1987), during which time numerous changes have taken place in orchid taxonomy that have not been compiled in an easily manageable source. Orchids of Palau: A field guide proficiently fills this void for an important component of orchid diversity in Micronesia. Palau's orchid flora is rich with showy, rare, and endemic species, but given that the islands’ remarkable marine environments often overshadow potential interests in their plant communities, it is encouraging to see that their orchids are being documented and showcased for a broad audience in a convenient field guide. Following the preliminary material [Credits, Acknowledgements, Table of Contents], an Introduction is presented that includes brief sections on Physical Geography, Vegetation of the Islands, History of Palauan Orchids (which includes an interesting list of botanists that have made taxonomic contributions), The Orchid Flora, The Structure of Orchids, The Flower, The Inflorescence, The Seed Capsule, and Vegetative Morphology, most of which include color photos. The main body of the text (Species Descriptions) follows the Introduction and consists of 39 species accounts, organized alphabetically. Each account includes two sections with information on the species’ distribution and habitat (globally and locally) and a species description that includes information on synonymy (in some cases), growth form, stems, leaves, flowers, and phenology. Multiple color photographs of growth form, leaves, flowers, and capsules from co-author Makoto Uesugi and several other contributors also accompany each species account and offer sufficient detail to permit recognition of plants in the field. Although the guide is limited in that it only provides descriptions for less than half of the known orchid species in Palau, it makes up for this in part through a subsequent section of Orchid Plates that includes photos of an additional 12 species. Furthermore, a checklist of 80 recorded species follows the plates section and is a very useful element for consolidating information on the orchids specifically found in Palau. The checklist includes details on phenology (including a monthly calendar) and information on distribution status (Native, Endemic, Introduced, Invasive). The field guide concludes with a Glossary emphasizing orchid morphology and a References section. As with any first edition book, particularly those that cover subjects such as floristics and taxonomy, which are continuously in flux and subject to updates, occasional limitations and errors have inevitably found their way into the publication. In a few instances, photos appear to be captioned incorrectly (e.g., Taeneophyllum palawense, p. 13). Another limitation is that some of the more cryptic species are not included in the Species Descriptions section or in the Plates Section, making it difficult to compare and differentiate closely related species in the field based on the information and photos provided, particularly in the absence of a dichotomous key. In some cases, the taxonomic nomenclature needs to be updated as well, although some of the potential changes are currently under debate (e.g., Oberonia spp., Moerenhoutia spp.). The caption for the checklist also has some missing information for species status symbology (status G), which is omitted. Lastly, it should be noted that the phenology dataset is incomplete, something the authors recognize, and thus it only documents when a species has been observed in bloom by the authors, but not necessarily the true seasonality of the species. Nevertheless, the authors acknowledge that the guide is a work in progress and assert that they are gathering new photographs and added information on seasonality for updated volumes in the future. Despite minor issues with the first edition, I strongly recommend this field guide for any biology department or natural history institute with interests in the flora of Micronesia or southeast Asia. I believe that this book is a valuable resource for botanists focusing on the orchids or flora of Micronesia and a convenient field guide for ecotourists and natural history guides in the Republic of Palau.

NaturalHeritage: Bridging Belgian natural history collections

The Royal Belgian Institute of Natural Sciences (RBINS), the Royal Museum for Central Africa (RMCA) and Meise Botanic Garden house more than 50 million specimens covering all fields of natural history. While many different research topics have their own specificities, throughout the years it became apparent that with regards to collection data management, data publication and exchange via community standards, collection holding institutions face similar challenges (James et al. 2018, Rocha et al. 2014). In the past, these have been tackled in different ways by Belgian natural history institutions. In addition to local and national collaborations, there is a great need for a joint structure to share data between scientific institutions in Europe and beyond. It is the aim of large networks and infrastructures such as the Global Biodiversity Information Facility (GBIF), the Biodiversity Information Standards (TDWG), the Distributed System of Scientific collections (DiSSCo) and the Consortium of European Taxonomic Facilities (CETAF) to further implement and improve these efforts, thereby gaining ever increasing efficiencies. In this context, the three institutions mentioned above, submitted the NaturalHeritage project (http://www.belspo.be/belspo/brain-be/themes_3_HebrHistoScien_en.stm) granted in 2017 by the Belgian Science Policy Service, which runs from 2017 to 2020. The project provides links among databases and services. The unique qualities of each database are maintained, while the information can be concentrated and exposed in a structured way via one access point. This approach aims also to link data that are unconnected at present (e.g. relationship between soil/substrate, vegetation and associated fauna) and to improve the cross-validation of data. (1) The NaturalHeritage prototype (http://www.naturalheritage.be) is a shared research portal with an open access infrastructure, which is still in the development phase. Its backbone is an ElasticSearch catalogue, with Kibana, and a Python aggregator gathering several types of (re)sources: relational databases, REpresentational State Transfer (REST) services of objects databases and bibliographical data, collections metadata and the GBIF Internet Publishing Toolkit (IPT) for observational and taxonomical data. Semi-structured data in English are semantically analysed and linked to a rich autocomplete mechanism. Keywords and identifiers are indexed and grouped in four categories (“what”, “who”, “where”, “when”). The portal can act also as an Open Archives Initiatives Protocol for Metadata Harvesting (OAI-PMH) service and ease indexing of the original webpage on the internet with microdata enrichment. (2) The collection data management system of DaRWIN (Data Research Warehouse Information Network) of RBINS and RMCA has been improved as well. External (meta)data requirements, i.e. foremost publication into or according to the practices and standards of GBIF and OBIS (Ocean Biogeographic Information System: https://obis.org) for biodiversity data, and INSPIRE (https://inspire.ec.europa.eu) for geological data, have been identified and evaluated. New and extended data structures have been created to be compliant with these standards, as well as the necessary procedures developed to expose the data. Quality control tools for taxonomic and geographic names have been developed. Geographic names can be hard to confirm as their lack of context often requires human validation. To address this a similarity measure is used to help map the result. Species, locations, sampling devices and other properties have been mapped to the World Register of Marine Species and DarwinCore (http://www.marinespecies.org), Marine Regions and GeoNames, the AGRO Agronomy and Vertebrate trait ontologies and the British Oceanographic Data Centre (BODC) vocabularies (http://www.obofoundry.org/ontology/agro.html). Extensive mapping is necessary to make use of the ExtendedMeasurementOrFact Extension of DarwinCore (https://tools.gbif.org/dwca-validator/extensions.do). External (meta)data requirements, i.e. foremost publication into or according to the practices and standards of GBIF and OBIS (Ocean Biogeographic Information System: https://obis.org) for biodiversity data, and INSPIRE (https://inspire.ec.europa.eu) for geological data, have been identified and evaluated. New and extended data structures have been created to be compliant with these standards, as well as the necessary procedures developed to expose the data. Quality control tools for taxonomic and geographic names have been developed. Geographic names can be hard to confirm as their lack of context often requires human validation. To address this a similarity measure is used to help map the result. Species, locations, sampling devices and other properties have been mapped to the World Register of Marine Species and DarwinCore (http://www.marinespecies.org), Marine Regions and GeoNames, the AGRO Agronomy and Vertebrate trait ontologies and the British Oceanographic Data Centre (BODC) vocabularies (http://www.obofoundry.org/ontology/agro.html). Extensive mapping is necessary to make use of the ExtendedMeasurementOrFact Extension of DarwinCore (https://tools.gbif.org/dwca-validator/extensions.do).

The European Journal of Taxonomy: Enhancing taxonomic publications for dynamic data exchange and navigation

The European Journal of Taxonomy (EJT) was initiated by a consortium of European natural history publishers to take advantage of the shift from paper to electronic-only publishing (Benichou et al. 2011). Whilst originally publishing in PDF format has been considered the state of the art, it became recently obvious that complementary dissemination channels help to disseminate taxonomic data - one of the pillars of Natural History institutions research - more widely and efficiently (Côtez et al. 2018). The adoption of semantic markup and assignment of persistent identifiers for content allow more comprehensive citations of the article, including elements therein, such as images, taxonomic treatments, and materials citation. It also allows more in-depth analyses and visualization of the contribution of collections, authors, or specimens to taxonomic output and third parties, such as the Global Biodiversity Information Facility, for reuse of the data or building the catalogue of life. In this presentation, EJT will be used to outline the nature of natural history publishers and their technical set up. This is followed by a description of the post-publishing workflow using the Plazi workflow and dissemination via the Biodiversity Literature Repository (BLR) and TreatmentBank. It outlines switching the publishing workflow to an increased use of extended markup language (XML) and visualization of the output and concludes by publishing guidelines that enable more efficient text and data mining of the content of taxonomic publications.

Database Tools to Meet the Nagoya Protocol Requirements in a Collection Management System

The Nagoya Protocol (NP) of the Convention on Biological Diversity requires that genetic resource holders and users obtain, preserve and keep relevant documentation. Users and third parties need to be informed on terms of access, which utilisation is allowed, and which benefits need to be shared when respective genetic resources or associated traditional knowledge is utilised in the meaning of the NP. Following the recommendations in the Code of Conduct & Best Practices of the Consortium of European Taxonomic Facilities (CETAF) CETAF Legislations and Regulations Liaison Group 2019, institutions should implement appropriate data management systems to support compliance with the protocol and keep records on acquisition of biological material, utilization of genetic resources, transfers to third parties, benefits derived and shared, and deaccessioning of specimens or disposal of consumed samples. Here we describe how we have implemented the first set of tools to meet the NP requirements in the Kotka Collection Management System (CMS), which is used by eleven Natural History Museums in Finland. The Kotka CMS is used for storing and managing specimen data and for handling material transactions (loans, exchanges, donations and consumptive loans). Users can enter and store all necessary documentation for both incoming and outgoing material as material transactions, which hold information on e.g., the transaction type, description of the material, important dates, correspondent organization and contact person. Specimens are linked to transactions by their unique identifiers and each transaction also has a unique stable identifier. The first version of the tools for meeting the requirements of the Nagoya protocol on both in situ and ex situ accession of genetic resources have been integrated into the transaction section of the system. For genetic resource users to be able to enter, save and provide all the required information about an incoming genetic resource, we have implemented a set of fields to be completed in the transactions in Kotka CMS (Fig. 1). Users can record, for example, a possible IRCC number (Internationally Recognized Certificate of Compliance), acquisition date and providing country, description of the material, information on Prior Informed Consent, Mutually Agreed Terms, Material Transfer Agreement and other possible permits. The Finnish genomic resource legislation requires a notification within one month of acquisition to the Competent National Authority (CNA; The Finnish Environment Institute and Natural Resources Institute Finland) for any imported genetic resources. The required data for the notification is compiled in Kotka CMS and then sent to the CNA. All the documentation and conditions regulating the utilisation of each specimen and derived samples must follow with the specimen data at all times. To accomplish this all the necessary information and documents are linked from the material transactions to the relevant specimens by unique specimen or sample identifiers. In the specimen view page, links to the full transaction details and history are given, as a single specimen or a derived sample can be part of several different types of transactions. Users also see a summary of the transaction information directly in the specimen view, most importantly whether the specimen is available for genetic research or has any restrictions for use. The Kotka CMS transaction section makes use of the Application Programming Interface (API) provided by the Access and Benefit Sharing Clearing House (ABS-CH). Using the API, Kotka CMS validates the IRCC number if given and provides links to the ABS-CH, for example to the relevant country profile page, the contact details of the CNA, and specific requirements for access to genetic resources when applicable. This way, we provide Kotka CMS users up-to-date information from the original source to support their genetic resource management. We will further improve and develop the tools during the years 2019-2020. Now that the first version is in use, we will make adjustments according to user feedback. We also have a few changes planned, for example, the tools for transferring the necessary information on permits and other details with outgoing specimens to a user in another institution abroad will be updated. All users in Finnish natural history institutions have access to all the information directly in Kotka CMS, as it is a national system. Additionally, both specimen and transaction information searchability will be refined.

Natural history values and meanings in nineteenth-century Chile

In nineteenth-century Chile, naturalists and their supporters argued that scientific work and study, including natural history, were good for individuals and society because they developed and tempered the character of their practitioners. These practitioners and boosters, Chileans, European visitors and European immigrants, made this argument in a context in which Chilean state support for natural history institutions, publications and education helped disseminate scientific training, perspectives and practices. Examining this nineteenth-century discourse of beneficial science is important for three reasons: first, the discourse of value-laden sciences offered this field a powerful justification for its development, especially in the face of criticism; second, because naturalists believed in this discourse, it helps explain what their work meant to them, and, finally, these values highlight the disjuncture between discourses about natural history and its links to military conquests, as well as the ways in which natural history was an exclusionary practice.

Overcoming the Tyranny of Distance: Revealing Type Collections Down-Under.

Auckland Museum’s Natural Science collections contain several thousands of biological primary types, some dating back to well over a 100 years. Biological type specimens are important for the recognition of new species, because they are the specimens on which species names and descriptions are based, and so they are the standards against which all potentially new species are measured. As by definition there can only ever be one primary type for each species, these are the unique specimens with highest scientific value. Fun fact one: More than almost any other country, New Zealand has a very high percentage of endemic fauna and flora, which means species that are found nowhere else. Fun fact two: In New Zealand we only know about 50% of our biodiversity, which means half of all our species are yet to be discovered and described. Therefore, our type collections are actively growing as more and more species are discovered and more and more type specimens are lodged in our collections. Because they are unique, types are of great interest to researchers. However, because of our remote position on the globemany researchers request loans of our type specimens rather than travel the long distance to Auckland. Although such practices were common in the past, we, like many other modern natural history institutions no longer allow the loan of many of these unique items. The risk of damage or loss en route to the recipient and back is considered too great. However, it is a disservice to science not to make types available for study. So in 2008 we launched a project to digitise our type collections. This talk will focus on how high resolution images of our primary types, and their online publication, has removed much of the need for loans and thereby lessened the risks to these important specimens. At the same time it has made our type collections more visible and accessible to a much greater audience.

Planning the future of plant systematics: Report on a special colloquium at the Royal Netherlands Academy of Arts and Sciences.

Planning the future of plant systematics: Report on a special colloquium at the Royal Netherlands Academy of Arts and Sciences.

Content Analysis of Life Exhibitions in Japanese Science Museums and Centres

Life exhibitions in Japanese science museums (SMs) face difficulties in coping with rapid progress in the life sciences owing to certain constraints around the frequency of exhibit renovations, and the Japanese indigenous understanding of the natural world (Shizen) that Japanese visitors unconsciously bring with them. To what extent do current life exhibitions reflect aspects of Japanese Shizen as well as recent progress in the life sciences? The purpose of this study was twofold: to analyse the contents of life exhibitions in nine Japanese SMs from both a Japanese Shizen and a contemporary life science perspective. The major findings were: (1) educational missions in natural history institutions appreciated and reflected Japanese indigenous understanding of Shizen in addition to having a scientific understanding of life phenomena; (2) from a life science perspective, among the ‘common traits of life’, ‘evolution’ was the most commonly exhibited trait, while ‘genome’ was the least; and (3) the importance of DNA and genomes in contemporary life sciences was not yet fully appreciated in most of the institutions. The findings implied that in natural history institutions life exhibitions could emerge as a kind of amalgam of Shizen and life science to the visitors. The need for a careful means to avoid the potential misunderstanding of life sciences by visitors is discussed.

European Journal of Taxonomy: A Public Collaborative Project in Open Access Scholarly Communication

Most natural history institutions in Europe have been scientific publishers sincetheir foundation and have a long scholarly publishing tradition. Nowadays, they areconfronted with rapid technological developments and face complex strategic andtechnical questions related to visibility, access, format, and the financial structure oftheir titles. These issues require a common vision and an international strategy toensure that the community acts in a consistent and coordinated way. A consortiumof institutions is thus launching the European Journal of Taxonomy to provide analternative public open-access business model, where neither authors nor readers haveto pay fees for subscriptions or publication. This paper focuses on the benefits for theinstitutions on taking greater control over their communication process.

EDIT's Taxonomy and Biodiversity Information Services for Biogeographers

agora ISSN 1948-6596 EDIT's Taxonomy and Biodiversity Information Services for Bio- geographers In recent meetings, the opinion has grown that the burgeoning field of biodiversity informatics was being led, perhaps dominated, by descriptive taxonomists. This came as something of a surprise to many of the leading players in the field, so here we want to explore how a taxonomic initiative may have real benefits for other fields, like bio- geography. The European Distributed Institute of Tax- onomy (EDIT; http://www.e-taxonomy.eu/) is a consortium of 29 natural history institutions in Europe and beyond. It works to provide better, faster and more accountable tools to taxonomists, to significantly accelerate the global production of taxonomic knowledge. We are currently just start- ing the final year of a 5-year project. We organise year-round All-Taxa Biodiver- sity Inventory and Monitoring programmes, we develop an Internet Platform for Cybertaxonomy with software for the management of taxonomy and biodiversity data, we create collaborative Scratchpad websites to empower research com- munities across the globe and we improve the training of the next generation’s taxonomists. All this is in addition to helping the most powerful taxonomic institutions in the world work better together. In this article we try to describe what the biogeographical community can gain by partner- ing with the recent developments in computer- aided taxonomy. It seems obvious to us that both sides can only grow from such a partnership: the increasing applied importance of taxonomy makes it rely more and more on geographical data, and the teeming mass of such data would be very hard indeed to navigate for biogeographers without an adequate taxonomic backbone. Cybertaxonomy Platform tools http://cybertaxonomy.org/ Part of EDIT’s work is to develop a series of tools to accelerate and simplify scientific work. These are originally focused on taxonomy, but many of them can be of tremendous use to biogeogra- phers. The Cybertaxonomy Platform has now reached an open-release stage, and can be ac- cessed at http://cybertaxonomy.org/. All of the tools are free and developed using an open source process. They can be downloaded on any platform and used in the field, with or without an internet connection. We aim at provid- ing a comprehensive, robust, intuitive platform to support scientific analysis, respecting interna- tional standards, but without burdening the user with technical details. The system works with minimal components to install. The user interface should not change dramatically if new technolo- gies or standards are adopted. This allows re- searchers to use these tools on a daily basis. Here we offer a selection of tools with a biogeographi- cal interest. 1) EDIT MapViewer (http://edit.csic.es/geo/ mapviewer/edit.html). We are aware of the benefits a taxonomist can get simply by visualizing his georeferenced records on a screen along with other geographic data. It not only enables you to get a good overview of your data, but also to discover distribution patterns; moreover, with the appropriate analysis tools, you can visualize and catch the probable location of well and insufficiently surveyed regions. EDIT mapViewer allows you to do it without installing any software: simply access the website, upload your point data, create your maps and print them in high-quality (maximum 600 dpi) (see Figure 1). You can also get the legend of your sym- bolized points as well as the main map in different formats (JPEG, TIFF, PNG…) and colour or black and white. Other utilities include: browse GBIF data, perform some spatial analysis, query your data, draw your own polygons, choose from different projections, etc. © 2010 the authors; journal compilation © 2010 The International Biogeography Society — frontiers of biogeography 2.1, 2010