142 results on '"Cybertaxonomy"'
Search Results
2. Luchando contra los déficits Linneano y Wallaceano en el avance del conocimiento de la diversidad de los escarabajos del estiércol: el caso de los géneros Onthophagus Latreille, 1802 y Phanaeus MacLeay, 1819 (Coleoptera: Scarabaeidae).
- Author
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Moctezuma, Victor
- Subjects
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BIOLOGICAL classification , *PALEO-Indians , *INSECTS , *DUNG beetles - Abstract
An introduction is presented on the importance of insects (particularly dung beetles), and the origin and importance of two major limitations for the studies on diversity: the Linnaean and Wallacean shortfalls. Afterwards, the most recent progress in the taxonomic and geographic knowledge of the genera Onthophagus Latreille, 1802 and Phanaeus MacLeay, 1819 are synthesized; and some unpublished ideas on the current lack of knowledge on the taxonomy and distribution of the genera are presented as a reference for future studies. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
3. Scanning holotypes from the Vertebrate Paleontology Collection at the Museu Paraense Emilio Goeldi (Brazil): Tools for research and science outreach.
- Author
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Kerber, Leonardo, Moraes–Santos, Heloísa, and Ramos, Maria Inês Feijó
- Abstract
The scanning of paleontological collections is increasingly important for morphological studies and science outreach. In addition to ensuring data sharing, digitization contributes to preserving morphological information in case of damage to the original specimens. In this communication, we aim to report digital versions of the holotypes from the Vertebrate Paleontology Collection at the Museu Paraense Emilio Goeldi, Brazil. For this purpose, eighteen holotypes of Early/Middle Miocene Teleostei from Pirabas Formation, northern Brazil, were scanned using microtomography, and cybertypes were proposed. The CT‐Scan data were stored in a virtual repository, can be freely accessed, and are available for future studies on the morphology of these specimens. Furthermore, these specimens are tiny and fragile, and digital versions can be an alternative to safely handling them. Finally, the digitization of important specimens, at least of holotypes, needs to be a standard practice in museum collections over the next years. [ABSTRACT FROM AUTHOR]
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- 2023
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4. Integration or minimalism: twenty-one new species of ghost spiders (Anyphaenidae: Anyphaena) from Mexico
- Author
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Andrés Rivera-Quiroz and Fernando Álvarez-Padilla
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diversity ,Neotropic ,Araneae ,cybertaxonomy ,species online documentation ,Zoology ,QL1-991 ,Botany ,QK1-989 - Abstract
The rhythm of biodiversity loss vastly surpasses the number of new species described per year, with several taxa going extinct without us even knowing about their existence. After more than 250 years of traditional taxonomy, it is clear that the rate of biodiversity description and discovery needs to be improved. Molecular data has greatly increased the speed of species discovery and accuracy of taxonomic delimitation. Phenotypic documentation, although relatively slower, is still crucial to identify species and communicate taxonomic discoveries to a broader audience. Here, we integrate these data sources to describe a relatively large number of new species of the spider genus Anyphaena and look into its internal phylogenetic relationships. Our findings support the existence of several species groups within Anyphaena (as currently defined), but failed to recover the monophyly of this genus, suggesting a more comprehensive revision of its species groups and closely related anyphaenid genera is necessary. The 21 new species described here are: Anyphaena adnani sp. nov., A. bifurcata sp. nov., A. dulceae sp. nov., A. epicardia sp. nov., A. fernandae sp. nov., A. franciscoi sp. nov., A. ibarrai sp. nov., A. jimenezi sp. nov., A. megamedia sp. nov., A. miniducta sp. nov., A. natachae sp. nov., A. noctua sp. nov., A. porta sp. nov., A. quadrata sp. nov., A. rebecae sp. nov., A. salgueiroi sp. nov., A. sofiae sp. nov., A. stigma sp. nov., A. tonoi sp. nov., A. triangularis sp. nov. and A. urieli sp. nov.
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- 2023
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5. Taxonomic revision of the mydas-fly genera Eremohaplomydas Bequaert, 1959, Haplomydas Bezzi, 1924, and Lachnocorynus Hesse, 1969 (Insecta, Diptera, Mydidae).
- Author
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Boschert, Claire and Dikow, Torsten
- Abstract
The genera Eremohaplomydas Bequaert, 1959, Haplomydas Bezzi, 1924, and Lachnocorynus Hesse, 1969 (Diptera: Mydidae: Syllegomydinae) are revised. Currently, four species are known from southern Africa, i.e., Eremohaplomydas desertorum Bequaert, 1959 from north-western Namibia, Haplomydas crassipes Bezzi, 1924 widespread in southern Africa, Lachnocorynus chobeensis Hesse, 1969 from northern Botswana, and Lachnocorynus kochi Hesse, 1969 from northern Namibia. Four new species, Eremohaplomydas gobabebensis sp. nov. and Eremohaplomydas whartoni sp. nov. from the central Namib desert of Namibia, Eremohaplomydas stomachoris sp. nov. from the northern Namib desert in Namibia, and Lachnocorynus stenocephalus sp. nov. from north-eastern Zimbabwe are described. Lachnocorynus kochi is synonymized with Lachnocorynus chobeensis. Distribution, biology, occurrence in biodiversity hotspots sensu Conservation International and seasonal imago flight activity are discussed. Descriptions/redescriptions, photographs, specimen occurrence data, and identification keys (both dichotomous and matrix-based) to species are provided and made openly accessible in data repositories to support and accelerate future studies of the included taxa. An updated identification key to the Mydidae genera of the Afrotropical Region is provided. The placement of the three genera in the subfamily taxon Syllegomydinae is discussed and several morphological features, such as an extremely reduced proboscis in some species, a unique wing venation in Eremohaplomydas gobabebensis sp. nov., and the unique metathoracic coxa, are discussed. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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6. Cactaceae at Caryophyllales.org – a dynamic online species-level taxonomic backbone for the family.
- Author
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Korotkova, Nadja, Aquino, David, Arias, Salvador, Eggli, Urs, Franck, Alan, Gómez-Hinostrosa, Carlos, Guerrero, Pablo C., Hernández, Héctor M., Kohlbecker, Andreas, Köhler, Matias, Luther, Katja, Majure, Lucas C., Müller, Andreas, Metzing, Detlev, Nyffeler, Reto, Sánchez, Daniel, Schlumpberger, Boris, and Berendsohn, Walter G.
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SPINE , *PERSONAL names , *CARYOPHYLLALES , *LITERARY sources , *BOTANY , *CACTUS - Abstract
This data paper presents a largely phylogeny-based online taxonomic backbone for the Cactaceae compiled from literature and online sources using the tools of the EDIT Platform for Cybertaxonomy. The data will form a contribution of the Caryophyllales Network for the World Flora Online and serve as the base for further integration of research results from the systematic research community. The final aim is to treat all effectively published scientific names in the family. The checklist includes 150 accepted genera, 1851 accepted species, 91 hybrids, 746 infraspecific taxa (458 heterotypic, 288 with autonyms), 17,932 synonyms of accepted taxa, 16 definitely excluded names, 389 names of uncertain application, 672 unresolved names and 454 names belonging to (probably artificial) named hybrids, totalling 22,275 names. The process of compiling this database is described and further editorial rules for the compilation of the taxonomic backbone for the Caryophyllales Network are proposed. A checklist depicting the current state of the taxonomic backbone is provided as supplemental material. All results are also available online on the website of the Caryophyllales Network and will be constantly updated and expanded in the future. Citation: Korotkova N., Aquino D., Arias S., Eggli U., Franck A., Gómez-Hinostrosa C., Guerrero P. C., Hernández H. M., Kohlbecker A., Köhler M., Luther K., Majure L. C., Müller A., Metzing D., Nyffeler R., Sánchez D., Schlumpberger B. & Berendsohn W. G. 2021: Cactaceae at Caryophyllales.org – a dynamic online species-level taxonomic backbone for the family. – Willdenowia 51: 251–270. Version of record first published online on 31 August 2021 ahead of inclusion in August 2021 issue. Data published through:http://caryophyllales.org/cactaceae/Checklist [ABSTRACT FROM AUTHOR]
- Published
- 2021
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7. Automated Plant Species Identification: Challenges and Opportunities
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Mata-Montero, Erick, Carranza-Rojas, Jose, Rannenberg, Kai, Editor-in-chief, Sakarovitch, Jacques, Series editor, Goedicke, Michael, Series editor, Tatnall, Arthur, Series editor, Neuhold, Erich J., Series editor, Pras, Aiko, Series editor, Tröltzsch, Fredi, Series editor, Pries-Heje, Jan, Series editor, Whitehouse, Diane, Series editor, Reis, Ricardo, Series editor, Furnell, Steven, Series editor, Furbach, Ulrich, Series editor, Gulliksen, Jan, Series editor, Rauterberg, Matthias, Series editor, Mata, Francisco J., editor, and Pont, Ana, editor
- Published
- 2016
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8. Accelerating ocean species discovery and laying the foundations for the future of marine biodiversity research and monitoring
- Author
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Rogers, Alex David, Appiah-madson, Hannah, Ardron, Jeff A., Bax, Nicholas J., Bhadury, Punyasloke, Brandt, Angelika, Buttigieg, Pier-luigi, De Clerck, Olivier, Delgado, Claudia, Distel, Daniel L., Glover, Adrian, Gobin, Judith, Guilhon, Maila, Hampton, Shannon, Harden-davies, Harriet, Hebert, Paul, Hynes, Lisa, Lowe, Miranda, Macintyre, Sandy, Madduppa, Hawis, De Azevedo Mazzuco, Ana Carolina, Mccallum, Anna, Mcowen, Chris, Nattkemper, Tim Wilhelm, Odido, Mika, O’hara, Tim, Osborn, Karen, Pouponneau, Angelique, Provoost, Pieter, Rabone, Muriel, Ramirez-llodra, Eva, Scott, Lucy, Sink, Kerry Jennifer, Turk, Daniela, Watanabe, Hiromi Kayama, Weatherdon, Lauren V., Wernberg, Thomas, Williams, Suzanne, Woodall, Lucy, Wright, Dawn J., Zeppilli, Daniela, Steeds, Oliver, Rogers, Alex David, Appiah-madson, Hannah, Ardron, Jeff A., Bax, Nicholas J., Bhadury, Punyasloke, Brandt, Angelika, Buttigieg, Pier-luigi, De Clerck, Olivier, Delgado, Claudia, Distel, Daniel L., Glover, Adrian, Gobin, Judith, Guilhon, Maila, Hampton, Shannon, Harden-davies, Harriet, Hebert, Paul, Hynes, Lisa, Lowe, Miranda, Macintyre, Sandy, Madduppa, Hawis, De Azevedo Mazzuco, Ana Carolina, Mccallum, Anna, Mcowen, Chris, Nattkemper, Tim Wilhelm, Odido, Mika, O’hara, Tim, Osborn, Karen, Pouponneau, Angelique, Provoost, Pieter, Rabone, Muriel, Ramirez-llodra, Eva, Scott, Lucy, Sink, Kerry Jennifer, Turk, Daniela, Watanabe, Hiromi Kayama, Weatherdon, Lauren V., Wernberg, Thomas, Williams, Suzanne, Woodall, Lucy, Wright, Dawn J., Zeppilli, Daniela, and Steeds, Oliver
- Abstract
Ocean Census is a new Large-Scale Strategic Science Mission aimed at accelerating the discovery and description of marine species. This mission addresses the knowledge gap of the diversity and distribution of marine life whereby of an estimated 1 million to 2 million species of marine life between 75% to 90% remain undescribed to date. Without improved knowledge of marine biodiversity, tackling the decline and eventual extinction of many marine species will not be possible. The marine biota has evolved over 4 billion years and includes many branches of the tree of life that do not exist on land or in freshwater. Understanding what is in the ocean and where it lives is fundamental science, which is required to understand how the ocean works, the direct and indirect benefits it provides to society and how human impacts can be reduced and managed to ensure marine ecosystems remain healthy. We describe a strategy to accelerate the rate of ocean species discovery by: 1) employing consistent standards for digitisation of species data to broaden access to biodiversity knowledge and enabling cybertaxonomy; 2) establishing new working practices and adopting advanced technologies to accelerate taxonomy; 3) building the capacity of stakeholders to undertake taxonomic and biodiversity research and capacity development, especially targeted at low- and middle-income countries (LMICs) so they can better assess and manage life in their waters and contribute to global biodiversity knowledge; and 4) increasing observational coverage on dedicated expeditions. Ocean Census, is conceived as a global open network of scientists anchored by Biodiversity Centres in developed countries and LMICs. Through a collaborative approach, including co-production of science with LMICs, and by working with funding partners, Ocean Census will focus and grow current efforts to discover ocean life globally, and permanently transform our ability to document, describe and safeguard marine species.
- Published
- 2023
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9. Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data
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Pavel Stoev, Ana Komerički, Nesrine Akkari, Shanlin Liu, Xin Zhou, Alexander Weigand, Jeroen Hostens, Christopher Hunter, Scott Edmunds, David Porco, Marzio Zapparoli, Teodor Georgiev, Daniel Mietchen, David Roberts, Sarah Faulwetter, Vincent Smith, and Lyubomir Penev
- Subjects
Cybertaxonomy ,gene sequence data ,micro-CT ,data integration ,molecular systematics ,caves ,Biology (General) ,QH301-705.5 - Abstract
We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.
- Published
- 2016
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10. A Set of Simple Tools For Assembling, Annotating, Versioning and Publishing Taxonomies.
- Author
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Rocha Prado, Laura
- Subjects
TAXONOMY ,BIODIVERSITY ,NATURAL history catalogs & collections ,BOTANICAL nomenclature ,APPLICATION program interfaces - Abstract
Biodiversity data publishers rely on virtually assembled taxonomic hierarchies to structure their data, with operational units involving scientific names, nomenclatural acts and taxonomic trees. The main goal for the majority of biodiversity aggregators, databases, and software developed specifically for managing scientific names, biological samples and other occurrences has been to establish a single, unified biological classification, to serve as their structural "taxonomic backbone." Resources to produce and publish biological classifications digitally are thus, typically restricted to those generating unified taxonomic backbones, leaving individual researchers and decentralized communities with few options to assemble, visualize, version and disseminate multiple taxonomies online. To aid the creation of a culture of assembling, annotating, versioning, and publishing taxonomies online, and to help users interested in taxonomic classifications that lack digital communities, the development of a set of modular and independent tools is proposed, based on the following complementary features: • A web application to serve as the taxonomy curator (referred to as the Curator) • A web application to serve as the optional taxonomic database and information provider (referred to as the Aggregator) These tools are being designed and built following modern software development standards, in a modular architecture consisting of front-end clients, databases, and back-end applications, with the provision for a public Application Programming Interface (API) that will make data available for any interested parties and can be potentially integrated into large-scale projects like the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), Symbiota (Gries et al. 2014), and Plazi (Agosti and Egloff 2009). Curator tool The Curator tool will be a publicly accessible front-end web application, with which users can assemble, curate, and export taxonomies. The primary focus is to support the userpreferred taxonomy generation, with manual inputs and optional annotations of the resulting product. Users can pick between three modes of taxonomy assembly: 1. manual mode with assisted taxon search, 2. automated generation from an online source, and 3. automated generation from a file upload. Taxonomies can be edited and annotated as necessary. Once a user is satisfied with their taxonomy, they can save it in one or all of the available formats for exporting and external usage (common formats include, among others, JSON (JavaScript Object Notation), CSV (comma-separated values), and XML). Logged in users can also opt to save the taxonomy in the Aggregator database, which will make the taxonomy publicly available. Ideally, all fields in the Curator forms should correspond to terms included in the Darwin Core standard (Wieczorek et al. 2012) or Plazi's TaxonX schema (Agosti and Egloff 2009) (for hierarchies available in published treatments). Aggregator tool The Aggregator tool will communicate with the database and will provide users with a number of functionalities, such as: • Store and publish versioned taxonomies generated with the Curator • API endpoints for automation (JSON/XML formats/CSV download) • Optional unique identifier/DOI generation for published taxonomies • Search engine with user-friendly interface as well as API endpoint for querying the database The possibility of making taxonomies available as an API endpoint, as well as exporting taxonomies in different formats, will ensure that this tool behaves as a taxonomic source that can be used by virtually any interested party or application. The tools are being modelled as a decentralized community resource that can be used for any or all taxonomic groups and, as such, its scale and impact will be driven by bottom-up community use. The goal is not to provide extensive coverage of all biological organisms, but rather to provide an open digital toolkit and space for biodiversity researchers and projects that lack access to open, structured, online taxonomic publication venues and dedicated tools. Practical examples of usage for these tools include: • A user generates multiple taxonomic concepts for organisms they are studying, which can then be queried and analyzed by scripts that make taxonomic alignments to compare different scientific hypotheses throughout time; • An institution wants to publish a regional Symbiota portal to manage specimens in a particular collection, so they establish an annotated working taxonomic backbone with the Curator that Symbiota will then be able to ingest before samples can be imported into the portal; • A researcher wants to export a biodiversity portal taxonomy at a given moment and wants to annotate and publish this version in an upcoming paper to establish scientific baselines for proper taxonomic communication. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
11. TaxonWorks: Character state matrices and identification tools.
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Dmitriev, Dmitry A. and Yoder, Matthew
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TAXONOMISTS ,BIODIVERSITY ,DATA management ,ACQUISITION of data ,COLLECTION management (Museums) - Abstract
TaxonWorks is an integrated web-based application for practicing taxonomists and biodiversity specialists. It is focused on promoting collaboration between researchers and developers. TaxonWorks has a modular structure that enables various components of the application to target specific needs and requirements of different groups of users. Specific areas of interest may include nomenclature-related tasks (Yoder and Dmitriev 2021) designed to help assemble and validate scientific name checklists of a target group of organisms; and collection management tasks, including interfaces to create, filter, and edit collecting events, collection objects, and loans. This presentation focuses on matrix-related tools integrated into TaxonWorks. A matrix, which could either be used for phylogenetic analysis or to build an identification key, is structured as a table where columns represent numerous characters that could be used to describe a set of entities, taxa or specimens (presented as rows of the table). Each cell of the table may contain observations for specific character/entity combinations. TaxonWorks does not generate a table for each a particular matrix--all observations are stored as graphs. This structure allows building of a matrix of an unlimited size as well as reuse of individual observations in multiple matrices. For matrix columns, TaxonWorks supports a variety of different kinds of characters or descriptors: qualitative, presence/absence, quantitative, sample, gene, free text, and media. Each character may have specific properties, for example a qualitative descriptor may have numerous characters states, and a quantitative descriptor may have a measurement unit defined. For an entity in a matrix row, TaxonWorks supports either collection objects (specimens) or taxa as Operational Taxonomic Units (OTU). OTUs could either be linked to nomenclature or be stand alone entities (e.g., representing undescribed species). The matrix, once built, could serve several purposes. A matrix based on qualitative and quantitative characters could be used to build an interactive key (Fig. 1), construct standardized natural language descriptions for each entity, and determine a diagnosis (a minimal set of characters that separate one entity from all others). It could also be exported and used for phylogenetic analysis or to build an interactive key in an external application. TaxonWorks supports export files in several formats, including Nexus, TNT, NeXML. Application Programming Interfaces (API) are also available. A matrix based on media descriptors could be used as a pictorial identification tool (Fig. 2). [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
12. Review of Anasillomos Londt, 1983 with the description of a new species (Insecta: Diptera: Asilidae)
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Torsten Dikow
- Subjects
Afrotropical ,assassin flies ,identification keys ,cybertaxonomy ,data sharing ,Biology (General) ,QH301-705.5 - Abstract
The southern African assassin-fly genus Anasillomos Londt, 1983 is reviewed. A new species, Anasillomos juergeni sp. n., is described from the Namib desert and represents the second species in the genus. Descriptions/re-descriptions, photographs, and identification keys are provided to aid in the identification. Distribution, occurrence in biodiversity hotspots sensu Conservation International, and seasonal incidence are discussed.
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- 2015
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13. A Linnaeus NG interactive key to the species of Glomera (Orchidaceae, Coelogyninae) from Southeast Asia.
- Author
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Wati, Richa Kusuma, van Vugt, Rogier R., and Gravendeel, Barbara
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ORCHIDS , *EPIPHYTES - Abstract
We present a multilingual interactive key available online (http://glomera.linnaeus.naturalis.nl) that can be used on any web browser without the need for installing additional software. The key includes 169 species of Glomera, a genus within the necklace orchids (Coelogyninae) not yet comprehensively treated in any recent field guide or web-based survey. With this key, plants can be identified using a combination of vegetative and floristic characters in addition to distribution and ecology as a first step to further taxonomic revisions. We urge anyone with an interest in wild orchids in Southeast Asia to contribute new observations to update current information on the distribution of these overlooked plants as a first step for a taxonomic revision and to gain more insight into their conservation status. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
14. Using the EDIT Platform for Cybertaxonomy to prepare and publish a treatment for the Caryophyllales Network: an online synthesis of the Nepenthaceae.
- Author
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Berendsohn, Walter G., Borsch, Thomas, Güntsch, Anton, Kohlbecker, Andreas, Korotkova, Nadja, Luther, Katja, Müller, Andreas, Plitzner, Patrick, and Mering, Sabine Von
- Subjects
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CARYOPHYLLALES , *NEPENTHES , *PLANT phylogeny , *PLANT classification , *PHYTOGEOGRAPHY - Abstract
The Caryophyllales Network strives to assemble an online dynamic synthesis of the order Caryophyllales, uniting the current knowledge about the phylogeny of the order with up-to-date information on the individual taxa contained. Capturing taxonomic data and the decision processes involved in the definition and circumscription of the taxa requires highly complex specialized software. The Caryophyllales Network uses the EDIT Platform for Cybertaxonomy for that purpose. In the context of the online treatment of the family Nepenthaceae, we describe the steps taken to assemble the database, the interaction with other electronic sources, the links with the World Flora Online initiative, and the prospects for the maintenance and further development of the Nepenthaceae segment of the Caryophyllales database. Nepenthaceae constitute an example of a family with a relatively recent flora treatment (Flora Malesiana, published in 2001), which to a large extent covers its total range of distribution, but with further species subsequently described as new to science in mostly regional treatments, and with an analysis of relationships and species limits on the basis of evolutionary methods just emerging. A snapshot of the current state of the database is provided as an annotated checklist in PDF format in the Supplementary Material online, which includes 176 species and nine naturally occurring named hybrids and treats 435 species and infraspecific names. Citation: Berendsohn W. G., Borsch T., Güntsch A., Kohlbecker A., Korotkova N., Luther K., Müller A., Plitzner P. & Mering S. von 2018: Using the EDIT Platform for Cybertaxonomy to prepare and publish a treatment for the Caryophyllales Network: an online synthesis of the Nepenthaceae. – Willdenowia 48: 335–344. doi: https://doi.org/10.3372/wi.48.48301 Version of record first published online on 17 September 2018 ahead of inclusion in December 2018 issue. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
15. Taxonomic revision of the assassin-fly genus Microphontes Londt, 1994 (Insecta, Diptera, Asilidae).
- Author
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Markee, Amanda and Dikow, Torsten
- Subjects
- *
ROBBER flies , *TAXONOMY , *OPEN access publishing websites , *FLY behavior , *SPECIES distribution - Abstract
The genus Microphontes Londt, 1994 (Diptera: Asilidae: Brachyrhopalinae) is revised. Currently, three species are known from Namibia and western South Africa, i.e. Microphontes megoura Londt, 1994 from north-western South Africa, Microphontes safra Londt, 1994 from Namibia and Microphontes whittingtoni Londt, 1994 from western South Africa. Four new species, Microphontes ericfisheri sp. n. from the Little Karoo of South Africa, Microphontes gaiophanes sp. n. from the Namib desert of Namibia and Microphontes jasonlondti sp. n. and Microphontes kryphios sp. n. from western South Africa, are described. Distribution, occurrence in biodiversity hotspots sensu Conservation International and seasonal incidence are discussed. Descriptions/redescriptions, photographs and identification keys are provided and made openly accessible in data repositories to support future studies of the included taxa. An unusual flight pattern of male Microphontes gaiophanes sp. n. is discussed. A unique morphological feature on tergite 8 of Microphontes females, termed postero-paramedian T8 pores, is described, illustrated and discussed. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
16. Taxonomic revision of the mydas-fly genera Eremohaplomydas Bequaert, 1959, Haplomydas Bezzi, 1924, and Lachnocorynus Hesse, 1969 (Insecta, Diptera, Mydidae)
- Author
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Claire Boschert and Torsten Dikow
- Subjects
Eremohaplomydas ,Haplomydas ,Insecta ,Lachnocorynus ,Arthropoda ,Diptera ,Saxifragaceae ,Saxifraga ,Paleontology ,Mydas flies ,Biota ,Afrotropical ,Karoo ,Mydidae ,Tracheophyta ,Magnoliopsida ,Namib Desert ,Insect Science ,Animalia ,Animal Science and Zoology ,cybertaxonomy ,Plantae ,open-access ,Saxifragales ,Ecology, Evolution, Behavior and Systematics - Abstract
The genera Eremohaplomydas Bequaert, 1959, Haplomydas Bezzi, 1924, and Lachnocorynus Hesse, 1969 (Diptera: Mydidae: Syllegomydinae) are revised. Currently, four species are known from southern Africa, i.e., Eremohaplomydas desertorum Bequaert, 1959 from north-western Namibia, Haplomydas crassipes Bezzi, 1924 widespread in southern Africa, Lachnocorynus chobeensis Hesse, 1969 from northern Botswana, and Lachnocorynus kochi Hesse, 1969 from northern Namibia. Four new species, Eremohaplomydas gobabebensissp. nov. and Eremohaplomydas whartonisp. nov. from the central Namib desert of Namibia, Eremohaplomydas stomachorissp. nov. from the northern Namib desert in Namibia, and Lachnocorynus stenocephalussp. nov. from north-eastern Zimbabwe are described. Lachnocorynus kochi is synonymized with Lachnocorynus chobeensis. Distribution, biology, occurrence in biodiversity hotspots sensu Conservation International and seasonal imago flight activity are discussed. Descriptions/redescriptions, photographs, specimen occurrence data, and identification keys (both dichotomous and matrix-based) to species are provided and made openly accessible in data repositories to support and accelerate future studies of the included taxa. An updated identification key to the Mydidae genera of the Afrotropical Region is provided. The placement of the three genera in the subfamily taxon Syllegomydinae is discussed and several morphological features, such as an extremely reduced proboscis in some species, a unique wing venation in Eremohaplomydas gobabebensissp. nov., and the unique metathoracic coxa, are discussed.
- Published
- 2022
17. A review of the tribes of Deltocephalinae (Hemiptera: Auchenorrhyncha: Cicadellidae)
- Author
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Chris Dietrich and James N. Zahniser
- Subjects
Leafhopper ,classification ,taxonomy ,phylogeny ,database ,interactive key ,cybertaxonomy ,Zoology ,QL1-991 ,Botany ,QK1-989 - Abstract
The classification of the largest subfamily of leafhoppers, Deltocephalinae, including 38 tribes, 923 genera, and 6683 valid species, is reviewed and revised. An updated phylogeny of the subfamily based on molecular (28S, Histone H3) and morphological data and an expanded taxon sample (37 taxa not included in previous analyses) is presented. Based on the results of these analyses and on the morphological examination of many representatives of the subfamily, the classification of the tribes and subtribes of Deltocephalinae is revised. Complete morphological descriptions, illustrations, lists of the included genera, and notes on their distribution, ecology, and important vector species are provided for the 38 recognized tribes and 18 subtribes. A dichotomous key to the tribes is provided. All names in the taxonomic treatments are hyperlinked to online resources for individual taxa which are supported by a comprehensive database for Deltocephalinae compiled using the taxonomic database software package 3I. The online functionality includes an interactive key to tribes and subtribes and advanced database searching options. Each taxon (subspecies through subfamily) has a unique taxon webpage providing nomenclatural information, lists of included taxa, an automated description (if available), images (if available), distributional information, bibliographic references and links to outside resources. Some observations and trends regarding the history of taxonomic descriptions in Deltocephalinae are reported. Four new tribes are described: Bahitini tribe nov. (25 genera), Bonsapeiini tribe nov. (21 genera), Phlepsiini tribe nov. (4 genera), and Vartini tribe nov. (7 genera). The circumscription and morphological characterization of Scaphoideini Oman, 1943 (61 genera) is substantially revised. Eleven new species are described: Acostemma stilleri sp. nov., Arrugada linnavuorii sp. nov., Drabescus zhangi sp. nov., Parabolopona webbi sp. nov., Goniagnathus emeljanovi sp. nov., Hecalus hamiltoni sp. nov., Scaphoideus omani sp. nov., Dwightla delongi sp. nov., Abimwa knighti sp. nov., Gannia viraktamathi sp. nov., and Doratulina dmitrievi sp. nov. Some family-group level taxonomic changes are made: Platymetopiini Haupt, 1929, Anoterostemmini Haupt, 1929, and Allygidiina Dmitriev, 2006 are synonymized with Athysanini Van Duzee, 1892, syn. nov.; Procepitini Dmitriev, 2002 is synonymized with Cicadulini Van Duzee, 1892, syn. nov.; Listrophorini Boulard, 1971 is synonymized with Chiasmini Distant, 1908, syn. nov.; Adamini Linnavuori & Al-Ne’amy, 1983, Dwightlini McKamey, 2003, and Ianeirini Linnavuori, 1978 are synonymized with Selenocephalini Fieber, 1872 syn.nov., and all three are now recognized as valid subtribes in their parent tribe. New placements of many genera to tribe and subtribe are made, and these are described in individual taxon treatments.
- Published
- 2013
- Full Text
- View/download PDF
18. Extracting Data from Legacy Taxonomic Literature: Applications for planning field work.
- Author
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Rivera-Quiroz, Francisco Andres and Miller, Jeremy A.
- Subjects
BIOLOGICAL databases ,DIGITIZATION of archival materials ,SPIDERS - Abstract
Traditional taxonomic publications have served as a biological data repository accumulating vast amounts of data on species diversity, geographical and temporal distributions, ecological interactions, taxonomic relations, among many other types of information. However, the fragmented nature of taxonomic literature has made this data difficult to access and use to its full potential. Current anthropogenic impact on biodiversity demands faster knowledge generation, but also making better use of what we already have. This could help us make better-informed decisions about conservation and resources management. In past years, several efforts have been made to make taxonomic literature more mobilized and accessible. These include online publications, open access journals, the digitization of old paper literature and improved availability through online specialized repositories such as the Biodiversity Heritage Library (BHL) and the World Spider Catalog (WSC), among others. Although easy to share, PDF publications still have most of their biodiversity data embedded in strings of text making them less dynamic and more difficult or impossible to read and analyze without a human interpreter. Recently developed tools as GoldenGATEImagine (GGI) allow transforming PDFs in XML files that extract and categorize taxonomically relevant data. These data can then be aggregated in databases such as Pla zi TreatmentBank, where it can be re-explored, queried and analyzed. Here we combined several of these cybertaxonomic tools to test the data extraction process for one potential application: the design and planning of an expedition to collect fresh material in the field. We targeted the ground spider Teutamus politus and other related species from the Teutamus group (TG) (Araneae; Liocranidae). These spiders are known from South East Asia and have been cataloged in the family Liocranidae; however, their relations, biology and evolution are still poorly understood. We marked-up 56 publications that contained taxonomic treatments with specimen records for the Liocranidae. Of these publications, 20 contained information on members of the TG. Geographical distributions and occurrences of 90 TG species were analyzed based on 1,309 specimen records. These data were used to design our field collection in a way that allowed us to optimize the collection of adult specimens of our target taxa. The TG genera were most common in Indonesia, Thailand and Malaysia. From these, Thailand was the second richest but had the most records of T. politus. Seasonal distribution of TG specimens in Thailand suggested June and July as the best time for collecting adults. Based on these analyses, we decided to sample from mid-July to mid- August 2018 in the three Thai provinces that combined most records of TG species and T. politus. Relying on the results of our literature analyses and using standard collection methods for ground spiders, we captured at least one specimen of every TG genus reported for Thailand. Our one-month expedition captured 231 TG spiders; from these, T. politus was the most abundant species with 188 specimens (95 adults). By comparison, a total of 196 specimens of the TG and 66 of T. politus had been reported for the same provinces in the last 40 years. Our sampling greatly increased the number of available specimens, especially for the genera Teutamus and Oedignatha. Also, we extended the known distribution of Oedignatha and Sesieutes within Thailand. These results illustrate the relevance of making biodiversity data contained within taxonomic treatments accessible and reusable. It also exemplifies one potential use of taxonomic legacy data: to more efficiently use existing biodiversity data to fill knowledge gaps. A similar approach can be used to study neglected or interesting taxa and geographic areas, generating a better biodiversity documentation that could aid in decision making, management and conservation. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
19. TaxonWorks: Character state matrices and identification tools
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Matthew J. Yoder and Dmitry A. Dmitriev
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Character (mathematics) ,business.industry ,Computer science ,Identification (biology) ,Pattern recognition ,General Medicine ,Artificial intelligence ,State (functional analysis) ,bioinformatics ,cybertaxonomy ,interactive identification key ,business ,matrix - Abstract
TaxonWorks is an integrated web-based application for practicing taxonomists and biodiversity specialists. It is focused on promoting collaboration between researchers and developers. TaxonWorks has a modular structure that enables various components of the application to target specific needs and requirements of different groups of users. Specific areas of interest may include nomenclature-related tasks (Yoder and Dmitriev 2021) designed to help assemble and validate scientific name checklists of a target group of organisms; and collection management tasks, including interfaces to create, filter, and edit collecting events, collection objects, and loans. This presentation focuses on matrix-related tools integrated into TaxonWorks. A matrix, which could either be used for phylogenetic analysis or to build an identification key, is structured as a table where columns represent numerous characters that could be used to describe a set of entities, taxa or specimens (presented as rows of the table). Each cell of the table may contain observations for specific character/entity combinations. TaxonWorks does not generate a table for each a particular matrix—all observations are stored as graphs. This structure allows building of a matrix of an unlimited size as well as reuse of individual observations in multiple matrices. For matrix columns, TaxonWorks supports a variety of different kinds of characters or descriptors: qualitative, presence/absence, quantitative, sample, gene, free text, and media. Each character may have specific properties, for example a qualitative descriptor may have numerous characters states, and a quantitative descriptor may have a measurement unit defined. For an entity in a matrix row, TaxonWorks supports either collection objects (specimens) or taxa as Operational Taxonomic Units (OTU). OTUs could either be linked to nomenclature or be stand alone entities (e.g., representing undescribed species). The matrix, once built, could serve several purposes. A matrix based on qualitative and quantitative characters could be used to build an interactive key (Fig. 1), construct standardized natural language descriptions for each entity, and determine a diagnosis (a minimal set of characters that separate one entity from all others). It could also be exported and used for phylogenetic analysis or to build an interactive key in an external application. TaxonWorks supports export files in several formats, including Nexus, TNT, NeXML. Application Programming Interfaces (API) are also available. A matrix based on media descriptors could be used as a pictorial identification tool (Fig. 2).
- Published
- 2021
20. Jewelled spider flies of North America: a revision and phylogeny of Eulonchus Gerstaecker (Diptera, Acroceridae).
- Author
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Borkent, Christopher J., Gillung, Jessica P., and Winterton, Shaun L.
- Subjects
- *
ANTRODIAETIDAE , *SPIDERS , *PHYLOGENY , *TARANTULAS , *BIODIVERSITY - Abstract
The spider fly genus Eulonchus Gerstaecker is found throughout the Nearctic Region. Six species are recognized and intraspecific morphological variation is documented in several species. A phylogeny of Eulonchus based on DNA sequence data of three molecular markers (COI, CAD, and 16S) is presented and relationships of species are discussed in the light of biogeography and host usage. All six species of Eulonchus are redescribed using natural language descriptions exported from a character matrix, and a key to species is presented. Lectotypes are designated for E. sapphirinus Osten Sacken, E. smaragdinus Gerstaecker, and E. tristis Loew. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
21. The application of '-omics' technologies for the classification and identification of animals.
- Author
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Raupach, Michael, Amann, Rudolf, Wheeler, Quentin D., and Roos, Christian
- Subjects
- *
ANIMAL classification , *IDENTIFICATION of animals , *ANIMAL morphology , *THREE-dimensional printing , *SPECIES diversity , *ANATOMY - Abstract
The correct classification of organisms based on specific rules is essential in biological sciences. Traditionally, morphological characteristics such as size, shape, color, and anatomical structures have been used to identify and classify species. However, as consequence of the tremendous advances in molecular technologies during the last years, new approaches have become available for taxonomic research. Various modern high-throughput technologies allow the detailed characterization of the genome, proteome, metabolome as well as the morphology of an organism. Furthermore, the open access storage of such comprehensive data sets as part of an uprising digital cybertaxonomy enables highly fascinating digital dimensions for modern taxonomy, including the buildup of virtual collections as well as data sets for 3D printing techniques that can be used to replicate complete voucher specimens or at least important diagnostic characters. As a result of these advances, we are now able to document, describe, and identify species much more comprehensively than just a few years ago. In this review we provide an overview about the technical advances in taxonomic research in recent years and discuss their power and limitations. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
22. Systematics, Epidermal defense and Bioprospecting of Wild Orchids
- Author
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Kusuma Wati, R. (Richa) and Kusuma Wati, R. (Richa)
- Abstract
This thesis presents the systematics, epidermal defense, and bioprospecting of wild orchids. I mainly targeted Indonesian orchids, with particular emphasis on the genus Glomera with 169 species. Four main challenges of this group of orchids were tackled. First of all, a web-based multilingual interactive key of Glomera, one of the lesser-known genera in the horticulturally popular necklace orchids, was constructed. This key simplifies species identification for further taxonomic revisions by both specialists and amateur orchid enthusiasts. Secondly, identification of non-flowering Glomera specimens in botanical gardens was sped up by producing DNA barcodes of herbarium p
- Published
- 2021
23. Systematics, epidermal defense and bioprospecting of wild orchids
- Author
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Kusuma Wati, R., Smets, E.F., Gravendeel, B., Wezel, G.P. van, Schilthuizen, M., Andel, T.R. van, Boer, H. de, Kessler, P., Wesselingh, R., and Leiden University
- Subjects
Bioprospecting ,Epidermal Defense ,Indonesia ,Attachment force ,Safety Factor ,Necklace orchids ,Cybertaxonomy ,Snail Herbivory ,DNA Barcoding ,Glomera - Abstract
This thesis presents the systematics, epidermal defense, and bioprospecting of wild orchids. I mainly targeted Indonesian orchids, with particular emphasis on the genus Glomera with 169 species. Four main challenges of this group of orchids were tackled. First of all, a web-based multilingual interactive key of Glomera, one of the lesser-known genera in the horticulturally popular necklace orchids, was constructed. This key simplifies species identification for further taxonomic revisions by both specialists and amateur orchid enthusiasts. Secondly, identification of non-flowering Glomera specimens in botanical gardens was sped up by producing DNA barcodes of herbarium preserved flowering type specimens. These DNA barcodes were matched with data obtained from vegetative fresh plants. Thirdly, improving protection of orchids in botanic gardens and nature reserves against herbivory was investigated. Centrifuge and feeding experiments showed that leaf trichomes and wax layers reduce both the adhesion and appetite of herbivorous snails. Lastly, bioprospecting was explored to help financing the maintenance of orchid collections in botanical gardens and protection of nature reserves. For this, traditional medicinal use was compiled from the literature and plotted on a molecular phylogeny. Potential clades with high antimicrobial potential were traced by employing two different methods: organ targeted and biological response based. The latter proved to be more effective. The research presented in this thesis provides new approaches to improve identification, protection against herbivory, and bioprospecting of wild orchids cultivated in botanical gardens and preserved in nature reserves.
- Published
- 2021
24. A Set of Simple Tools For Assembling, Annotating, Versioning and Publishing Taxonomies
- Author
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Laura Rocha Prado
- Subjects
Set (abstract data type) ,Computer science ,Simple (abstract algebra) ,Publishing ,business.industry ,Programming language ,biological classifications ,General Medicine ,cybertaxonomy ,business ,computer.software_genre ,computer ,Software versioning - Abstract
Biodiversity data publishers rely on virtually assembled taxonomic hierarchies to structure their data, with operational units involving scientific names, nomenclatural acts and taxonomic trees. The main goal for the majority of biodiversity aggregators, databases, and software developed specifically for managing scientific names, biological samples and other occurrences has been to establish a single, unified biological classification, to serve as their structural "taxonomic backbone." Resources to produce and publish biological classifications digitally are thus, typically restricted to those generating unified taxonomic backbones, leaving individual researchers and decentralized communities with few options to assemble, visualize, version and disseminate multiple taxonomies online. To aid the creation of a culture of assembling, annotating, versioning, and publishing taxonomies online, and to help users interested in taxonomic classifications that lack digital communities, the development of a set of modular and independent tools is proposed, based on the following complementary features: A web application to serve as the taxonomy curator (referred to as the Curator) A web application to serve as the optional taxonomic database and information provider (referred to as the Aggregator) A web application to serve as the taxonomy curator (referred to as the Curator) A web application to serve as the optional taxonomic database and information provider (referred to as the Aggregator) These tools are being designed and built following modern software development standards, in a modular architecture consisting of front-end clients, databases, and back-end applications, with the provision for a public Application Programming Interface (API) that will make data available for any interested parties and can be potentially integrated into large-scale projects like the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), Symbiota (Gries et al. 2014), and Plazi (Agosti and Egloff 2009). Curator tool The Curator tool will be a publicly accessible front-end web application, with which users can assemble, curate, and export taxonomies. The primary focus is to support the user-preferred taxonomy generation, with manual inputs and optional annotations of the resulting product. Users can pick between three modes of taxonomy assembly: manual mode with assisted taxon search, automated generation from an online source, and automated generation from a file upload. Taxonomies can be edited and annotated as necessary. manual mode with assisted taxon search, automated generation from an online source, and automated generation from a file upload. Taxonomies can be edited and annotated as necessary. Once a user is satisfied with their taxonomy, they can save it in one or all of the available formats for exporting and external usage (common formats include, among others, JSON (JavaScript Object Notation), CSV (comma-separated values), and XML). Logged in users can also opt to save the taxonomy in the Aggregator database, which will make the taxonomy publicly available. Ideally, all fields in the Curator forms should correspond to terms included in the Darwin Core standard (Wieczorek et al. 2012) or Plazi’s TaxonX schema (Agosti and Egloff 2009) (for hierarchies available in published treatments). Aggregator tool The Aggregator tool will communicate with the database and will provide users with a number of functionalities, such as: Store and publish versioned taxonomies generated with the Curator API endpoints for automation (JSON/XML formats/CSV download) Optional unique identifier/DOI generation for published taxonomies Search engine with user-friendly interface as well as API endpoint for querying the database Store and publish versioned taxonomies generated with the Curator API endpoints for automation (JSON/XML formats/CSV download) Optional unique identifier/DOI generation for published taxonomies Search engine with user-friendly interface as well as API endpoint for querying the database The possibility of making taxonomies available as an API endpoint, as well as exporting taxonomies in different formats, will ensure that this tool behaves as a taxonomic source that can be used by virtually any interested party or application. The tools are being modelled as a decentralized community resource that can be used for any or all taxonomic groups and, as such, its scale and impact will be driven by bottom-up community use. The goal is not to provide extensive coverage of all biological organisms, but rather to provide an open digital toolkit and space for biodiversity researchers and projects that lack access to open, structured, online taxonomic publication venues and dedicated tools. Practical examples of usage for these tools include: A user generates multiple taxonomic concepts for organisms they are studying, which can then be queried and analyzed by scripts that make taxonomic alignments to compare different scientific hypotheses throughout time; An institution wants to publish a regional Symbiota portal to manage specimens in a particular collection, so they establish an annotated working taxonomic backbone with the Curator that Symbiota will then be able to ingest before samples can be imported into the portal; A researcher wants to export a biodiversity portal taxonomy at a given moment and wants to annotate and publish this version in an upcoming paper to establish scientific baselines for proper taxonomic communication. A user generates multiple taxonomic concepts for organisms they are studying, which can then be queried and analyzed by scripts that make taxonomic alignments to compare different scientific hypotheses throughout time; An institution wants to publish a regional Symbiota portal to manage specimens in a particular collection, so they establish an annotated working taxonomic backbone with the Curator that Symbiota will then be able to ingest before samples can be imported into the portal; A researcher wants to export a biodiversity portal taxonomy at a given moment and wants to annotate and publish this version in an upcoming paper to establish scientific baselines for proper taxonomic communication.
- Published
- 2021
25. Avances tecnológicos y sus aplicaciones en la cibertaxonomía.
- Author
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CIGLIANO, María Marta, POCCO, Martina E., and PEREIRA, Hernán L.
- Subjects
- *
INSECT collection & preservation , *BIOINFORMATICS , *ENTOMOLOGY , *DIGITAL image processing , *BIODIVERSITY , *TECHNOLOGICAL innovations - Abstract
The rapid advances in cyber-infrastructure, bioinformatics, digital imaging and related information technologies facilitate the access to taxonomic data and allow generating new information on a scale appropriate to meet the decline in biodiversity, Basic taxonomic information, such as taxonomic literature, catalogues, specimen- level data, location of types, and interactive keys are already available, at least for some groups, on the Web. In this article we explore the modern means of disseminating taxonomic information, mostly entomological information, in the Internet; we review some of the different ways taxonomists have so far made use of the Web or will be able to do so in the near future, and how modern means of sharing data, especially via the Internet, are being used to streamline taxonomic work and improve links with end users. [ABSTRACT FROM AUTHOR]
- Published
- 2014
26. Guide to image editing and production of figures for scientific publications with an emphasis on taxonomy
- Author
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Bevilaqua, Marcus
- Subjects
taxonomy ,Adobe Lightroom ,image bank ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,software application ,Adobe Camera Raw ,digital photography ,Adobe Photoshop ,cybertaxonomy - Abstract
Figures for scientific publications go through various stages from the planning, to the capturing of images, to the production of finished figures for publication. This guide is meant to familiarise the reader with the main image-editing software used by professional photographers. The guide’s focus is on digital photo editing and the production of figures using Adobe Photoshop to produce publication-quality figures for scientific publications. This guide will be of fundamental use for the academic public, especially taxonomists and others who work with images. Besides, it should be useful for anyone interested in becoming familiar with the basic tools of image editing.
- Published
- 2020
27. EDIT Platform output model for botany v. 2.05
- Author
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Luther, Katja, Müller, Andreas, Kohlbecker, Andreas, Güntsch, Anton, and Berendsohn, Walter G.
- Subjects
500 Natural sciences and mathematics::590 Zoological sciences::591 Zoology ,Systematics ,500 Natural sciences and mathematics::580 Plants::581 Botany ,000 Computer science, information, and general works::000 Computer Science, knowledge, systems::005 Computer programming, programs, data ,Cybertaxonomy ,Taxonomy - Abstract
The Common Data Model (CDM) is the underlying data structure of the EDIT Platform for Cybertaxonomy, representing a complete model of data used in biological taxonomy and systematics. CDM-light is a set of relational tables produced by one of the export functions of the EDIT Platform. As compared to the CDM itself, the relational model is simplified and data are partially aggregated. CDM-light may be used as a transfer format, to generate statistics about the data in a CDM database, to control data quality, or to produce document-type output from CDM databases.
- Published
- 2020
28. Guide to image editing and production of figures for scientific publications with an emphasis on taxonomy
- Author
-
Bevilaqua, Marcus Vinícius Oliveira
- Subjects
Digital photography ,Image bank ,Adobe Lightroom ,Adobe Camera Raw ,Adobe Photoshop ,Cybertaxonomy ,Software application ,Taxonomy - Abstract
Figures for scientific publications go through various stages from the planning, to the capturing of images, to the production of finished figures for publication. This guide is meant to familiarise the reader with the main image-editing software used by professional photographers. The guide's focus is on digital photo editing and the production of figures using Adobe Photoshop to produce publication-quality figures for scientific publications. This guide will be of fundamental use for the academic public, especially taxonomists and others who work with images. Besides, it should be useful for anyone interested in becoming familiar with the basic tools of image editing. © 2020.
- Published
- 2020
29. Taxonomic revision of the assassin-fly genus Microphontes Londt, 1994 (Insecta, Diptera, Asilidae)
- Author
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Torsten Dikow and Amanda Markee
- Subjects
0106 biological sciences ,Insecta ,Arthropoda ,Microphontes ,lcsh:QH1-199.5 ,010607 zoology ,Zoology ,Biology ,lcsh:General. Including nature conservation, geographical distribution ,010603 evolutionary biology ,01 natural sciences ,Genus ,lcsh:QH540-549.5 ,Animalia ,lcsh:Science ,Ecology, Evolution, Behavior and Systematics ,female postero-paramedian T8 pores ,Diptera ,Asilidae ,robber fly ,Paleontology ,biology.organism_classification ,male flight behaviour ,Insect Science ,Assassin fly ,Animal Science and Zoology ,lcsh:Q ,lcsh:Ecology ,cybertaxonomy ,open-access - Abstract
The genus Microphontes Londt, 1994 (Diptera: Asilidae: Brachyrhopalinae) is revised. Currently, three species are known from Namibia and western South Africa, i.e. Microphontesmegoura Londt, 1994 from north-western South Africa, Microphontessafra Londt, 1994 from Namibia and Microphonteswhittingtoni Londt, 1994 from western South Africa. Four new species, Microphontesericfisherisp. n. from the Little Karoo of South Africa, Microphontesgaiophanessp. n. from the Namib desert of Namibia and Microphontesjasonlondtisp. n. and Microphonteskryphiossp. n. from western South Africa, are described. Distribution, occurrence in biodiversity hotspots sensu Conservation International and seasonal incidence are discussed. Descriptions/redescriptions, photographs and identification keys are provided and made openly accessible in data repositories to support future studies of the included taxa. An unusual flight pattern of male Microphontesgaiophanessp. n. is discussed. A unique morphological feature on tergite 8 of Microphontes females, termed postero-paramedian T8 pores, is described, illustrated and discussed.
- Published
- 2018
30. A Linnaeus NG interactive key to the species of Glomera (Orchidaceae, Coelogyninae) from Southeast Asia
- Author
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Richa Kusuma Wati, Rogier R van Vugt, and Barbara Gravendeel
- Subjects
0106 biological sciences ,Triphoreae ,epiphytes ,Ecology (disciplines) ,Liliopsida ,Distribution (economics) ,Asparagales ,Plant Science ,010603 evolutionary biology ,01 natural sciences ,necklace orchids ,Floristics ,Papua New Guinea ,Genus ,lcsh:Botany ,Plantae ,Orchidaceae ,Taksonomi Siber ,Ecology, Evolution, Behavior and Systematics ,Glomera ,Coelogyninae ,biology ,Valdiviesoa ,business.industry ,Ecology ,05 social sciences ,050301 education ,anggrek kalung ,biology.organism_classification ,Arethuseae ,lcsh:QK1-989 ,epifit ,pengamatan ,Tracheophyta ,monitoring ,Geography ,Indonesia ,Conservation status ,Key (lock) ,Cybertaxonomy ,business ,0503 education - Abstract
We present a multilingual interactive key available online (http://glomera.linnaeus.naturalis.nl) that can be used on any web browser without the need for installing additional software. The key includes 169 species ofGlomera, a genus within the necklace orchids (Coelogyninae) not yet comprehensively treated in any recent field guide or web-based survey. With this key, plants can be identified using a combination of vegetative and floristic characters in addition to distribution and ecology as a first step to further taxonomic revisions. We urge anyone with an interest in wild orchids in Southeast Asia to contribute new observations to update current information on the distribution of these overlooked plants as a first step for a taxonomic revision and to gain more insight into their conservation status.
- Published
- 2018
31. A review of the assassin-fly genus Laphyctis Loew, 1858 with descriptions of two new species (Diptera, Asilidae, Laphriinae)
- Author
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Torsten Dikow and Jason G.H. Londt
- Subjects
0106 biological sciences ,Insecta ,Arthropoda ,lcsh:QH1-199.5 ,010607 zoology ,assassin fly ,Zoology ,lcsh:General. Including nature conservation, geographical distribution ,01 natural sciences ,Genus ,lcsh:QH540-549.5 ,Animalia ,lcsh:Science ,Ecology, Evolution, Behavior and Systematics ,biology ,Diptera ,Asilidae ,Paleontology ,biology.organism_classification ,Afrotropical ,010602 entomology ,Insect Science ,lcsh:Q ,Animal Science and Zoology ,lcsh:Ecology ,Laphriinae ,cybertaxonomy - Abstract
The asilid genus Laphyctis Loew, 1858 is revised. The genus is restricted to the Afrotropical Region where it has been confused with the more widely distributed Laphystia Loew, 1847, which currently has no Afrotropical representatives. Three previously described species are recognised: Laphyctisgigantella (Loew, 1852), type of the genus, Laphyctisargenteofasciata (Engel, 1929), reinstated from the synonymy of L.gigantella, and Laphyctisorichalcea (Lindner, 1973). Two new species are described, Laphyctiseremia sp. n. from Namibia and Laphyctisiota sp. n. from South Africa. The genus has a wide distribution ranging from northern Kenya to eastern South Africa and to western Namibia. Species are associated with dry, sandy habitats.
- Published
- 2018
32. Biodiversity into your hands - A call for a virtual global natural history 'metacollection'.
- Author
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Balke, Michael, Schmidt, Stefan, Hausmann, Axel, Toussaint, Emmanuel F.A., Bergsten, Johannes, Buffington, Matthew, Häuser, Christoph L., Kroupa, Alexander, Hagedorn, Gregor, Riedel, Alexander, Polaszek, Andrew, Ubaidillah, Rosichon, Krogmann, Lars, Zwick, Andreas, Fikáček, Martin, Hájek, Jiř, Michat, Mariano C., Dietrich, Christopher, Salle, John La, and Mantle, Beth
- Subjects
- *
NATURAL history , *BIODIVERSITY , *ROBOTICS , *CONSERVATION biology , *NUCLEIC acid isolation methods , *VIRTUAL communities - Abstract
Background: Many scientific disciplines rely on correct taxon delineations and identifications. So does a great part of the general public as well as decision makers. Researchers, students and enthusiastic amateurs often feel frustrated because information about species remains scattered, difficult to access, or difficult to decipher. Together, this affects almost anyone who wishes to identify species or verify identifications. Many remedies have been proposed, but we argue that the role of natural history collections remains insufficiently appreciated. We suggest using state-of-the-art mass imaging technology and to join forces to create a global natural history metacollection on the internet, providing access to the morphology of tens of millions of specimens and making them available for automated digital image analysis. Discussion: Robotic high-resolution imaging technology and fast (high performance) computer-based image stitching make it now feasible to digitize entire collection drawers typically used for arthropod collections, or trays or containers used for other objects. Resolutions of 500 megapixels and much higher are already utilized to capture the contents of 40x50 cm collection drawers, providing amazing detail of specimens. Flanked by metadata entry, this helps to create access to tens of thousands of specimens in days. By setting priorities and combining the holdings of the most comprehensive collections for certain taxa, drawer digitizing offers the unique opportunity to create a global, virtual metacollection. The taxonomic and geographic coverage of such a collection could never be achieved by a single institution or individual. We argue that by joining forces, many new impulses will emerge for systematic biology, related fields and understanding of biodiversity in general. Digitizing drawers containing unidentified, little-curated specimens is a contribution towards the beginning of a new era of online curation. It also will help taxonomists and curators to discover and process the millions of "gems" of undescribed species hidden in museum accessions. Summary: Our proposal suggests creating virtual, high-resolution image resources that will, for the first time in history, provide access for expert scientists as well as students and the general public to the enormous wealth of the world's natural history collections. We foresee that this will contribute to a better understanding, appreciation and increased use of biodiversity resources and the natural history collections serving this cause. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
33. Three new species in the harvestmen genus Acuclavella (Opiliones, Dyspnoi, Ischyropsalidoidea), including description of male Acuclavella quattuor Shear, 1986.
- Author
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Richart, Casey H. and Hedin, Marshal
- Subjects
- *
OPILIONES , *CLADISTIC analysis , *NUCLEOTIDE sequence , *MORPHOMETRICS , *FIELD research - Abstract
In Shear's (1986) cladistic analysis of the Ischyropsalidoidea, he described the new genus Acuclavella including four new species from the Pacific Northwest states of Washington and Idaho. Several of these species descriptions were based on very limited sample sizes. Our recent field work has increased by more than an order of magnitude both the number of specimens and known localities for Acuclavella. We use this new material to interpret species limits in Acuclavella using morphometric analyses and DNA sequence data from four gene regions. We sequence for the first time the protein-coding homolog of the Wnt2 gene for phylogenetic reconstruction in Opiliones. Our multi-locus phylogeny corroborates a sister relationship between Acuclavella and Ceratolasma, as hypothesized using morphology by Shear (1986). Within Acuclavella, morphometric clusters and reciprocal allelic monophyly allows recognition of three additional species: Acuclavella leonardi sp. n., A. sheari sp. n., and A. makah sp. n. This work also describes the previously unknown male of Acuclavella quattuor, from specimens collected at the type locality. Our research identifies a number of novel morphologies for Acuclavella, including females with four pairs of spines, individuals with three pairs of spines on scute areas I-III, and a population with two pairs of spines disjunct from A. quattuor, which was diagnosed with this spination character. We were unable to assign these populations to existing species, and conservatively do not yet recognize them as new. Intrageneric morphometrics and phylogenetic inference in Acuclavella were often concordant. However, we demonstrate that species delimitation signal would not be detected if only a single line of evidence were utilized. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
34. The unappreciated, fundamentally analytical nature of taxonomy and the implications for the inventory of biodiversity.
- Author
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Sluys, Ronald
- Subjects
BIODIVERSITY ,BIOLOGICAL classification ,NATURE conservation ,DNA ,TAXONOMY - Abstract
Several ways have been suggested to improve the poor status of taxonomy as well as to overcome the taxonomic impediment and thus to speed up species discovery and documentation, such as: DNA barcoding, creation of databases of taxa and identification tools, online quantum contributions, standardization of morphological features, training of a new generation of taxonomists. The paper comments on the desirability and effectiveness of these presumed remedies. It is argued that the analytical, hypothesis-testing nature of taxonomic research is not well understood or appreciated and forms a major constraint on the rate of taxonomic descriptions. The various components of the taxonomic method, such as exploration, data, analysis, and results, interact in a complex manner that resembles the erratic, bouncing behaviour of a pinball machine. Species hypotheses probably are the most tested hypotheses in the natural sciences. The introduction of cybertaxonomy instrumentation and infrastructure will not alleviate the time-consuming, intrinsically analytical and hypothesis-testing process underlying the description and/or identification of each taxon. Long-term survival of the discipline of taxonomy, thus guaranteeing the future cumulative taxonomic output of amateurs and professionals, is endangered by a diminishing workforce of adequately trained professional systematists. The only way to increase the pace of a well-documented and scientifically useful taxic inventory of the world's biodiversity is to increase the number of professional taxonomists. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
35. Micro-computed tomography: Introducing new dimensions to taxonomy.
- Author
-
Faulwetter, Sarah, Vasileiadou, Aikaterini, Kouratoras, Michail, Dailianis, Thanos, and Arvanitidis, Christos
- Subjects
- *
THREE-dimensional imaging , *BIOLOGICAL classification , *POLYCHAETA , *SPECIES distribution , *DISPERSAL (Ecology) , *ELECTRONIC data processing - Abstract
Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called "cybertypes", and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
36. Extracting Data from Legacy Taxonomic Literature: Applications for planning field work
- Author
-
Rivera-Quiroz, F.A. (Francisco Andres), Miller, J.A. (Jeremy), Rivera-Quiroz, F.A. (Francisco Andres), and Miller, J.A. (Jeremy)
- Abstract
Traditional taxonomic publications have served as a biological data repository accumulating vast amounts of data on species diversity, geographical and temporal distributions, ecological interactions, taxonomic relations, among many other types of information. However, the fragmented nature of taxonomic literature has made this data difficult to access and use to its full potential. Current anthropogenic impact on biodiversity demands faster knowledge generation, but also making better use of what we already have. This could help us make better-informed decisions about conservation and resources management. In past years, several efforts have been made to make taxonomic literature more mobilized and accessible. These include online publications, open access journals, the digitization of old paper literature and improved availability through online specialized repositories such as the Biodiversity Heritage Library (BHL) and the World Spider Catalog (WSC), among others. Although easy to share, PDF publications still have mos
- Published
- 2019
- Full Text
- View/download PDF
37. New Australian stiletto flies: revision of Manestella Metz and description of Medomega gen. n. (Diptera, Therevidae, Agapophytinae).
- Author
-
Winterton, Shaun L. and Lambkin, Christine L.
- Subjects
- *
FLIES , *SPECIES distribution , *BIOLOGICAL classification , *DISPERSAL (Ecology) , *DIPTERA , *THEREVIDAE - Abstract
The previously monotypic genus Manestella Metz, 2003 is revised with a single species, M. tristriata (Mann, 1933), redescribed and an additional 14 new species described: Manestella caesia sp. n., M. campestris sp. n., M. canities sp. n., M. cooloola sp. n., M. fumosa sp. n., M. incompleta sp. n., M. nubis sp. n., M. obscura sp. n., M. ocellaris sp. n., M. persona sp. n., M. poecilothorax sp. n., M. umbrapennis sp. n., M. vasta sp. n. and M. vespera sp. n. The putative sister genus to Manestella, Medomega gen. n., is described containing six new species: Medomega averyi sp. n., M. bailmeup sp. n., M. chlamydos sp. n., M. danielsi sp. n., M. gigasathe sp. n., and M. nebrias sp. n. Complete taxonomic descriptions were generated from a character matrix developed in Lucid Builder from which natural language descriptions (NLD) were parsed. Images of all species of Manestella and Medomega gen. n. are included, along with dichotomous keys to species. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
38. A charismatic new species of green lacewing discovered in Malaysia (Neuroptera, Chrysopidae): the confluence of citizen scientist, online image database and cybertaxonomy.
- Author
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Winterton, Shaun L., Guek, Hock Ping, and Brooks, Stephen J.
- Subjects
- *
SPECIES , *CHRYSOPIDAE , *NEUROPTERA , *TAXONOMISTS - Abstract
An unusual new species of green lacewing (Neuroptera: Chrysopidae: Semachrysa jade sp. n.) is described from Selangor (Malaysia) as a joint discovery by citizen scientist and professional taxonomists. The incidental nature of this discovery is underscored by the fact that the species was initially photographed and then released, with images subsequently posted to an online image database. It was not until the images in the database were randomly examined by the professional taxonomists that it was determined that the species was in fact new. A subsequent specimen was collected at the same locality and is described herein along with another specimen identified from nearby Sabah. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
39. Review of Australasian spider flies (Diptera, Acroceridae) with a revision of Panops Lamarck.
- Author
-
Winterton, Shaun L.
- Subjects
- *
SPIDER behavior , *ACROCERIDAE , *ANIMAL species - Abstract
The Australasian spider flies (Diptera: Acroceridae) are reviewed, with all eight currently recognized genera diagnosed and figured. The panopine genus Panops Lamarck, 1804 from Australia and Indonesia is revised with four new species described, increasing the total number of species in the genus to nine: P. aurum sp. n., P. danielsi sp. n., P. jade sp. n. and P. schlingeri sp. n. Five species of Panops are redescribed: Panops austrae Neboiss, 1971, P. baudini Lamarck, 1804, P. boharti (Schlinger, 1959), comb. n., P. conspicuus (Brunetti, 1926) and P. grossi (Neboiss, 1971), comb. n. The monotypic genera Neopanops Schlinger, 1959 and Panocalda Neboiss, 1971 are synonymized with Panops. Keys to genera of Australasian Acroceridae and species of Panops, Helle Osten Sacken, 1896 and Australasian Pterodontia Gray, 1832 are included. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
40. From taxonomic literature to cybertaxonomic content.
- Author
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Miller, Jeremy, Dikow, Torsten, Agosti, Donat, Sautter, Guido, Catapano, Terry, Penev, Lyubomir, Zhi-Qiang Zhang, Pentcheff, Dean, Pyle, Richard, Blum, Stan, Parr, Cynthia, Freeland, Chris, Garnett, Tom, Ford, Linda S., Muller, Burgert, Smith, Leo, Strader, Ginger, Georgiev, Teodor, and Bénichou, Laurence
- Subjects
- *
TAXONOMY , *BIOLOGICAL classification , *SPECIES , *GENETICS , *ORGANISMS - Published
- 2012
- Full Text
- View/download PDF
41. Systematics, Biodiversity, Biogeography, and Host Associations of the Miridae (Insecta: Hemiptera: Heteroptera: Cimicomorpha).
- Author
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Cassis, G. and Schuh, R.T.
- Subjects
- *
MIRIDAE , *INSECT nomenclature , *BIOGEOGRAPHY , *GEOGRAPHICAL distribution of insects , *TRICHOBOTHRIUM - Abstract
The Miridae, a hyperdiverse family containing more than 11,020 valid described species, are discussed and the pertinent literature is reviewed. Diagnoses for the family and subfamilies are given. Color habitus photos are presented for representatives of most of the 35 currently recognized tribes. Key morphological character systems are discussed and illustrated, including pretarsal structures, femoral trichobothria, external efferent system of the metathoracic glands, male and female genitalia, and molecular markers. A historical comparison of tribal classifications and the most up-to-date classification are presented in tabular form. A brief history of the classification of each of the eight recognized subfamilies is presented. Distributional patterns and relative generic diversity across biogeographic regions are discussed; generic diversity by biogeographic region is presented in tabular form. Taxonomic accumulation graphs are presented by biogeographic region, indicating an ongoing need for taxonomic work in the Southern Hemisphere, and most particularly in Australia. Host plant associations are evaluated graphically, showing high specificity for many taxa and a preference among phytophagous taxa for the Asteridae and Rosidae. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
42. Bush Blitz aids description of three new species and a new genus of Australian beeflies (Diptera, Bombyliidae, Exoprosopini).
- Author
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Lambkin, Christine L. and Bartlett, Justin S.
- Subjects
- *
PHYLOGENY , *TAXONOMY , *NATIONAL Reserve System (Australia) , *BOMBYLIIDAE - Abstract
Bush Blitz is a three-year multimillion dollar program to document the plants and animals in hundreds of properties across Australia's National Reserve System. The core focus is on nature discovery - identifying and describing new species of plants and animals. The Bush Blitz program has enabled the collection and description of beeflies (Diptera, Bombyliidae) from surveys in Western Australia and Queensland. Three new species of Australian beeflies belonging to the Exoprosopini are described; Palirika mackenziei Lambkin, sp. n., Palirika culgoafloodplainensis Lambkin, sp. n., and Larrpana bushblitz Lambkin, sp. n. Phylogenetic analysis of 40 Australian exoprosopine species belonging to the Balaana generic-group Lambkin & Yeates, 2003 supports the placement of the three new species into existing genera, and the erection and description of the new genus Ngalki Lambkin, gen. n. for Ngalki trigonium (Lambkin & Yeates, 2003), comb. n. Revised keys are provided for the genera of the Australian Balaana genus-group and the species of Palirika Lambkin & Yeates, 2003 and Larrpana Lambkin & Yeates, 2003. With the description of the three new species and the transferral of Munjua trigona Lambkin & Yeates, 2003 into the new genus Ngalki Lambkin, gen. n., three genera are rediagnosed; Munjua Lambkin & Yeates, 2003, Palirika and Larrpana. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
43. Sphaerosyllis levantina sp. n. (Annelida) from the eastern Mediterranean, with notes on character variation in Sphaerosyllis hystrix Claparède, 1863.
- Author
-
Faulwetter, Sarah, Chatzigeorgiou, Georgios, Galil, Bella S., Nicolaidou, Artemis, and Arvanitidis, Christos
- Subjects
- *
POLYCHAETA , *SYLLIDAE , *TAXONOMY - Abstract
Examination of polychaete specimens from Haifa Bay (Israel, eastern Mediterranean Sea) revealed several individuals exhibiting morphological characteristics similar to Sphaerosyllis hystrix Claparede, 1863. A detailed morphometrical analysis of the Israeli specimens in comparison to specimens of S. hystrix and S. boeroi Musco, Cinar & Giangrande, 2005 supported the description of the former as a new species, S. levantina sp. n. Individuals of S. hystrix formed a very heterogeneous group with strong character variations in the analysis and the presumed cosmopolitan distribution of the species is discussed based on literature records. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
44. New genera of philopotine spider flies (Diptera, Acroceridae) with a key to living and fossil genera.
- Author
-
Gillung, Jéssica P. and Winterton, Shaun L.
- Subjects
- *
ACROCERIDAE , *DIPTERA , *FLIES - Abstract
In this paper we describe two new genera of philopotine Acroceridae: Schlingeriella irwini gen. et sp. n. (New Caledonia) and Quasi fisheri gen. et sp. n. (Mexico). The Baltic amber species Eulonchiella eocenica Meunier, 1912 is rediagnosed and a neotype designated based on a newly discovered specimen. We also provide a dichotomous key to the world genera of Philopotinae, both living and fossil. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
45. Revision of the stiletto fly genera Acupalpa Kröber and Pipinnipons Winterton (Diptera, Therevidae, Agapophytinae) using cybertaxonomic methods, with a key to Australasian genera.
- Author
-
Winterton, Shaun L.
- Subjects
- *
THEREVIDAE , *CLASSIFICATION of insects , *DIPTERA , *NUMBERS of species - Abstract
Australian stiletto flies of the sister-genera Acupalpa Kröber, 1912 and Pipinnipons Winterton, 2001 (Diptera: Therevidae: Agapophytinae) are revised. Twelve new species of Acupalpa are described, while Acupalpa imitans (White, 1915), comb. n. is transferred from Pipinnipons and Acupalpa albimanis (Kröber, 1914), comb. n. is transferred from Ectinorhynchus Macquart as a senior synonym of Acupalpa pollinosa Mann. The total number of species of Acupalpa is therefore increased to 19: A. albimanis (Kröber), comb. n., A. albitarsa Mann, A. boharti sp. n., A. divisa (Walker), A. dolichorhyncha sp. n., A. glossa sp. n., A. imitans (White), comb. n., A. irwini Winterton, A. melanophaeos sp. n., A. miaboolya sp. n., A. minuta sp. n., A. minutoides sp. n., A. notomelas sp. n., A. novayamarna sp. n., A. rostrata Kröber, A. semirufa Mann, A. westralica sp. n., A. yalgoo sp. n. and A. yanchep sp. n. Three new species of Pipinnipons are described, increasing the total number of species to five: P. chauncyvallis sp. n., P. fascipennis (Kröber), P. kampmeierae sp. n., P. kroeberi Winterton, and P. sphecoda sp. n. Pipinnipons and Acupalpa are rediagnosed in light of the new species presented herein and revised keys to species are included. A dichotomous key to genera of Australasian Therevidae is included. As an empirical example of cybertaxonomy, taxonomic descriptions were composed using a character matrix developed in Lucid Builder (in Structured Descriptive Data (SDD) format) to generate natural language descriptions supplemented by online specimen and image databases. Web resources are provided throughout the document including: a) links to high resolution colour images of all species on Morphbank, b) registration of authors, publications, taxon names and other nomenclatural acts in Zoobank, with assignment of Life Science Identifiers (LSIDs) for each, c) links to Genbank accession records for DNA sequences, and d) assignment of LSIDs to specimen records with links to respective records in an online Therevidae specimen database. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
46. How many species in the Southern Ocean? Towards a dynamic inventory of the Antarctic marine species
- Author
-
De Broyer, Claude and Danis, Bruno
- Subjects
- *
MARINE biodiversity , *MARINE species diversity , *INVENTORIES , *DATA analysis , *BIOGEOGRAPHY , *DATABASES ,ANTARCTIC exploration - Abstract
Abstract: The IPY sister-projects CAML and SCAR-MarBIN provided a timely opportunity, a strong collaborative framework and an appropriate momentum to attempt assessing the “Known, Unknown and Unknowable” of Antarctic marine biodiversity. To allow assessing the known biodiversity, SCAR-MarBIN “Register of Antarctic Marine Species (RAMS)” was compiled and published by a panel of 64 taxonomic experts. Thanks to this outstanding expertise mobilized for the first time, an accurate list of more than 8100 valid species was compiled and an up-to-date systematic classification comprising more than 16,800 taxon names was established. This taxonomic information is progressively and systematically completed by species occurrence data, provided by literature, taxonomic and biogeographic databases, new data from CAML and other cruises, and museum collections. RAMS primary role was to establish a benchmark of the present taxonomic knowledge of the Southern Ocean biodiversity, particularly important in the context of the growing realization of potential impacts of the global change on Antarctic ecosystems. This, in turn, allowed detecting gaps in knowledge, taxonomic treatment and coverage, and estimating the importance of the taxonomic impediment, as well as the needs for more complete and efficient taxonomic tools. A second, but not less important, role of RAMS was to contribute to the “taxonomic backbone” of the SCAR-MarBIN, OBIS and GBIF networks, to establish a dynamic information system on Antarctic marine biodiversity for the future. The unknown part of the Southern Ocean biodiversity was approached by pointing out what remains to be explored and described in terms of geographical locations and bathymetric zones, habitats, or size classes of organisms. The growing importance of cryptic species is stressed, as they are more and more often detected by molecular studies in several taxa. Relying on RAMS results and on some case studies of particular model groups, the question of the potential number of species that remains to be discovered in the Southern Ocean is discussed. In terms of taxonomic inputs to the census of Southern Ocean biodiversity, the current rate of progress in inventorying the Antarctic marine species as well as the state of taxonomic resources and capacity were assessed. Different ways of improving the taxonomic inputs are suggested. [Copyright &y& Elsevier]
- Published
- 2011
- Full Text
- View/download PDF
47. The centipede genus Eupolybothrus Verhoeff, 1907 (Chilopoda: Lithobiomorpha: Lithobiidae) in North Africa, a cybertaxonomic revision, with a key to all species in the genus and the first use of DNA barcoding for the group.
- Author
-
Stoev, Pavel, Akkari, Nesrine, Zapparoli, Marzio, Porco, David, Enghoff, Henrik, Edgecombe, Gregory D., Georgiev, Teodor, and Penev, Lyubomir
- Subjects
- *
LITHOBIUS , *LITHOBIIDAE , *CENTIPEDES , *MYRIAPODA , *GENETIC genealogy , *TAXONOMY , *ANIMAL species , *ANIMAL classification - Abstract
Thee centipede genus Eupolybothrus Verhoeff, 1907 in North Africa is revised. A new cavernicolous species, E. kahfiStoev & Akkari, sp. n., is described from a cave in Jebel Zaghouan, northeast Tunisia. Morphologically, it is most closely related to E. nudicornis (Gervais, 1837) from North Africa and Southwest Europe but can be readily distinguished by the long antennae and leg-pair 15, a conical dorso-median protuberance emerging from the posterior part of prefemur 15, and the shape of the male first genital sternite. Molecular sequence data from the cytochrome c oxidase I gene (mtDNA-5' COI-barcoding fragment) exhibit 19.19% divergence between E. kahfiand E. nudicornis, an interspecific value comparable to those observed among four other species of Eupolybothrus which, combined with a low intraspecific divergence (0.3-1.14%), supports the morphological diagnosis of E. kahfias a separate species. Theis is the first troglomorphic myriapod to be found in Tunisia, and the second troglomorph lithobiomorph centipede known from North Africa. E. nudicornis is redescribed based on abundant material from Tunisia and its post-embryonic development, distribution and habitat preferences recorded. E. cloudsley-thompsoni Turk, 1955, a nominal species based on Tunisian type material, is placed in synonymy with E. nudicornis. To comply with the latest technological developments in publishing of biological information, the paper implements new approaches in cybertaxonomy, such as fine granularity XML tagging validated against the NLM DTD TaxPub for PubMedCentral and dissemination in XML to various aggregators (GBIF, EOL, Wikipedia), vizualisation of all taxa mentioned in the text via the dynamically created Pensoft Taxon Profile (PTP) page, data publishing, georeferencing of all lo calities via Google Earth, and ZooBank, GenBank and MorphBank registration of datasets. An interactive key to all valid species of Eupolybothrus is made with DELTA software. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
48. The flower fly genus Eosphaerophoria Frey (Diptera, Syrphidae).
- Author
-
Mengual, Ximo and Ghorpadé, Kumar
- Subjects
- *
SYRPHIDAE , *DIPTERA , *INSECTS , *ANIMAL species , *ANIMAL classification - Abstract
The flower fly genus Eosphaerophoria is revised. Eight new species are described (adornata sp. n. Mengual, bifi da sp. n. Mengual, brunettii sp. n. Ghorpadé, hermosa sp. n. Mengual, luteofasciata sp. n. Mengual, nigrovittata sp. n. Mengual, symmetrica sp. n. Mengual, and vietnamensis sp. n. Mengual), and an identifi cation key is provided. Redescriptions, illustrations, synonymies, diagnoses and distributional data are given for all 11 known species of Eosphaerophoria. The new described species increase the genus' distribution, now recorded from Nepal and Sri Lanka east to New Guinea. All information data, images and drawings, as well as additional images and relevant information, are available online via the internet as an example of the utility of international standards for biodiversity informatics. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
49. TaxonWorks: An experience of migrating large datasets into the new cybertaxonomic infrastructure
- Author
-
Dmitry A. Dmitriev
- Subjects
taxonomy ,TaxonWorks ,dataset ,nomenclature ,General Medicine ,bioinformatics ,cybertaxonomy ,database - Abstract
TaxonWorks (http://taxonworks.org) in an integrated, open-source, cybertaxonomic web application serving taxonomists and biodiversity scientists. It is designed to facilitate efficient data capture, storage, manipulation, and retrieval. It integrates a wide variety of data types used by biodiversity scientists, including, but not limited to, taxonomy (with validation based on codes of zoological, botanical, bacterial, and viral nomenclature), specimen data, bibliographies, media (images, PDFs, sounds, videos), morphology (character/trait matrices), distribution, biological associations. Available TaxonWorks web interfaces currently provide various data entry forms for simple and advanced querying of the database. TaxonWorks has integrated batch uploader functionality. But, for larger datasets, specialized migration scripts were used. Several projects, historically build in 3i (http://dmitriev.speciesfile.org), MX (http://mx.phenomix.org), SpeciesFiles (http://software.speciesfile.org), and other databases, have been or are being migrated into TaxonWorks. Of the projects moving into TaxonWorks, it is worth mentioning several: 3i World Auchenorrhyncha Database, LepIndex, Universal Chalcidoidea Database, Orthoptera SpeciesFile, Plecoptera SpeciesFile, Illinois Natural History Survey Insect Collection database, and several others. An experience of the data migration will be shared during the presentation.
- Published
- 2019
50. Extracting Data from Legacy Taxonomic Literature: Applications for planning field work
- Author
-
Francisco Andres Rivera-Quiroz, Jeremy A. Miller, and Staff publications
- Subjects
Biological data ,Liocranidae ,Teutamus ,Plazi ,Computer science ,computer.internet_protocol ,Process (engineering) ,Biodiversity ,General Medicine ,XML ,computer.software_genre ,Data science ,PDF ,Field (computer science) ,GoldenGATE-Imagine ,Data extraction ,Araneae ,cybertaxonomy ,computer ,Digitization ,Interpreter - Abstract
Traditional taxonomic publications have served as a biological data repository accumulating vast amounts of data on species diversity, geographical and temporal distributions, ecological interactions, taxonomic relations, among many other types of information. However, the fragmented nature of taxonomic literature has made this data difficult to access and use to its full potential. Current anthropogenic impact on biodiversity demands faster knowledge generation, but also making better use of what we already have. This could help us make better-informed decisions about conservation and resources management. In past years, several efforts have been made to make taxonomic literature more mobilized and accessible. These include online publications, open access journals, the digitization of old paper literature and improved availability through online specialized repositories such as the Biodiversity Heritage Library (BHL) and the World Spider Catalog (WSC), among others. Although easy to share, PDF publications still have most of their biodiversity data embedded in strings of text making them less dynamic and more difficult or impossible to read and analyze without a human interpreter. Recently developed tools as GoldenGATE-Imagine (GGI) allow transforming PDFs in XML files that extract and categorize taxonomically relevant data. These data can then be aggregated in databases such as Plazi TreatmentBank, where it can be re-explored, queried and analyzed. Here we combined several of these cybertaxonomic tools to test the data extraction process for one potential application: the design and planning of an expedition to collect fresh material in the field. We targeted the ground spider Teutamus politus and other related species from the Teutamus group (TG) (Araneae; Liocranidae). These spiders are known from South East Asia and have been cataloged in the family Liocranidae; however, their relations, biology and evolution are still poorly understood. We marked-up 56 publications that contained taxonomic treatments with specimen records for the Liocranidae. Of these publications, 20 contained information on members of the TG. Geographical distributions and occurrences of 90 TG species were analyzed based on 1,309 specimen records. These data were used to design our field collection in a way that allowed us to optimize the collection of adult specimens of our target taxa. The TG genera were most common in Indonesia, Thailand and Malaysia. From these, Thailand was the second richest but had the most records of T. politus. Seasonal distribution of TG specimens in Thailand suggested June and July as the best time for collecting adults. Based on these analyses, we decided to sample from mid-July to mid-August 2018 in the three Thai provinces that combined most records of TG species and T. politus. Relying on the results of our literature analyses and using standard collection methods for ground spiders, we captured at least one specimen of every TG genus reported for Thailand. Our one-month expedition captured 231 TG spiders; from these, T. politus was the most abundant species with 188 specimens (95 adults). By comparison, a total of 196 specimens of the TG and 66 of T. politus had been reported for the same provinces in the last 40 years. Our sampling greatly increased the number of available specimens, especially for the genera Teutamus and Oedignatha. Also, we extended the known distribution of Oedignatha and Sesieutes within Thailand. These results illustrate the relevance of making biodiversity data contained within taxonomic treatments accessible and reusable. It also exemplifies one potential use of taxonomic legacy data: to more efficiently use existing biodiversity data to fill knowledge gaps. A similar approach can be used to study neglected or interesting taxa and geographic areas, generating a better biodiversity documentation that could aid in decision making, management and conservation.
- Published
- 2019
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