More Like this

1. TaxonWorks: a Use Case in Documenting of Etymology of Generic Names in Auchenorrhyncha (Hemiptera)

   https://doi.org/10.3897/biss.2.25724  

   Dmitriev, Dmitry ( May 2018 , Biodiversity Information Science and Standards)

   The 3i World Auchenorrhyncha database (http://dmitriev.speciesfile.org) is being migrated into TaxonWorks (http://taxonworks.org) and comprises nomenclatural data for all known Auchenorrhyncha taxa (leafhoppers, planthoppers, treehoppers, cicadas, spittle bugs). Of all those scientific names, 8,700 are unique genus-group names (which include valid genera and subgenera as well as their synonyms). According to the Rules of Zoological Nomenclature, a properly formed species-group name when combined with a genus-group name must agree with the latter in gender if the species-group name is or ends with a Latin or Latinized adjective or participle. This provides a double challenge for researchers describing new or citing existing taxa. For each species, the knowledge about the part of speech is essential information (nouns do not change their form when associated with different generic names). For the genus, the knowledge of the gender is essential information. Every time the species is transferred from one genus to another, its ending may need to be transformed to make a proper new scientific name (a binominal name). In modern day practice, it is important, when establishing a new name, to provide information about etymology of this name and the ways it should be used in the future publications: the grammatical gender formore »a genus, and the part of speech for a species. The older names often do not provide enough information about their etymology to make proper construction of scientific names. That is why in the literature, we can find numerous cases where a scientific name is not formed in conformity to the Rules of Nomenclature. An attempt was made to resolve the etymology of the generic names in Auchenorrhyncha to unify and clarify nomenclatural issues in this group of insects. In TaxonWorks, the rules of nomenclature are defined using the NOMEN onthology (https://github.com/SpeciesFileGroup/nomen).« less
2. Nomenclature over 5 years in TaxonWorks: Approach, implementation, limitations and outcomes

   https://doi.org/10.3897/biss.5.75441  

   Yoder, Matthew ; Dmitriev, Dmitry ( September 2021 , Biodiversity Information Science and Standards)

   We are now over four decades into digitally managing the names of Earth's species. As the number of federating (i.e., software that brings together previously disparate projects under a common infrastructure, for example TaxonWorks) and aggregating (e.g., International Plant Name Index, Catalog of Life (CoL)) efforts increase, there remains an unmet need for both the migration forward of old data, and for the production of new, precise and comprehensive nomenclatural catalogs. Given this context, we provide an overview of how TaxonWorks seeks to contribute to this effort, and where it might evolve in the future. In TaxonWorks, when we talk about governed names and relationships, we mean it in the sense of existing international codes of nomenclature (e.g., the International Code of Zoological Nomenclature (ICZN)). More technically, nomenclature is defined as a set of objective assertions that describe the relationships between the names given to biological taxa and the rules that determine how those names are governed. It is critical to note that this is not the same thing as the relationship between a name and a biological entity, but rather nomenclature in TaxonWorks represents the details of the (governed) relationships between names. Rather than thinking of nomenclature as changingmore »(a verb commonly used to express frustration with biological nomenclature), it is useful to think of nomenclature as a set of data points, which grows over time. For example, when synonymy happens, we do not erase the past, but rather record a new context for the name(s) in question. The biological concept changes, but the nomenclature (names) simply keeps adding up. Behind the scenes, nomenclature in TaxonWorks is represented by a set of nodes and edges, i.e., a mathematical graph, or network (e.g., Fig. 1). Most names (i.e., nodes in the network) are what TaxonWorks calls "protonyms," monomial epithets that are used to construct, for example, bionomial names (not to be confused with "protonym" sensu the ICZN). Protonyms are linked to other protonyms via relationships defined in NOMEN, an ontology that encodes governed rules of nomenclature. Within the system, all data, nodes and edges, can be cited, i.e., linked to a source and therefore anchored in time and tied to authorship, and annotated with a variety of annotation types (e.g., notes, confidence levels, tags). The actual building of the graphs is greatly simplified by multiple user-interfaces that allow scientists to review (e.g. Fig. 2), create, filter, and add to (again, not "change") the nomenclatural history. As in any complex knowledge-representation model, there are outlying scenarios, or edge cases that emerge, making certain human tasks more complex than others. TaxonWorks is no exception, it has limitations in terms of what and how some things can be represented. While many complex representations are hidden by simplified user-interfaces, some, for example, the handling of the ICZN's Family-group name, batch-loading of invalid relationships, and comparative syncing against external resources need more work to simplify the processes presently required to meet catalogers' needs. The depth at which TaxonWorks can capture nomenclature is only really valuable if it can be used by others. This is facilitated by the application programming interface (API) serving its data (https://api.taxonworks.org), serving text files, and by exports to standards like the emerging Catalog of Life Data Package. With reference to real-world problems, we illustrate different ways in which the API can be used, for example, as integrated into spreadsheets, through the use of command line scripts, and serve in the generation of public-facing websites. Behind all this effort are an increasing number of people recording help videos, developing documentation, and troubleshooting software and technical issues. Major contributions have come from developers at many skill levels, from high school to senior software engineers, illustrating that TaxonWorks leads in enabling both technical and domain-based contributions. The health and growth of this community is a key factor in TaxonWork's potential long-term impact in the effort to unify the names of Earth's species.« less
3. A catalogue of the tribe Sepidiini Eschscholtz, 1829 (Tenebrionidae, Pimeliinae) of the world

   https://doi.org/10.3897/zookeys.844.34241  

   Kamiński, Marcin J. ; Kanda, Kojun ; Lumen, Ryan ; Ulmer, Jonah M. ; Wirth, Christopher C. ; Bouchard, Patrice ; Aalbu, Rolf ; Mal, Noël ; Smith, Aaron D. ( May 2019 , ZooKeys)

   This catalogue includes all valid family-group (six subtribes), genus-group (55 genera, 33 subgenera), and species-group names (1009 species and subspecies) of Sepidiini darkling beetles (Coleoptera: Tenebrionidae: Pimeliinae), and their available synonyms. For each name, the author, year, and page number of the description are provided, with additional information (e.g., type species for genus-group names, author of synonymies for invalid taxa, notes) depending on the taxon rank. Verified distributional records (loci typici and data acquired from revisionary publications) for all the species are gathered. Distribution of the subtribes is illustrated and discussed. Several new nomenclatural acts are included. The generic names Phanerotomea Koch, 1958 [= Ocnodes Fåhraeus, 1870] and Parmularia Koch, 1955 [= Psammodes Kirby, 1819] are new synonyms (valid names in square brackets). The following new combinations are proposed: Ocnodesacuductusacuductus (Ancey, 1883), O. acuductusufipanus (Koch, 1952), O. adamantinus (Koch, 1952), O. argenteofasciatus (Koch, 1953), O. arnoldiarnoldi (Koch, 1952), O. arnoldisabianus (Koch, 1952), O.barbosai (Koch, 1952), O.basilewskyi (Koch, 1952), O.bellmarleyi (Koch, 1952), O. benguelensis (Koch, 1952), O. bertolonii (Guérin-Méneville, 1844), O. blandus (Koch, 1952), O. brevicornis (Haag-Rutenberg, 1875), O. brunnescensbrunnescens (Haag-Rutenberg, 1871), O. brunnescensmolestus (Haag-Rutenberg, 1875), O. buccinator (Koch, 1952), O. bushmanicus (Koch, 1952), O. carbonarius (Gerstaecker, 1854), O. cardiopterus (Fairmaire,more »1888), O. cataractus (Koch, 1952), O. cinerarius (Koch, 1952), O. complanatus (Koch, 1952), O. confertus (Koch, 1952), O. congruens (Péringuey, 1899), O. cordiventris (Haag-Rutenberg, 1871), O. crocodilinus (Koch, 1952), O. dimorphus (Koch, 1952), O. distinctus (Haag-Rutenberg, 1871), O. dolosus (Péringuey, 1899), O. dorsocostatus (Gebien, 1910), O. dubiosus (Péringuey, 1899), O. ejectus (Koch, 1952), O. epronoticus (Koch, 1952), O. erichsoni (Haag-Rutenberg, 1871), O. ferreiraeferreirae (Koch, 1952), O. ferreiraezulu (Koch, 1952), O. fettingi (Haag-Rutenberg, 1875), O. fistucans (Koch, 1952), O. fraternus (Haag-Rutenberg, 1875), O. freyi (Koch, 1952), O. freudei (Koch, 1952), O. fulgidus (Koch, 1952), O. funestus (Haag-Rutenberg, 1871), O. gemmeulus (Koch, 1952), O. gibberosulus (Péringuey, 1908), O. gibbus (Haag-Rutenberg, 1879), O. globosus (Haag-Rutenberg, 1871), O. granisterna (Koch, 1952), O. granulosicollis (Haag-Rutenberg, 1871), O.gridellii (Koch, 1960), O. gueriniguerini (Haag-Rutenberg, 1871), O. guerinilawrencii (Koch, 1954), O. guerinimancus (Koch 1954), O. haemorrhoidalishaemorrhoidalis (Koch, 1952), O. haemorrhoidalissalubris (Koch, 1952), O. heydeni (Haag-Rutenberg, 1871), O. humeralis (Haag-Rutenberg, 1871), O. humerangula (Koch, 1952), O. imbricatus (Koch, 1952), O.imitatorimitator (Péringuey, 1899), O. imitatorinvadens (Koch, 1952), O. inflatus (Koch, 1952), O. janssensi (Koch, 1952), O. javeti (Haag-Rutenberg, 1871), O. junodi (Péringuey, 1899), O. kulzeri (Koch, 1952), O. lacustris (Koch, 1952), O. laevigatus (Olivier, 1795), O. lanceolatus (Koch, 1953), O. licitus (Peringey, 1899), O. luctuosus (Haag-Rutenberg, 1871), O. luxurosus (Koch, 1952), O. maputoensis (Koch, 1952), O. marginicollis (Koch, 1952), O. martinsi (Koch, 1952), O. melleus (Koch, 1952), O. mendicusestermanni (Koch, 1952), O. mendicusmendicus (Péringuey, 1899), O. miles (Péringuey, 1908), O. mimeticus (Koch, 1952), O. misolampoides (Fairmaire, 1888), O. mixtus (Haag-Rutenberg, 1871), O. monacha (Koch, 1952), O. montanus (Koch, 1952), O. mozambicus (Koch, 1952), O. muliebriscurtus (Koch, 1952), O. muliebrismuliebris (Koch, 1952), O. muliebrissilvestris (Koch, 1952), O. nervosus (Haag-Rutenberg, 1871), O.notatum (Thunberg, 1787), O. notaticollis (Koch, 1952), O. odorans (Koch, 1952), O. opacus (Solier, 1843), O. osbecki (Billberg, 1815), O. overlaeti (Koch, 1952), O. ovulus (Haag-Rutenberg, 1871), O. pachysomaornata (Koch, 1952), O. pachysomapachysoma (Péringuey, 1892), O. papillosus (Koch, 1952), O. pedator (Fairmaire, 1888), O. perlucidus (Koch, 1952), O. planus (Koch, 1952), O. pretorianus (Koch, 1952), O. procursus (Péringuey, 1899), O. protectus (Koch, 1952), O. punctatissimus (Koch, 1952), O. puncticollis (Koch, 1952), O. punctipennisplanisculptus (Koch, 1952), O. punctipennispunctipennis (Harold, 1878), O. punctipleura (Koch, 1952), O. rhodesianus (Koch, 1952), O. roriferus (Koch, 1952), O. rufipes (Harold, 1878), O. saltuarius (Koch, 1952), O.scabricollis (Gerstaecker, 1854), O. scopulipes (Koch, 1952), O. scrobicollisgriqua (Koch, 1952), O. scrobicollissimulans (Koch, 1952), O. semirasus (Koch, 1952), O. semiscabrum (Haag-Rutenberg, 1871), O. sericicollis (Koch, 1952), O.similis (Péringuey, 1899), O. sjoestedti (Gebien, 1910), O. spatulipes (Koch, 1952), O. specularis (Péringuey, 1899), O. spinigerus (Koch, 1952), O. stevensoni (Koch, 1952), O. tarsocnoides (Koch, 1952), O. temulentus (Koch, 1952), O. tenebrosusmelanarius (Haag-Rutenberg, 1871), O. tenebrosustenebrosus (Erichson, 1843), O. tibialis (Haag-Rutenberg, 1871), O. torosus (Koch, 1952), O. transversicollis (Haag-Rutenberg, 1879), O. tumidus (Haag-Rutenberg, 1871), O. umvumanus (Koch, 1952), O. vagus (Péringuey, 1899), O. vaticinus (Péringuey, 1899), O. verecundus (Péringuey, 1899), O. vetustus (Koch, 1952), O. vexator (Péringuey, 1899), O. virago (Koch, 1952), O. warmeloi (Koch, 1953), O. zanzibaricus (Haag-Rutenberg, 1875), Psammophanesantinorii (Gridelli, 1939), and P.mirei (Pierre, 1979). The type species [placed in square brackets] of the following genus-group taxa are designated for the first time, Ocnodes Fåhraeus, 1870 [ Ocnodesscrobicollis Fåhraeus, 1870], Psammodophysis Péringuey, 1899 [ Psammodophysisprobes Péringuey, 1899], and Trachynotidus Péringuey, 1899 [ Psammodesthoreyi Haag-Rutenberg, 1871]. A lectotype is designated for Histrionotusomercooperi Koch, 1955 in order to fix its taxonomic status. Ulamus Kamiński is introduced here as a replacement name for Echinotus Marwick, 1935 [ Type species. Aviculaechinata Smith, 1817] (Mollusca: Pteriidae) to avoid homonymy with Echinotus Solier, 1843 (Coleoptera: Tenebrionidae).« less
4. The demise of Monechma: new combinations and a new classification in the resurrected genera Meiosperma and Pogonospermum (Acanthaceae)

   https://doi.org/10.1007/s12225-022-10003-w  

   Darbyshire, Iain ; Kiel, Carrie A. ; Chase, Frances M. ; Manzitto-Tripp, Erin A. ( March 2022 , Kew Bulletin)

   Summary Recent molecular phylogenetic results have demonstrated that Monechma s.l., a group of plants with ecological importance in the savanna and succulent biomes of sub-Saharan Africa, is polyphyletic with two discrete lineages recognisable. In the present work, we recognise Monechma Groups I and II at the generic rank, which can be distinguished by differences in inflorescence characteristics and seed morphology. The nomenclatural implications of these findings are investigated. The lectotype of Monechma , M. bracteatum Hochst., is a part of a small lineage of plants closely allied to Justicia L. sect. Harnieria (Solms) Benth. for which the earliest valid name is found to be Meiosperma Raf. Hence, Monechma is synonymised within Meiosperma , which comprises six accepted species and two undescribed taxa. The majority of species of former Monechma s.l. are resolved within the second lineage for which the only validly published generic name is Pogonospermum Hochst. This resurrected genus comprises 34 accepted species plus two undescribed taxa. Pogonospermum displays considerable morphological variation and is here subdivided into six sections based primarily on differences in plant habit, inflorescence form, calyx, bract and bracteole venation, and seed indumentum. The new combinations and new sections are validated, and seven accepted species namesmore »are lectotypified.« less
5. Ontology and values anchor indigenous and grey nomenclatures: a case study in lichen naming practices among the Sámi, Sherpa, Scots, and Okanagan

   https://doi.org/10.1016/j.shpsc.2020.101340  

   Kendig, Catherine ( November 2021 , Integrated HPS Conference Proceedings)

   Schickore, Jutta (Ed.)

   Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not be comparable if the ontological commitments employed differ. Comparisons between different nomenclatures cannot assume that either the naming practices or the object to which these names are intended to apply identifies some universally agreed upon object of interest. Investigating this suite of philosophical problems, I explore the role grey nomenclatures play in classification. ‘Grey nomenclatures’ are defined as those that employ names that are either intentionally or accidently non-Linnaean. The classification of the lichen thallus (a symbiont) has been classified outside the Linnaean system by botanists relying on the International Code of Nomenclature for algae, fungi, and plants (ICN). But, I argue, the use of grey names is not isolated and does not occur exclusively within institutionalized naming practices.more »I suggest, ‘grey names’ also aptly describe nomenclatures employed by indigenous communities such as the Sámi of Northern Finmark, the Sherpa of Nepal, and the Okanagan First Nations. I pay particular attention to how naming practices are employed in these communities; what ontological commitments they hold; for what purposes are these names used; and what anchors the community's nomenclatural practices. Exploring the history of lichen naming and early ethnolichenological research, I then investigate the stakes that must be considered for any attempt to preserve, retain, integrate, or compare the knowledge contained in both academically formalized grey names and indigenous nomenclatures in a way that preserves their source-specific informational content.« less