Published October 22, 2021 | Version v1
Journal article Restricted

Towards a global list of accepted species V. The devil is in the detail

  • 1. Bernice Pauahi Bishop Museum, Hawai'i, Honolulu, USA
  • 2. CSIR-National Botanical Research Institute, Lucknow, India
  • 3. Southern Cross University, Coffs Harbour, Australia
  • 4. Centre for Logic and Philosophy of Science, KU Leuven, Leuven, Belgium
  • 5. Faculty of Bioscience and Aquaculture, Nord Universitet, Bodø, Norway & School of Environment, University of Auckland, Auckland, New Zealand
  • 6. Global Wildlife Conservation, Austin, TX, USA
  • 7. Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT 0909, Australia
  • 8. Species 2000, Canberra, Australia
  • 9. Royal Botanic Gardens Kew, Richmond, UK
  • 10. School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
  • 11. Integrated Taxonomic Information System, National Museum of Natural History, Smithsonian Institution, Washington,
  • 12. Marine Biological Laboratory, Woods Hole, MA, USA
  • 13. Chelonian Research Institute, Oviedo, FL, USA
  • 14. Kenya Marine and Fisheries Research Institute, Mombasa, Kenya

Description

Pyle, Richard L., Barik, Saroj K., Christidis, Les, ConiX, Stijn, Costello, Mark John, Dijk, Peter Paul van, Garnett, Stephen T., Hobern, Donald, Kirk, Paul M., Lien, Aaron M., Orrell, Thomas M., Remsen, David, Thomson, Scott A., Wambiji, Nina, Zachos, Frank E., Zhang, Zhi-Qiang, Thiele, Kevin R. (2021): Towards a global list of accepted species V. The devil is in the detail. Organisms Diversity & Evolution 21 (4): 657-675, DOI: 10.1007/s13127-021-00504-0, URL: http://dx.doi.org/10.1007/s13127-021-00504-0

Files

Restricted

The record is publicly accessible, but files are restricted to users with access.

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:6921FFDBB33E4E4841560C315834FFED

References

  • Alvarez, M., & Luebert, F. (2018). The taxlist package: Managing plant taxonomic lists in R. Biodiversity Data Journal, 6, e23635. https:// doi.org/10.3897/BDJ.6.e23635
  • Anonymous. (2002). VegBank taxonomic data models. Ecological Society of America. Retrieved May 31, 2021, from http://www. vegbank.org/vegdocs/design/planttaxaoverview.html
  • Ardelean, A., Kervin, K., Kansakar, S., & Fautin, D. G. (2009). Syngraph: An application for graphic display and interactive use of synonym lists. Zootaxa, 2283, 29-39. https://doi.org/10.11646/ zootaxa.2283.1.3
  • Balakrishnan, R. (2005). Species concepts, species boundaries and species identification: A view from the tropics. Systematic Biology, 54(4), 689-693.
  • Berendsohn, W. G. (1995). The concept of "potential taxa" in databases. Taxon, 44, 207-212.
  • Berendsohn, W. G. (1997). A taxonomic information model for botanical databases: The IOPI Model. Taxon, 46, 283-309.
  • Berendsohn, W. G., Anagnostopoulos, A., Hagedorn, G., Jakupovic, J., Nimis, P. L., Valdes, B., Giintsch, A., Pankhurst, R. J., & White, R. J. (1999). A comprehensive reference model for biological collections and surveys. Taxon, 48, 511-562.
  • Blum, S., Barker, K., Baskauf, S. J., Berendsohn, W. G., Buttigieg, P. L., Doring, M., Droege, G., Fichtmueller, D., Glockler, F., Guntsch, A., & Guralnick, R. (2019). Integrating ABCD and DarwinCore: Toward a better foundation for biodiversity information standards. Biodiversity Information Science and Standards, 3, e37491. https://doi.org/10.3897/biss.3.37491
  • Brickell, C. D., Alexander, C., David, J. C., Hetterscheid, W. L. A., Leslie, A. C., Malecot, V., Xiaobai, J., & Cubey, J. J. (2009). International Code of Nomenclature for cultivated plants (8th ed.). International Society for Horticultural Science.
  • Callomon, P. (2016). The nature of names: Japanese vernacular nomenclature in natural science. Drexel University.
  • Catapano, T. (2010). TaxPub: An extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions. Proceedings of the Journal Article Tag Suite Conference 2010. http://www.ncbi. nlm.nih.gov/books/NBK47081
  • Chen, M., Yu, S., Franz, N., & Bowers, S. (2014). Euler/X: A toolkit for logic-based taxonomy integration. arXiv preprint, 1402.1992.
  • Chesser, R. T., Burns, K. J., Cicero, C., Dunn, J. L., Kratter, A. W., Lovette, I. J., Rasmussen, P. C., Remsen, J. V., Rising, J. D., Stotz, D. F., & Winker, K. (2017). Fifty-eighth supplement to the American Ornithological Society' s check-list of North American birds. The Auk, 134(3), 751-773. https://doi.org/10.1642/AUK-17-72.1
  • Conix, S. (2018). Values, regulation, and species delimitation. Zootaxa, 4415(2), 390-392. https://doi.org/10.11646/zootaxa.4415.2.9
  • Conix, S., Garnett, S. T., Thiele, K. R., Christidis, L., van Dijk, P. P., Banki, O. S., Barik, S. K., Buckeridge, J. S., Costello, M. J., Hobern, D., Kirk, P. M., Lien, A., Nikolaeva, S., Pyle, R. L., Thomson, S. A., Zhang, Z.-Q., & Zachos, F. E. (2021). Towards a global list of accepted species III: Independence and stakeholder inclusion. Org Divers Evol. https://doi.org/10.1007/ s13127-021-00496-x
  • Conniff, R. (2011). The species seekers: Heroes, fools, and the mad pursuit of life on earth. W. W. Norton & Company.
  • Conniff, R. (2021). The wall of the dead: A memorial to fallen naturalists. Retrieved February 7, 2021, from https://strangebehaviors. wordpress.com/2011/01/14/the-wall-of-the-dead/
  • Corliss, J. O. (1995). The ambiregnal protists and the codes of nomenclature: A brief review of the problem and of proposed solutions. Bulletin of Zoological Nomenclature., 52, 11-17.
  • Correia, R. A., Jaric, I., Jepson, P., Malhado, A. C., Alves, J. A., & Ladle, R. J. (2018). Nomenclature instability in species culturomic assessments: Why synonyms matter. Ecological Indicators, 90, 74-78. https://doi.org/10.1016/j.ecolind.2018.02.059
  • Costello, M. J., Bouchet, P., Boxshall, G., Fauchald, K., Gordon, D. P., Hoeksema, B. W., Poore, G. C. B., van Soest, R. W. M., Stohr, S., Walter, T. C., Vanhoorne, B., Decock, W., & Appeltans, W. (2013a). Global coordination and standardisation in marine biodiversity through the World Register of Marine Species (WoRMS) and related databases. PLoS One 8(1), e51629.
  • Costello, M. J., May, R. M., & Stork, N. E. (2013b). Can we name Earth' s species before they go extinct? Science, 339, 413-416.
  • Costello, M. J., & Wieczorek, J. (2014). Best practice for biodiversity data management and publication. Biological Conservation, 173, 68-73.
  • Costello, M. J., Appeltans, W., Bailly, N., Berendsohn, W. G., de Jong, Y., Edwards, M., Froese, R., Huettmann, F., Los, W., Mees, J., Segers, H., & Bisby, F. A. (2014). Strategies for the sustainability of online open-access biodiversity databases. Biological Conservation, 173, 155-165.
  • Costello, M. J., Horton, T., & Kroh, A. (2018). Sustainable biodiversity databasing: International, collaborative, dynamic, centralised. Trends in Ecology and Evolution, 33(11), 803-805.
  • Cotterill, F. P., Groves, C. P., & Taylor, P. J. (2017). Taxonomy: Refine rather than stabilize. Nature, 547(7662), 162-162. https://doi.org/ 10.1038/547162d
  • Council of Heads of Australasian Herbaria. (2010). Australian plant census https://biodiversity.org.au/nsl/services/apc
  • Doring, M., & Ower, G. D. (2019). The Catalogue of Life Data Package - A new format for exchanging nomenclatural and taxonomic information. Biodiversity Information Science and Standards, 3, e38711. https://doi.org/10.3897/biss.3.38771
  • Fichtmueller, D., Berendsohn, W. G., Droege, G., Glockler, F., Guntsch, A., Hoffmann, J., Holetschek, J., Petersen, M., & Reimeier, F. (2019). ABCD 3.0 Ready to use. Biodiversity Information Science and Standards, 3, e37214. https://doi.org/10.3897/biss.3.37214
  • Franz, N. M., Peet, R. K., & Weakley, A. S. (2008). On the use of taxonomic concepts in support of biodiversity research and taxonomy. In The new taxonomy (Wheeler QD, ed.). Systematics Association Special Volume, Taylor & Francis, 76, 63-84.
  • Franz, N. M., & Cardona-Duque, J. (2013). Description of two new species and phylogenetic reassessment of Perelleschus Wibmer & O' Brien, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013. Systematics and Biodiversity, 11(2), 209-236. https://doi.org/10.1080/14772000.2013.806371
  • Franz, N. M., & Thau, D. (2010). Biological taxonomy and ontology development: Scope and limitations. Biodiversity Informatics 7(1), 45-66. https://journals.ku.edu/index.php/jbi/article/view/3927
  • Franz, N., Gilbert, E., Ludascher, B., & Weakley, A. (2016). Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal. Research Ideas and Outcomes, 2, e10610. https://doi.org/10.3897/rio.2.e10610
  • Funk, V. A., Herendeen, P., & Knapp, S. (2017). Taxonomy: Naming algae, fungi, plants. Nature, 546(7660), 599-599. https://doi.org/ 10.1038/546599c
  • Garnett, S. T., & Christidis, L. (2017). Taxonomy anarchy hampers conservation. Nature, 546(7656), 25-27. https://doi.org/10.1038/ 546025a
  • Garnett, S. T., Christidis, L.Science-based taxonomy still needs better governance: Response to Thomson, , et al. (2018a). PLoS Biology, 16(3), e2005249. https://doi.org/10.1371/journal.pbio.2005249
  • Garnett, S. T., & Christidis, L. (2018b). Better governance will lead to better taxonomy: Response to Raposo et al.(2017). Zootaxa, 4418(3): 296-298. https://doi.org/10.11646/zootaxa.4418.3.7
  • Garnett, S. T., Christidis, L., Pylem R. L., & Thomson, S. A. (2020a). How a scientific spat over how to name species turned into a big plus for nature. The conversation, https://theconversation.com/ how-a-scientific-spat-over-how-to-name-species-turned-into-abig-plus-for-nature-138887 26 July 2020.
  • Garnett, S. T., Christidis, L., Conix, S., Costello, M. J., Zachos, F. E., Banki, O. S., et al. (2020). Principles for creating a single authoritative list of the world' s species. PLoS Biology, 18(7).
  • Geoffroy, M., & Berendsohn, W. G. (2003). The concept problem in taxonomy: Importance, components, approaches. In: MoReTax: Handling factual information linked to taxonomic concepts in biology (W.G. Berendsohn WG, ed.). Schriftenreihe fur Vegetationskunde, Federal Agency for Nature Conservation, Bonn, Germany. 39, 5-14.
  • Gewirtz, P. (1996). On 'I know it when I see it.' Yale Law Journal, 105, 1023-1047.
  • Gradstein, S. R., Sauer, M., Braun, M., Koperski, M., & Ludiwig, G. (2001). TaxLink, a program for computer-assisted documentation of different circumscriptions of biological taxa. Taxon, 50, 1075-1084.
  • Hayward, B.W., Le Coze, F., Vachard, D.,& Gross, O. (2021). World Foraminifera Database. Retrieved January 25, 2021, from http:// www.marinespecies.org/foraminifera https://doi.org/10.14284/305
  • Hobern, D., Barik, S. K., Christidis, L., Garnett, S. T. Kirk, P., Orrell, T. M., Pape, T., Pyle, R. L., Thiele, K. R., Zachos, F. E., & Banki, O. (2021). Towards a global list of accepted species VI. The Catalogue of Life checklist. Org Divers Evol. https://doi.org/10.1007/ s13127-021-00516-w
  • Holetschek, J., Droge, G., Guntsch, A., & Berendsohn, W. G. (2012). The ABCD of primary biodiversity data access. Plant Biosystems- an International Journal Dealing with All Aspects of Plant Biology, 146(4), 771-779. https://doi.org/10.1080/11263504.2012. 740085
  • Hollingsworth, P. M. (2017). Taxonomy: Avoid extra bureaucracy. Nature, 546(7660), 600-600. https://doi.org/10.1038/546600a
  • Holstein, N., & Luebert, F. (2017). Taxonomy: Stable taxon boundaries. Nature, 548(7666), 158-158. https://doi.org/10.1038/548158d
  • International Commission on Zoological Nomenclature (ICZN) (1999). International Code of Zoological Nomenclature. International Trust for Zoological Nomenclature.
  • Jackson, M.D., Scherz, M. D., & Zona, S. (2017). Taxonomy is not beholden to its dependencies: A rebuttal to Garnett and Christidis (2017) PeerJ, 5, e3060v1. https://doi.org/10.7287/peerj.preprints. 3060v1
  • Kennedy, J., Hyam, R., Kukla, R., & Paterson, T. (2006). Standard data model representation for taxonomic information. OMICS: A Journal of Integrative Biology 10, 220-230. https://doi.org/10. 1089/omi.2006.10.220
  • King, A. M., Lefkowitz, E., Adams, M. J., & Carstens, E. B. (eds.) (2011). Virus taxonomy: Ninth report of the International Committee on Taxonomy of Viruses (Vol. 9). Elsevier.
  • Koperski, M., Sauer, M., Braun, W., & Gradstein, S. R. (2000). Referenzliste Der Moose Deutschlands. Schriftenreihe Vegetationsk., 34, 1-519.
  • Krell, F. T., & Pyle, R. L. (2010). ZooBank progress report. Bulletin of Zoological Nomenclature, 67(4), 271.
  • Kroh, A., Costello, M. J., & Horton, T. (2019). Biodiversity databases in the future: Reply to Cene Fiser. Trends in Ecology and Evolution, 34(3), 185-186.
  • Lambertz, M. (2017). Taxonomy: Retain scientific autonomy. Nature, 546(7660), 600-600. https://doi.org/10.1038/546600b
  • Lepage, D., Vaidya, G., & Guralnick, R. (2014). Avibase-a database system for managing and organizing taxonomic concepts. ZooKeys, 420, 117. https://doi.org/10.3897/zookeys.420.7089
  • Le Renard, J. (2000). TAXIS, a taxonomic information system for managing large biological collections. in: Abstracts. TDWG 2000: Digitizing biological collections. Taxonomic Databases Working Group (p. 18), 16th Annual Meeting, Frankfurt, November 10-12, 2000.
  • Lien, A. M., Conix, S., Zachos, F. E., Christidis, L., van Dijk, P. P., Banki, O. S., Barik, S. K., Buckeridge, J. S., Costello, M. J., Hobern, D., Montgomery, N., Nikolaeva, S., Pyle, R. L., Thiele, K., Thomson, S. A., Zhang, Z.-Q., & Garnett, S. T. (2021). Towards a global list of accepted species IV. Overcoming fragmentation in the governance of taxonomic lists. Org Divers Evol. https://doi.org/10.1007/s13127-021-00499-8
  • Linnaeus, C. (1753). Species plantarum, exhibentes plantas rite cognitas, ad genera relatas, cum differentiis specificis, nominibus trivialibus, synonymis selectis, locis natalibus, secundum systema sexuale digestas. Impensis Laurentii Salvii
  • Linnaeus, C. (1758). Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Editio decima, reformata. Impensis Laurentii Salvii
  • McClure, C. J. W., Lepage, D., Dunn, L., Anderson, D. L., Schulwitz, S. E., Camacho, L., Robinson, B. W., Christidis, L., Schulenberg, T. S., Iliff, M. J., Rasmussen, P. C., & Johnson, J. (2020). Towards reconciliation of the four world bird lists: Hotspots of disagreement in taxonomy of raptors. Proceedings of the Royal Society B: Biological Sciences, 287(1929), 20200683. https://doi.org/10. 1098/rspb.2020.0683
  • Midford, P. E., Dececchi, T. A., Balhoff, J. P., Dahdul, W. M., Ibrahim, N., Lapp, H., Lundberg, J. G., Mabee, P. M., Sereno, P. C., Westerfield, M., & Vision, T. J. (2013). The vertebrate taxonomy ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics, 4(1), 1-6. https://doi.org/ 10.1186/2041-1480-4-34
  • Murray, A. E., Freudenstein, J., & Reysenbach, A.-L. (2020). Roadmap for naming uncultivated archaea and bacteria. Nature Microbiology, 5, 987-994.
  • Nakada, T. (2010). Nomenclatural notes on some ambiregnal generic names (comments to Ozdikmen, 2009). Munis Entomology & Zoology, 5(1), 204-208.
  • Parker, C. T., Tindall, B. J., Garrity, G. M. Eds (2019). International Code of Nomenclature of prokaryotes: Prokaryotic code (2008 revision). International Journal of Systematic and Evolutionary Microbiology, 69(1A), S1-S111 https://doi.org/10.1099/ijsem.0. 000778
  • Page, L. M., Espinosa-Perez, H., Findley, L. T., Gilbert, C. R., Lea, R. N., Mandrak, N. E., & Mayden, R. L. (2013). New seventh edition of common and scientific names of fishes: Changes include capitalization of common names. Fisheries. 38(4), 188-189.
  • Patterson, C. (1981). Significance of fossils in determining evolutionary relationships. Annual Review of Ecology and Systematics, 12, 195-223.
  • Patterson, D. J. (1986). Some problems of ambiregnal taxonomy and a possible solution. Symposia Biologica Hungarica, 33, 87-93.
  • Patterson, D. J., & Larsen, J. (1992). A perspective on protistan nomenclature. The Journal of Protozoology, 39(1), 125-131.
  • Patterson, D. J., Cooper, J., Kirk, P. M., Pyle, R. L., & Remsen, D. P. (2010). Names are key to the big new biology. Trends in Ecology & Evolution, 25(12), 686-691. https://doi.org/10.1016/j.tree. 2010.09.004
  • Pullan, M. R., Watson, M. F., Kennedy, J. B., Raguenaud, C., & Hyam, R. (2000). The Prometheus Taxonomic Model: A practical approach to representing multiple classifications. Taxon, 49, 55-75.
  • Pyle, R. L. (2004). Taxonomer: A relational data model for managing information relevant to taxonomic research. Phyloinformatics, 1, 1-54. https://doi.org/10.5281/zenodo.59790
  • Pyle, R. L. (2016). Towards a Global Names Architecture: The future of indexing scientific names. ZooKeys, 550, 261. https://doi.org/ 10.3897/zookeys.550.10009
  • Pyle, R. L., & Michel, E. (2008). ZooBank: Developing a nomenclatural tool for unifying 250 years of biological information. Zootaxa, 1950(1), 39-50. https://doi.org/10.11646/zootaxa.1950.1.6
  • Raposo, M. A., Stopiglia, R., Brito, G. R. R., Bockmann, F.A., Kirwan, G. M., Gayon, J., & Dubois, A. (2017). What really hampers taxonomy and conservation? A riposte to Garnett and Christidis (2017). Zootaxa, 4317(1), 179-184. https://doi.org/10.11646/zootaxa.4317.1.10
  • Raguenaud, C. (2002), Managing complex taxonomic data in an object-oriented database. [Unpublished manuscript representing partial PhD thesis, Napier University.] http://www.soc.napier.ac. uk/publication/op/getpublication/publicationid/1845313
  • Ruggiero, M. A., Gordon, D. P., Orrell, T. M., Bailly, N., Bourgoin, T., Brusca, R. C., Cavalier-Smith, T., Guiry, M. D., & Kirk, P. M. (2015). A higher level classification of all living organisms. PLoS ONE, 10(4), e0119248. https://doi.org/10.1371/journal. pone.0119248
  • Senderov, V., Simov, K., Franz, N., Stoev, P., Catapano, T., Agosti, D., Sautter, G., Morris, R. A., & Penev, L. (2018). OpenBiodiv- O: Ontology of the OpenBiodiv knowledge management system. Journal of Biomedical Semantics, 9(5), 1-15. https://doi.org/10. 1186/s13326-017-0174-5
  • Spencer, R. D., & Cross, R. G. (2007). The International Code of Botanical Nomenclature (ICBN), the international code of nomenclature for cultivated plants (ICNCP), and the cultigen. Taxon, 56(3), 938-940.
  • Stearn, W. T. (Ed.). (1953). International Code of Nomenclature for cultivated plants. Royal Horticultural Society.
  • Thiele, K. R., Conix, S., Pyle, R. L., Barik, S. K., Christidis, L., Costello, M. J., van Dijk, P. P., Kirk, P., Lien, A., Thomson, S. A., Zachos, F. E., Zhang, Z.-Q., & Garnett, S. T. (2021). Towards a global list of accepted species I. Why taxonomists sometimes disagree, and why this matters. Org Divers Evol. https://doi.org/ 10.1007/s13127-021-00495-y
  • Thomson, S. A., Pyle, R. L., Ahyong, S. T., Alonso-Zarazaga, M., Ammirati, J., Araya, J. F., et al. (2018). Taxonomy based on science is necessary for global conservation. PLoS Biology, 16, e2005075. https://doi.org/10.1371/journal.pbio.2005075
  • Thomson, S. A., Thiele, K., Conix, S., Christidis, L., Costello, M. J., Hobern, D., Nikolaeva, S., Pyle, R. L., van Dijk, P. P., Weaver, H., Zachos, F. E., Zhang, Z.-Q., & Garnett, S. T. (2021). Towards a global list of accepted species II. Consequences of inadequate taxonomic list governance. Org Divers Evol. https://doi.org/10. 1007/s13127-021-00518-8
  • Trehane, P. (2002). 50 years of the International Code of Nomenclature for Cultivated Plants: Future prospects for the Code. In XXVI International Horticultural Congress: IV International Symposium on Taxonomy of Cultivated Plants (pp. 17-27).
  • Turland, N. J., Wiersema, J. H., Barrie, F. R., Greuter, W., Hawksworth, D. L., Herendeen,P. S., Knapp, S., Kusper, W.-H., Li, D.-Z., Marhold, K., May, T. W., McNiell, J., Monro,A.M., Prado,J., Price, M. J., & Smith, G. F. (2018). International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Koeltz Botanical Books. https://doi.org/10.12705/Code.2018
  • Wheeler, Q. D., & Meier, R. (eds.) (2000). Species concepts and phylogenetic theory: A debate. Columbia University Press.
  • Wieczorek, J., Bloom, D., Guralnick, R., Blum, S., Doring, M., Giovanni, R., Robertson, T., & Vieglais, D. (2012). Darwin Core: An evolving community-developed biodiversity data standard. PloS ONE, 7(1), e29715. https://doi.org/10.1371/journal.pone.0029715
  • Ytow, N., Morse, D. R., & Roberts, & D. M. . (2001). Nomencurator: A nomenclatural history model to handle multiple taxonomic views. Biological Journal of the Linnean Society, 73(1), 81-98. https:// doi.org/10.1111/j.1095-8312.2001.tb01348.x
  • Zachos, F. E. (2018). (New) Species concepts, species delimitation and the inherent limitations of taxonomy. Journal of Genetics, 97(4), 811-815. https://doi.org/10.1007/s12041-018-0965-1
  • Zhong, Y., Jung, S., Pramanik, S., & Beaman, J. H. (1996). Data model and comparison and query methods for interacting classifications in a taxonomic database. Taxon, 45, 223-241.