New Concepts and Methods for Phylogenetic Taxonomy and Nomenclature in Zoology, Exemplified by a New Ranked Cladonomy of Recent Amphibians (Lissamphibia)
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Megataxa 005 (1): 001–738 ISSN 2703-3082 (print edition) https://www.mapress.com/j/mt/ MEGATAXA Copyright © 2021 Magnolia Press ISSN 2703-3090 (online edition) https://doi.org/10.11646/megataxa.5.1.1 http://zoobank.org/urn:lsid:zoobank.org:pub:FDD3A5EB-123D-4567-83D4-72A9A231731D MEGATAXA 5 New concepts and methods for phylogenetic taxonomy and nomenclature in zoology, exemplified by a new ranked cladonomy of recent amphibians (Lissamphibia) ALAIN DUBOIS1, ANNEMARIE OHLER2 & R. ALEXANDER PYRON3 1 Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France. �[email protected]; https://orcid.org/0000-0002-6463-3435 2 Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France. �[email protected]; https://orcid.org/0000-0001-6531-464X; Phone: +33 140 79 34 86 3 Department of Biological Sciences, The George Washington University, Washington DC, USA. �[email protected]; https://orcid.org/0000-0003-2524-1794; Phone: +1 (202) 994 6616 Magnolia Press Auckland, New Zealand Submitted: 30 May 2020; accepted by Zhi-Qiang Zhang 30 Nov. 2020; published: 26 Feb. 2021 Licensed under Creative Commons Attribution-N.C. 4.0 International https://creativecommons.org/licenses/by-nc/4.0/ ALAIN DUBOIS, ANNEMARIE OHLER & R. ALEXANDER PYRON New concepts and methods for phylogenetic taxonomy and nomenclature in zoology, exemplified by a new ranked cladonomy of recent amphibians (Lissamphibia) (Megataxa 5) 738 pp.; 30 cm. 26 February 2021 ISBN 978-1-77688-192-5 (Paperback) ISBN 978-1-77688-193-2 (Online edition) FIRST PUBLISHED IN 2021 BY Magnolia Press P.O. Box 41-383 Auckland 1041 New Zealand e-mail: [email protected] https://www.mapress.com/j/mt © 2021 Magnolia Press ISSN 2703-3082 (Print edition) ISSN 2703-3090 (Online edition) • Megataxa 005 (1) © 2021 Magnolia Press DUBOIS et al. Table of Contents 2.3.4.3.5.2. Non-differential diagnoses .... 65 2.3.4.3.5.3. Diagnosis unconnected with Abstract...................................................................................... 5 new taxon ................................................. 66 Keywords.................................................................................... 6 2.3.4.3.5.4. Notes for the future ............... 67 Terminology, conventions and abbreviations .................... 6 2.3.4.4. Conclusion ............................................. 67 1. Introduction .......................................................................... 9 2.3.5. Categories of usage of nomina..................... 68 2. Materials and methods: phylogeny, taxonomy and 2.3.6. Taxonomic allocation of nomina ................. 68 nomenclature ........................................................................... 15 2.3.6.1. Family-series nomina ............................. 68 .. Phylogeny ............................................................... 15 2.3.6.2. Class-series nomina ............................... 69 2.1.1. Phylogenetic reconstruction ......................... 15 2.3.7. Validity and correctness of nomina .............. 70 2.1.2. The lability of phylogenetic hypotheses 2.3.7.1. Introduction ............................................ 70 and the use of the term clade ................................. 17 2.3.7.2. Priority ................................................... 71 .. Taxonomy ............................................................... 18 2.3.7.3. Airesy (first reviser) ............................... 71 2.2.1. Taxonomic paradigms .................................. 18 2.3.7.4. Proedry (rank precedence)..................... 71 2.2.2. Phylogenetic taxonomies .............................. 20 2.3.7.5. Eugraphy ................................................ 72 2.2.3. Taxonomic categories and 2.3.7.6. Reversal of precedence .......................... 74 nomenclatural ranks .............................................. 21 2.3.7.6.1. Article 23.9 ..................................... 74 2.2.4. Taxonomic concepts and Criteria ................ 22 2.3.7.6.2. Other Articles resulting in 2.2.4.1. General situation ................................... 22 reversal of precedence .................................... 75 2.2.4.2. Species taxonominal level ...................... 23 2.3.7.7. Sozoidy ................................................... 78 2.2.4.3. Genus taxonominal level ........................ 23 2.3.7.8. Archoidy (Commission’s Plenary 2.2.4.4. Suprageneric taxonominal levels ........... 25 Power) ................................................................. 80 2.2.5. Taxonomic scope of the present work .......... 25 2.3.7.9. Conclusion ............................................. 80 2.2.5.1. Species taxonominal level ...................... 25 2.3.8. Comprehensive lists of supraspecific 2.2.5.2. Genus taxonominal level ........................ 26 nomina of Lissamphibia ........................................ 80 2.2.5.3. Suprageneric taxonominal levels ........... 27 2.3.9. ‘Vernacular’, ‘common’ and scientific .. Nomenclature ......................................................... 30 names ...................................................................... 81 2.3.1. Introduction .................................................. 30 .4. A new methodology for taxonomic and 2.3.2. Nomenclatural Rules, recommendations nomenclatural transcription of a tree into a and conventions ...................................................... 31 cladonomy ..................................................................... 83 2.3.3. Nominal-series, nominal-sets and 2.4.1. Introduction .................................................. 83 nomenclatural ranks .............................................. 32 2.4.2. Allocation, assignment, attribution and 2.3.4. Nomenclatural availability ........................... 35 allotment of nomina ............................................... 86 2.3.4.1. Publication availability .......................... 38 2.4.3. The two basic mandatory ranks between 2.3.4.2. Nominal-series assignment of genus and class: family and order ........................ 87 suprageneric nomina .......................................... 38 2.4.4. Nominal-series saturation ............................ 88 2.3.4.3. Nomen and onomatergy availability ...... 45 2.4.5. Recognition of suprageneric taxa and 2.3.4.3.1. General situation ............................ 45 their rank attribution: the ‘Ten Criteria 2.3.4.3.2. Metagraphs ..................................... 51 Procedure’ [TCP] .................................................... 88 2.3.4.3.3. Categories of homonymy ............... 53 2.4.5.1. General Criteria ..................................... 89 2.3.4.3.4. Ectonyms ........................................ 58 2.4.5.1.1. Criterion [CNC]: the 2.3.4.3.4.1. Oligocaconyms: ‘Consistent Naming Criterion’ ....................... 89 non-binominal specific nomenclature ...... 59 2.4.5.1.1.1. Statement of Criterion ........... 89 2.3.4.3.4.2. Hypercaconyms: 2.4.5.1.1.2. Rationale and use of this plurinominal nomina above the Criterion ................................................... 89 species-series ............................................ 59 2.4.5.1.2. Criterion [NPC]: the 2.3.4.3.4.3. Anemonyms: nomina ‘Nomenclatural Precedence Criterion’ ........... 90 unassignable to a nominal-series .............. 59 2.4.5.1.2.1. Statement of Criterion ........... 90 2.3.4.3.4.4. Notharchonyms: alternative 2.4.5.1.2.2. Rationale and use of nomenclatural systems ............................. 60 Criterion ................................................... 90 2.3.4.3.4.5. Anhypsonyms: unranked or 2.4.5.1.3. Criterion [CHC]: the ‘Consistent pseudoranked nomenclatural systems, Hierarchy Criterion’ ....................................... 91 mero-systems or pseudo-systems ............. 61 2.4.5.1.3.1. Statement of Criterion ........... 91 2.3.4.3.5. Acceptable tolerance for 2.4.5.1.3.2. Rationale and use of this borderline gymnonymy .................................. 63 Criterion ................................................... 91 2.3.4.3.5.1. Polythetic diagnoses .............. 64 2.4.5.1.3.3. Examples of use of this NEW LISSAMPHIBIAN CLADONOMY Megataxa 005 (1) © 2021 Magnolia Press • Criterion ................................................... 91 2.4.5.2.6.3. Consequences of the use 2.4.5.1.4. Criterion [FPC]: the ‘Family- of this Criterion ...................................... 103 Series Precedence Criterion’ .......................... 92 2.4.6. Implementation of the [TCP] and rank 2.4.5.1.4.1. Statement of Criterion ........... 92 attribution of suprageneric taxa.................................. 103 2.4.5.1.4.2. Rationale and use of this 2.4.6.1. A general summary of the Ten Criterion ................................................... 92 Criteria Procedure [TCP] ................................. 103 2.4.5.1.4.3. Examples of use of this 2.4.6.2. Theoretical examples ........................... 105 Criterion ................................................... 93 2.4.6.2.1. Example T1 .................................. 105 2.4.5.2. Criteria applying only or particularly 2.4.6.2.2. Example T2 .................................. 106 to families ............................................................ 93 2.4.6.3. Real examples ...................................... 108 2.4.5.2.1. Criterion [UQC]: the ‘Upper 2.4.6.3.1. Example