Phylogeny, taxonomy and nomenclature:the problem of taxonomic categories and of nomenclatural ranks

Zootaxa ◽  
2007 ◽  
Vol 1519 (1) ◽  
pp. 27-68 ◽  
Author(s):  
ALAIN DUBOIS

The use of ranks and nominal-series in zoological nomenclature has recently been challenged by some authors who support unranked systems of nomenclature. It is here shown that this criticism is based on a double misunderstanding: (1) the confusion between nomenclatural ranks and taxonomic categories; (2) the request for a monosemic nomenclatural system, not for scientific reasons, but to please non-taxonomists, especially customers of the web. It is here argued that nomenclatural ranks and taxonomic categories should be clearly distinguished and designated by different terms, and that the Code should be modified in order to make this distinction clear. Whereas taxonomic categories have biological definitions, nomenclatural ranks do not, as they express only a position in a taxonomic hierarchy. If used consistently (which is not always the case), the system of nomenclatural ranks is very useful for the storage and retrieval of taxonomic and phylogenetic information. Taxa referred to a given rank in different groups cannot therefore be considered equivalent by any criterion, so that using ranks for comparisons between taxa (e.g., for biodiversity richness assessment) is irrelevant and misleading. Although the current Code needs to be improved in several respects, the superiority of this nomenclatural system, which is theory-free regarding taxonomy as it relies on ostensional allocation of nomina to taxa rather than on intensional definitions of nomina, is again stressed. It is suggested that all taxonomists should follow the Code for the allocation and validity of nomina, whatever taxonomic theory they favour, and in particular whatever kinds of definitions or diagnoses they wish to use for taxa. This would avoid the considerable loss of manpower, time and energy that would be required by the implementation of a new nomenclatural system (e.g., in order to require “phylogenetic definitions” for nomina, or to make nomenclature fully monosemic), and the confusion that would result for most users of nomina. The new paradigm imposed to biology by the combination of the taxonomic impediment and of the biodiversity crisis requires from taxonomists, who are already considerably much less numerous than required by this new situation, to concentrate on what should be their priority at the beginning of the century of extinctions, namely the inventory of the living species of our planet before they get extinct.

Bionomina ◽  
2011 ◽  
Vol 2 (1) ◽  
pp. 1-104 ◽  
Author(s):  
Alain DUBOIS

At the beginning of the century of extinctions, science has only inventoried a very small proportion of the living species of the globe. In order to face the taxonomic urgency that results from this taxonomic gap combined with the biodiversity crisis, zootaxonomy needs efficient, rigorous and automatic nomenclatural Rules, that allow to spend a minimal time on nomenclatural problems—rather than investing time, energy and money in renaming millions of already named taxa in order to follow alternative nomenclatural systems, e.g., “phylogenetic” ones, that furthermore do not show theoretical superiority to the current Linnaean-Stricklandian one. The current Code, result of a 250-year improvement process, is based on very sound and healthy Rules, being theory-free regarding taxonomy, relying on objective allocation of nomina to taxa by a system of ostension using onomatophores, and on an objective basic Principle, priority, for recognizing the valid nomen of a taxon in case of synonymy or homonymy. Nevertheless, this nomenclatural system is certainly not perfect. It should be modified at least in nine directions: (1) it should adopt a technical terminology avoiding possible misinterpretations from outsiders of the field and even from specialists, and allowing a precise formalisation of its mode of functioning; (2) its plan should be drastically modified; (3) its Principles should be redefined, and some added; (4) material evidence for the allocation of nomina to taxa through specimens deposited in permanent collections should be given more weight; (5) it should incorporate all nomina of higher taxa, providing clear and strict universal Rules for their naming, whereas conserving the traditional nomina largely used in non-specialized systematic literature; (6) it should allow for the recognition of many more ranks at lower nomenclatural levels, i.e., just above genus, between genus and species, and below species; (7) it should provide much more stringent Rules for the protection against priority of “wellknown” nomina or sozonyms; (8) various “details” should be addressed, various Rules and Recommendations changed before a new edition of the Code is published; (9) the procedure of implementations of changes in the Code should be modified in order to involve zootaxonomists of the whole world in the decisions. In several instances, the Rules of the Code should become much more compulsory for all zoologists, editors and publishers, to avoid the publication of endless and sometimes most detrimental discussions among taxonomists which give a poor image of nomenclature and taxonomy among the biological sciences, such as bitter discussions about the “best” nomen to be used under a so-called “usage” philosophy, or about nomina to be applied to higher taxa. Code-compliance in zootaxonomic publications should be highlighted, and editors and publishers should require from authors who follow alternative nomenclatural Rules (or no rule at all) to make it clear by using particular modes of writing their nomina. It is argued here that if the Code of the 21st century does not evolve to incorporate these changes, it will prove unable to play its role in front of several important recent theoretical and practical developments of taxonomy and run the risk of being abandoned by a part of the international community of zootaxonomists. The latter could then adopt alternative “phylogenetic” nomenclatural Rules, despite the severe practical problems and theoretical flaws posed by such projects. This would be most detrimental for all comparative biological disciplines including systematics, and even for the unity of biology. In the course of this discussion, a few recommendations are given concerning the standards and guidelines suggested by recent authors for a good, modern, integrative taxonomy.


Zootaxa ◽  
2008 ◽  
Vol 1950 (1) ◽  
pp. 51-86 ◽  
Author(s):  
ALAIN DUBOIS

Taxonomic paradigms have changed several times during the history of taxonomy, yet a single nomenclatural system, socalled Linnaean, has remained in force all along. It is theory-free regarding taxonomy as it relies on ostensional allocation of nomina to taxa, rather than on intensional definitions of nomina (e.g., “phylogenetic definitions”). Nomina are not descriptions, definitions or theories but simple labels designating taxa. Both for theoretical and practical reasons, this system should be maintained for the allocation and validity of nomina under a cladistic taxonomic paradigm. Whereas taxa can be cladistically defined by apognoses or cladognoses, nomina should remain attached to taxa through onomatophores, combined in some cases with a Principle of Coordination. Under such a system, the allocation of nomina to taxa is automatic, unambiguous and universal, and nomenclature does not infringe upon taxonomic freedom. However, to avoid misunderstandings and to solve some current problems, the current Code of zoological nomenclature should be improved in several respects. The distinction should be made clear between taxonomic categories, which have biological definitions, and nomenclatural ranks, which do not, as they give only a position in a nomenclatural hierarchy: if used consistently under a cladistic paradigm, they simply allow to express hypotheses about successive branchings and sistertaxa relationships. Taxa referred to a given rank in different groups cannot therefore be considered equivalent by any biological criterion. The nomenclatural rules should cover the whole taxonomic hierarchy, which is currently not the case in zoology. The recent strong increase in the number of higher taxa which results from cladistic analyses may quickly lead to chaos and problems in communication if the nomina of these taxa continue to be based on personal tastes and opinions. There is an urgent need for the zoological Code to cover these nomina with automatic and stringent rules leaving no place to subjective interpretation. Just like for those currently covered by the Code, the status of these nomina should be established in their first publication (nomenclatural founder effect). The Code should be protected against alternative nomenclatural systems by rejecting as unavailable all nomina and nomenclatural acts published without respecting the basic Linnaean system of nomenclatural hierarchy of ranks.


Zootaxa ◽  
2010 ◽  
Vol 2426 (1) ◽  
pp. 1 ◽  
Author(s):  
ALAIN DUBOIS

Taxonomy is currently facing a major crisis and is likely to have strong difficulties to reduce significantly the taxonomic gap before the biodiversity crisis has wiped out a large proportion of the living species of the earth. In this context, taxonomists should pay great attention to the nomenclatural Rules, and care for them to help them in this urgent task, rather than diverting their time and energy to secondary or useless questions or debates. A major purpose of the Code is to promote nomenclatural stability in zoology. This requires stability in the Rules, or at least that a great care be taken, when establishing new Rules, to avoid that they can have unexpected deleterious consequences for stability. In particular, in most cases, it is crucial to deny retroactivity to the new Rules. Several examples of problems created in zoological nomenclature by introduction of changes in Articles dealing with the spellings of nomina are examined in detail. These Articles were modified, with retroactive value, in the 1985 edition (Art. 32, 33, 35 and 39) and in the 1999 edition (Art. 24) of the Code. It is shown that these changes, which have no clear “philosophical” or practical justifications and which result in no clear benefits, have in fact had negative impacts on nomenclatural practice. Their implementation requires heavy useless additional work from taxonomists and has negative results in nomenclatural stability that had clearly not been anticipated by the ICZN when promulgating them. In a few sets of nomina tested below, the changes in the 1985 edition resulted in spelling changes for 10.0 to 22.2 % of the nomina, and those in the 1999 edition for 21.7 to 33.3 % of the nomina, roughly a quarter of them on the whole (24.5 %). Among others that are less emblematic, a striking case is that of the fish generic nomen Tetraodon, widely used especially since the genome of a species of this genus has been sequenced, and which should be changed to Tetrodon because of the unwarranted introduction of the new Art. 24.2.4 into the Code. It is suggested that these changes should be cancelled, or at least denied retroactivity from the years of their promulgations. In order to make this discussion easier, a “taxonomy” of the different kinds of spellings of nomina, and a dichotomic key to such situations, are provided. This stresses the fact that detailed discussions on very precise aspects of the functioning of nomenclatural Rules, as well as the computerization of nomenclatural data for online databases, require to use a specialized technical terminology to designate the nomenclatural concepts and tools, not vague “common language” terms like “name” or “type”: “keep the Rules, but change the terms”. The problems outlined here should be kept in mind by the ICZN before implementing drastic changes in the Rules of nomenclatural availability, as recently suggested.


Zootaxa ◽  
2019 ◽  
Vol 4590 (2) ◽  
pp. 296
Author(s):  
HIROAKI KARASAWA

The name, Galathea keijii, was given to a Miocene fossil species of squat lobster from Japan by Karasawa (1993: 39, pl. 6, figs. 1, 2, 3, 10). In the same year, the name, Galathea keijii, was established for a living species from the Andaman Sea and Arabian Sea (Tirmizi & Javed 1993: 50, fig. 22). Therefore, both names are homonymous. The description of Karasawa was published in the Bulletin of the Mizunami Fossil Museum, no. 20, which, on the inside back cover states the date of publication as December 25, 1993. The description of Tirmizi & Javed was published in “Indian Ocean galatheids (Crustacea: Anomura)” by the Marine Reference Collection and Resource Centre, University of Karachi. This work was published in 1993 but the day and month of publication were not cited in the publication. In the absence of evidence to the contrary, the date of publication for “Indian Ocean galatheids (Crustacea: Anomura)” is deemed to be the last day of 1993, by application of Article 21.3.2 of the International Code of Zoological Nomenclature (ICZN 1999: 20). As such, application of Article 52 on the principle of homonymy of the International Code of Zoological Nomenclature (ICZN, 1999: 56) shows that Galathea keijii Karasawa, 1993, takes precedence over Galathea keijii Tirmizi & Javed, 1993. In accordance with Article 60 on the replacement of junior homonyms (ICZN 1999: 62, 63) a new replacement name, Galathea nasimae, is here proposed for Galathea keijii Tirmizi & Javed, 1993. It is dedicated to the late Dr. Nasima M. Tirmizi (Marine Reference Collection and Resource Centre, University of Karachi).


1999 ◽  
Vol 33 (3) ◽  
pp. 689-732 ◽  
Author(s):  
Arild Engelsen Ruud

The Subaltern studies project has been a major contribution towards rethinking the role of groups such as peasants, lower castes, labourers or women in forming the course of Indian history. The project has also brought the issues of culture, ideology and consciousness to the forefront of Indian history writing. Although the importance of non-elite action on the historical developments of the Indian independence movement has already been noted by more mainstream historians, the concertedness of the project has created a whole new situation in which the subalternist perspective has become a new paradigm for Indian history writing, indeed, the subalternist perspective has increasingly come to dominate the formation of perspectives and concepts. As Masselos points out, the Subaltern studies has become the establishment.


Zootaxa ◽  
2008 ◽  
Vol 1965 (1) ◽  
pp. 61-68 ◽  
Author(s):  
JOSÉ ANTONIO GONZÁLEZ-OREJA

One of the most crucial questions of twenty-first century systematic biology deals with the determination of the real number of living species currently sharing the Earth with us (Cracraft 2002); answers vary widely, but commonly range between 3 and 100 million (see, for example, Stork 1997 or May 2002 and references therein). However, in terms of completeness and correctness, our current inventory of living species is certainly unsatisfactory (Dubois 2003), as the total number of species described so far is known to correspond to only a very small fraction of the Earth´s biodiversity. Indeed, large numbers of species remain to be discovered, primarily insects, small invertebrates and, above all, microorganisms (Chevalier et al. 1997). On the other hand, this gap of knowledge regarding the magnitude of the Earth´s biodiversity limits our capacity to properly manage the world´s biotic resources and conserve biological diversity in this so-called Century of Extinctions (Dubois 2003): the current biodiversity crisis is wiping out a significant fraction of living species at an alarming rate and, sadly, an unknown number of species is being forever lost before being discovered, described, and named. Likewise, conservation priorities are clearly constrained by our limited knowledge of the total biodiversity (Dubois 2003, Scotland et al. 2003).


2019 ◽  
Vol 66 (2) ◽  
pp. 119-145 ◽  
Author(s):  
Sarah Meierotto ◽  
Michael J. Sharkey ◽  
Daniel H. Janzen ◽  
Winnie Hallwachs ◽  
Paul D. N. Hebert ◽  
...  

Here we elucidate and justify a DNA barcode approach to insect species description that can be applied to name tens of thousands of species of Ichneumonoidea and many other species-rich taxa. Each description consists of a lateral habitus image of the specimen, a COI barcode diagnosis, and the holotype specimen information required by the International Code of Zoological Nomenclature. We believe this approach, or a slight modification of it, will be useful for many other underdescribed hyperdiverse taxa, especially in the tropics. Due to the extreme species-richness of the Ichneumonoidea, the very low percentage of described species, and the lack of detailed biological information for most described species, the standard taxonomic approach is inefficient and overwhelmingly time consuming. A DNA barcode-based approach to initial description will provide a solid foundation of species hypotheses from which more comprehensive descriptions can be developed as other data, time, and budgets permit. Here we elucidate this view and detailed methodology that can generally be applied to species-rich underdescribed taxa. A real example is given by describing species in two genera, Hemichoma and Zelomorpha, reared from the Área de Conservación Guanacaste in northwestern Costa Rica. The generic type species Zelomorphaarizonensis is given a DNA barcode diagnosis and the following new species are described: Zelomorphaangelsolisi, Zelomorphabobandersoni, Zelomorphadanjohnsoni, Zelomorphadonwindsori, Zelomorphaeffugia, Zelomorphajohnchemsaki, Zelomorphakellyanneae, Zelomorphalarrykirkendalli, Zelomorphamariyavladmirovnae, Zelomorphamikeiviei, Zelomorphamyricagaleae, Zelomorphanoahjaneae, Zelomorphapaulgoldsteini, Zelomorphaterryerwini, Zelomorphawillsflowersi, Hemichomadonwhiteheadi, Hemichomafrankhovorei, and Hemichomajohnkingsolveri.


Zootaxa ◽  
2018 ◽  
Vol 4375 (4) ◽  
pp. 587 ◽  
Author(s):  
HIROAKI KARASAWA

The name Mursia minuta Spiridonov & Apel, 2007, was given to a living species from the Indian Ocean (Spiridonov & Apel 2007: 2870, figs. 2G, H, 4E, F, 8C, 10A–D, 11A, B, 12A, B). This name is preoccupied by the senior primary homonym Mursia minuta Karasawa, 1993, for a Pliocene fossil species from Japan (Karasawa 1993: 45, pl. 8, figs. 8, 10, 13, 14). In accordance with Article 60 of the International Code of Zoological Nomenclature (ICZN 1999: 62, 63) a new replacement name, Mursia spiridonovi is here proposed for Mursia minuta Spiridonov & Apel, 2007. It is named for V. A. Spiridonov (Institute of Oceanology of the Russian Academy of Sciences, Moscow), in honor of his pioneering work on the extant decapods. 


Author(s):  
Victor Rodriguez-Herola

The North Atlantic Treaty Organisation (NATO) is shifting towards Net-centric operations paradigms driven by the nature of the new missions that the Alliance will likely be facing in the coming years. This new situation has forced the Alliance to pursue the achievement of the so-called NATO Network-Enabled Capability (NNEC). In this framework, the concept of a system of systems should give way to the new paradigm of federation of services, where any capability needs to be seen as a loosely-couple service. From the perspective of any of these services, one of the biggest issues will be to discover available services and, more importantly, the information provided for such services can be consumed. For this purpose, we present in this chapter the use of Semantic Web as a technology that will facilitate the explicit description of the services available on the Net that will eventually help in selecting the right services. The technology will also mediate between service consumers and service providers, so information is given a well-defined meaning and is comprehensible. Based on the foundations of the Semantic Web, we propose a concept demonstrator called SISearch, where well defined vocabularies from apparently different domains are defined by using ontology languages. Then, these different vocabularies are interpreted with respect to the vocabulary defined by a potential service consumer. Assisted by this interpretation and by inference services, the SISearch will translate both consumer-based queries to service provider specific-queries (using different vocabularies), and aggregating and interpreting the results with respect to the service consumer vocabulary. This approach will allow extending to new potential service consumer or service providers without having to develop specific modules or components.


2000 ◽  
Vol 179 ◽  
pp. 177-183
Author(s):  
D. M. Rust

AbstractSolar filaments are discussed in terms of two contrasting paradigms. The standard paradigm is that filaments are formed by condensation of coronal plasma into magnetic fields that are twisted or dimpled as a consequence of motions of the fields’ sources in the photosphere. According to a new paradigm, filaments form in rising, twisted flux ropes and are a necessary intermediate stage in the transfer to interplanetary space of dynamo-generated magnetic flux. It is argued that the accumulation of magnetic helicity in filaments and their coronal surroundings leads to filament eruptions and coronal mass ejections. These ejections relieve the Sun of the flux generated by the dynamo and make way for the flux of the next cycle.


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