Is Myxomycetes (Amoebozoa) a Truly Ambiregnal Group? A Major Issue in Protist Nomenclature

NOMENCLATURE OF CULTIVATED PLANTS: A HISTORICAL BOTANICAL STANDPOINT

To the Editor: Our 2002 article in Emerging Infectious Diseases about nomenclature changes for organisms in the genus Pneumocystis (1) has been widely cited and probably will remain a source for persons seeking information about this subject. Therefore, we need to correct an error in 1 of the species names presented in our article and in the 1999 article by Frenkel (2) on which our article was based. In the 1999 article, Frenkel proposed that the species of Pneumocystis found in humans be named to honor the Czech parasitologist, Otto Jirovec. The 1999 article was his second proposal for this change. In 1976, he first named the human pathogen Pneumocystis jiroveci (3), at which time it was classified as a protozoan and therefore named according to the International Code of Zoological Nomenclature. By 1999, it had become clear that the organisms in the genus Pneumocystis are fungi, which are named according to the International Code of Botanical Nomenclature (ICBN) (4). Differences between the International Code of Zoological Nomenclature and ICBN resulted in the realization of an error in the species epithet proposed by Frenkel in 1999, and our 2002 article contained this error. Frenkel’s 1999 article should have modified the species epithet from “jiroveci” to “jirovecii,” (ICBN Articles 32.7 and 60.11 and Rec. 60C.1b). The correct and valid name under ICBN is Pneumocystis jirovecii. Redhead et al. further explain the basis for this correction (5).

Bibliography resembles some species complexes with such overlapping diversity that they can be regarded as a single polymorphic species or as an assemblage of several closely allied and subtly distinguishable species or as a hybrid swarm derived from intercrossing in past. It is a matter of definition. As John Carter has said in his ABC for Book-Collectors (1952), may be enumerative, analytical or descriptive; broadly defined, it is the description or knowledge of books in regard to their authors, subjects, editions and history. Thus in biological terms biblio­ graphy is a polymorphic species embracing numerous variants, i.e. lines of enquiry. Some of these, however, interest only bibliophiles. Others are highly relevant to procedures in natural history and have accordingly received much attention within Natural History Museum during past hundred years; moreover their utility will continue. The importance of bibliography for such an institution as Natural History Museum at South Kensington, which is primarily taxonomic in its research, comes from importance of printed record as a long-lasting continuously usable source of taxonomic information. For this information to be retrievable with minimum of inconvenience and loss of time, stability of nomenclature and resolving of synonymy are in turn important. As stated in International Code of Botanical Nomenclature, principle III, the nomenclature of a taxonomic group is based upon priority of publication. The International Code of Zoological Nomenclature puts same emphasis on priority: the valid name of a taxon is oldest available name applied to it... provided that name is not invalidated by any provision of this Code or has not been suppressed by Commission. Relative dates of publication of competing different names for same organism or of like names for different organisms can thus determine name which should be adopted. To ascertain relative dates of publication often involves difficult and time-consuming bibliographical enquiry but this must nevertheless be undertaken when result may be crucial for correct nomenclature. That is why Natural History Museum has long been a major centre of such bibliographical enquiry and why Society for Bibliography of Natural History was formed under Museum's auspices in 1936 and has received so much support from Museum. The Society has never been officially part of Museum, but this Museum support has been vital to its maintenance and success. On other hand Society, by publishing results of bibliographic al and associated biographical enquiry relevant to natural history, has much benefited workers in Museum and elsewhere. The relations of two, in biological terms, have not been simply commensal but symbiotic.

The typographical layout of the present Draft conforms to that of the International code of botanical nomenclature (Tokyo Code) (Greuter & al. in Regnum Veg. 131. 1994, abbreviated ICBN hereafter) and therefore differs from the usual Taxon style, and also from that of the current editions of the International code of zoological nomenclature (Ride & al., London, 1985: the ICZN) and of the International code of nomenclature of bacteria (Lapage & al., Washington, 1992: the BC). The Draft does not yet include Recommendations, Notes, or Examples. For further relevant explanations, botanists may find it useful to refer to the Introductory comments by Greuter & Nicolson (in Taxon 45: 343-348. 1996), a document initially prepared for the benefit of members of the General Committee on Botanical Nomenclature, now published in a slightly updated form. A set of explanatory Notes addressed to all biologists interested in nomenclatural matters is in preparation and expected to be ready for distribution at a half-day symposium on The New Bionomenclature at the Fifth International Congress of Systematic and Evolutionary Biology (ICSEB V) in Budapest, 17-24 August 1996 (see Hawksworth in Taxon 44: 447-456. 1995). To help all interested biologists who wish to compare the proposed new rules with the corresponding entries in the current Codes (BC, ICBN, ICZN), cross-references

A proposal is submitted to the ICSP to change the wording of General Consideration 5 of the International Code of Nomenclature of Prokaryotes (ICNP), deleting the words Schizophycetes, Cyanophyceae and Cyanobacteria from the groups of organisms whose nomenclature is covered by the Code. It is further proposed to change the terms Zoological Code and International Code of Botanical Nomenclature in General Consideration 5 and in Principle 2 to International Code of Zoological Nomenclature and International Code of Nomenclature for algae, fungi and plants, respectively.

Changes to the International Code of Botanical Nomenclature are decided upon every six years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18–22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (e.g. MycoBank). Draft text of the new articles to do with publication is provided and best practice is outlined. © The Authors. Journal compilation © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 133–136. To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in BMC Evolutionary Biology, Botanical Journal of the Linnean Society, Brittonia, Cladistics, MycoKeys, Mycotaxon, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, Plant Diversity and Resources, Systematic Botany and Taxon.

In the July issue of Journal of Paleontology, 84(4), Sánchez (2010) proposed the new genus nameEmiliodontafor the Ordovician bivalve genusEmilianiaSánchez, 1999 because of assumed homonymy withEmilianiaHay and Mohler, 1967 (in Hay et al., 1967). The supposed senior name, the genusEmilianiaHay and Mohler, belongs to the coccolithophores, a group of unicellular eukaryotic algae, which have traditionally been treated as plants (e.g., Glaessner, 1945; Tappan, 1980; see also Green and Jordan, 1994; Andersen, 2004 for modern classification) and to which the International Code of Botanical Nomenclature (ICBN) applies. In the original description ofEmilianiaHay and Molher the ICBN was used (Hay et al., 1967, p. 447) and the name was validly published under its rules. Animals such as the bivalveEmilianiaSánchez, 1999, in contrast, are treated under the International Code for Zoological Nomenclature (ICZN). Both codes are independent (ICBN, Principle I: Greuter et al., 1993, 2000; McNeill et al., 2006; ICZN Article 1: Ride et al., 1985, 1999), and therefore the same names (“homonyms” sensu lato) can coexist under different codes. Consequently,EmilianiaSánchez andEmilianiaHay and Molher are not homonyms in a taxonomic sense but are both legitimate names under the respective code. Furthermore, the nameEmiliodontaSánchez 2010 is superfluous and illegitimate, as “[…] the name of an animal taxon is not to be rejected merely because it is identical with the name of a taxon that is not animal.” (ICZN Article 1.4: Ride et al., 1999).

(258–260) Proposals to eliminate contradiction between Articles 11.7 and 11.8 and to equate non‐fossil with fossil names of dinophytes for purposes of priority

A revised six-kingdom system of life is presented, down to the level of infraphylum. As in my 1983 system Bacteria are treated as a single kingdom, and eukaryotes are divided into only five kingdoms: Protozoa, Animalia, Fungi, Plantae and Chromista. Intermediate high level categories (superkingdom, subkingdom, branch, infrakingdom, superphylum, subphylum and infraphylum) are extensively used to avoid splitting organisms into an excessive number of kingdoms and phyla (60 only being recognized). The two 'zoological' kingdoms, Protozoa and Animalia, are subject to the International Code of Zoological Nomenclature, the kingdom Bacteria to the International Code of Bacteriological Nomenclature, and the three 'botanical' kingdoms (Plantae, Fungi, Chromista) to the International Code of Botanical Nomenclature. Circumscriptions of the kingdoms Bacteria and Plantae remain unchanged since Cavalier-Smith (1981). The kingdom Fungi is expanded by adding Microsporidia, because of protein sequence evidence that these amitochondrial intracellular parasites are related to conventional Fungi, not Protozoa. Fungi are subdivided into four phyla and 20 classes; fungal classification at the rank of subclass and above is comprehensively revised. The kingdoms Protozoa and Animalia are modified in the light of molecular phylogenetic evidence that Myxozoa are actually Animalia, not Protozoa, and that mesozoans are related to bilaterian animals. Animalia are divided into four subkingdoms: Radiata (phyla Porifera, Cnidaria, Placozoa, Ctenophora), Myxozoa, Mesozoa and Bilateria (bilateral animals: all other phyla). Several new higher level groupings are made in the animal kingdom including three new phyla: Acanthognatha (rotifers, acanthocephalans, gastrotrichs, gnathostomulids), Brachiozoa (brachiopods and phoronids) and Lobopoda (onychophorans and tardigrades), so only 23 animal phyla are recognized. Archezoa, here restricted to the phyla Metamonada and Trichozoa, are treated as a subkingdom within Protozoa, as in my 1983 six-kingdom system, not as a separate kingdom. The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some 'rhizopods' and is therefore renamed Cercozoa. The number of protozoan phyla is reduced by grouping Mycetozoa and Archamoebae (both now infraphyla) as a new subphylum Conosa within the phylum Amoebozoa alongside the subphylum Lobosa, which now includes both the traditional aerobic lobosean amoebae and Multicilia. Haplosporidia and the (formerly microsporidian) metchnikovellids are now both placed within the phylum Sporozoa. These changes make a total of only 13 currently recognized protozoan phyla, which are grouped into two subkingdoms: Archezoa and Neozoa the latter is modified in circumscription by adding the Discicristata, a new infrakingdom comprising the phyla Percolozoa and Euglenozoa). These changes are discussed in relation to the principles of megasystematics, here defined as systematics that concentrates on the higher levels of classes, phyla, and kingdoms. These principles also make it desirable to rank Archaebacteria as an infrakingdom of the kingdom Bacteria, not as a separate kingdom. Archaebacteria are grouped with the infrakingdom Posibacteria to form a new subkingdom, Unibacteria, comprising all bacteria bounded by a single membrane. The bacterial subkingdom Negibacteria, with separate cytoplasmic and outer membranes, is subdivided into two infrakingdoms: Lipobacteria, which lack lipopolysaccharide and have only phospholipids in the outer membrane, and Glycobacteria, with lipopolysaccharides in the outer leaflet of the outer membrane and phospholipids in its inner leaflet. (ABSTRACT TRUNCATED)

ABSTRACTA revised six‐kingdom system of life is presented, down to the level of infraphylum. As in my 1983 system Bacteria are treated as a single kingdom, and eukaryotes are divided into only five kingdoms: Protozoa, Animalia, Fungi, Plantae and Chromista. Intermediate high level categories (superkingdom, subkingdom, branch, infrakingdom, superphylum, subphylum and infraphylum) are extensively used to avoid splitting organisms into an excessive number of kingdoms and phyla (60 only being recognized). The two ‘zoological’ kingdoms, Protozoa and Animalia, are subject to the International Code of Zoological Nomenclature, the kingdom Bacteria to the International Code of Bacteriological Nomenclature, and the three ‘botanical’ kingdoms (Plantae, Fungi, Ghromista) to the International Code of Botanical Nomenclature. Circumscriptions of the kingdoms Bacteria and Plantae remain unchanged since Cavalier‐Smith (1981). The kingdom Fungi is expanded by adding Microsporidia, because of protein sequence evidence that these amitochondrial intracellular parasites are related to conventional Fungi, not Protozoa. Fungi are subdivided into four phyla and 20 classes; fungal classification at the rank of subclass and above is comprehensively revised. The kingdoms Protozoa and Animalia are modified in the light of molecular phylogenetic evidence that Myxozoa are actually Animalia, not Protozoa, and that mesozoans are related to bilaterian animals. Animalia are divided into four subkingdoms: Radiata (phyla Porifera, Cnidaria, Placozoa, Ctenophora), Myxozoa, Mesozoa and Bilateria (bilateral animals: all other phyla). Several new higher level groupings are made in the animal kingdom including three new phyla: Acanthognatha (rotifers, acanthocephalans, gastrotrichs, gnathostomulids), Brachiozoa (brachiopods and phoronids) and Lobopoda (onychophorans and tardigrades), so only 23 animal phyla are recognized. Archezoa, here restricted to the phyla Metamonada and Trichozoa, are treated as a subkingdom within Protozoa, as in my 1983 six‐kingdom system, not as a separate kingdom. The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some ‘rhizopods’ and is therefore renamed Cercozoa. The number of protozoan phyla is reduced by grouping Mycetozoa and Archamoebae (both now infraphyla) as a new subphylum Conosa within the phylum Amoebozoa alongside the subphylum Lobosa, which now includes both the traditional aerobic lobosean amoebae andMulticilia. Haplosporidia and the (formerly microsporidian) metchnikovellids are now both placed within the phylum Sporozoa. These changes make a total of only 13 currently recognized protozoan phyla, which are grouped into two subkingdoms: Archezoa and Neozoa; the latter is modified in circumscription by adding the Discicristata, a new infrakingdom comprising the phyla Percolozoa and Euglenozoa). These changes are discussed in relation to the principles of megasystematics, here defined as systematics that concentrates on the higher levels of classes, phyla, and kingdoms. These principles also make it desirable to rank Archaebacteria as an infrakingdom of the kingdom Bacteria, not as a separate kingdom. Archaebacteria are grouped with the infrakingdom Posibacteria to form a new subkingdom, Unibacteria, comprising all bacteria bounded by a single membrane. The bacterial subkingdom Negibacteria, with separate cytoplasmic and outer membranes, is subdivided into two infrakingdoms: Lipobacteria, which lack lipopolysaccharide and have only phospholipids in the outer membrane, and Glycobacteria, with lipopolysaccharides in the outer leaflet of the outer membrane and phospholipids in its inner leaflet. This primary grouping of the 10 bacterial phyla into subkingdoms is based on the number of cell‐envelope membranes, whilst their subdivision into infrakingdoms emphasises their membrane chemistry; definition of the negibacterial phyla, five at least partly photosynthetic, relies chiefly on photosynthetic mechanism and cell‐envelope structure and chemistry corroborated by ribosomal RNA phylogeny. The kingdoms Protozoa and Chromista are slightly changed in circumscription by transferring subphylum Opalinata (classes Opalinea, Proteromonadea, Blastocystea cl. nov.) from Protozoa into infrakingdom Heterokonta of the kingdom Chromista. Opalinata are grouped with the subphylum Pseudofungi and the zooflagellateDevelopayella elegans(in a new subphylum Bigyromonada) to form a new botanical phylum (Bigyra) of heterotrophs with a double ciliary transitional helix, making it necessary to abandon the phylum name Opalozoa, which formerly included Opalinata. The loss of ciliary retronemes in Opalinata is attributed to their evolution of gut commensalism. The nature of the ancestral chromist is discussed in the light of recent phylogenetic evidence.

Virus taxonomy: one step forward, two steps back.

Additional modern and fossil genera of the Pyrrhophyta are catalogued, and an indication is given as to their validity under the International Code of Botanical Nomenclature or International Code of Zoological Nomenclature. Eighty-seven taxonomic entries are cited in addition to those in the original index and five supplements. A type species is selected for Pseudopyrocystis, a correction is made to the type species of Cystodinedria, comment is made concerning the relationship of Tuberculodinium and Trioperculodinium, and a new combination is made for the type species of Manchudinium. Sixty-two references are cited in the accompanying bibliography.

(219) The Editorial Committee is instructed to provide a glossary of technical terms in the ICBN: A glossary would facilitate interpretation of the Code by obviating the need to find the appropriate entry in the index and then find the definition in the text. More importantly, having the Editorial Committee focus on the definition of terms may help them guard against inconsistencies, redundancies, and ambiguities in the Code. For example, the word is used in at least three different ways. In available element (Art. 9.17; Art. 10.5) the word is used in ordinary sense referring to potential types, but available (Art. 11.5; Art. 58) is a technical term meaning an epithet that does not form a later homonym in its new position or rank. An available (Art. 6.4, Ex. 4; Art. 53.1, Ex. 2) is a name that is either initially legitimate name that has not been suppressed by conservation or sanctioning or initially illegitimate name that has been made legitimate by conservation or sanctioning. An unavailable (Art. 15.2) is a name that may not be used either because it is illegitimate or because it is suppressed by conservation or sanctioning. It would be useful to clarify these various usages and terms in a glossary. Ironically, the International Code of Botanical Nomenclature contains a definition of available as used in the International Code of Zoological Nomenclature (Art. 45, Ex. 4, fn.).

Additional modern and fossil genera of the Pyrrhophyta are catalogued, and an indication is given as to their validity under the International Code of Botanical Nomenclature or International Code of Zoological Nomenclature. Eighty-seven taxonomic entries are cited in addition to those in the original index and five supplements. A type species is selected for Pseudopyrocystis, a correction is made to the type species of Cystodinedria, comment is made concerning the relationship of Tuberculodinium and Trioperculodinium, and a new combination is made for the type species of Manchudinium. Sixty-two references are cited in the accompanying bibliography.

The PhyloCode: naming of biodiversity at a crossroads