scholarly journals Roadmap for naming uncultivated Archaea and Bacteria

2020 ◽  
Vol 5 (8) ◽  
pp. 987-994 ◽  
Author(s):  
Alison E. Murray ◽  
John Freudenstein ◽  
Simonetta Gribaldo ◽  
Roland Hatzenpichler ◽  
Philip Hugenholtz ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Dna Sequences ◽  
Scientific Community ◽  
Consensus Statement ◽  
The Other ◽  
Type Material ◽  
International Code ◽  
Code Of Nomenclature ◽  
The Future ◽  
International Code Of Nomenclature

AbstractThe assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

scholarly journals International Mycological Congress: Guiding Vote on nomenclature proposals to amend Chapter F of the International Code of Nomenclature for algae, fungi, and plants

IMA Fungus ◽  
2018 ◽  
Vol 9 (2) ◽  
pp. xv-xxi ◽  
Author(s):  
Tom W. May ◽  
Andrew N. Miller
Keyword(s):  
Dna Sequences ◽  
International Code ◽  
Code Of Nomenclature ◽  
International Mycological Congress ◽  
International Code Of Nomenclature

Abstract Results are provided for the Guiding Vote on the seven formal proposals to amend the International Code of Nomenclature for algae, fungi, and plants to be decided by the Fungal Nomenclature Session (FNS) of the XI International Mycological Congress in July 2018. Te ballot for the Guiding Vote was provided online. Tere were 520 valid ballots, submitted by mycologists from 42 countries, belonging to 23 eligible groups and societies, along with authors of proposals. Tw o proposals F-005 and F-006, both concerning DNA sequences as types, exceeded the 75 % No vote that is the threshold above which proposals are considered rejected by the FNS unless formally re-introduced. Two options for amendments to future procedures for the Guiding Vote are proposed: adding eligibility via publication of a nomenclatural novelty among fungi and removing eligibility via membership of IMA MMOs.

Remarks and clarifications on the type material of Ximenesia encelioides (Verbesina encelioides; Asteraceae, Heliantheae), with a new lectotype designation

Phytotaxa ◽  
2016 ◽  
Vol 253 (2) ◽  
pp. 161
Author(s):  
MANUEL B. CRESPO ◽  
Mª ÁNGELES ALONSO
Keyword(s):  
Type Material ◽  
International Code ◽  
Code Of Nomenclature ◽  
Herbarium Sheet ◽  
Verbesina Encelioides ◽  
International Code Of Nomenclature

In a recent paper, the name Ximenesia encelioides was lectotypified on material conserved at MA. However, the selected “lectotype” includes several fragments collected at three different times, and that herbarium sheet is therefore to be considered to contain three different specimens as defined in Art. 8.2 of the International Code of Nomenclature of algae, fungi and plants. This fact makes that “lectotype” invalid since contrary to Art. 8.1, and hence the previous lectotypification is to be disregarded. Accordingly, a new lectotype is designated for that name, currently accepted as Verbesina encelioides.

scholarly journals Nomenclatural notes on the name Asarum longerhizomatosum (Aristolochiaceae)

Phytotaxa ◽  
2014 ◽  
Vol 172 (1) ◽  
pp. 57
Author(s):  
Yunfei Deng ◽  
Wenbin Yu
Keyword(s):  
Traditional Medicine ◽  
Type Material ◽  
Chinese Traditional Medicine ◽  
International Code ◽  
Code Of Nomenclature ◽  
International Code Of Nomenclature

Asarum longerhizomatosum C.F. Liang & C.S. Yang (Aristolochiaceae) in Liang (1975: 21) was originally described from Guangxi, China. It was widely adopted in Chinese floras (Liang 1991; Cheng & Yang 1988; Yang & Zhou 2000; Huang et al. 2003; Yang & Yang 2006). However, the name was not validly published in 1975 because two gatherings (C.L. Zhang 001 in CMMI and C.L. Zhang 002 in IBK) were designated as types contrary to the requirements of Article 40.1 & 40.2 of International Code of Nomenclature for Algae, Fungi and Plants (McNeil et al. 2012) for the names published on or after 1 January 1958. Huang et al. (2003) presumed the two elements represented duplicates of a single collection and treated the name as validly published. However,searching for type material in herbaria showed that C.L. Zhang 001 and C.L. Zhang 002 were two different gatherings. Three duplicates of C.L. Zhang 002 are found at IBK. Although no duplicate of C.L. Zhang 001 was traced by us, the previous literatures indicated that at least two duplicates exist, one in CMMI (Liang 1975) and another in PTM (Cheng & Yang 1983). It is noted that “PTM” was the acronym of “Beijing Chinese Traditional Medicine College” whose acronym is BCMM now in Index Herbariorum Sinicorum (Fu et al. 1993) and Index Herbariorum (Thiers, [continousely unpdated]).

scholarly journals Rectification of invalidly published new names for plants from the late Eocene of North Bohemia

2015 ◽  
Vol 55 (2) ◽  
pp. 209-212
Author(s):  
Zlatko Kvaček
Keyword(s):  
Relevant Information ◽  
Late Eocene ◽  
Type Material ◽  
International Code ◽  
Fossil Plant ◽  
International Botanical ◽  
International Botanical Congress ◽  
Code Of Nomenclature ◽  
English Translations ◽  
International Code Of Nomenclature

Abstract Valid publication of new names of fossil plant taxa published since 1 January 1996 requires a diagnosis or description in English, besides other requirements included in the International Code of Nomenclature for algae, fungi, and plants (Melbourne Code) adopted by the Eighteenth International Botanical Congress, Melbourne, Australia, July 2011 (McNeill et al. 2012). In order to validate names published from the late Eocene flora of the Staré Sedlo Formation, North Bohemia, diagnosed only in German (Knobloch et al. 1996), English translations are provided, including references to the type material and further relevant information.

scholarly journals Begonia intermedia, an illegitimate name and taxonomic synonym of B. wuzhishanensis

Phytotaxa ◽  
2014 ◽  
Vol 172 (1) ◽  
pp. 59
Author(s):  
DAIKE TIAN
Keyword(s):  
Hainan Island ◽  
Type Material ◽  
International Code ◽  
Wild Populations ◽  
Code Of Nomenclature ◽  
International Code Of Nomenclature

It came to our attention that Begonia ×intermedia Veitch ex van Houtte (1873: 39) was published in Flore des Serres and therefore, B. intermedia D.K. Tian et al. (2014: 116) is a later homonym and not legitimate according to the International code of nomenclature for algae, fungi and plants (McNeill et al. 2012: Art. 53). Furthermore, the article by Tian et al. was published on 24 Apr 2014 in Phytotaxa while B. wuzhishanensis C.I. Peng et al. (2014: 3) was published on 5 Feb 2014 in Botanical Studies for the same species based on type material collected from different locations on Hainan Island of China. In total, extant wild populations of this species have been found in at least the three places belonging to one city (Wuzhishan) and two counties (Qiongzhong and Lingshui), respectively (Fig 1).

scholarly journals Emendation of circumscriptions of taxa in the Lists of Changes in Taxonomic Opinion

2020 ◽  
Vol 70 (4) ◽  
pp. 2163-2164
Author(s):  
Aharon Oren ◽  
George M. Garrity
Keyword(s):  
International Code ◽  
Diagnostic Characters ◽  
The Past ◽  
Higher Taxa ◽  
Code Of Nomenclature ◽  
The Future ◽  
Evolutionary Microbiology ◽  
International Code Of Nomenclature

In the past 3 years, a large number of emendations of circumscriptions of species, subspecies and higher taxa were published outside the International Journal of Systematic and Evolutionary Microbiology (IJSEM) that only marginally modify the earlier circumscription and may not meet the requirements of Rule 35 of the International Code of Nomenclature of Prokaryotes. Thus far, these emendations were included in the Lists of Changes in Taxonomic Opinion in the IJSEM. The list editors propose to list in the future only meaningful emendations that in their opinion significantly modify the diagnostic characters or the circumscription of taxa.

Typifications and nomenclatural notes in Passiflora section Dysosmia (Passifloraceae)

Phytotaxa ◽  
2016 ◽  
Vol 288 (2) ◽  
pp. 101 ◽  
Author(s):  
HARLAN T. SVOBODA ◽  
JOHN M. MACDOUGAL ◽  
HARVEY E. BALLARD, JR.
Keyword(s):  
Type Material ◽  
International Code ◽  
Code Of Nomenclature ◽  
Orthographic Errors ◽  
Author Citations ◽  
International Code Of Nomenclature

Names within Passiflora section Dysosmia (Passifloraceae) were evaluated for proper typification and nomenclatural clarity. Because several names lacked type material, 13 lectotypes, two neotypes, and four epitypes are here designated to maintain nomenclatural stability. Many more names suffered from other nomenclatural discrepancies and thus four orthographic errors, six author citations, and 12 type designations are here corrected to comply with the International Code of Nomenclature (ICN). Seven names in Dysosmia are treated as ambiguous and 12 names are identified as either invalid or illegitimate.

scholarly journals Lists of names of prokaryotic Candidatus taxa

2020 ◽  
Vol 70 (7) ◽  
pp. 3956-4042 ◽  
Author(s):  
Aharon Oren ◽  
George M. Garrity ◽  
Charles T. Parker ◽  
Maria Chuvochina ◽  
Martha E. Trujillo
Keyword(s):  
International Committee ◽  
Type Material ◽  
International Code ◽  
Gene Sequences ◽  
Code Of Nomenclature ◽  
Evolutionary Microbiology ◽  
International Code Of Nomenclature

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

scholarly journals XI International Mycological Congress: report of Congress action on nomenclature proposals relating to fungi

IMA Fungus ◽  
2018 ◽  
Vol 9 (2) ◽  
pp. xxii-xxvii ◽  
Author(s):  
Tom W. May ◽  
Scott A. Redhead ◽  
Lorenzo Lombard ◽  
Amy Y. Rossman
Keyword(s):  
Dna Sequences ◽  
Plenary Session ◽  
International Code ◽  
Division Iii ◽  
Editorial Committee ◽  
Nomenclature Committee ◽  
Code Of Nomenclature ◽  
Congress Report ◽  
International Mycological Congress ◽  
International Code Of Nomenclature

Abstract Procedures, appointments and outcomes of the Fungal Nomenclature Session (FNS) of the 11th International Mycological Congress (IMC11) are summarized, including the composition of the Fungal Nomenclature Bureau and the Nominating Committee of the IMC. Nearly 150 mycologists attended the FNS, at which formal proposals to amend Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICN) were debated. The 18 proposals considered included 10 “from the floor”. Four proposals were withdrawn, two were sent to the Editorial Committee, five were sent to two Special-purpose Committees, four were rejected, and three were accepted (concerning: using the identifier in place of the author citation; mis-citation of identifiers; and indication of sanctioning). Proposals to amend Division III of the ICN were deemed out of scope of the FNS because they did not relate to Chapter F. The two Special-purpose Committees authorized were: “DNA Sequences as Types for Fungi” and “Names of Fungi with the Same Epithet”. Appointments made by the FNS included the Secretary of the Fungal Nomenclature Bureau for IMC12, and officers and members of the Permanent Nomenclature Committee for Fungi. Decisions and appointments of the FNS were ratified in a resolution accepted by the plenary session of the Congress.

scholarly journals Cyanobacterial systematics and nomenclature as featured in the International Bulletin of Bacteriological Nomenclature and Taxonomy / International Journal of Systematic Bacteriology / International Journal of Systematic and Evolutionary Microbiology

2011 ◽  
Vol 61 (1) ◽  
pp. 10-15 ◽  
Author(s):  
Aharon Oren
Keyword(s):  
New Taxa ◽  
Botanical Nomenclature ◽  
International Code ◽  
Systematic Bacteriology ◽  
Code Of Nomenclature ◽  
The Future ◽  
Evolutionary Microbiology ◽  
International Code Of Nomenclature ◽  
Highly Cited

Surprisingly few papers on cyanobacteria have been published in the International Bulletin of Bacteriological Nomenclature and Taxonomy / International Journal of Systematic Bacteriology / International Journal of Systematic and Evolutionary Microbiology (IBBNT/IJSB/IJSEM) during its 60 years of existence. The first papers featuring the group appeared in volume 28 and, in the 32 years that have passed since, 42 articles on cyanobacteria have been published in the journal. Very few of these papers deal with the description of new taxa and this is understandable in view of the current difficulty in validly publishing new names of cyanobacteria under the rules of the International Code of Nomenclature of Prokaryotes (ICNP). Other papers discuss the problems of the nomenclature of the group under the International Code of Botanical Nomenclature (ICBN)/ICNP and the ICBN. The largest group of articles on cyanobacteria consists of papers on systematics, in which isolates are compared using different approaches, without any implications for the nomenclature of the group under either Code. The fact that on average these papers have been highly cited shows that IJSEM and its predecessors have been an excellent framework for publications on cyanobacteria and should remain so in the future.

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