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Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes.

ABSTRACT: The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (https://gtdb.ecogenomic.org). In the case of union of taxa, GTDB names were applied based on the priority of publication. The division of taxa or change in rank led to the formation of new Latin names above the rank of genus that were only made publicly available via the GTDB website without associated published taxonomic descriptions. This has sometimes led to confusion in the literature and databases. A number of the provisional GTDB names were later published in other studies, while many still lack authorships. To reduce further confusion, here we propose names and descriptions for 329 GTDB-defined prokaryotic taxa, 223 of which are suitable for validation under the International Code of Nomenclature of Prokaryotes (ICNP) and 49 under the Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode). For the latter, we designated 23 genomes as type material. An additional 57 taxa that do not currently satisfy the validation criteria of either code are proposed as Candidatus.

SUBMITTER: Chuvochina M

PROVIDER: S-EPMC10408702 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes.

Chuvochina Maria M Mussig Aaron J AJ Chaumeil Pierre-Alain PA Skarshewski Adam A Rinke Christian C Parks Donovan H DH Hugenholtz Philip P

FEMS microbiology letters 20230101

The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (https://gtdb.ecogenomic.org). In the case of union of taxa, GTDB names were applied based on the priority of publication. The division of taxa or change in rank led to the formation of new Latin names above the rank of genus that ...[more]

PMID: 37480240

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Project description:BackgroundWe use taxonomy to organize the world into recognizable units. Folk taxonomy deals with the naming and classification of organisms through culture. Unlike its scientific counterpart, folk taxonomy is mostly undocumented, the Zoological Code of Nomenclature does not regulate it, and the resulting names are specific to each culture. A growing body of literature is steadily shedding light on the principles underlying this pre-scientific taxonomy. Vernacular names can be an instrument to increase participation of non-scientists in biodiversity matters. In South Africa, great strides have been made in standardizing and increasing relatability of vernacular amphibian names in English and Afrikaans. However, there is a need to achieve the same with the country's autochthonous languages which are used by a majority of the population.MethodsThis study investigates amphibian-related folk taxonomy using a semi-structured interview process in KwaZulu-Natal's Zululand region and pilots methods of applying folk taxonomy principles to compile a comprehensive list of standardized indigenous frog names.ResultsFolk taxonomy in Zululand is systematic, developed, and bears similarities to other indigenous taxonomies around the world. Similarities also exist between folk and scientific taxonomy. Six uninomial indigenous names were found to be used for the 58 amphibian species occurring in the study area. The 58 species were assigned individual indigenous names using folk taxonomy guidelines supplemented with guidelines for modern taxonomies.ConclusionsThere is a gap in the documentation and investigation of amphibian folk taxonomy in South Africa. Standardization of indigenous frog names is required to increase their universality. Similarities between folk and modern taxonomies allow for supplementation of indigenous guidelines when compiling a comprehensive indigenous species list. Through this study, social inclusion in wildlife matters is increased, indigenous knowledge systems are promoted, and a contribution is made to the development of an indigenous South African language.

Dataset Information

Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes.

Publications

Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes.

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