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. 2013 Nov 1:(346):29-41.
doi: 10.3897/zookeys.346.5753. eCollection 2013.

GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources

Prosanta Chakrabarty  1 , Melanie Warren, Lawrence M Page, Carole C Baldwin
Affiliations

GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources

Prosanta Chakrabarty et al. Zookeys. .

Abstract

An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the "Genetypes" naming system, which some have been reluctant to adopt because of the use of the "type" suffix in the terminology. In the new nomenclature, genetic sequences are labeled "genseq," followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an indication of the likely reliability of taxonomic identification of the voucher. Included in this ranking system, in descending order of taxonomic reliability, are the following: sequences from primary types - "genseq-1," secondary types - "genseq-2," collection-vouchered topotypes - "genseq-3," collection-vouchered non-types - "genseq-4," and non-types that lack specimen vouchers but have photo vouchers - "genseq-5." To demonstrate use of the new nomenclature, we review recently published new-species descriptions in the ichthyological literature that include DNA data and apply the GenSeq nomenclature to sequences referenced in those publications. We encourage authors to adopt the GenSeq nomenclature (note capital "G" and "S" when referring to the nomenclatural program) to provide a searchable tag (e.g., "genseq"; note lowercase "g" and "s" when referring to sequences) for genetic sequences from types and other vouchered specimens. Use of the new nomenclature and ranking system will improve integration of molecular phylogenetics and biological taxonomy and enhance the ability of researchers to assess the reliability of sequence data. We further encourage authors to update sequence information on databases such as GenBank whenever nomenclatural changes are made.

Keywords: GenBank; genetics; molecular phylogenetics; systematics; taxonomy.

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Figures

Figure 1.
Figure 1.
Example of how the GenSeq ranking system of sequences from various sources (Table 1) can be used to assess the trustworthiness of data used to reconstruct phylogenetic relationships. The rankings (the # in the “genseq-#”) make it clear that the relationship recovered between Species 3 and Species 4, from primary and secondary types, should be trustworthy because the taxonomic identifications of the voucher specimens are considered to be highly reliable. In contrast, the recovered sister relationship between Species 1 and Species 2 may be less trustworthy because of the weak reliability rankings of these sequences from non-types. Species 1 lacks both a specimen or photo voucher and therefore does not have a GenSeq ranking.
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