| Literature DB >> 24223486 |
Prosanta Chakrabarty1, Melanie Warren, Lawrence M Page, Carole C Baldwin.
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.Entities:
Keywords: GenBank; genetics; molecular phylogenetics; systematics; taxonomy
Year: 2013 PMID: 24223486 PMCID: PMC3821064 DOI: 10.3897/zookeys.346.5753
Source DB: PubMed Journal: Zookeys ISSN: 1313-2970 Impact factor: 1.546
Ranking Sequence Reliability. Ranking of source materials of genetic sequences based on reliability of taxonomic identification. Examples of the source material are listed in the third column with the last column providing the corresponding GenSeq nomenclature.
| Reliability Ranking | Source Materials | Examples | Corresponding GenSeq Nomenclature |
|---|---|---|---|
| Highest 1ST | Primary Types | Holotype, Lectotype, Syntype, Isosyntype, Neotype, Isotype | genseq-1 |
| 2nd | Secondary Types | Paratype, Paralectotypes, etc. | genseq-2 |
| 3rd | Topotypes (vouchered), or non-type specimens listed in original description or redescription | Topotype, Non-type specimen listed in original description or redescription | genseq-3 |
| 4th | Collections-vouchered non-types (not from original description or redescription) | Vouchered specimen | genseq-4 |
| 5th | Photo voucher only | No specimen voucher but photo voucher available | genseq-5 |
| Lowest | No voucher | Non-vouchered | No classification |
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.
Example Reporting Table. Examples of how links between genetic sequences and vouchers in institutional collections could be displayed as a table in publications reporting new sequences.
| Species | Specimen Catalog # | GenBank # | GenSeq Nomenclature | |
|---|---|---|---|---|
| COI | ND1 | |||
| LSUMZ 13636 (a holotype) | genseq-1 COI, ND1 | |||
| AMNH 229558 (a paratype) | NA | genseq-2 COI | ||
| UMMZ 236321 (a topotype) | genseq-3 COI, ND1 | |||
| FMNH 96353 (a non-type specimen voucher) | genseq-4 COI, ND1 | |||
| NMNH 12345PV2 (a photo voucher) | NA | genseq-5 ND1 | ||
Results of Search for Sequences from Types. GenSeq nomenclature applied to DNA sequences of fishes described from 2010–2011. The data were mined from GenBank and Google Scholar. Institutional abbreviations follow Sabaj-Perez (2012) except GSDNA which is the Natural History Gallery of Casalina. ◆ indicates that the catalog number of the voucher was reported with the genetic sequences in the published original description. ○ indicates that the catalog number of the voucher was recorded in GenBank with the sequences. Lack of either symbol indicates that the authors were e-mailed to find the link between a voucher and a sequence.
| Species (Group) | Citation | Type of type | Voucher catalog | GenBank # | GenSeq |
|---|---|---|---|---|---|
| Holotype | AMNH 251650 | genseq-1 COI | |||
| Paratypes | 16 examples | 16 examples | genseq-2 COI | ||
| Holotype | USNM 398105 | genseq-1 COI | |||
| Paratypes | AMNH 251648 | genseq-2 COI | |||
| USNM 398102 | |||||
| USNM 398103 | |||||
| USNM 398106 | |||||
| USNM 398107 | |||||
| USNM 398109 | |||||
| USNM 398112 | |||||
| Paratypes | MNHN 2007-1557 | genseq-2 COI | |||
| MNHN:2007-1555 | |||||
| MNHN:2007-1567 | |||||
| MNHN:2007-1579 | |||||
| Holotype | ZFMK 41613 | genseq-1 16S | |||
| Paratypes | UFRJ 6782.1 | genseq-2 CytB | |||
| UFRJ 6782.2 | |||||
| UFRJ 6782.3 | |||||
| UFRJ 6782.4 | |||||
| Holotype | CU 95318 | genseq-1 CytB | |||
| Paratypes | CU 93218.1 | genseq-2 CytB | |||
| CU 93218.2 | |||||
| CU 93218.3 | |||||
| CU 93218.4 | |||||
| CU 93219 | |||||
| Holotype | USNM 398932 | genseq-1 COI | |||
| Paratypes | USNM 398939 | genseq-2 COI | |||
| USNM 398933 | |||||
| USNM 398936 | |||||
| USNM 398934 | |||||
| USNM 398935 | |||||
| USNM 398938 | |||||
| USNM 398940 | |||||
| Paratypes | USNM 399658 | genseq-2 COI | |||
| USNM 399659 | |||||
| Paratypes | USNM 399649 | genseq-2 COI | |||
| USNM 399653 | |||||
| USNM 399652 | |||||
| USNM 399651 | |||||
| USNM 399656 | |||||
| USNM 399655 | |||||
| Paratypes | USNM 397396 | genseq-2 COI | |||
| Paratypes | USNM 399909 | genseq-2 COI | |||
| USNM 399911 | |||||
| Paratypes, Topotypes | USNM 398922 | genseq-2 COI, genseq-3 COI | |||
| USNM 398921 | |||||
| USNM 398920 | |||||
| Holotype | GSDNA1 | genseq-1 COI, CytB | |||
| Paratype | LSUMZ 13637 | genseq-2 ND2, CytB, COI | |||
| Holotype | ZMUB 19686 | genseq-1 mitogenome | |||
| Paratype | ZUEC 6349 | genseq-2 16S, 12S | |||
| Paratype | CIUFES 0317 | genseq-2 CytB | |||
| CIUFES 1279 | |||||
| CIUFES 1474 | |||||
| CIUFES 1475 | |||||
| USNM 397005 | |||||
| Paratype | NRM 57780 | genseq-2 CytB, rhodopsin | |||
| Paratype | MACN-ict 9430.1 | genseq-2 trnQ, trnM, ND2, trnW, trnA | |||
| MACN-ict 9430.2 |