Rockefeller University

Program for the Human Environment

The Barcode Blog

A mostly scientific blog about short DNA sequences for species identification and discovery. I encourage your commentary. -- Mark Stoeckle

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Names

In Systema Natura 250 (Andrew Polaszek, ed; CRC Press), a new collection of essays on the state of taxonomy, David Schindel and Scott Miller address how to speed up “naming” of specimens without causing chaos, in chapter entitled “Provisional nomenclature: The on-ramp to taxonomic names.” The authors observe the increasing numbers of undescribed and undescribable specimens (eg fragments, mixed environmental samples) and propose to standardize provisional names (preferred designation of these standardized hu7temporary placeholders is “taxon label”). As they note, there are many provisional names in GenBank (e.g. Ocyptamus sp. MZH S143_2004), so this is not a change in usual practice, except that the format of provisional names is standardized. As a starting point, Schindel and Miller propose a scheme developed by Council of the Heads of Australian Herbariums (CHAH) and recommend review by Biodiversity Information Standards (TDWG). The CHAH format is:

Genus_name sp. Locality (Voucher identifier) Source, where “(Voucher-specimen identifier) is a two-part field consisting of a collector’s name and the voucher specimen number attached to the exemplar of the taxon concept,” and “Source refers to the name of the concept’s proposer.”  Regarding sequence data as identifiers, such labels could be generated by a clustering algorithm for DNA barcodes for example. Schindel and Miller discuss short and long-term advantages to taxonomic workflow, academic credit, and scientific sharing.

A standardized format for provisional names is a simple, powerful proposal with many downstream benefits. I hope TDWG will adopt!

This entry was posted on Friday, January 22nd, 2010 at 11:56 pm and is filed under General. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

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Contact: mark.stoeckle@rockefeller.edu

About this site

This web site is an outgrowth of the Taxonomy, DNA, and Barcode of Life meeting held at Banbury Center, Cold Spring Harbor Laboratory, September 9-12, 2003. It is designed and managed by Mark Stoeckle, Perrin Meyer, and Jason Yung at the Program for the Human Environment (PHE) at The Rockefeller University.

About the Program for the Human Environment

The involvement of the Program for the Human Environment in DNA barcoding dates to Jesse Ausubel's attendance in February 2002 at a conference in Nova Scotia organized by the Canadian Center for Marine Biodiversity. At the conference, Paul Hebert presented for the first time his concept of large-scale DNA barcoding for species identification. Impressed by the potential for this technology to address difficult challenges in the Census of Marine Life, Jesse agreed with Paul on encouraging a conference to explore the contribution taxonomy and DNA could make to the Census as well as other large-scale terrestrial efforts. In his capacity as a Program Director of the Sloan Foundation, Jesse turned to the Banbury Conference Center of Cold Spring Harbor Laboratory, whose leader Jan Witkowski prepared a strong proposal to explore both the scientific reliability of barcoding and the processes that might bring it to broad application. Concurrently, PHE researcher Mark Stoeckle began to work with the Hebert lab on analytic studies of barcoding in birds. Our involvement in barcoding now takes 3 forms: assisting the organizational development of the Consortium for the Barcode of Life and the Barcode of Life Initiative; contributing to the scientific development of the field, especially by studies in birds, and contributing to public understanding of the science and technology of barcoding and its applications through improved visualization techniques and preparation of brochures and other broadly accessible means, including this website. While the Sloan Foundation continues to support CBOL through a grant to the Smithsonian Institution, it does not provide financial support for barcoding research itself or support to the PHE for its research in this field.