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

Subscribe to this blog

Sign up for email notifications

«
»

Embedding standardized DNA analysis in taxonomic practice

In 17 September 2007 Zootaxa (open access full article) researchers from Museo Nacional de Ciencias Naturales-CSIC, Madrid, make a plea for routinely incorporating standardized DNA sequence analysis, ie DNA barcoding, into modern taxonomic practice. In their view, “integrative taxonomists should use and produce DNA barcodes.” Of course, this is already happening in many areas, but new practices diffuse slowly through the fragmented world of taxonomy, and so Padial and de la Riva’s exhortation is an important step. With growing DNA barcode libraries and increasingly inexpensive sequencing technologies, DNA testing will likely be the fastest way to sort specimens into species and will enable identification of multiple forms that now go unnamed or misidentified while waiting for an expert, waiting for eggs and larva to mature, or waiting to find an identifiable adult male or a recognizable fragment in stomach contents.

One might view taxonomic science as an effort to construct detailed, reliable “maps” of species and their historical relationships. Adopting Padial’s and de la Riva’s advice to routinely “use and produce DNA barcodes” will speed taxonomic research and, more importantly, will naturally produce a “map of species” with general scientific and public utility. Few persons can have the requisite knowledge to distinguish larval fish for example, whereas anyone can submit a sample for DNA sequence analysis. In this way, a DNA barcode library is a map of species, one that anyone can read with the right device, a DNA sequencer. Of course, more work is needed to identify the best approaches for assigning sequences to named species and for flagging divergent sequence clusters that might represent new species. With improved analytic software and as more species and specimens per species are analyzed, the reliability of DNA barcode maps will increase. Based on results so far, I expect rapid growth in mail-order identification services, analogous to today’s DNA ancestry companies, that do DNA barcode analysis of submitted specimens, and, as others have envisioned, soon enough there will be table-top or hand-held devices that pinpoint where the specimen in hand belongs on the biodiversity map. Best wishes to all this holiday season!

This entry was posted on Friday, December 21st, 2007 at 11:14 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.

2 Responses to “Embedding standardized DNA analysis in taxonomic practice”

  1. Scott Says:
    December 22nd, 2007 at 3:09 pm

    “Adopting Padial’s and de la Riva’s advice to routinely “use and produce DNA barcodes” will speed taxonomic research and, more importantly, will naturally produce a “map of species” with general scientific and public utility.”

    Very good point and a concept which should be taken on board throughout the Taxonomic industry. Lets just hope there’s no infrastructure issues on the introduction of this kind of large-scale communication concept with DNA barcodes. Hopefully some of Padial’s advice and guidance will be taken into account.

  2. Max Seo Says:
    January 5th, 2008 at 1:47 pm

    Another point which should noted is that Fossils and Prehistoric remains would also be classified through this means.

    Mark Stoeckle replies: DNA can be recovered from some ancient samples (see for example Lambert et al 2005 “Is a large-scale inventory of ancient life possible? ( http://jhered.oxfordjournals.org/cgi/content/abstract/esi035v1 ) although not from fossils.

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.