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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Counting angels with DNA: update

“It is impossible to describe biological diversity with traditional approaches. Molecular methods are the way forward–especially, perhaps in the form of DNA barcodes” observed Mark Blaxter in a 2003 Nature commentary, “Counting angels with DNA“, on the first paper proposing “DNA barcodes” as a standardized method for identifying species.

Five years on, how do things look? I believe the scientific and practical value of molecular (ie DNA-based) identification of species is established. Of course visual methods will often be the method of choice to identify specimens in the lab and in the field, but the standardized genetic libraries (aka DNA barcode databases) linked to specimens stored in museums are an increasingly valuable reference for assigning specimens to known species and as a means of species discovery (for more, see www.barcoding.si.edu; www.barcodinglife.org).

In addition to helping identify what is already known, DNA analysis can reveal what would otherwise remain hidden. In 16 May 2008 Science, researchers from Cornell College, Smithsonian Institution, US Department of Agriculture, University of Maryland, and Ithaca College use DNA to reveal hidden diversity in Blepharoneura, a neotropical genus of tephritid fruit flies that feeds within the flowers or fruits of plants in the cucumber family (Cucurbitaceae). To skip to the conclusion, mtCOI sequencing of 2857 flies reared from 24 cucurbit host species collected in six locations in Central and South America revealed 52 morphologically similar species (most were entirely indistinguishable) with “highly conserved patterns of specificity to host taxa and host parts.” Nuclear genes showed the same pattern of genetic clustering as mitochondrial COI.   

This report highlights an exciting scientific challenge raised by genetic surveys of biodiversity, including DNA barcoding: there are far more species, each with biologically specialized traits, than anyone has recognized. Condon et al report “diversity exceeding the original morphologic estimates by an order of magnitude” but conclude this must be an underestimate because of limited sampling (usually along single transects in one season at 6 sites in 5 countries), considering the vast expanse of neotropical forests in Central and South America. Also they used a conservative 4% mtCOI divergence as a cutoff (if 1% cutoff were used, an additional 10 species would be recognized, and several generalist species would be split into narrowly specialized ones).

In closing, I wish the authors had sequenced the barcode region of COI (they analyzed a 693 bp fragment from the 3′ end of the gene which does not overlap with the 5′ DNA barcode region). It would be interesting for example to compile these results with data from the tephritid fly initiative, which aims to collect DNA barcodes from the 4500 known tephritid species. Perhaps these valuable Blepharoneura DNA samples can be reanalyzed for barcode region COI.

This entry was posted on Wednesday, May 28th, 2008 at 9:02 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.