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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New places to find DNA

In 29 july 2008 Fish Biology scientists from Macquarie University, Sydney describe successful recovery of mitochondrial DNA from contemporary and historical shark teeth and jaws. After developing the method on 11 recently collected teeth from Gray nurse shark Carcharias taurus and Ornate wobbegong (excellent name!) Orectolobus halei, Ahonen and Stowe applied it to 20-40 year old museum specimens, including 5 jaws from 3 species and 19 individual teeth from 2 species. They collected approximately 0.02-0.06 g of “tooth powder” by drilling several small holes into a tooth or jaw; DNA was extracted using a standard silica-based method or Qiagen DNAeasy tissue kit.

The authors are interested in historical population sizes for sharks; following the theory that genetic variation within species is an indicator of population size, they picked the hypervariable control region as their target. As an aside, results so far with mitochondrial surveys including DNA barcoding generally show very low variation within most animal species and no relationship between intraspecific variation and census population size. In any case, a 700 bp fragment of mtDNA control region was amplified with a single pair of primers. The two extraction methods gave similar results.  DNA was amplified and sequenced from 100% of the contemporary samples and 15/34 (44%) historical samples. 700 bp is a relatively long sequence to amplify from historical samples, suggesting it may be possible to obtain standard COI barcodes (648 bp) from museum skeletons of sharks and bony fish, which would be particularly useful for those species which are rare or otherwise difficult to collect. A standard set of fish primers (see for example Hubert et al June 2008 PLoS ONE) amplifies COI barcode region from most fish (more than 5,000 species so far, including including representatives of all major divisions of Chondrichthyes (cartilaginous fish) and Osteichthyes (bony fish), both marine and freshwater).

To date most fish specimens are preserved in formaldehyde, which makes routine DNA recovery difficult or impossible. If DNA can be recovered from skeletons, there are many museum specimens that might be used. For example, the American Museum of Natural History Icthyology Department collection includes over 35,000 fish skeletons as compared to about 2,500 tissue samples so far.

This entry was posted on Monday, October 6th, 2008 at 11:10 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.