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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mtDNA recovery from old bones hints at DNA durability, ubiquity

In another seeming step towards Jurassic Park, two groups of researchers recovered full-length mitochondrial DNA sequences from 22,000 to 44,000 year-old bones of extinct European and North American bears. Full-length mtDNA has been recovered from similarly ancient specimens, but in those cases frozen tissues preserved in permafrost were used. Both groups used specialized PCR protocols employing several hundred primer pairs designed to recover short fragments, rather than one of the newer sequencing technologies, demonstrating the continued power of DNA amplification.

In 28 july 2008 BMC Evol Biol Proc a group of 18 researchers led by Johannes Krause, Max Planck Institute, Germany, recovered full-length mtDNA from a 44,000 year old Ursus spelaeus (European cave bear) bone found in an Austrian cave, and from a 22,000 year-old skull of Arcdotus simus (American giant short-faced bear) from Eldorado Creek, Canada. In 11 november 2008 Proc Natl Acad Sci USA, 14 researchers led by Jean-Marc Elalouf, Institute de Biologie et Technologies de Saclay, France, report full-length U. spelaeus mitochondrial genome from a 32,000 year-old bone from the legendary Chauvet-Pont d’Arc Cave, home to the oldest rock art pictures ever found.  

If we found a bone from one of these extinct bears in our backyard, could it be identified by its COI barcode? Submitting the long-ago bears’ COI barcode region sequences (positions 48 to 705) to BOLD ID engine flags both species as not in database, with a NJ tree similar to that created by full-length genomes (ie the extinct U. spelaeus is sister to U. arctos (Brown bear) and U. maritimus (Polar bear), and extinct Arcdotus simus is sister to Tremarctos ornatus (Spectacled bear). Of course it would be difficult to recover a full-length sequence–what about the 130 base pair “mini barcode” proposed for broad-scale biodiversity analysis? This is within the size range(ie < 180 bp) that Elalouf and colleagues report best for recovery of ancient DNA. Remarkably, A. simus mini-barcode submitted to BOLD ID engine gives NJ tree correctly showing T. ornatus as its sister species and U. spelaeus mini-barcode correctly picks out U. arctos and U. maritimus as most closely-related species.

Recovering DNA from ancient bones leads to CSI-like thoughts of where else we might usefully recover DNA for species identification. DNA has been recovered from naturally shed feathers, flakes of seal skin at breathing holes in polar ice, hair and saliva left by predators of sheep, bird faeces, and, turning to world of commerce, ancient and modern processed leather goods (Long 2007). I look forward to analyses of the many processed foods with what is currently an unverifiable “list of ingredients.”

This entry was posted on Tuesday, December 23rd, 2008 at 12:39 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.