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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DNA barcodes suggest fractal nature of genome

Growing data sets demonstrate DNA barcoding usually works, but why? Why does a very short stretch of DNA, such as a DNA barcode which usually represents less than one one-millionth of the genome, enable identification of most animal species? In computer language, Rod Page describes a DNA barcode as “embedded metadata“. Here I suggest an analogy to fractals, which might help convey what DNA barcodes reveal about how genomes are constructed.

DNA barcoding usually works because patterns seen in very short DNA sequences usually reflect patterns seen in longer sequences. In this way, DNA barcodes demonstrate “self-similarity”, a fundamental property of fractals. In March 28, 2007 PLoS One, researchers from Concordia University, Quebec, analyze 849 complete animal mitochondrial genomes, comparing GC composition in 648 bp COI barcode region to GC composition in the mitochondrial genome as a whole. Min and Hickey found “such short sequences can yield important, and surprisingly accurate, information about the [mitochondrial] genome as a whole. In other words, for unsequenced genomes, the DNA barcodes can provide a quick preview of the whole genome.” It will be of great interest to extend this analysis to compare mitochondrial barcodes to nuclear genomes; the general success of barcoding approach suggests there will be similarly close correlation.

Overall, the patterning of barcode differences supports the emerging view that selective sweeps prune mitochondrial diversity within species and mitochondrial and nuclear co-evolution are tightly linked.





This entry was posted on Saturday, May 26th, 2007 at 10:07 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.

3 Responses to “DNA barcodes suggest fractal nature of genome”

  1. Brian Says:

    Interesting – I was not aware that small sections of DNA exhibit self-similarity. Yet another area to apply quantum methods to…

  2. Richard Zander Says:

    I’m not sure this applies. Note that the fractal nature of a part of a fractal image can de determined by examination of both the smaller details and the larger details. This is not the case with barcodes, where the smaller details of the sequence do not reflect exactly the organization of the whole genome. It is like saying that tossing a coin a few times is representative of many tosses. One cannot predict the long frequency data from a particular coin from only a few tosses. One needs sufficient data to do a chi-square test. Same with barcode data.

  3. Dr. Andras J. Pellionisz Says:

    Here comes FractoGene ( – with the collapse of both “Genes” thesis and “JunkDNA” antithesis (with “genes” appearing obviously fragmented and the “Junk” proving to be anything, but), fractal properties (such as “barcode”) are found both in the DNA and are visible e.g. in the arborization of the fern.

    Another isntance of “self-similarity” is represented by the onion – though some species of onions have enormously greater amount of formerly “Junk” DNA than others.

    Very loose and mostly peri-scientific blogs, such as Panda’s thumb are on record now to measure our understanding of the function of the whole genome by the ability to “pass the onion test”, best formulated by Ryan Gregory (essentially the same as Richard Dawkins’ “Salamander paradox”; that different sub-species of Salamandra have a great diversity in their size of “junk DNA”).

    Thus far, FractoGene came forward with an explanation – awaiting other theoretical accounts …


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.