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 data point to need for better theories about species formation

Insiders can be mistaken, in science and in other fields. At the beginning of the Human Genome Project, “the great majority of scientists dismissed the original proposal with hostility or indifference” (Great 15-year project to decipher genes stirs opposition. New York Times, June 5, 1990). The Times article details some of the initial negative reactions:

“Even if scientists manage to finish the genome project, it will have generated enormous reams of uninterpretable and often useless data”.

“The human genome project is bad science, it’s unthought-out science, it’s hyped science” said Dr. Martin Rechsteiner, a biochemist at the University of Utah. Some critics have begun aggressive letter-writing campaigns, urging colleagues who harbor similar sentiments to write Congress.

“Everybody I talk to thinks this is an incredibly bad idea,” said Dr. Michael Syvanen, a microbiologist at the Medical School of the University of California at Davis and a stout antagonist of the genome project.

Professional societies weighed in as well. A resolution adopted by the Council of the American Society for Biochemistry and Molecular Biology, and endorsed by the Federation of American Societies for Experimental Biology stated: “A large scale, massive effort to ascertain the sequence of the entire genome cannot be adequately justified at the present time… The Council wants to state in the clearest possible terms our opposition to any current proposal that envisions the establishment of one or a few large centers that are designed to map and/or sequence the human genome.” https://www.fasebj.org/cgi/reprint/1/6/502 

This history comes to mind in reading the article by Hickerson, Meyer, and Moritz in October 2006 Syst Biol 55:729. According to their analysis, mathematical modelling predicts that DNA barcoding will often fail to discover young species. Their analysis is based on a classical model of speciation (Bateson-Dobzhansky-Muller) and “well-established population genetic theory”. I should tread lightly here, not being a population biologist! To my reading, these mathematical models are either unsupported or disproved by experimental evidence. The BDM model of biological species formation is “well-characterized, tractable, and its dynamics captures a range of speciation times implicit across many pre- and post-zygotic isolation models”, ie good for modelling, but is not derived from actual genetic data on differences between sister species. Genetic surveys including growing barcode libraries demonstrating limited intraspecific variation in diverse species across enormous differences in population size and generation time indicate that “well established population genetic theory” does not explain intraspecific mitochondrial diversity (Bazin et al 2006 Science 28:570).

Instead of making predictions about why barcoding will fail, I hope the same mathematic rigor will be applied to understanding why barcoding works as well as it does, why the variation within most species is low, why the distances between most species are large, and what determines the exceptions.

This entry was posted on Tuesday, November 7th, 2006 at 12:44 am 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.