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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Resolving leaves and branches?

COI barcoding is a standardized approach to identifying species by DNA, helping resolve the “leaves” on the tree of life.  Will the growing arrays of COI sequences also help provide insight into evolutionary history, the “branches” of the tree? I am struck that in some cases, simple genetic arithmetic with COI sequences creates trees very similar to modern phylogenies painstakingly created from multiple nuclear and mitochondrial genes, multiple morphologic characters, and exhaustive computerized analysis. Shown at right, a neighbor-joining analysis of COI barcodes of 264 species of North American birds creates a tree that is quite similar to the most recent understanding of relationships among modern birds, with anseriformes (ducks and geese) next to galliformes (grouse and quail) at the top, passeriformes (perching birds) at the bottom, and most of the other established orders appearing as single lineages in between. Most of the families and groupings of families within these orders also match current understanding, including for example, that flycatchers appear as the basal lineage within passeriformes, and a group of New World passerines called nine-primaried oscines appear together at the bottom of the tree. Of course, a systematist would immediately note that the statistical support for these higher-order branches is weak or absent. I should tread lightly here or not at all, since phylogenetics is the province of mathematical experts, but I will plunge ahead anyway and suggest that, if the single gene neighbor-joining distance tree is “right” say 8 times out of 10, then the apparent lack of statistical support for higher order branches is misleading. There are cases where the COI gene tree is incorrect (eg Hajibabaei et al Genome 49:851 2006).

I close with a picture inspired by the data. If single gene trees usually correspond to evolutionary history, this implies strong barriers to gene flow arise concurrent with differences in the single gene and are continuously maintained.

This entry was posted on Tuesday, April 17th, 2007 at 9:54 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.