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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Beginning to build a neotropical bird species index with DNA barcodes

Photo by Arthur Grosset: Planalto Slaty-Antshrike Thamnophilus pelzelniDNA barcodes index species. In most animal species studied so far, mtDNA differences within species are much smaller than those between species. As a result, species appear as distinct clusters in a simple neighbor-joining tree of COI barcodes. The uniformity of this patterning gives confidence that a DNA barcode library based on relatively few individuals per species will be a reliable index for assigning unknown specimens to known species.  Although we are just at the beginning of compiling barcodes, and although we need phylogenetically-informed mathematical analysis about how to define clusters particularly in groups not well-studied, I am struck by how obvious most species clusters are. There are of course exceptions and limits (hybridization, young species, slow mitochondrial DNA evolution) but it is likely that someone with no knowledge other than a neighbor-joining tree of DNA barcodes could reconstruct most species categories, although they wouldn’t know anything about the biology of the organisms. This suggests viewing DNA barcoding as a diagnostic tool that links to biological knowledge, just as a laboratory test is used to detect HIV for example, and thereby point to a large body of biological knowledge. 

                                                                                           There are more bird species in the Neotropics than anywhere else. Over 4,000 of the approximately 10,000 world bird species live in South and Central America and the Caribbean, including over 3000 endemics. The large number of speciose families and the fact that intraspecific genetic variation is generally thought to be greater in the tropics than in temperate regions (eg Balakrishnan 2005 Syst Biol 54:689) might challenge DNA barcoding. In what I believe is the first explicit application of DNA barcoding to Neotropical birds (Vilaca 2006 Revista Brasileira Ornitologia 14:7) researchers analyzed 16 species of antbirds in the Atlantic Forest region of southeastern Brazil, with half of specimens obtained as blood samples from birds in the field. All species form distinct clusters in a neighbor-joining tree with 99% bootstrap support, including the recently split pair Thamnophilus pelzelni (shown above) and T. ambiguus. Maximum intraspecific variation is less than 1% except in T. caerulescens which shows 2 distinct lineages, highlighting a good candidate for further study. 

 

 

 

This entry was posted on Saturday, June 24th, 2006 at 11:18 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.