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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DNA plus morphology speeds taxonomy

In May 2008 PLoS One researchers from California Academy of Sciences and University of Guelph analyze morphology and COI barcodes of Madagascar ants in genera Anochetus and Odontomachus.  Their taxonomic revision is “based on arthropod surveys in Madagascar that included over 6,000 leaf litter samples, 4,000 pitfall traps, and 8,000 additional collecting events…from 1992 to 1996”–phew!  Researchers Fisher and Smith used COI sequence data of 501 individuals to speed their analysis and provide an accessible reference for future work. 

First, COI barcodes enable associating the various caste forms including males and females within species. Second, DNA barcodes provide an additional tool for matching names with type specimens. For example, Meusnier et al have recently applied broad-range primers to amplify a 130 base pair “universal mini-barcode” (this lies within the 648 full-length COI barcode sequence). The mini-barcode can more easily be amplified from older museum material with partly degraded DNA, and usually contains enough sequence information to associate older specimens with more recently collected material. Third, distinct genetic clusters within morphologically undifferentiated ant species suggest avenues for future study. Fourth, DNA barcodes establish a method for future workers, not skilled in ant morphology, to identify specimens. For example, not many persons will be able to recognize males of Malagasy Anochetus by “shortest distance between lateral ocellus and margin of compound eye smaller than maximum length of ocellus. Petiolar node as seen from front or rear with lateral corners rounded, without acute spine or sharp tooth.” There are multiple high-resolution photos of each described species posted on AntWeb; I find these just as mysterious as the text descriptions.

As a test of how DNA barcoding might work for the interested ant novice, I collected the tiny specimen at left in Rincon, Puerto Rico, and submitted its COI barcode to BOLD ID engine. This gave 100% match to Paratrechina longicornis, and on the corresponding  Encyclopedia of Life page, I learned the common name is “Crazy ant”, an invasive species found worldwide, plus found many interesting links including to AntWeb P. longicornis pages. It was amusing to learn that Crazy ants overran Biosphere II and were one factor leading to demise of the project (link to NYT article). Of course not all 100+ Paratrechina spp are in BOLD, and there may be a closely-related species with similar or identical COI barcode sequences as P. longicordis, so more work is needed to build up the database!

This entry was posted on Sunday, September 14th, 2008 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.