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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Learning how to apply DNA barcoding to species discovery

In 7 June 2006 Systematics and Biodiversity Andrew Brower examines application of DNA barcodes to identifying and defining new species. His Perspective piece “Problems with DNA barcodes for species delimitation: ‘ten species’ of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae)” reviews Hebert et al’s 2004 PNAS paper “Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. My short summary is that we are still learning about how best to use DNA barcodes for identifying new species. In an April 2006 post responding to another worry piece I wrote: “DNA barcoding is a taxonomic tool for a) assigning specimens to known species and b) speeding discovery of new species. More work is needed to determine the best use of DNA barcodes in species discovery.” 

credit Dan JanzenBrower’s article argues about how many Astraptes species are supported by the sequence data, worries about possible consequences of the rise of DNA barcoding, and misses the scientific opportunity to examine this very young species complex with a large set of morphologic, ecologic, and sequence data. He concedes “there are probably at least three species” but declines to put forth what criteria can be used to delimit species. I was surprised to read that the question of whether two sequences “belong to the ‘same species’ is a metaphysical one”. 

A brief summary may be helpful. The PNAS Astraptes paper reports on 25 years of ecological and morphological work on Astraptes fulgerator larva and adults in a conservation area in northwestern Costa Rica. Approximately 40% of the 2,592 A. fulgerator caterpillars collected over this interval were successfully raised to adult; DNA barcodes were derived from the adult specimens. Differences in larval morphology and food plants and in some cases subtle differences in adult morphology suggested the presence of 6-7 cryptic species. When ADDED to this very large natural history knowledge base, DNA barcoding supported these inferences and highlighted another possible 3 or 4 species.  The number of individuals sequenced is larger (4-103 per putative species; 7 of 10 with more than 40 specimens sequenced) than in any other single species study I am aware of. Despite the large sample sizes and detailed information on biological co-variation in ecological and morphological traits, Brower seems to read the paper as defining species based on DNA barcodes. According to his own analysis, NJ bootstrap recovered 7 species and cladistic haplotype analysis recovered 8, albeit with low statistical support. The argument over whether some of the putative species are established to be distinct biological entities is important for the Astraptes specialist, but misses the point of how well barcode lineages in the neighbor-joining tree match differences in biology in this VERY YOUNG species complex. To my reading, the findings suggest that if one were starting over, or starting with a unstudied group, using DNA barcoding as a first step would be the fastest way for taxonomists to sort specimens and find new species.  

This entry was posted on Tuesday, June 6th, 2006 at 10:10 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.