Check it out at Wired here!

DNA barcoding exposes fake ferns in international plant trade

Barcoding endangered sea turtles

Sand fly barcoding in Panama reveals Leishmania strain and its potential control

Hidden habits and movements of insect pests revealed by DNA barcoding

Mercury is higher in some tuna species, according to DNA barcoding

Unknowingly consuming endangered tuna

CU-Boulder team identifies DNA barcodes to help track illegal trading of wildlife products

And don’t forget the series of reports of widespread market substitution in market fishes. For example, check out my friend and colleague Bob Hanner discussing this topic on a recent episode of Marketplace:

Next week, I’m off to Nairobi for the inaugural meeting of HealthBOL, of which I am international Scientific Coordinator: a project within the International Barcode of Life (iBOL) initiative focused on vectors, parasites, and pathogens.

Experience is required in PCR, DNA sequencing, and related analytical approaches, as well as expertise in one or more of protists, nematodes, flatworms, or insect vectors. In addition, applicants must possess excellent written and oral communication skills in English as well as strong leadership qualities.

Salary and benefits will total $45,000 (CDN) per year, with a further $5,000 per year in individual research support. The successful candidate will have access to a high-throughput biodiversity genomics facility under the co-supervision of Ryan Gregory (Department of Integrative Biology) and Paul Hebert (Biodiversity Institute of Ontario). The position will be co-funded by the Ministry of Research and Innovation through the Ontario Post-Doctoral Fellowship Program, Round 3.

Candidates must meet the following additional requirements:

• Have completed their PhD no earlier than June 15, 2007.
• Be available to begin work no later than Oct. 31, 2009.
• Be eligible to work in Ontario, Canada.

Applicants should send a CV including a brief overview of experience and research interests to rgregory(at)uoguelph.ca

Review of applications will commence June 15, 2009.

For more information, visit:

• Canadian Centre for DNA Barcoding
• International Barcode of Life (iBOL) project

Note the following from the introduction by my friends/colleagues Brian Golding, Bob Hanner, and Paul Hebert:

Despite some popular misconceptions, the goal of DNA barcoding is neither to determine the tree of life nor to carry out phylogenetic studies. The goal of DNA barcoding is also not molecular taxonomy, as it is not intended to replace classical taxonomy. Its purpose is to carry out species identifications so that even non-experts can determine what species might be at hand, and to do so in a rapid and inexpensive manner. This does not mean that barcodes lack phylogenetic information, or that the sequences do not contribute to taxonomic knowledge. Barcodes can provide evidence for cryptic species, and contribute to knowledge of phylogeny and biogeography. Each of these, however, requires corroboration from additional sources of information for robust support of the hypotheses generated by barcoding. For example, no one would attempt to reconstruct the phylogenetic history of the Diptera from 600 bp of mitochondrial sequence.

Central to the DNA barcoding enterprise is a database of previously identified reference specimens and their corresponding COI sequences. This requires taxonomists to apply their knowledge and to provide identifications of specimens that can then be barcoded. They must provide their intimate knowledge of the species ranges and morphologies to direct sampling strategies that would cover the greatest likely range of genetic variation. It is then these couplets of information that can be used to identify an unknown specimen.

Here are the papers, all open access thanks to support from NSERC and Genome Canada (before the cuts):

Molecular Ecology Resources

Volume 9 Issue s1 May 2009

Special Issue on Barcoding Life

Preface (p iv-vi)
G. B. GOLDING, R. HANNER, P. D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02654.x

Abstract | PDF

KEYNOTE ARTICLE

Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity (p 1-26)
DANIEL H. JANZEN, WINNIE HALLWACHS, PATRICK BLANDIN, JOHN M. BURNS, JEAN-MARIE CADIOU, ISIDRO CHACON, TANYA DAPKEY, ANDREW R. DEANS, MARC E. EPSTEIN, BERNARDO ESPINOZA, JOHN G. FRANCLEMONT, WILLIAM A. HABER, MEHRDAD HAJIBABAEI, JASON P. W. HALL, PAUL D. N. HEBERT, IAN D. GAULD, DONALD J. HARVEY, AXEL HAUSMANN, IAN J. KITCHING, DON LAFONTAINE, JEAN-FRANÇOIS LANDRY, CLAUDE LEMAIRE, JACQUELINE Y. MILLER, JAMES S. MILLER, LEE MILLER, SCOTT E MILLER, JOSE MONTERO, EUGENE MUNROE, SUZANNE RAB GREEN, SUJEEVAN RATNASINGHAM, JOHN E. RAWLINS, ROBERT K. ROBBINS, JOSEPHINE J. RODRIGUEZ, RODOLPHE ROUGERIE, MICHAEL J. SHARKEY, M. ALEX SMITH, M. ALMA SOLIS, J. BOLLING SULLIVAN, PAUL THIAUCOURT, DAVID B. WAHL, SUSAN J. WELLER, JAMES B. WHITFIELD, KEITH R. WILLMOTT, D. MONTY WOOD, NORMAN E. WOODLEY, JOHN J. WILSON
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02628.x

Abstract | PDF

BARCODING METHODOLOGY AND APPLICATIONS

The front-end logistics of DNA barcoding: challenges and prospects (p 27-34)
ALEX V. BORISENKO, JAYME E. SONES, PAUL D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02629.x

Abstract | PDF

Express barcodes: racing from specimen to identification (p 35-41)
NATALIA V. IVANOVA, ALEX V. BORISENKO, PAUL D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02630.x

Abstract | PDF

DNA barcoding and the mediocrity of morphology (p 42-50)
LAURENCE PACKER, JASON GIBBS, CORY SHEFFIELD, ROBERT HANNER
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02631.x

Abstract | PDF

Biological agent detection technologies (p 51-57)
JOHN P. JAKUPCIAK, RITA R. COLWELL
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02632.x

Abstract | PDF

Efficient algorithms for the discovery of DNA oligonucleotide barcodes from sequence databases (p 58-64)
M. ZAHARIEV, V. DAHL, W. CHEN, C. A. LÉVESQUE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02651.x

Abstract | PDF

BARCODING MICRO- AND MESO-FAUNA

Barcoding diatoms: Is there a good marker? (p 65-74)
MÓNICA B. J. MONIZ, IRENA KACZMARSKA
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02633.x

Abstract | PDF

Development of primers for the mitochondrial cytochrome c oxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminths (p 75-82)
ANNA MOSZCZYNSKA, SEAN A. LOCKE, J. DANIEL McLAUGHLIN, DAVID J. MARCOGLIESE, TERESA J. CREASE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02634.x

Abstract | PDF

BARCODING FUNGI

Progress towards DNA barcoding of fungi (p 83-89)
KEITH A. SEIFERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02635.x

Abstract | PDF

Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium (p 90-98)
SCOTT R. GILMORE, TOM GRÄFENHAN, GERRY LOUIS-SEIZE, KEITH A. SEIFERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02636.x

Abstract | PDF

Evaluation of mitochondrial genes as DNA barcode for Basidiomycota (p 99-113)
AGATHE VIALLE, NICOLAS FEAU, MATHIEU ALLAIRE, MARYNA DIDUKH, FRANCIS MARTIN, JEAN-MARC MONCALVO, RICHARD C. HAMELIN
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02637.x

Abstract | PDF

A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium (p 114-129)
W. CHEN, K.A. SEIFERT, C.A. LÉVESQUE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02638.x

Abstract | PDF

BARCODING PLANTS

Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? (p 130-139)
ARON J. FAZEKAS, PRASAD R. KESANAKURTI, KEVIN S. BURGESS, DIANA M. PERCY, SEAN W. GRAHAM, SPENCER C. H. BARRETT, STEVEN G. NEWMASTER, MEHRDAD HAJIBABAEI, BRIAN C. HUSBAND
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02652.x

Abstract | PDF

Routine DNA barcoding of Canadian Gracilariales (Rhodophyta) reveals the invasive species Gracilaria vermiculophylla in British Columbia (p 140-150)
GARY W. SAUNDERS
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02639.x

Abstract | PDF

Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae) (p 151-163)
JULIAN R. STARR, ROBERT F. C. NACZI, BRIANNA N. CHOUINARD
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02640.x

Abstract | PDF

DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India (p 164-171)
SUBRAMANYAM RAGUPATHY, STEVEN G. NEWMASTER, MARUTHAKKUTTI MURUGESAN, VELUSAMY BALASUBRAMANIAM
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02641.x

Abstract | PDF

Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae) (p 172-180)
STEVEN G. NEWMASTER, RAGUPATHY SUBRAMANYAM
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02642.x

Abstract | PDF

BARCODING ARTHROPODS

DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach (p 181-187)
ADRIANA E. RADULOVICI, BERNARD SAINTE-MARIE, FRANCE DUFRESNE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02643.x

Abstract | PDF

DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea) (p 188-195)
R. G. FOOTTIT, H. E. L. MAW, N. P. HAVILL, R. G. AHERN, M. E. MONTGOMERY
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02644.x

Abstract | PDF

DNA barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies (p 196-207)
CORY S. SHEFFIELD, PAUL D. N. HEBERT, PETER G. KEVAN, LAURENCE PACKER
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02645.x

Abstract | PDF

DNA barcode accumulation curves for understudied taxa and areas (p 208-216)
M. ALEX SMITH, JOSE FERNANDEZ-TRIANA, ROB ROUGHLEY, PAUL D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02646.x

Abstract | PDF

Combining DNA barcoding and morphological analysis to identify specialist floral parasites (Lepidoptera: Coleophoridae: Momphinae: Mompha) (p 217-223)
VIRGINIA J. EMERY, JEAN-FRANÇOIS LANDRY, CHRISTOPHER G. ECKERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02647.x

Abstract | PDF

Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae) (p 224-236)
JULIO RIVERA, DOUGLAS C CURRIE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02648.x

Abstract | PDF

BARCODING VERTEBRATES

DNA barcoding reveals overlooked marine fishes (p 237-242)
TYLER S. ZEMLAK, ROBERT D. WARD, ALLAN D. CONNELL, BRONWYN H. HOLMES, PAUL D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02649.x

Abstract | PDF

Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach (p 243-256)
EUGENE H.-K. WONG, MAHMOOD S. SHIVJI, ROBERT H. HANNER
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02653.x

Abstract | PDF

Countering criticisms of single mitochondrial DNA gene barcoding in birds (p 257-268)
ALLAN J. BAKER, ERIKA SENDRA TAVARES, REBECCA F. ELBOURNE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02650.x

Abstract | PDF

[Excerpt from Genomes of Other Organisms: DNA Barcoding and Metagenomics]

Partial Gene Sequences

The method of comparative genomics can be applied not just to full genome sequences, but also to single genes and gene fragments to study their function and help establish relationships among species. Indeed, a species‘ place on an evolutionary tree is a valuable predictor of the structure and function of neighboring taxa.

The current convention of describing (defining) organisms new to science and establishing their evolutionary relationships is based on total evidence; in other words, the organisms’ genetic, morphological, and ecological characters are described and analyzed against other sets of data. Taken together, these techniques can be very informative, having thus far provided us with a detailed road map of Earth’s biota. But for systematics – the study of biological diversity and common ancestry – rapid technological advances in the field of comparative genomics are both a blessing and a curse. Consider, for example, the technique called DNA bar coding, which is based on using short fragments of mitochondrial gene CO1 to uniquely identify and document animal species (Savolainen, 2005). This technique has applications across all living organisms, but the precise genetic methodology is still being developed. In addition, the debate among scientists regarding the use and the utility of DNA bar coding has been quite vociferous. On one hand, this technique brings the promise of instant species identification to a much wider community with minimal biological training. Indeed, it is hypothetically possible to carry a hand-held device out in the field and input species sequences into a rapidly expanding database; all for a fraction of the price, knowledge, and effort associated with the conventional manual method or with human-curated taxonomic identification. So what’s the catch?

One major problem with DNA bar coding is that it operates on the assumption that species have evolved in perfect percentile distances of genetic diversion. Thus, with this technique, in order for any two organisms to be deemed the same species, they must share 88-98% of genetic code at the chosen CO1 mitochondrial gene fragment (Savolainen, 2005). The exact suggested threshold has to be characterized for each group, and neither the threshold nor the groups have been clearly defined for most taxa. Thus, DNA bar coding has been called a “quick fix” and an oversimplification of systematics. Indeed, wide variation in the CO1 gene is found not only among species, but also within them, and even between the cells of an individual organism – a phenomenon known as mitochondrial heteroplasmy (Kmiec & Woloszynska, 2006). Furthermore, there is a broad overlap of inter- and intraspecific genetic distances among closely related species (Goldstein et al., 2000).

These issues come into focus when you consider the devastating malaria epidemic that kills one to three million people worldwide every year. The pathogens that cause malaria are protozoan parasites from the genus Plasmodium that are transmitted through the bite of mosquitoes of the genus Anopheles. Both of these animal genera contain hundreds of species, although only a few are involved in transmitting malaria in humans. Recent genetic studies of the symbiotic bacteria in the midgut of the Anopheles stephensi mosquitoes have yielded promising results: Enterobacter agglomerans bacteria were genetically engineered to display two anti-Plasmodium effector molecules that kill the parasite before it is transmitted to humans (Riehle et al., 2007). Now consider the genetic and physiological differences between the wild-type and genetically modified Anopheles stephensi mosquitoes: they are still the same species by all major standards of species definition, yet what a difference it would make for humankind if the Plasmodium-resistant genetically modified strain were dominant. This example highlights the importance of studying genomes and biological associations of the narrowest niches of life. It also underlines the vital potential for the unpredictable outcomes of genome sequencing-major advances are often made using information generated for completely unrelated reasons.

Ok. The last paragraph has nothing to do with DNA barcoding. As to the critique of DNA barcodes, I find it odd that the author a) does not cite any papers by people who do DNA barcoding, and b) cites a paper from 2000 (i.e., 3 years before DNA barcoding began) as showing that sequences overlap. Nevermind that the paper a) does not discuss COI data, and b) is co-authored by Rob DeSalle and Alfried Vogler (my two postdoc advisors), neither of whom is against the use of DNA in species identifications (though both would prefer cladistic methodology).

The bias is obvious, but at least they could have included some proper references (goodness knows there are enough vocal opponents).

See the clip here (their segment starts at 13:05).

Note: the segment before theirs, which begins at 8:55 and includes Sean Carroll, refutes the myth about Darwin’s finches instigating his evolutionary views (replacing them with mockingbirds), but presents an apparently misattributed “Darwin quote”.

Here’s a story in the New York Times about the importance of identifying which species are involved in airplane bird strikes.

Identifying the Bird, When Not Much Bird Is Left

It talks about the use of feathers and feet (i.e., morphology) and also describes the use of DNA (new word: “snarge“). It does not mention DNA barcoding per se, but it bears noting that the FAA and USAF support DNA barcoding efforts at the Smithsonian. In general, it would be best to have as many tools as possible, including sequencing DNA and comparing this against the bird DNA barcode dataset, which already encompasses more than 2600 species (out of about 10,000) and means to include every bird on the planet within the next several years.

1) In our genes, old fossils take on new roles
by David Brown, Washington Post

It turns out that about 8 percent of the human genome is made up of viruses that once attacked our ancestors. The viruses lost. What remains are the molecular equivalents of mounted trophies, insects preserved in genomic amber, DNA fossils.

2) Gaming evolves
by Carl Zimmer, New York Times

Evolutionary biologists like Dr. Near and Dr. Prum, who have had a chance to try the game, like it a great deal. But they also have some serious reservations. The step-by-step process by which Spore’s creatures change does not have much to do with real evolution. “The mechanism is severely messed up,” Dr. Prum said.

Nevertheless, Dr. Prum admires the way Spore touches on some of the big questions that evolutionary biologists ask. What is the origin of complexity? How contingent is evolution on flukes and quirks? “If it compels people to ask these questions, that would be great,” he said.

I may have to check out this game.

3) Research raises questions about DNA barcoding methodology
by Andrea Anderson, GenomeWeb Daily News

This one is about the PNAS article by Song et al. that at first seemed like it was going to get a lot of hype (it did from NSF, but other venues decided it wasn’t worth a story). A lot of silliness going on with this one that I can’t really talk about, but suffice it to say I am not impressed with this paper or the conduct of the authors. I’ll just quote from the linked story.

“Sadly, the authors of this paper do not understand barcoding protocols,” Paul Hebert, director of the Biodiversity Institute of Ontario at the University of Guelph, told GenomeWeb Daily News. Calling the title of the paper misleading, he said barcoders have been aware of nuclear pseudogenes for years and have already designed some strategies for dealing with the problems described in the paper.

…

“Given that pseudogenes were reported 25 years ago, it’s not new news to us,” Hebert said. He said the team focused on species in which numts are particularly common and drew conclusions based on these eight species. Barcoding projects such as iBOL, he said, include data from thousands of species and are carried out using methods that differ from those described in the paper.

Hebert emphasized that the Barcoding of Life Data Systems, or BOLD, database scours sequences for indels, stop codons, and other tell-tale pseudogene signs. Barcoding sequences are also screened against a pool of sequences representing known contaminants, he said. Sequences that raise red flags are then set aside for further assessment, including longer sequence analysis or RT-PCR.

And, he noted, large barcoding studies typically amalgamate DNA barcode data with information provided by taxonomy, morphology, ecology, and other biological measures. “We’ve never advocated that sequence information alone is declarative for species boundaries,” he said.

…

For his part, Crandall conceded that large barcoding projects such as iBOL “have excellent strategies for quality control of data” and are already applying many of the steps he and his colleagues recommended. Still, he said, even though some people are already worrying about numts does not mean everyone in the field is addressing the problems appropriately.