Outstanding applicants are sought for a two-year postdoctoral position at the University of Guelph, focusing on the development of molecular identification methodology (“DNA barcoding”) for a wide range of pathogens, parasites, and disease vectors. This will include both original research and participation in the assembly and coordination of large-scale international collaborations.

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

The journal Molecular Ecology Resources has just published a special issue on DNA barcoding. This is the result of a conference held at the Royal Ontario Museum.

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

I received an email about Scitable, a new online resource by Nature Education. I notice that they have a link to my 2005 paper in Nature Reviews Genetics. Overall, I think the site looks interesting. On a more curious note, I was checking out the material about comparative genomics, and came across this, um, bizarre discussion of DNA barcoding:

[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).

I don’t know if the same people are giving the same arguments against DNA barcoding anymore as I have pretty much stopped following those old discussions out of exhaustion. We can argue about how much influence DNA methods should have on alpha taxonomy (ranging from “none” to “who needs names, just use DNA sequences” — the latter being DNA taxonomy rather than DNA barcoding, and not a position that I endorse). What is silly to argue is that DNA barcoding would not have any practical roles that can’t already be covered just as easily, cheaply, and accurately by morphology-based identification.

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.

John Wilkins, who apparently didn’t learn the first time, has repeated his ill-informed claim that “Barcoding syphons off money and resources from real systematics.” I have said it before: DNA barcoding has brought in money from sources that never supported systematics (a prime example being Genome Canada). I co-authored some of these grants. I have been in the field with some of the taxonomists who are supported by them. I am around a five minute walk from the world’s major barcoding facility, which hosts systematist postdocs and collaborators and processes material from a large network of taxonomists. Wilkins, on the other hand, gets all his information from critics of barcoding.

I want to share a few quotes about DNA barcoding. Some of these are from critics of barcoding (Roe and Sperling 2007) and some are from proponents of DNA barcoding (Hebert and Gregory 2005). For fun, see if you can guess which is which, and then see if you can guess why critics keep saying the same thing despite what barcoding actually involves.

This shortfall suggests that mtDNA is not as universally successful as suggested by DNA-barcoding advocates. Additional markers are clearly essential to clarify species boundaries, providing additional support for an integrative, multilocus approach to delimiting species.

_________

References

Hebert, P.D.N. and T.R. Gregory. 2005. The promise of DNA barcoding for taxonomy. Systematic Biology 54: 582-859.

Roe, A.D. and F.A.H. Sperling. 2007. Population structure and species boundary delimitation of cryptic Dioryctria moths: an integrative approach. Molecular Ecology 16: 3617-3633.

Gather ’round, and I will tell you the tale of the Matrix Beetle.

It began in England — London, to be precise — during the second half of my two-year NSERC postdoc. I had spent the first year in New York at the incredible American Museum of Natural History, and decided to spend the second in the UK at the equally remarkable Natural History Museum. Time well spent in both cases. In London, I joined the lab of Alfried Vogler, an expert on tiger beetles, accomplished molecular systematist, and all-around excellent person. Alfried is, like many of my colleagues, interested in the applications of molecular tools to the problem of identifying the probable 10 million species on the planet. He takes it a step farther in some cases and would like to see a “DNA taxonomy” and not just “DNA barcoding” (there is a big difference, folks), but the basic point remains that he is interested in exploring how modern genetic methods can inform the identification of life.

Every Friday at the NHM, people would gather for inexpensive (by UK standards), though certainly not cheap, beer; it was here that I discovered Leffe, which, to my delight, is also available in Canada (at the LCBO, not the Beer Store, in case you’re looking for it in Ontario). One evening whilst enjoying said brew, Alfried remarked that someone in the lab had shown him a DNA sequence that morning, and that he had looked at it and said “That’s not from a tiger beetle”. He then noted — jokingly, of course — that if he had seen the real beetle he may not have been so sure. “What are you, like the Matrix?,” I snorted, “You just see DNA sequences raining down all over?”.

Deciding to follow up on this amusing notion, I created an image of a tiger beetle as seen in a Matrix world of DNA sequences. I put this on the computers in the lab, and hilarity ensued. Someone joked that it would be funny if we managed to get that on a journal cover. I agreed, but left it at that.

For those of you who follow the literature, you’ll know that there is a vocal opposition to DNA barcoding. Most of this comes from (some) taxonomists who see barcoding as a threat to their discipline. A debate on this issue was held at the PEET meeting in 2004 (watch the video), with a follow-up “discussion” to be held in the pages of Systematic Biology. By this time, I was back in Guelph, and Paul Hebert and I were neck deep in writing a multi million dollar Genome Canada grant (which, incidentally, took exactly $0.00 from the pockets of taxonomists and delivered a sizable chunk of funds to many non-molecular types). As a result, Paul was regretfully planning to withdraw from submitting his paper to the journal issue. I thought this would be a mistake, busy though he was, because it would have let the anti-barcoding side have the only word. We agreed to work on the paper together, which consisted of answering a series of questions that had arisen from the PEET meeting.

When the papers were accepted, the journal editors asked if anyone had ideas for a cover image. On a lark, I sent in the “Matrix Beetle” — and they wanted it.

And so, from the beer gardens of the NHM to the cover of Systematic Biology Volume 54 Number 5, I give you… the Matrix Beetle:

Cover Illustration: The recent proposal to use short, standardized gene sequences as unique identifiers of species – known as DN barcoding – has generated both strong support and vocal opposition in certain biological circles. The potential impact of DNA barcoding as either a help or a hindrance to taxonomic research represents an especially polarizing point of contention. A debate on the issues of DNA barcoding was held at the fifth biennial conference of the Partnerships for Enhancing Expertise in Taxonomy (PEET) in September 2004 at the University of Illinois at Urbana-Champaign. The debate was moderated by Vincent Smith, and involved Paul Hebert, the lead proponent of DNA barcoding, and Kipling Will, a vocal barcoding opponent. As a follow up to this debate, two contrasting position papers dealing with DNA barcoding are provided in this issue, moderated once again by a contribution from Smith. On the pro-barcoding side, Hebert and Gregory outline what they consider to be the beneficial aspects of DNA barcoding for taxonomy and other biological disciplines, where as Will et al. provide an opposing perspective in which they argue that DNA barcoding will be detrimental to taxonomic science. Neither set of authors has been permitted to read the others’ contribution prior to publication. Image © 2005 by T. Ryan Gregory.