Rewriting the invention of DNA barcoding

Today I got an email from David E. Schindel, who is the Executive Secretary of the Consortium for the Barcode of Life, announcing Google funding for DNA barcoding. The project aims to create a reference library of endangered species COI sequences so that DNA barcoding can be used as a tool against wildlife trafficking. Good for them, this is a good use of money.

However I was shocked to read later in the email

DNA barcoding is a technique developed at a Canadian university for identifying species using a short, standardized gene sequence

What? Either this was typed and not checked in a bad moment or we have entered the world of barcoding political spin. I assume that ‘at a Canadian university’ refers to Guelph, where the the Canadian Centre for DNA Barcoding is based, lead by Paul Hebert.

The problem is that this Canadian group didn’t invent barcoding, neither the name nor the discipline. I can’t really go into a detailed history of DNA barcoding in this post but the statement in this email makes me squirm, just like when I hear politicians take credit for natural events or someone else’s work. But the meme is out there, the Consortium for the Barcoding of Life begins

In 2003, researchers at the University of Guelph in Ontario, Canada, proposed ‘DNA barcoding’ as a way to identify species.

I don’t want to deny Paul Hebert’s contribution, nor that of the barcoding organisations. They have together popularised, formalised, extended and refined DNA barcoding. DNA barcoding is a force for good in the world and they have explained it beautifully to many diverse biologists, gained funding for several large studies, and refined the methodologies. Good for them.

I would like someone unconnected to the international barcoding groups to write a history of the discipline in a broad context, not just the projects labelling themselves ‘DNA barcoding’. The origins of the methodology and approach probably lie with the bacterial 16S sequencers like Norm Pace. They used short standardised gene segments to identify species and although some bacterial projects were undoubtedly environmental surveys, assigning taxa into molecular clusters with little extra biological information, many others incorporated well-characterised reference strains, which is exactly what most people would describe as DNA barcoding. Jonathan Eisen has an article (“Barcoding” researchers keep ignoring microbes) of relevance here- make sure to read the comments. The first use of the exact term “DNA barcoding” is unclear to me, and may possibly be in classic Hebert (2003) paper, although Blaxter used something essentially the same in the title of his 2002 paper “Molecular barcodes for soil nematode identification” which also employed a short standardised segment of 18S rRNA (Floyd et al 2012). Although there are some who dismiss these sorts of similarity based groupings as ‘environmental surveys’ like those used for bacteria, Floyd et al.  also use a phylogenetic approach to link their environmental sequence clusters (MOTUs) to known, classically-described species that have been identified through morphology and vouchers lodged in museums- see Fig 4 in Floyd et al 2002. This is DNA barcoding and differs from typical studies only in the reference locus used. Ritz and Trudgill (1999) cited Blaxter as talking about a ‘molecular bar-code’ a few years earlier in a 1999 publication.

Screenshot 2018-10-29 at 17.20.43
Baker and Palumbi (1999) tree identifying whale meat samples by comparison to whale voucher specimen sequences.

So what about mtDNA studies? Well, I haven’t done real research, I’m just trying to remember stuff, and I would be delighted to hear of examples in the comments. It wouldn’t surprise me at all to find that John Avise’s group (pioneers of mtDNA analysis) had used mtDNA to match unknown samples to voucher specimens. They tended to use whole mtDNA and RFLPs though rather than sequencing, would that still count, what do you think? Certainly Silberman and Walsh (1992) were identifying lobster larvae by RFLPs of PCR amplified rRNA early on, does that count? Alan Wilson’s lab developed some of the first ‘universal’ mtDNA primers used in ecology and evolution (Kocher et al 1989) and again I wouldn’t be surprised to learn that they had assigned unknown specimens to type by DNA barcoding. But they usually chose cytochrome b or 12S rRNA, so would that still count?

A classic DNA barcoding study was published in Science in 1994 (Baker and Palumbi 1994). They took ‘whale’ meat samples from Japanese markets and tried to identify which species they really belonged to. This is almost identical to many classic DNA barcoding studies (Wong and Hanner 2008) in all but that they used a standardised section of the mitochondrial control region rather than COI. I could also mention Hoelzel (2001) “Shark fishing in a fin soup” who identified the species present in shark fin soup using cytb and NADH2 sequences compared to the database.

So what about COI? Folmer et al (1994) designed some of the earliest (and best) COI universal primers. These are great primers and still the most commonly used for DNA barcoding. I was unaware of the Folmer primers when I designed my own universal primers (Lunt 1994 PhD thesis) and several labs were doing this. In Godfrey Hewitt’s lab at UEA we had up to that point been using conserved mtDNA primers from Richard Harrison’s lab at Cornell (they were in pairs named after US presidents and their wives). We weren’t barcoding, the primers were being used for phylogeography, phylogeny and molecular evolution studies. This background just illustrates that COI primers had been around and used widely in all types of evolutionary biology for over a decade before the famous Hebert et al 2003 paper. So had anyone used DNA sequencing of COI with universal primers to match unknown specimens to described vouchered species? Had anyone used this approach to discover and describe cryptic species (another important aspect of DNA barcoding)? Definitely, probably lots of people! A study I designed with Africa Gomez and published in 2002 did exactly this (Gomez et al 2002). We had known rotifer isolates characterised by morphology, mating, ecology etc. We had lots of unknown eggs and identified them using a phylogenetic analysis of COI with the standard barcoding primers. Were we the first? Definitely not, we never thought for a minute that we were the first to do this, but I couldn’t tell you who was. Let me just repeat that, we were NOT the first, we did NOT invent DNA barcoding, not even in animals. I just wish people would stop claiming to have ‘invented’ DNA barcoding and instead understand the context in which their work stands. I doubt very much that DNA barcoding in any meaningful sense had a single origin. It was not a moment of inspiration, it was incremental change, as almost all scientific advance is.

If you know any good science journalists please buy them beers and persuade them to write the history of ‘DNA barcoding’ in the wide sense, and especially of the work of the bacterial 16S pioneers, I’d like to read that.

 

Baker CS, Palumbi SR. Which whales are hunted? A molecular genetic approach to monitoring whaling. Science. 1994;265: 1538–1539. doi:10.1126/science.265.5178.1538

Floyd R, Abebe E, Papert A, Blaxter M. Molecular barcodes for soil nematode identification. Mol Ecol. 2002;11: 839–850.

Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 1994;3: 294–299.

Gómez A, Serra M, Carvalho GR, Lunt DH. Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera). Evolution. 2002;56: 1431–1444.

Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proc Biol Sci. 2003;270: 313–321. doi:10.1098/rspb.2002.2218

Hoelzel AR. Shark fishing in fin soup. Conserv Genet. 2001;2: 69–72. doi:10.1023/A:1011590517389

Lunt DH. mtDNA differentiation across Europe in the meadow grasshopper Chorthippus parallelus (Orthoptera: acrididae). University of East Anglia. 1994. ISNI: 0000 0001 3614 061X

Kocker TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villabianca FX, et al. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci U S A. 1989;86: 6196–6200.

Ritz K, Trudgill DL. Utility of nematode community analysis as an integrated measure of the functional state of soils: perspectives and challenges. Plant Soil. 1999;212: 1–11. doi:10.1023/A:1004673027625

Silberman JD, Walsh PJ. Species identification of spiny lobster phyllosome larvae via ribosomal DNA analysis. Mol Mar Biol Biotechnol. 1992;1: 195–205.

Wong EH-K, Hanner RH. DNA barcoding detects market substitution in North American seafood. Food Res Int. 2008;41: 828–837. doi:10.1016/j.foodres.2008.07.005

6 Comments Add yours

  1. Stephen Thorpe says:

    Are you surprised that the world of DNA barcoding is a world of spin and politics? I am not! That is why it has been so successful, very little to do with the science. And the irony is that it takes funding away from taxonomy, and yet a barcode without a reliable species name associated with it is next to useless! Bar coding is only good for sheep and trees!! 🙂

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    1. Dave Lunt says:

      I share your frustration, but don’t confuse with a DNA barcoding critic, I’m a supporter of the science just not the spin!

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  2. Stephen Thorpe says:

    I suuport it as well, in it’s place, but it’s place isn’t first in the queue … it is potentially great for associating adults with immatures (insects, I mean!) and associating dimorphic sexes, but so little of that seems to get done …

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  3. I strongly believe that hebert et al made a huge mistake dubbing their work as DNA Barcoding. they did not insert any barcode into any organism but simply distinguished species by differences in their naturally existing wild genomes…. a barcode is not inherent in an organism nor any product. there for I strongly believe that there is a huge misuse of the term “DNA BARCODING”. A barcoded organism must be a genetically modified organism with a foreign sequence deliberately inserted into its genome for specific reasons just as UPC barcodes are inserted into finished goods for specific purposes. What Herbert and his colleagues have done is synonymous to DNA fingerprinting or profiling which have been in existence for long.I am not surprised though, because this is what happens when taxonomists venture into the field of genetics without thorough consultation of geneticists.

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  4. CT says:

    Well this is an incredibly insightful and useful rant.

    Like

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