DaveLunt.net - Dr Dave Lunt | Rewriting the invention of DNA barcoding
post-template-default,single,single-post,postid-16403,single-format-standard,ajax_fade,page_not_loaded,,side_area_uncovered_from_content,qode-theme-ver-9.1.3,hide_inital_sticky,wpb-js-composer js-comp-ver-4.5.3,vc_responsive

Rewriting the invention of DNA barcoding

04 Dec 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 paper [cite]12614582[/cite], 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 [cite]11972769[/cite]. 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 (Ritz K and Trudgill DL 1999 Plant and Soil 212: 1–11).

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 [cite]1364049[/cite] 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 [cite]2762322[/cite] 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 [cite]17801528[/cite]. 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 [cite source=’doi’]10.1016/j.foodres.2008.07.005[/cite] 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 designed some of the earliest (and best) COI universal primers [cite]7881515[/cite]. 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)[cite]8799733[/cite] 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 an published in 2002 did exactly this [cite]12206243[/cite]. 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.