[Taxacom] Taxonomy &DNA barcoding

[Stephen Thorpe]

This may be the way barcoding gets in the door, but what will it do  
once inside? Let's hope it isn't a trojan sheep ... horse, horse, ...  
!!!

Quoting Rodolphe Rougerie <rrougeri at uoguelph.ca>:

> Dear Doug,
>
> Just a few thoughts from an "insider" working at the Canadian Centre  
> for DNA Barcoding ;-). I am not sure if most taxacomers have a  
> detailed understanding of what DNA barcoding is and where it is  
> going... so I'm just giving my perspective as a taxonomist, and  
> instead of looking at barcoding as a massively funded initiative  
> competing with other taxonomy projects, I find it more constructive  
> to look into how this large international project can actually be  
> benefitial for taxonomists. It must be of interest, otherwise why  
> would there be so many taxonomists contributing to barcoding  
> projects or creating their owns?
>
> I observe daily that the data generated here (and it's certainly  
> true for any lab in the world producing barcodes or any other DNA  
> marker used for taxonomic purposes) are quite useful to taxonomists  
> who had no or limited access to molecular data so far.
> More precisely, within the community of taxonomists I am directly  
> collaborating with - that is mostly lepidopterists, both "hobbyists  
> and pros" - I can see the combination of the DNA barcodes and  
> morphology slowly making its way into a number of taxonomic projects  
> and then to publications (some not peer-reviewed - as inherent to  
> most taxonomic journals; I can send some references to those  
> interested, it goes from a formal analysis of the sequences in  
> relation to other characters to the mere citation of the sequence  
> for the type and some statements about genetic distances).
>
> This use of DNA barcodes by taxonomists constitutes IMHO a direct  
> support from DNA barcoding to the taxonomic community and its work.  
> I don't think we can expect much more within the current context,  
> especially since major (but not all) barcoding fundings aim at  
> building a reference library, not at solving taxonomic problems...  
> the later is - I think - a cool by-product of the former, and this  
> is appealing enough already for many taxonomists to send us  
> thousands of samples and invest a huge amount of their time doing  
> that.
>
> Of course, it would be even more positive if DNA barcoding proves,  
> in the future, to be an efficient leverage to be used by taxonomists  
> in their own grant applications. If a "fashion effect" can make  
> applications more succesful, then it's great - I don't think that  
> adding barcodes or other molecular markers to one's toolbox is a too  
> big price to pay. Can someone talk from the experience with  
> phylogenetics? Can we say that the development of molecular  
> phylogenetics somewhat permitted some morphological works to be  
> carried out? I would assume yes, if only for the controversy  
> inherent to the approach while still new (and DNA barcode has its  
> share ;-)). As for myself, my PhD project had a molecular component  
> in it (small one, 10% DNA / 90% morphology), but it was mostly to  
> make it more sexy since what I really wanted to do was morphology ;  
> I am sure it helped getting the scholarship at that time.
>
> About the use of type specimens in barcoding studies and a broader  
> "legacy" concept:
>
> First, a number of campaigns here are developped by taxonomists  
> and/or in close collaboration with expert taxonomists; they are one  
> of the main source of the samples we receive, meaning that the  
> identification coming with them is based on their conception of a  
> 'species name' by reference to what they know of the name-bearing  
> type. Sometimes - hopefully quite often - it ain't to be questioned  
> and all is just fine with barcodes then correctly associated to that  
> name in the reference library.
> As such, it looks to me as if the records in this library represent  
> a new "legacy" (based on new material, right) but with an indirect  
> reference to the type via the taxonomist expertise.
>
> Second, when things are not so simple and when f.i. possible cases  
> of cryptic diversity or synonymy are revealed through analysis of  
> DNA barcodes, there are different options:
> (a) taxonomists, strong of that new information can get back to the  
> specimens (including the types or the OD at least), look for  
> overlooked differences, look at their distributions, etc... In a  
> number of cases the group can be better understood and new taxa  
> described or raised from/sunk into synonymy (see f.i. our paper in  
> Zootaxa last year:  
> http://www.mapress.com/zootaxa/2008/f/zt01923p036.pdf)
>
> (b) more directly connected to your point: there are protocols (at  
> least for lepidoptera -other groups will certainly follow)  
> permitting to obtain barcodes from very old specimens. The complete  
> barcode region was recovered for specimens as old as 160 years old  
> or more, and partial sequences for specimens older than that, but  
> still providing enough data to link the type to some recent  
> specimens through their barcodes. This approach is used in a paper  
> in press in Zootaxa (Hausmann et al.; should be available within the  
> next few weeks) and the protocol will be published separately. When  
> the type, because of its sex f.i., or because of its poor condition,  
> is of no help to solve a taxonomic/nomenclatural question, then  
> barcodes can be a good alternative over designation of a neotype  
> (which is quite a complex process if the type isn't lost or  
> destroyed). On the other hand, the approach was seen by some  
> colleagues in charge of collections as a way to preserve the  
> integrity of the type by removing a leg instead of dissecting its  
> abdomen.
>
> Hopefully, the "no problem" or "problem solved through  
> re-examination of material" options are usual enough so that there  
> won't be a need for point (b) in « >95% of the existing holotypes ».
>
> The protocol used for old types is still quite costy when compared  
> to fresh specimens, and it isn't integrated in high-throughput  
> workflows (though the 96-wells format and robotic liquid-handling  
> can be used as well, as long as you get very cautious against  
> contamination...) - the good side of it is that a single specimen,  
> the holotype, is certainly worth a hundred fresh ones once  
> sequenced...
> BTW, I would add that for insects (tissue samples from dry museum  
> specimens) the routine protocols currently used here can recover  
> with a very reasonable success (70-80%) DNA barcodes from specimens  
> collected between 1980 and 2000 or so, which is not so bad and gives  
> access to a fairly large amount of material in museum collections.  
> Obviously, the fresher the better, but when necessary, for material  
> difficult to find or re-collect, it's good to know that there are  
> ways around it.
>
> Finally, as far as leps are concerned, all records of primary types  
> are made public on BOLD  
> (http://www.barcodinglife.org/views/login.php; click on the  
> published projects link, top left corner), including DNA sequences  
> and all voucher information (institution storing, collecting data,  
> image). There are only 175 records so far, 112 being sphingid moths,  
> but species newly described by collaborators are systematically  
> added and old types as well on a case by case basis, along with the  
> progress of some revisions which have been including barcodes of old  
> types. This may not be a direct support to the institution hosting  
> the types, but in a way it brings an additional value to the  
> collections that their curator may be able to exploit.
>
> Damn, it's long... and late... Let's say this was my "propaganda"  
> for taxacomers to look into the potential of DNA barcoding as a tool  
> for taxonomists, rather than as a competing initiative.
>
> Cheers,
>
> Rodolphe
>
>
>> Quoting Robert Hanner <rhanner at uoguelph.ca>:
> [snip]
>>> In fact, the barcode community is responsibe for the first concerted
>>> effort to make structured linkages between GenBank Accessions and
>>> Museum Voucher Specimens.
>
> This is NOT the same as work based on "legacy" museum specimens; the  
> typical morphological taxonomist uses MOSTLY material which is from  
> 30-100 years old, but DNA barcoding does not - unless you have  
> references showing barcoding projects based primarily on OLD  
> specimens, in which case many of us here would be very interested in  
> seeing them. Since most of the material in the world's museums is  
> from 30-100 years old, the barcoding community and the museum  
> community are not entirely "on the same page" here. Most pointedly,  
> if one cannot do a barcode for >95% of the existing holotypes, that  
> leaves very little overlap between the *foundation* of traditional  
> taxonomy and nomenclature - the type specimen - and the barcoding  
> methodology.
>
> The original quote, alluded to by Stephen, was in this context: the  
> idea that basing names on old museum specimens was quaint and  
> outdated, and barcoding represented a chance to start from scratch;  
> i.e., that legacy material would no longer occupy the place of honor  
> in systematics once everyone saw how barcoding worked, became  
> convinced that it was indeed a panacea, and then (presumably) we all  
> admitted that holotypes that cannot be barcoded serve no purpose,  
> since no one can ever know what taxa they truly represent.
>
> Maybe you can allay our concerns by answering the following  
> question: how much of the funding for CBoL projects (such as the one  
> you mention by Packer) goes to the maintenance and curation of  
> un-sequenceable legacy material?
>
> If CBoL support extends, blanket-wise, to the care of legacy  
> material, and if this represents a real increase in support to  
> institutions with large holdings of such legacy material, then maybe  
> there isn't as much of an issue with "competing" for funding dollars  
> as it would appear. But if the money is going to build *new*  
> collections composed of *new* specimens, while existing museums  
> elsewhere are closing their doors, then the "zero-sum" problems are  
> genuine, and worrisome.
>
> Sincerely,
>
>
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