This is an excellent question but my answer may not be to everyone's liking. With an uncurated database such as GenBank, one is wholly reliant on the validity of the submitter's identification of the taxon or gene in question. Thus if an error is made in the first instance, the "label" can become assigned to further submissions and thus the magnitude of the error increases. Examples from my experience that spring to mind are predominantly in cases where supposedly new species are shown to be examples of already extant species - 'Campylobacter hyoilei' is C. coli, 'Helicobacter sp. Mainz' H. cinaedi. Such errors can occur even where a whole genome sequence is obtained if the requisite cross-checking for phylogenetic assignment is not done. Methods such as rMLST now make that far easier to check than before, but the potential for mislabelling and thus misidentification remain. I personally favour a polyphasic approach to identification for this reason.

Hi, Stephen, thanks a lot for the input. So, it seems that users have to rely entirely on the submitter’s identification which is a conclusion made by the submitter from whatever evidences not always made accessible to the user. (By the way, is it assumed that the submitter or his research group made the identification if not otherwise acknowledged?)

Back to the problem, I was worrying with the misidentifications when uploading sequences and by “circular” identifications by using “BLASTS” – a colleague of mine explained me this method is used for species identifications - , because when the goal is to trace the site of origin of invasive species that have become widespread or set the timing of any particular evolutionary change, colonization event or appearance of a new genera, radiation etc the results basing on molecular phylogenies using barcodes of incorrectly identified species can be quite misleading.

I will try to highlight potential problems that can arise from misidentifications when studying invasive species. For example, here in Northern Spain we have a few invasive oyster species some of which have been misidentified as Crassostrea gigas. There are researcher that are barcoding them and labelling them with - I suspect - the wrong species identification and will sooner or later upload their barcodes in GenBank.

The material from which the DNA has been extracted and sequenced is deposited here in the University in the zoological collections, but the vouchers are not yet available to the public. I’m putting all my efforts to load all the information relative to the material that has been barcoded into an online database and make it accessible to everybody together with pictures through the webpage of the University. Unluckily this needs time. Besides,  I’m not the researcher who  will upload the sequences to GenBank, give the information relative to the species identification, site and date of collection to GenBank and neither who is responsible for the labelling and providing the species name that at the end will be accessible in GenBank.  Thus there is a “disconnection” between voucher database and GenBank database that will make it difficult to trace the “vouchers” of the barcoded specimens in Genbank. Given this (and probably given many other cases in which vouchers are not accessible, lost or destroyed after the study) if GenBank has not a kind of quality control that put as a requisite facilitating other than the DNA sequence any additional information of independent source for the species identification,  this would mean that users of the GenBank have no objective criteria to evaluate the “quality and traceability ” of the sequences and as a consequence are not critically evaluating the material they use from GenBank for their publications other than recognizing the “authority” of the submitter.  I consider that even in such cases where sequences come from a recognised authority in the field and since misidentifications may occur, researchers using the sequences from GenBank should have available from GenBank independent, objective information relative to the sequence that will allow them to critically select or discard sequences. And I’m afraid as I see that there is little option to critically check sequences and threre is no requirement of vouchers deposition.

By the way, what is exactly rMLST?. A colleague of mine made me aware that BOLD have vouchers, this is a great achievement . However, GenBank not only have sequences provided from BOLD and still is widely used.

In the case of Crassostrea oysters, the misidentification and the uncritical use of their sequences from Genbank can lead to many errors with bad consequences. The species has been shown to hybridize with other species from the same genus, and it may become extremely complex with time to trace the introduction vector, source of introduction or impact on other native Crassostrea oysters if barcodes of wrongly identified species are uploaded to genBank and labelled as C. gigas and used later for further studies. I suspect thus that if there have been earlier misidentifications of C. gigas and researcher are trying now to identify poorly known cryptogenic species or non native Crassostrea oysters by using barcodes from Genbank, suddenly “C. gigas” may become more widespread and the magnitude of the impact and dispersal capacity and adaptation of this species may be overestimated. At the same time, measurements effective against real C. gigas may not apply to the other species wrongly taken for C. gigas or even native Crassostrea oysters may be taken as an invasive Crassostrea oyster. Making experiments with the misidentified species trying to detect the species specifity of parasites become also complicated.

The status of native species or non native species of a poorly known Crassostrea species, may also be misinterpreted if the species identification is based on these barcodes. For example, C. angulata is considered by certain authors as an introduced species from the Indo-Pacific because it appears from a molecular point of view closely related to C. gigas. Some even consider them identical with C. gigas. But what if the sequences available come from misidentified specimens and there is no chance to check the vouchers? Errors can be perpetuated obviously and in some cases political decisions are made on the results of researchers.

All this reflections arises because of observing quite unprofessional ways of identifying species whose sequences are uploaded to GenBank – there may be who dislike what I say here – and because of strange results in a few studies dealing with sympatric speciations and invasive species.

“The demanding/alarming question for taxonomist”

I am not a taxonomist, working on assemblage structure of intertidal macrobenthos. During my research I come across a limpet species which has three morphotype. By interest, I tried to identify it by phenotypic characters but got failed. As an amateur, I used DNA barcoding technique and submit sequences to the GenBank and BOLD with the help of experts. My question becomes more difficult. I found lots of sequences uploaded without any photograph or voucher details. The question is that, as an ecologist, should I trust on this submitted sequences or identification? However, DNA barcoding can magnificently be a better system also for identification of species if we use it in a good manner. It permits better evaluation of the taxonomic crisis and can solve thousands of our questions regarding evolution. If it will use wrongly, it can create a big problems to a scientific society which working on taxonomy and evolution and published thousands of landmark papers with the help of these systems. After all we all are trying to understand creation of nature.

I have not answer for this question, I just sharing my experience. I think, many researchers are facing same problems. “Actually these systems are good but we are not using it in a scientific manner”.

Thanks for raising this question.

Hi Paresh, thanks for sharing with us your experience.

Barcoding is a good tool, but I consider that without having the chance to link the sequence with the specimen from which it comes, you loose important and useful information that would allow you to define the animal and look for diagnostic characters that can  easily be corroborated in other specimens.

So if you are going to make BLASTS with the sequences in genBank I would recommend you to take only those that come from a pubblication in which the animal from which the DNA has been extracted has been described or figured. So at least, you know whith what you are dealing and then you can go back to the original description of the species and check if your identification is right or wrong.

Today you can download so many old books from bioheritage library with so many beautiful pictures and exhaustive comments and descriptions that identifying species are costeless and feasible. It only takes a bit time, but to extract DNA, sequence  etc you need money and time and to be member of a group that can afford to make this investments, while anybody with a bit practice and patience can crack the shell  and have a look inside the animal under the binocular. I did not need to use barcode to differ among Littorina arcana and L. saxatilis. I just had a look inside the pallial cavity and read the articles about the ecology, biology and orginal descriptions. It took me less than a few hour to dissect the animals and see the differences. But of course, before I made a bibliographic search and read the work and had an intense correspondence with other colleagues that were seding me works and pictures.

Of course, sometimes it is difficult to distinguish cryptic species complexes and barcoding can be useful but at the end there are alsways differences easily visible: different types of development, reproductive strategies and even details in the internal anatomy.

to sum up, for me and in my circumstances (I'm not a project leader and don't belong to a multidisciplinary research group) using barcode for species indentification is worth but only after the easy and cheap approach doesn't work and in any case as long as I can also check the voucher and compare it with my  animal.