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specimens barcoded:  19243
 
species barcoded:  2779
 
unnamed barcode  
clusters found: 
858
 
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FAQs
Q:    Where should voucher specimens collected for the "Trichoptera Barcode of Life" campaign be housed? In cases where the donors do not need the specimens shipped back, should all of these donated specimens be curated and housed in one location? Will housing DNA voucher specimens in different locations (under different databases) make things easier or harder for future students/researchers wanting access to them (to describe new species, re-check ID's, work on associations, look at specimens for phylogenetic work, etc.)?
A:    Presumably, the majority of the caddisfly specimens contributed to barcoding will go back to the original donors. Alternatively, if the donors do not need to keep the specimens, specimens will be deposited at Guelph. However, the Canadian Centre for DNA Barcoding (CCDB) does not have the capacity to store and curate a large amount of specimens, especially pinned materials. So we encourage our collaborators to take the responsibility to store specimens that are used for DNA barcoding. We appreciate the extra efforts needed on the collaborators' side to cooperate with barcoding initiatives. Hopefully, we can come up with a reasonable system that will reduce the investment of time of the collaborators while meeting the basic requirements for DNA barcoding (that is to store barcoded specimens individually, each attached with a unique sample ID). Also, an effective tracking system should be developed so that people who needs to reach a specific individual specimen is able to retrieve that information from the Barcode of Life Data System (BOLD).

    Currently, Matrix boxes are most frequently used for transferring tissues. For example, insect legs are routinely assembled into these boxes while the pinned specimens stay in the original museums. However, storing voucher specimens individually will take up extra space and efforts. At the moment, we can offer two kinds of containers, Matrix Box (12.6cm X 8.5cm X 5.8cm) and Matrix Plate (12.6cm X 8.5cm X 2.7cm), both in 96-matrix format and can hold up to 94 specimens. Matrix Boxes have longer tubes than Matrix Plates (5.2 cm vs. 2.1 cm), and are more suitable for big specimens. On the other hand, some collaborators prefer to move the barcoded specimens back to the original vials from which they were taken. In this case, the small tubes in Matrix Plates can be separated and stored in bigger container while each tube remains self-sealed.

    Detailed information for all barcoded specimens are deposited on BOLD, including SampleID and donor’s contact information. Using this system, we should be able to trace all individual specimens that are used for barcoding. Of course, our collaborators may have their own systems on their ends to make easy access to these specimens.

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Q:    Who will ultimately "own" the DNA? For example, many (if not most) of the caddisfly species are known from only a very few specimens. Some of these may be old. Some of these may be from recently collected material, itself the result of much effort to collect, curate, identify, store, etc. Let's say we "sacrifice" a specimen of one of these few individuals for DNA barcoding. You extract the DNA and sequence the COI barcode region. What happens to the rest of the DNA? What if one of my students wanted to use that DNA to sequence other gene regions for phylogenetic research? Would they have access to it?
A:    As a general policy, we are willing to share aliquots of DNA with collaborators who donated the specimens from which the DNA was extracted. The routine protocol of DNA extraction at the CCDB produces 40 ul of genomic DNA, 2 ul of which is needed for each PCR amplification. Typically, there should be enough DNA extractions left for sharing after the barcode is generated. Protocols of shipping DNA in dried condition under room temperature has been developed, making exchange of DNA samples easy via regular mail carriers.

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Q:    What is the procedure for Trichoptera workers to get more DNA data for specimens besides the COI? If someone is interested in sequencing other gene fragments for phylogenetic or other purposes, can they provide funding to Guelph to have the sequencing done there?
A:    The major focus of the barcoding initiatives is mitochondrial COI. However, if common interests arise along projects process and multi-gene analysis is needed, running non-COI genes is possible especially if some funds can be allocated to the CCDB to compensate chemical consumables and technicians' time. However, the feasibility will depend on the availability of the facilities at the CCDB and the time that the person at the lab end can contribute.

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Q:    What is the policy on data sharing and authorship? Let’s say we send you all of the species in a genus of caddisflies, and you sequence the COI region and publish on it. Would we share authorship? On the other hand, let's say you get the COI sequence you want, and we use the remaining DNA aliquot to sequence other regions for phylogenetic study. Would you or someone at your institution demand authorship on the phylogenetic paper that results? The main thing I am thinking about is the tremendous amount of effort (in time and money) it has taken us (and taxonomists in general) to collect, curate, maintain, identify, etc. all of this material - as well as the commitment to maintain the voucher specimens from your DNA barcoding effort - as this effort relates to the use and sharing of the data that result.
A:    Because of the efforts made by collaborators (collecting, curating, identifying, and etc.), they are considered as co-authors of the resultant DNA barcoding publications. On the other hand, we do not automatically demand authorship for other publications, such as taxonomic or phylogenetic works, that are generated merely using the DNA we produce. Of course, if the collaborators have agreements with people in our institute, and we do make further contributions to the publication (for example if the co-author at Guelph agrees to contribute personal time to sequence additional genes with allocation of some funds from the collaborators to compensate chemicals, in which way the sequencing cost can be greatly reduced using Guelph facilities), we would be honored to share authorship. Of course, that will only happen upon reciprocal agreements. In addition, as we mentioned in the proposal, sequence data will be shared among collaborators even before they are published.

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Q:    Will the DNA be automatically made public or would it wait until I had published it?
A:    The COI sequences will not be publicly accessible unless the project coordinator pushes the "Publish" button. Normally, the collaborator and the project coordinator would come up agreements on how and when to publish the data. The collaborator can also share data with other people whomever he wants to include in the project. The sequence data and progress will be kept confidential between collaborators and project coordinator for a particular project.

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Q:    What is the typical turnaround time for processing specimens at Guelph?
A:    All specimens will go through a chain of processes until the data reach the BOLD system. Typically, it takes 1-2 weeks from the DNA extraction step to the final upload of sequences. And the process can be speeded up upon urgent needs. However, it is not unusual that the pre-lab steps can take enormous amount of extra time, specifically, entering and reformatting data entries that come with the specimens. To standardize the data format, we will provide some examples that meet the BOLD requirements at later stage. These examples and other relevant documents will be available on the constructed "Trichoptera Barcode of Life" website.

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