GenBank and vouchers

[Stuart G. Poss]

Jim,

A tag in the GenBank database as well as a collections "legacy" database
would still be helpful in tying specimen data to molecular data.  While
I would agree that publications should reference both, this is often not
done when considerable amounts of material have been studied.  Much more
often then we are left with only the GenBank sequence reference, without
a reference to the voucher.

While most collections probably record that particular specimens were
used as vouchers, few maintain extensive on-line lists of publications
using the collections, and few yet do so in a coordinate manner in terms
of standardized data structures.  Molecular biologists often do not send
copies or notification of their publications to the curators of
collections so that they can be recorded.  It is otherwise difficult for
curators to track this kind of information, since the archive (catalog)
numbers so not appear in GenBank.  Perhaps reestablishing this tradition
would be extremely helpful in developing dialog between both
communities.   Nonetheless, we would do well to maintain both numbers
(GenBank and traditional) in both respective databases, so that one
would not need to go to the time and expense to consult the specific
publication that is probably not on line, except perhaps in abstract
form.  It would also permit the programming of agent methods to
associate data in much more interesting ways than has been possible
previously, perhaps to remind curators to remind molecular works that
materials sent for archival have incomplete collections data, or to
remind molecular biologist to remind curators that sequence data
appearing in GenBank has yet to receive catalog numbers that are needed
for publication.

Your suggestion is a good one for "traditional" collections to consider,
since maintaining a uniform method of molecular voucher materials would
make "traditional" collections more relevant to molecular biologists,
particularly in their early stages of their careers.  Many collections
are attempting to do so, albeit not in a highly coordinated manner.  My
sense is that most curators would agree to assume the general
responsibity.  However, adequate funding for deposition of large amounts
of material accruing from multiple sources, without some willingness on
the part of the molecular biological/systematic community to pay for the
service, would over time place an unacceptable burden on collections,
which must  purchase the jars or other preservation media, process and
sort the materials, verify the identifications, enter and maintain the
data, produce the label and other records, and maintain the fluid or
other preservation media in perpetuity.  Curation and maintenance of
specimens requires much more than just the recording of the data.

With regards to "the appropriate site for molecular vouchers", I would
be surprised if it were any one place.  It would be better to be a
distributed network of archives, both for reasons of safety, as well as
ease of access to the materials by the community at large.

Stuart Poss




Jim Whitfield wrote:

>         I have argued in the literature (see refs. below if you are
> interested)  that when molecular sequence data are published upon,
> they should be deposited in GenBank, voucher specimens (e. g.
> specimen remnants, preferably also with intact specimens from the
> same collection series, etc.) with the GenBank numbers should be
> deposited in a museum, and the publication should reference both.
> That way, morphology- based taxonomy has the same direct access to
> specimens used for molecular work as those used for original
> descriptions, etc.    In other words, museum collections are an
> appropriate place to have material with labels referencing GenBank
> numbers.   To me, this is one of the nice ways in which museums can
> help integrate molecular and morphological systematics at the
> specimen level.

>
>         I would be very interested in opinions about the appropriate
> site for molecular vouchers, and whether museum curators want to take
> this on.
>

>                                         Cheers,  Jim Whitfield
>
> (Those refs.)
> I'd be happy to supply copies to whomever cannot get them easily...
>
> Whitfield, J. B. & S. A. Cameron. 1994.  Museum policies concerning
> specimen loans for molecular systematic research.  Molecular
> Phylogenetics and Evolution 3: 268-270.
> Cameron, S. A. & J. B. Whitfield. 1994.  Response to Dr. Hafner.
> Molecular Phylogenetics and Evolution 3: 271-272.
> Whitfield, J. B.  1999.  Destructive sampling and information
> management in molecular systematic research: an entomological
> perspective.  Chapter 18, pp. 301-314 in: Byers, S. and D. Metsger,
> eds., Managing the Modern Herbarium:  An Interdisciplinary
> Approach.   Society for Preservation of Natural History Collections
> and Royal Ontario Museum. 384 pp.
>
> --
> James B. Whitfield
> Associate Professor
> Department of Entomology
> University of Arkansas
> Fayetteville, AR 72701
> tel. 501-575-2482
> FAX 501-575-2452
> email jwhitfie at comp.uark.edu