[Nhcoll-l] eDNA voucher question

Fri Feb 22 16:28:40 EST 2019

Thank you all for your time, knowledge, and generosity. Have a good weekend.
Thomas Labedz
University of Nebraska State Museum

From: Nhcoll-l <nhcoll-l-bounces at mailman.yale.edu> On Behalf Of Dirk Neumann
Sent: Friday, February 22, 2019 11:41 AM
To: nhcoll-l at mailman.yale.edu
Subject: Re: [Nhcoll-l] eDNA voucher question

Hi Tom,

adding to my and the emails of Andy, John and Paul, the way Rob describes it surely is the best way to do it. In case that you have many small fishes in the same jar, we usually put tissued specimens in open glass tubes in the same jar and add a individual tissue ID into this glass tube. This helps to find tissued vouchers quickly and prevents (hopefully) loss of tags (which are hard to apply to such tiny fishes without damaging them anyway). We leave the tubes open to avoid plastics inside the storage fluid as these may release chemical compounds such as softeners.

Storage at room temperature for fluid stored tissue samples is not recommended, because you cannot control hydrolysis. If tissues are entirely (freeze)dried, things may be different.

All the best
Dirk

Am 22.02.2019 um 16:49 schrieb Rob Robins:
Tom,
Yes, this is the classic collection manager’s conundrum of: expend labor now to save space or conserve labor now at the expense of space.

It looks to me like you can satisfy both your concern over wasted space and the researcher’s concern regarding individual separation of the specimens by:

1.      Resampling each fish for dna.

2.      Linking those tissue samples to the individual specimens through the use of unique sampling locations on the body or small tags.

3.      Archiving the tiny, appropriately labeled tissue vials in an ultracold.

4.      Commingling your whole fish voucher specimens in locality/collecting event specific specimen lots (4 containers and not 35).

Or in other words, just reproduce the usual protocol for fishes coming from the field to the collection. I’m no DNA specialist, but I would think sampling the tissues now and storing them in the ultracold would also guard against room-temperature degradation of dna (I’m told this is a thing) in the specimens themselves and of course, give you that access to the whole specimens you desire.

Best,

Rob

Robert H. Robins
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Division of Ichthyology
[FLMNH                  Fishes logo email small]
Florida Museum of Natural History
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Gainesville, FL 32611-7800
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From: Nhcoll-l <nhcoll-l-bounces at mailman.yale.edu><mailto:nhcoll-l-bounces at mailman.yale.edu> On Behalf Of Thomas Labedz
Sent: Friday, February 22, 2019 10:31 AM
To: John E Simmons <simmons.johne at gmail.com><mailto:simmons.johne at gmail.com>
Cc: NHCOLL-L at mailman.yale.edu<mailto:NHCOLL-L at mailman.yale.edu>
Subject: Re: [Nhcoll-l] eDNA voucher question

NHCOLL readers
In an attempt to clarify my question to another responder I’ve copied below a more thorough explanation. Thanks to you all for your time and knowledge.
Thomas Labedz
University of Nebraska State Museum

The DNA work was done at another university, one that does not have collections to maintain vouchers. The DNA was collected and analyzed from these vouchers, the paper written and submitted for publication, and the author/researcher wants to deposit the individual fish as vouchers. Shoal Chub (Macrhybopsis hyostoma) are small, the largest maybe 5 cm long. My institution does not have any of the removed tissues that were analyzed for DNA, nor any products from that DNA, only the fish themselves. The researcher’s preference is for individual containers for each specimen should someone want to extract new tissue for DNA. Doing so would mean an approximately 10X increase in shelf space and material necessary to maintain these vouchers. Since we do not have the DNA samples or products, and are holding only the fish themselves, I submit that we should individually package each fish with its information but maintain all the samples from the same collecting locality in joint jars (4 jars instead of 35). Yes, cross-contamination would potentially occur between those jointly held samples, but since they are from the same collecting site cross-contamination would also be true in the natural environment where they were collected. Being small one option is to stuff them into individual tubes and put them in the freezers with tissues from other specimens where the vouchers are at this institution. That might work in this case but doesn’t lend itself  to ready access for species verification, nor does it function well as policy or protocol should another project produce larger numbers of samples from larger species.
Guess I’m addressing the balance between scientific need and budgetary/space constraints.

From: John E Simmons <simmons.johne at gmail.com<mailto:simmons.johne at gmail.com>>
Sent: Friday, February 22, 2019 9:26 AM
To: Thomas Labedz <tlabedz1 at unl.edu<mailto:tlabedz1 at unl.edu>>
Cc: NHCOLL-L at mailman.yale.edu<mailto:NHCOLL-L at mailman.yale.edu>
Subject: Re: [Nhcoll-l] eDNA voucher question

Tom,
I am not sure I understand the question. Do you mean the fish are vouchers from which DNA has been extracted and you want to keep the specimen separate to link it to the DNA sample, or do you mean fish from which DNA will be extracted in the future?

You will get contamination of the alcohol around the specimen from DNA from other specimens if you house them all together because protein is extracted over time by the alcohol (for example, see von Endt 1994, "Spirit collections: a preliminary analysis of some organic materials found in the storage fluid of mammals," Collection Forum 10(1):10-19). Whether that contamination would affect the DNA in the fish specimen itself has not been looked at, to my knowledge, but is an interesting question.

If you are storing these as whole-specimen vouchers from which DNA has already been sampled, I would go with Andy's suggestion of vials with polyester fiber plugs. If you are storing these for future DNA extraction, then they should be in 95.6% ETOH if they must be kept in alcohol.

Please let me know if I have misunderstood your question.

--John

John E. Simmons
Writer and Museum Consultant
Museologica
and
Associate Curator of Collections
Earth and Mineral Science Museum & Art Gallery
Penn State University
and
Investigador Asociado, Departamento de Ornitologia
Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima

On Thu, Feb 21, 2019 at 4:41 PM Thomas Labedz <tlabedz1 at unl.edu<mailto:tlabedz1 at unl.edu>> wrote:
Greetings from snowy central North America!
Has anyone developed policy or protocol for the receipt, treatment, and maintenance of eDNA fish voucher specimens? Would you share? The individual fish are small and the researcher recommends keeping each individual in a separate container (how they were delivered) to prohibit cross contamination of DNA via the ethanol solution. That is understandable but will utilize lots of space and containers.
Thomas
Thomas E. Labedz, Collections Manager
Division of Zoology and Division of Botany
University of Nebraska State Museum
Lincoln, Nebraska, U.S.A.
tlabedz1 at unl.edu<mailto:tlabedz1 at unl.edu>

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