[Taxacom] Identification by what method?

Fri Jul 31 09:35:09 CDT 2015

I agree entirely with Elena -- when students (especially, but not only) say "just sequence it," I point out that an accurate library of known sequences is needed, and they are almost universally dumbfounded.  A small detail seems to have been omitted in their training.

Plus for the group I work on -- anthozoans -- no single gene has been considered diagnostic, and I believe that is still the case, so the "library" is full of holes and far from complete taxonomically.  The "universal" Barcode (what I term a capital-B Barcode, to distinguish it from a lower-case barcode, which seems to have become the buzzword of choice for a sequence), COI, obviously works only for animals, and then for only some of them.  It does not work for anthozoans -- yet I often receive a message that someone has submitted COI sequences to some resource (they may differ but they are pretty much the big players) and a match has been found -- so, presto, that is the identification. Yes, I point out, the closest match will always be specified -- but that does not prove anything other than the sequences are similar (not necessarily identical -- more alike than anything else in the database).  For anthozoans, few COI sequences have been submitted in recent years because of the known problems with the gene for identification, so that makes the "match" all the more problematic.

Daphne G. Fautin
Professor, Ecology and Evolutionary Biology
University of Kansas
1200 Sunnyside Avenue
Lawrence, Kansas 66045 USA

telephone 1-785-864-3062
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skype user name daphne.fautin
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    database of hexacorals, including sea anemones
       most recent version released 2 January 2013
hercules.kgs.ku.edu/Hexacoral/Anemone2/index.cfm

________________________________________
From: Taxacom [taxacom-bounces at mailman.nhm.ku.edu] on behalf of Elena Kupriyanova [Elena.Kupriyanova at austmus.gov.au]
Sent: Thursday, July 30, 2015 12:23 AM
To: 'Timothy Jones'
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Identification by what method?

How do you *identify* something using gene sequencing??? You compare your sequence to another sequence that was obtained from a tissue of an organism identified HOW? Case closed and dismissed :)

Dr. Elena Kupriyanova
Research Scientist
Marine Invertebrates

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-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Timothy Jones
Sent: Thursday, 30 July 2015 2:54 PM
To: TAXACOM
Subject: [Taxacom] Identification by what method?

Howdy All,

Recently someone stated to me that the gold standard of biodiversity
identification was gene sequencing.   Which got me to thinking - how often
is gene sequencing used for ID as compared to traditional methods of identification?  My Google-fu is strong and can find zilch out there.  Anyone know of any papers that discuss this?

Thanks in advance,

Tim

--
Timothy M. Jones
Life Science Annex Building, Room A257
Louisiana State University
Baton Rouge, LA 70803
Website - http://www.herbarium.lsu.edu/keys/
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