[Taxacom] Identification by what method?

[Timothy Jones]

Thanks to everyone for the papers and replies.  In my search I finally
bumped into a hard number from Genbank itself on their taxonomy page (
http://www.ncbi.nlm.nih.gov/taxonomy).  They state that approximately 10 %
of known things are databased.  Realize this does not include other DBs
around the world.   So, keep keying.
Thanks again,
Tim

On Fri, Jul 31, 2015 at 11:26 AM, John Grehan <calabar.john at gmail.com>
wrote:

> which all points up to the fact observed by a friend of mine, that all too
> often a technological advance may be confused with a conceptual advance.
> The former does not call into existence the latter,
>
> John Grehan
>
> On Fri, Jul 31, 2015 at 10:35 AM, Fautin, Daphne G. <fautin at ku.edu> wrote:
>
>> 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
>> fax 1-785-864-5321
>> skype user name daphne.fautin
>> cv: www.nhm.ku.edu/inverts/daphne.html
>>
>>     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
>>
>> Associate Editor,
>> Records of the Australian Museum
>>
>> Australian Museum Research Institute
>> 6 College Street Sydney NSW 2010 Australia
>> t 61 2 9320 6340   m 61402735679   f 61 2 9320 6059
>> Visit: http://www.australianmuseum.net.au
>> Like: http://www.facebook.com/australianmuseum
>> Follow: http://www.twitter.com/austmus
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>> Inspiring the exploration of nature and cultures
>>
>>
>>
>> -----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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>
>


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