[Taxacom] Identification by what method?

[Doug Yanega]

On 7/29/15 9:53 PM, Timothy Jones wrote:
> 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?
>
In the context of linking an unknown living specimen to a species name, 
the statement makes no sense. Over 99% of all species on the planet have 
never been sequenced AND had that sequence definitively matched to a 
name, so you can't effectively use gene sequencing to identify anything 
- at least, from among that 99% - to species. A tool that can give you a 
species name for less than 1% of extant biodiversity is a pretty sorry 
excuse for a "gold standard". Traditional taxonomic tools can identify - 
by definition - essentially every single described species (somewhere 
between 1 and 2 million), which is about 10% of the existing diversity 
(there's debate over the actual figure), and can ALSO give you higher 
taxonomic ranks (above the species level) for increasingly higher 
percentages for every step up the hierarchy you go. Gene sequencing 
can't do that very well, either; for a novel sequence, all it can do is 
tell you which sequence (among those already available) is closest to 
the new one, and that's not a guarantee that it belongs in the same 
genus, or family, or order, etc. - though this is something traditional 
methods will tell you almost instantly. Can sequencing tell you when 
you've discovered a new genus? A new subspecies? A new family? A new 
order? Nope. It only really works at ONE level of classification, and 
its performance at that level is completely dependent on the size and 
scope of your genetic reference library - which is, presently, pitifully 
small.

In the context of identifying, say, an organism in a photo, you can 
identify a LOT of biodiversity that way (and a lot gets identified that 
way - just spend some time on BugGuide or FaceBook), but you can't 
sequence a photo. Likewise in the context of fossil taxa - we can 
identify a lot of extinct organisms by traditional methods, but 
sequencing will not help with this very much. ;-)

Sincerely,

-- 
Doug Yanega      Dept. of Entomology       Entomology Research Museum
Univ. of California, Riverside, CA 92521-0314     skype: dyanega
phone: (951) 827-4315 (disclaimer: opinions are mine, not UCR's)
              http://cache.ucr.edu/~heraty/yanega.html
   "There are some enterprises in which a careful disorderliness
         is the true method" - Herman Melville, Moby Dick, Chap. 82