[Taxacom] Identification by what method?

[Richard Pyle]

Hi Tim,

 

I’m happy to help!  Bear in mind that the 5-10% number is a very non-robust number I just sort of guestimated at without consulting any actual data whatsoever.  At best, it’s a Gestalt, with probably +/- 5-10% error (ish).  I suppose if I were a bit more diligent, I would start recording data and get a better sense for it.  But I’m not sure how useful those data would be in the grand scheme of things, as my group generally falls into Doug’s 1%, and even then, probably not the part of the 1% with economic/cultural/etc. importance.

 

Aloha,

Rich

 

From: Timothy Jones [mailto:tjone54 at tigers.lsu.edu] 
Sent: Thursday, July 30, 2015 6:21 PM
To: deepreef at bishopmuseum.org
Cc: TAXACOM
Subject: Re: [Taxacom] Identification by what method?

 

Rich,
So nice. Have had nothing but great responses,  yours included.  And thanks for the number;  mind if I cite you in a pers. comm. on this 5-10% value?   Will be used in a poster at a meeting.   

Tim

 

On Thu, Jul 30, 2015 at 2:13 AM, Richard Pyle <deepreef at bishopmuseum.org> wrote:

Hi Tim,

In my experience, gene sequencing is used only in cases where there is substantial ambiguity of identification via traditional methods.  Again, in my experience, I would guess that it's used in my (ichthyological) context somewhere in the range of 5-10% of the time (that's generous -- if I actually gathered data, I wouldn't be surprised if it was a lower percentage).  But, of course, in my context, species boundaries have been generally well-drawn based on traditional methods of identification.  As that changes (i.e., as species boundaries become increasingly defined by data established by gene sequencing), I suspect the need for gene sequencing to establish reliable identifications will only increase.

....which leads me to the premise of your question (someone telling you that gene sequencing is the gold standard for identification in biodiversity).  I have little doubt that the forward track of this thread on Taxacom will trend towards that part of your email, rather than your actual question (which is why I tried to answer your real question first!)  As I am currently in the field with tenuous internet access (and very limited time), I figured I'd get my quick shot in now...  Basically, it seems to me that most of us would agree that "Identification" is the process of mapping an organism (or population of organisms) to a taxon.  Further, most of us represent a taxon through a Linnean-style name (or some sort of label associated with a Linnean-style name, like "Aus sp.32").  And, finally, we'd like to think that we map Linnean-style species names to sets of organisms we regard to be the same taxon at a rank that a human thinks of as a "species".

So... the extent to which gene sequencing is the "gold standard" for identification is tightly linked to the concept that gene sequencing is the "gold standard" for defining boundaries between distinct species.  I think the latter is still under substantial debate, and therefore the former is not necessarily universally agreed.

Aloha,

Rich


Richard L. Pyle, PhD
Database Coordinator for Natural Sciences | Associate Zoologist in Ichthyology | Dive Safety Officer
Department of Natural Sciences, Bishop Museum, 1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115 <tel:%28808%29848-4115> , Fax: (808)847-8252 <tel:%28808%29847-8252>  email: deepreef at bishopmuseum.org
http://hbs.bishopmuseum.org/staff/pylerichard.html




> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
> Timothy Jones
> Sent: Thursday, July 30, 2015 3:54 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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>
> Celebrating 28 years of Taxacom in 2015.

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Celebrating 28 years of Taxacom in 2015.




-- 

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