[Taxacom] Identification by what method?

John Noyes j.noyes at nhm.ac.uk
Thu Aug 20 06:02:28 CDT 2015


Hi Tim,

To add to this, I would say that perhaps 20-30 out of 25,000 known species of Chalcidoidea (Hymenoptera) might be fairly reliably identified using DNA sequences alone. I say "might" and "fairly" because we can never be 100% sure even of these. This is partly because less than 2% of the described species of this group have any reliable sequences and in virtually all cases the limits of these species have not been set diagnostically.  Added to this, as there are probably at least 500,000 species of chalcidoids out there it could be said that DNA sequencing is about as useful as a chocolate teapot in identifying/delimiting species of this group. You can say the same thing about virtually all other groups of microhymenoptera and many other groups such as gall-forming Diptera, etc. etc.

John

John Noyes
Scientific Associate
Department of Life Sciences
Natural History Museum
Cromwell Road
South Kensington
London SW7 5BD 
UK
jsn at nhm.ac.uk
Tel.: +44 (0) 207 942 5594
Fax.: +44 (0) 207 942 5229

Universal Chalcidoidea Database (everything you wanted to know about chalcidoids and more):
www.nhm.ac.uk/chalcidoids 


-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Timothy Jones
Sent: 30 July 2015 09:13
To: Richard Pyle
Cc: TAXACOM
Subject: Re: [Taxacom] Identification by what method?

Thanks Rich,
Guarantee I will be soft about it,  no spotlights.  My number is much lower, so no worries -  my guesstimate for plants is > 5 %.  Figured this number was relatively low.  Yet still a guess.  Argh but happy about it.
At least I sorta' know.
Tim

On Thu, Jul 30, 2015 at 2:55 AM, Richard Pyle <deepreef at bishopmuseum.org>
wrote:

> 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, Fax: (808)847-8252 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.
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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/
>



--
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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