[Taxacom] Identification by what method?

Thu Jul 30 06:55:50 CDT 2015

Evolution is ongoing, and different features follow different patterns in
different species.  Both molecular and morphological characters may provide
clear differences or intergradation, and what works in one species may not
in another.  Freshwater mollusks are extremely subject to ecophenotypic
variation, and have also experienced major rounds of lumping and of
splitting, so there's little agreement on what is a valid species.  Thus,
molecular evidence is quite useful, though all of the already-mentioned
caveats apply.  However, molecular data turns up problems such as
contamination and paralogs.

A difficulty in calculating a percent is "out of what?"  The percent of
studies on freshwater mollusks that make some use of molecular data in
identification might be a bit higher (
http://ellipse.inhs.uiuc.edu:591/mollusk/biblio.html would allow the
generation of some statistics, remembering the possible biases of the
database).  But the percent of specimens identified by molecular means is
always going to be quite low, and there are still a lot of species not
analyzed.

Additionally, a molecular result does not automatically yield agreement on
the species status.  Lumpers and splitters remain.

On Thu, Jul 30, 2015 at 4:13 AM, Timothy Jones <tjone54 at tigers.lsu.edu>
wrote:

> 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/
> > > _______________________________________________
> > > Taxacom Mailing List
> > > Taxacom at mailman.nhm.ku.edu
> > > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> > > The Taxacom Archive back to 1992 may be searched at:
> > > http://taxacom.markmail.org
> > >
> > > Celebrating 28 years of Taxacom in 2015.
> >
> > _______________________________________________
> > Taxacom Mailing List
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> > The Taxacom Archive back to 1992 may be searched at:
> > http://taxacom.markmail.org
> >
> > 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/
> >
>
>
>
> --
> Timothy M. Jones
> Life Science Annex Building, Room A257
> Louisiana State University
> Baton Rouge, LA 70803
> Website - http://www.herbarium.lsu.edu/keys/
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> The Taxacom Archive back to 1992 may be searched at:
> http://taxacom.markmail.org
>
> Celebrating 28 years of Taxacom in 2015.
>

-- 
Dr. David Campbell
Assistant Professor, Geology
Department of Natural Sciences
Box 7270
Gardner-Webb University
Boiling Springs NC 28017