"types" - was Barcoding (animal) life

STEPHEN MANNING SDMANNING at ASUB.EDU
Wed Feb 5 09:38:28 CST 2003


At 10:24 AM 2/5/03 +1300, Michael Bayly wrote:
>Stephen,
>The "Type" concept is a nomenclatural one - and statistics don't really come
>into the matter, as I see it.  The concept ties a name to a specimen, and
>therefore makes the name definable in an exact sense (in that it refers at
>least to that specimen).  How widely you apply that name (e.g. to a range of
>other specimens) is a matter of interpretation, and there will often be
>seriously conflicting views on such matters.
>
>Modifying the type concept such that you would need multiple (geographically
>spread) specimens, would just be asking for trouble.  Two biologist could
>easily disagree as to whether the "types" represent one or more biological
>entities (species, subsp. etc) - no matter how carefully the work is done.
>If conflicting later classifications are proposed, what then happens about
>the application of names? You would probably end up (through
>lectotypification) with a re-narrowing of type concept for particular taxa -
>then aren't you back where you started?

Maybe so, but if this represents reality better and increases our knowledge
of that reality, then I submit that this would be good.  (I guess I am more
of a splitter than a lumper at this point in time.)

>Obviously for any study that seeks to assess the circumscriptions and/or
>relationships of taxa (using molecules, morphology, whatever) you need to
>include reasonable sample sizes to ensure the soundness of your conclusions.
>You also need to know where the "type" sits in relation to your assessment
>of variation - so you know how to apply names to the taxa you perceive.  But
>there is no need to think of "types" as representative of all (or most)
>variation in the taxa you recognise.

OK - but still, since molecular and some other workers choose other than
type specimens upon which to do research, and it would often be impossible
to use the type for such research even if they wanted to, it does seem that
as presently used the type specimen concept acts more as a constraint than
an enhancer of knowledge about the taxa of which they are types.

This really does get back to the issue, addressed recently by Richard Pyle
and others, of how to fit modern DNA and other phylogenetic information
into the Linnaean system of nomenclature.  I have said, or at least
thought, in other contexts that nomenclature has become the tail that wags
the taxonomic dog and don't particularly want to reopen that can of worms,
but still - I can remember perceiving this issue, at least dimly, back in
the 1980's and justifying doing essentially phenetic work on the basis that
"no one wants to overrule Linnaeus".  Well, maybe that is ultimately what
is needed.  Maybe we would actually feel liberated if we abandoned the
Linnaean system of nomenclature or at least relegated it to a subsidiary
role when there is a conflict, compared to measures based on quantifiable,
statistically valid measures of DNA and morphological divergence (which of
course would need their own reference points whether we called them "types"
or not.)

This does not mean that I am a "strict cladist" - no, I hypothesize that
the amount of convergent evolution and reticulate evolution are probably
underestimated in most present models.  Another reason why sometimes,
perhaps often, the type specimen may actually differ more genetically and
evolutionarily from other members assigned to the same taxon than
morphology would detect and why cladistic analyses may more often than not
be based on specimens significantly different from the types of the names
assigned to them.

Thanks,
Steve




>Mike
>
>
>----------------
>Dr Michael Bayly
>Research Scientist in Plant Biosystematics
>Museum of New Zealand Te Papa Tongarewa
>PO Box 467
>Wellington, New Zealand
>Ph: +644 381 7262
>Fax: +644 381 7070
>
>
>
>-----Original Message-----
>From: STEPHEN MANNING [mailto:SDMANNING at ASUB.EDU]
>Sent: Wednesday, 5 February 2003 9:31 a.m.
>To: TAXACOM at USOBI.ORG
>Subject: Re: Barcoding (animal) life
>
>
>At 11:12 AM 2/4/03 -0600, Richard Zander wrote:
> >A.M.:
> >By reliably identifying organisms, you mean like forensic DNA typing? Is
> >that what taxonomists do? Identify organisms?
> >
> >I think taxonomists do a lot more. As to money, we taxonomists have 250
> >years of the Linnaean endeavor behind us and have generated or mediated
> >great economic gains for the human race. A billion dollars is to laugh at.
> >(Oh, that's slightly rhetorical, since my 2004 research budget is presently
> >zero.)
> >
> >Sure, I agree with you that molecular and morphological work can proceed
> >simultaneously. The fact that it is mainly molecular work that is now
>funded
> >(grants, positions) indicates that such synergy must be rare and getting
> >rarer. The Planetary Biodiversity Inventory now supported by the U.S.'s
> >National Science Foundation is a worthy exception.
> >
> >_Everybody_ ducks my concerns about the statistical basis behind
>reliability
> >of phylogenetic estimation. Your response, Andrew, ("Yawwn") is at least
> >novel.
>
>Richard et al.,
>
>We have some things in common!  First, my research budget for 2004 is also
>zero.  Second, I have been troubled for quite awhile by the thought that
>phylogenetic analyses even at the family or higher level, let alone at the
>species level, based on either DNA or morphology, may be based on single
>specimen samples of the taxa represented.  It would seem that elementary
>statistics would dictate a sample size of AT LEAST ten randomly selected
>specimens be used for either DNA analysis or morphological analysis of the
>variation or lack thereof; and a sample of at least 100 specimens per taxon
>would be preferable and by no means excessive.
>
>I attribute most of the problem to the fact that taxonomists have not,
>traditionally, been statistically oriented.  Even the "type specimen"
>concept suffers from this deficiency.  There is no real reason to believe
>that a type specimen represents an average genotype or phenotype for the
>taxon of which it is the type, with obvious potential for error in
>phylogenetic and other analyses even if, as I think someone pointed out
>recently in this forum, the type specimen is what should be used to extract
>DNA for analysis.  Maybe the codes need to be modified to require a sample
>of ten or more specimens, as randomly selected and hopefully as
>ecologically and geographically diverse as possible, to qualify as the
>"type" of a taxon for future species descriptions, unless fewer than ten
>specimens are available.  I acknowledge that it probably won't be easy to
>require broadening the type specimen concept to the point of assuring its
>statistical validity, but nothing ventured nothing gained.
>
>If we ever do get to the point of using Bar Codes or other means of
>categorizing DNA diversity, I hope it can be made essentially mandatory
>that a sample of a statistically valid number of specimens (10?) (100?) and
>gene sequences per specimen (10?) (100?) be included in the DNA analysis in
>order for the analysis to be recognized as valid.  If this is done up front
>and becomes the tradition, it will be easier than it probably would to be
>to wait until later to do what is necessary for statistical validity, when
>less valid approaches would have become the norm.
>
>If  the above were implemented, it ought to be able to generate more
>funding for both morphological and molecular taxonomists!
>
>Steve Manning
>
> >R.Z.
> >______________________
> >Richard H. Zander
> >Bryology Group
> >Missouri Botanical Garden
> >PO Box 299
> >St. Louis, MO 63166-0299
> >richard.zander at mobot.org <mailto:richard.zander at mobot.org>
> >Voice: 314-577-5180
> >
> >
> >
> >-----Original Message-----
> >From: Andrew Mitchell [mailto:MitchellA at NU.AC.ZA]
> >Sent: Tuesday, February 04, 2003 9:18 AM
> >To: TAXACOM at USOBI.ORG
> >Subject: Re: [TAXACOM] Barcoding (animal) life
> >
> >We *sample* taxa not only
> >because of limits of time and money but because of the law of
> >diminishing returns. We want to be able to reliably identify organisms
> >and as an added bonus work out their evolutionary history, not count all
> >stomata on all specimens in the herbarium just for the fun of it.
> >
> >
> >Molecular and morphological/phenological/ecological etc. work can
> >proceed simultaneously.
> >
> > >
>
>Stephen D. Manning, Ph.D.
>Professor of Biology
>Mathematics and Science Division
>Arkansas State University - Beebe
>P. O. Box 1000
>Beebe, Arkansas 72012-1000
>USA
>Tel: 501-882-7162
>
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Stephen D. Manning, Ph.D.
Professor of Biology
Mathematics and Science Division
Arkansas State University - Beebe
P. O. Box 1000
Beebe, Arkansas 72012-1000
USA
Tel: 501-882-7162




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