[Taxacom] Exemplars, loci

Fri Jun 15 17:16:22 CDT 2007

Regarding large samples, I was referring to a possible increase in uncertainty in phylogenetic estimation of branching patterns. Not to the practice of barcoding itself, which is focused on identification of possible new species, and a helpful adjunct in (as Dave Schindel says) the context of traditional analysis.

Regarding the latter, large scale samples have apparently demonstrated the utility of barcoding in well-known groups, but not in poorly known groups (those without a well established phylogeny). See
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030422

= http://tinyurl.com/2f5h38 

for more into.

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Richard H. Zander 
Voice: 314-577-0276
Missouri Botanical Garden
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richard.zander at mobot.org
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and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
For FedEx and UPS use:
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> -----Original Message-----
> From: Schindel, David [mailto:schindeld at si.edu]
> Sent: Friday, June 15, 2007 2:57 PM
> To: Baum, Bernard; Richard Zander; Curtis Clark;
> taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] Exemplars, loci
> 
> I've made essentially the same statement on Taxacom and in print.
> Barcodes are a proxy for identification (i.e., assignment of specimens to
> known species).  Barcode data are also potentially useful characters for
> basic taxonomy, to be used alongside (NOT instead of) morphologic,
> ecologic, behavioral and other character traits.
> 
> David
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Baum, Bernard
> Sent: Friday, June 15, 2007 3:42 PM
> To: Richard Zander; Curtis Clark; taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Exemplars, loci
> 
> The real point is: how are species determined, defined and identified in
> the first place. It used to be by morphology for a long time, and then
> they were refined or altered by cytology and the rest you know.
> So, how does bar coding relates to this? At the most bar coding are an
> identifier and no more than that. The determination of species must rest
> on a multidisciplinary approach and definitely not on bar coding.
> 
> Bernard R. Baum, MSc, PhD, FRSC
> Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada
> Telephone/Téléphone: 613-759-1821
> Facsimile/Télécopieur: 613-759-1701
> Office Address/Adresse du bureau: ECORC, Neatby Bldg, 960 Carling Ave.
> City, Province/Ville: Ottawa, Ontario
> Postal Code (Code postal): K1A 0C6
> baumbr at agr.gc.ca
> res2.agr.gc.ca/ecorc/personnel/baum_b_e.htm
> 
>  Agriculture and Agri-Food Canada - Agriculture et Agroalimentaire Canada
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Richard Zander
> Sent: Friday, June 15, 2007 2:43 PM
> To: Curtis Clark; taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] Exemplars, loci
> 
> Well, what are those names terminal to lineages on cladograms? Are they
> species? or, rather, exemplars? Even if they are not species but
> exemplars, then they should be at least individuals, right? Not so. If
> the analysis is restricted to a particular DNA locus, then they are
> loci.
> 
> The cladogram analyzes loci. Only by inference does the cladogram
> analyze individuals, then by greater inference, species. How justified
> are these inferences?
> 
> And another thing, there was a fuss long ago about the very small number
> of individuals sampled from a taxon in molecular analysis. This seems to
> be no problem with anyone now, but I think it should be.
> 
> Analysis restricted to say only one exemplar per species were defended
> as a good start because it was expensive in many ways to do the
> analyses. Surely, surely we can start doing large scale sampling in
> species to see how heterogeneous a species is with respect to various
> useful DNA loci. If a species is genotypically heterogeneous, what about
> an ancestor? or an ancestor twice or thrice removed? Are all ancestors
> purified of sequence heterogeneity when speciation happens? is there
> only one individual ancestor per speciation event? or maybe can there be
> multiple say alloploid events of parallel speciation with one species
> derived from ancestors with different genotypes?
> 
> Lots of people on taxacom teach evolution and are more familiar with
> theory and experiment than I am. Have there been large scale sampling
> of, say, chloroplast and mitochondrial DNA with many individuals of each
> of several related species? What happens? Can you give a reference?
> 
> ******************************
> Richard H. Zander
> Voice: 314-577-0276
> Missouri Botanical Garden
> PO Box 299
> St. Louis, MO 63166-0299 USA
> richard.zander at mobot.org
> Web sites: http://www.mobot.org/plantscience/resbot/
> and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> For FedEx and UPS use:
> Missouri Botanical Garden
> 4344 Shaw Blvd.
> St. Louis, MO 63110
> ******************************
> 
> > -----Original Message-----
> > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> > bounces at mailman.nhm.ku.edu] On Behalf Of Curtis Clark
> > Sent: Thursday, June 14, 2007 9:47 PM
> > To: taxacom at mailman.nhm.ku.edu
> > Subject: Re: [Taxacom] invisible evolution/paraphyly
> >
> > On 2007-06-11 22:31, Rob Smissen wrote:
> > > Having spent too much time in the lab and not enough in a herbarium
> > > lately, it seems to me that monophyletic really means monophyletic
> at
> > > some fraction of loci
> >
> > In the sense that I and many other classical cladists use the term,
> > monophyletic is about grouping species, not loci.
> >
> > --
> > Curtis Clark            http://www.csupomona.edu/~jcclark/
> > Director, I&IT Web Development             +1 909 979 6371
> > University Web Coordinator, Cal Poly Pomona
> >
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