[Taxacom] Exemplars, loci

Fri Jun 15 14:08:09 CDT 2007

DNA barcoding is a source of the data you described - many specimens per
terminal taxon, sampled from across its geographic range.  Barcoding
most animal groups involves only one region (mitochondrial COI).  There
are a LOT of COI data already collected and the accumulation rate is
rising.  Land plants will probably require several plastid regions for
species-level separations.

We are finding two things about intraspecific barcode sequence
variability.  In some cases we are finding geographic or ecological
structure within what's been called a species.  These may be races,
ecological variants, or cryptic species, depending on the case and the
philosophy of the researchers.  In most cases we are finding very little
variability - too little, in fact.  The alternate explanations are that
species went through population bottlenecks at some point, leaving low
intraspecific variability as a founder effect.  Alternatively,
incompatibities between organellar and nuclear sequences could be
causing 'selective sweeps' that clean mt variability out of populations.
This is far from settled and is one of the interesting side-discoveries
of barcoding.

David E. Schindel, Executive Secretary

Consortium for the Barcode of Life
202/633-0812; fax 202/633-2938; portable 202/557-1149
Email: SchindelD at si.edu 
CBOL WEBSITE: http://www.barcoding.si.edu <http://www.barcoding.si.edu/>

Office and overnight delivery address:

   National Museum of Natural History
   Room CE-119
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   Washington, DC 20560

Postal mailing address:

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   P.O. Box 37012, MRC-105
   Washington, DC 20013-7012

-----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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