[Taxacom] Exemplars, loci

[Richard Zander]

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 
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Missouri Botanical Garden
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> -----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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