More on reticulation

[STEPHEN MANNING]

At 06:49 PM 2/6/02 -0800, Curtis Clark wrote:
>At 01:38 PM 2/5/02, STEPHEN MANNING wrote:
>>But yet botanical cladograms are constructed the same way as others, aren't
>>they?  If so, and for as long as this has occurred and continues to occur,
>>that is a warning flag for the methodology as a whole, from my
>>perspective.
>
>That's your call, of course, but most botanists I know won't reject a
>technique just because it's not infallible.

I don't either, but could it be improved?  It's not my field, but I
sometimes wonder whether a statistician could come up with, or has come up
with, a mathematical model which would take into account reticulation in
such a realistic way that it would often alter, based on probable
paleopolyploidy, what is determined to be the most parsimonious
cladogram.  If about 50% of plant species are polyploid, this seems a major
concern especially when analyzing relationships of species within genera,
or genera within families (as both are subject to hybridization events).

>>And how about the degree to which cladistic (and other?)
>>botanical studies use chloroplast and ribosomal rather than nuclear genes
>>from which to generalize?
>
>First, ribosomes don't have genes, they are the results of genes:
>cytoplasmic ribosomes are coded by nuclear DNA, chloroplast and
>mitochondrial ribosomes by their respective genomes.

Sorry, I was thinking mitochondrial and wrote ribosomal.

>Second, the comparison of chloroplast and nuclear gene trees is a common
>method for studying reticulation (as one line of evidence, of course).
>
>Third, chloroplast and mitochondrial genes are uniparental, but nuclear
>genes can recombine contributions from both parent species. These genetic
>chimeras are another way to study reticulation.
>
>
>--
>Curtis Clark                  http://www.csupomona.edu/~jcclark/
>Biological Sciences Department             Voice: (909) 869-4062
>California State Polytechnic University      FAX: (909) 869-4078
>Pomona CA 91768-4032  USA                  jcclark at csupomona.edu