molecular phylogeny

John Grehan jgrehan at SCIENCEBUFF.ORG
Thu Oct 9 11:50:56 CDT 2003

My questions, and clarifications, may indicate more my ignorance than a
necessary problem with the method. As for supporter of molecular phylogeny
- I do not intend to convey any pejorative connotation. It is the people
who actively use and apply the methods of molecular phylogeny that are
'supporters' and therefore in the best position to respond with
information. And I am genuinely appreciative of this and the other
responses so far.

>1. I don't follow your line of reasoning that just because a mutation
>event is random it shouldn't track speciation events. Simple descent
>with modification holds true even here: once a mutation has gone to
>fixation (and is now called a "substitution") then it can be passed on
>to future generations. no reason why this should be homoplasious. It
>sounds as if you are confounding "random" with substitutional

If a non-coding substitution of one base by another can chance in one
direction, why not in another - back again just as much such that there is
no necessary tracking of sequences with species lineages?

>2. Outgroup comparison, same as morphology! (although if there is
>really NO change then obviously you cannot make a tree at all and you
>need to find a more variable region of the genome...)

I did not express myself well here. I am suggesting a situation where one
can make a species tree because there are differences between he species,
but that these relationships are all primitive retentions inherited from
the ancestor rather than being new conditions representing the subsequent
speciation events. Is this possible?

>Andrew Mitchell
>Andrew Mitchell
>Senior Lecturer, Molecular Phylogenetics
>School of Molecular and Cellular Biosciences
>University of Natal
>Private Bag X01
>Scottsville, 3209
>Tel:  +27 (0)33 260 5815
>Fax: +27 (0)33 260 5462
> >>> LISTSERV at LISTSERV.NHM.KU.EDU 03/10/09 07:00:10 >>>
> >Date:    Wed, 8 Oct 2003 18:16:32 -0400
> >From:    John Grehan <jgrehan at SCIENCEBUFF.ORG>
> >Subject: molecular phylogeny
> >
> >I would be interested in what supporters of molecular phylogeny on
> >list would say with respect to the following two questions:
> >
> >1. If non-coding regions of DNA are supposed to be subject to random
> >mutational changes why should the genetic patterns between taxa match
> >phylogenetic sequence of taxageny (or speciation)?
> >
> >2. How would one deal with the possibility that there has been no
> >evolution at all between species for a group so that all that is
> >compared are the ancestral states with respect to the species being
> >compared and thus get a consistent pattern of molecular relationships
> >one that has nothing to do with speciation sequences?
> >
> >I realize that there are answers to these questions, but I have not
> >across them (or I overlooked them in the literature, or I
> >what I was reading).
> >
> >John Grehan
> >
>Please find our disclaimer at

Dr. John Grehan
Director of Science and Collections
Buffalo Museum of Science
1020 Humboldt Parkway
Buffalo, New York 14211-1293
Voice 716-896-5200 x372
Fax 716-897-6723
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