[Taxacom] Patterns of homoplasy

[Peter Stevens]

As the patterns of distribution of variation become more complex,  
part of the problem then becomes how to optimise characters on the  
tree (see e.g. papers by Donoghue, Ree et several al.); I find it  
excruciatingly difficult.  Distributions of individual characters  
might be homoplasy, but might not. Furthermore, our basic knowledge  
of much morphological s.l. variation is very incomplete indeed   
(e.g., think embryo sacs/endosperm  in flowering plants and what has  
been found here in the last few years) - and this is terribly  
important.  Indeed, as we find out more, our understanding of  
characters - and hence the very nature of the problem - changes.   
Given that, the distribution of things like nitrogen fixation in fl.  
pl. have long seemed to ask for an explanation, which may well have  
something to do with mycorrhizae and be at the molecular level. Plant  
chemists have weighed in on the remarkably erratic distribution of  
many secondary metabolites; Endress has written about larger patterns  
of variation in rosids (but he could do this only when he had  
assembled the basic information, much of it acquired by himself and  
his collaborators); and there is quite a bit more out there if you  
look at the literature (I don't know about animals so much).  The  
literature on developmental lability e.g. among ANITA grade  
angiosperms is also relevant here. Of course, there are several  
papers on "tendencies" from back in the 1980s and early 90s, but this  
line of thought didn't get very far then.

P.
On Aug 18, 2008, at 7:11 PM, Bob Mesibov wrote:

> There's a memorable courtroom scene in Oliver Stone's film 'JFK'  
> that I
> often think of when looking at tree-form phylogenetic hypotheses.
>
> New Orleans DA Jim Garrison is tracing the course of the bullet that
> killed Kennedy, *if* the findings of the official inquiry are  
> accepted.
> The bullet's track, with its supposed richochets and passages through
> people, is wildly improbable. It's far more likely that the
> interpretation of evidence by the official inquiry is flawed.
>
> The connection with phylogenetic hypotheses goes like this:
>
> We use character evidence (sequences, morphological character  
> states) to
> generate a set of phylogenetic hypotheses, and tentatively propose
> (usually) a single hypothetical tree based on that set. We know the
> assumptions involved and we're aware of the uncertainties involved in
> the 'phylogenising' method of choice. (Although as Richard Zander has
> pointed out, many phylogeneticists don't know how to determine those
> uncertainties, or aren't interested in them.)
>
> But inspection of the 'best' tree(s) always reveals character  
> conflict,
> or possible (minor?) disagreements with the evolutionary model we used
> to link raw sequences in a branching network. You might well then  
> say to
> yourself, 'Hmm. So this structure - if I accept the hypothesis -  
> appears
> here, then disappears in the lineage, then reappears later, and
> meanwhile appears independently over here. Wonder if other  
> structures do
> that?'
>
> What's more interesting to me is that I don't see this bullet-tracking
> in the systematic literature. It's as though homoplasy (in the case of
> morphology) is something of an embarrassment. We have our tree, we  
> don't
> want to think about what that means for character evolution. I'm aware
> that there are papers and books dealing with patterns of homoplasy,  
> but
> these seem to focus on similarity as a biological phenomenon, not  
> on the
> ins, outs, ricochets and surprising passages of individual homologue
> bullets.
>
> I'm wondering if study of homoplasy and sequence anomalies could  
> reveal
> widely occurring patterns of character and sequence evolution. Having
> discovered these, we might then have a new tool to assess a tree's
> plausibility.
>
> The first problem would be digging out those bullet-tracks from the
> systematics literature. Not many systematists do a Jim Garrison and  
> say,
> 'If we accept this best-supported tree, this means...'
> -- 
> Dr Robert Mesibov
> Honorary Research Associate
> Queen Victoria Museum and Art Gallery and
> School of Zoology, University of Tasmania
> Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
> (03) 64371195; 61 3 64371195
> http://www.qvmag.tas.gov.au/mesibov.html
>
>
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