[Taxacom] Why character-tracking doesn't happen?

[Richard Jensen]

I'll only attempt to respond to my contribution below.

What Platnick was saying, as I understood it, was that if we have a 
character that is homoplasious on the tree, i.e., the same state arises 
as a parallelism or convergence, then we have made a mistake in our 
interpretation of the character: what we are calling two states of the 
same character are really two different characters. Our assessment of 
homology is incorrect.

Dick J

Richard Jensen, Professor
Department of Biology
Saint Mary’s College
Notre Dame, IN 46556
Tel: 574-284-4674



John Grehan wrote:
>   
>> bounces at mailman.nhm.ku.edu] On Behalf Of Richard Jensen
>> Sent: Friday, September 12, 2008 11:05 AM
>> To: Bob Mesibov
>> Cc: taxacom at mailman.nhm.ku.edu
>> Subject: Re: [Taxacom] Why character-tracking doesn't happen?
>>
>> There's another way to view homoplasy. I believe it was Norm Platnick
>> who wrote that homoplasy is an indication that we have made incorrect
>> assumptions about homology. If character state 1 in taxon A and
>> character state 1 in unrelated Taxon B represent a homoplasy on the
>> tree, then they are not the same thing.
>>     
>
> But why could they not represent the "same" thing as a plesiomorphic
> character which is represented in just some members of the ingroup
> (being list in others) and the outgroup - or do I misunderstand?
>
>   
>> Bob Mesibov wrote:
>>     
>>> It works like this. A tree is built on an optimality criterion, say
>>> parsimony. Within this tree there's incongruence: not all the
>>> morphological characters, or all the sequences in a multi-locus gene
>>> set, will give the same tree when analysed separately. This
>>>       
> incongruence
>   
>>> is explained *after the fact* as due to homoplasy.
>>>       
>
> I thought homoplasy was just a term to describe character similarities
> that do not match the preferred tree, and as such they are not an
> explanation of anything. The homoplasies themselves are then 'explained'
> as convergence, parallelism etc.
>
>   
>>> Do people working at this higher level think something like: 'The
>>>       
> genes
>   
>>> and/or morphological characters disagree. I don't know why and it's
>>>       
> not
>   
>>> feasible to investigate. All I know is that this is a pretty good
>>>       
> tree
>   
>>> based on sound methodology'??
>>>       
>
> In morphology at least, the problem might sometimes lie more with
> character state identification and underlying assumptions. For example,
> there is supposed to be rampant homoplasy in the evolution of large
> bodied hominoids, but this extensive homoplasy only occurs when the best
> supported tree (human-orangutan) is rejected using other criteria (such
> as a prejudged preference for molecular trees), or characters are
> erroneously included because the outgroup is highlight restricted (e.g.
> just gibbons for the large bodied hominoids, or just one or two monkey
> species), or characters are just not correctly delineated (such as
> saying something is present when it is not).
>
> John Grehan
>
>