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Proof or counter-proof... this is how to do it.

Ludvig Mortberg Agneta.Guillemot at historia.umu.se
Fri Jul 14 16:58:54 EST 1995

higgins at ebi.ac.uk wrote:

- - - 
> what is it about the molecular clock hypothesis that arouses such
>antagonism (especially in some groups of people)??

Because the idea of the molecular clock has been elevated to a general
law without proof. I don't like that. Systematists that interpret
morphologic data have been working hard this century, trying to build
trees over the living world. And suddenly some people, without
convincing arguments or data  to demonstrate their theories, claim
that there is a "molecular clock" that can solve riddles in
phylogenetic research and may have priority over other methods. That's
how I feel about it anyway.

Well let's discuss the clock, shall we?

I wrote:

>> (1) Phylogenies, divergence dates etc, obtained by the clock,  
>> should conform with fossil data. 

higgins at ebi.ac.uk replied:

>Within the errors (stastical and experimantal) inherent in both types of data.

The question is, do they? In some cases yes, but in others no. 

I wrote:
>> (2) When different parts of the genome are used in an analysis the  
>> results should be the same. Different chromosomes, protein  
>> sequences etc should give the same divergent dates or  
>> phylogenies. Of course  it may not be possible to draw conclusions  
>> from data from a very slowly evolving protein. Histones for  
>> example. 

higgins at ebi.ac.uk replied:

>NO!!!!!  e.g. the Y chromosome (or parts of it) in mammals goes faster
>than the X.  e.g. different proteins go at totally different rates if you
>use amino acid distances or non-synonymous nucleotide distances.  

But proteins evolving at about the same speed should give similar
phylogenies, right? For example, if you use sequence data from both
the Y chromosome, (according to you a portion of the genome that
appears to evolve relativley fast) and from say the mitochondria (also
supposed to evolve fast, according to a message in this thread) you
should come up with the same phylogeny? Mitochondria and Y-chromosomes
can't give different phylogenies? Or...

I wrote:
>> (3) The Wilson relative rate test should be positive when applied  
>> to three reasonably closely related species. See illustration below: 
>>       / A 
>>     /  
>>   / 
>> /\    / B 
>>    \/ 
>>      \ C 
>> We have determined that B and C are closest. The distance from  
>> B to A, be it nuclear substitutions or melting temperatures for  
>> DNA-DNA hybrids, should of course be the same as the distance  
>> from C to A. Otherwise B and C have evolved with different  
>> speeds. 
>> The last test may be the one that is most useful in determining  
>> wether there is a clock or not. 
>> Now what does the data say?  

higgins at ebi.ac.uk replied:

>Why don't you look first??

Because I'm trying a shortcut by asking people on usenet.

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