Larry Moran wrote:
> On Tue, 25 May 2004 23:48:33 +0000 (UTC), 
> Anon.  wrote:
> 
>>Larry Moran wrote:
>>
>>>On Sun, 23 May 2004 18:07:23 +0000 (UTC), A
>>>non.  wrote:
>>
> 
> [snip]
> 
> 
>>>>I think I can still use my same question: Doesn't that depend on how 
>>>>you measure evolutionary change?  It's not clear to me that we have 
>>>>to measure it at the sequence level.  
>>>
>>>I didn't say you *have* to measure it at the sequence level. I just
>>>said that when you take into account ALL evolutionary change, including
>>>change at the sequence level, then drift is the main mechanism.
>>>
>>
>>To measure "all evolutionary change" you have to measure
both phenotypic 
>>and genotypic change.  How do you put these onto the same scale?  You 
>>have to weight them somehow, and it's not clear to me that there is a 
>>unique way of doing this - it will depend on your ideas about the 
>>relative importance of the genotypic and phenotypic levels in evolution. 
>>    You can, I think, get either selection, or drift, (or contingency?) 
>>as being the most important mechanism, depending on how you weight them.
> 
> 
> Why not give it a try? We already have an effective and quantitatvie way of 
> measuring evolution by looking at changes in DNA sequence. If you want to 
> find a more effective measure then let's see what you come up with. 

The first eigen value of the transition matrix for the changes in the 
phenotypic traits?  You can define the process in either discrete or 
continuous time.  You can even use a hierarchical model so that you can 
include discrete traits.

It's not clear to me that simply looking at changes in DNA sequence is a 
good measure of evolution - how do you deal with polymorphism?

Hmm, Actually, you can use the same sorts of models as I've suggested 
for phenotypic traits.

So
> far, all I've seen is some warm fuzzy feeling that "phenotypic change"
> should get a higher score in order to restore the supremacy of natural
> selection as a mechanism of evolution. Can you turn that subjective
> feeling into a scientific definition that we can examine?
> 
That's a mis-representation - I'm not arguing that phenotypic change 
should get a highe score, but rather that there is no obvious single 
score, so whatever measure you use is subjective.  Why remove phenotypic 
traits from evolution?

> Let's take the evolution of humans and chimps as an example. We already
> know that they differ by about 2% in DNA sequence. How would you evaluate
> the "phenotypic changes" along each lineage in order to arrive at some
> quantitative measure of the amount of evolution in each species from
> the time of the last common ancestor? How much of that is due to natural
> selection?
> 
That's actually something I'm starting to work on.  Over short time 
scales, one can compare Fst and Qst (e.g. Palo et al. 2003 Molecular 
Ecology, 12: 1963-1978) but some more work needs to be done to find a 
more quantitaive formulation.  I've started work with a colleague on the 
variation between species, but I'm not sure how that will pan out.

Bob

-- 
Bob O'Hara

Dept. of Mathematics and Statistics
P.O. Box 4 (Yliopistonkatu 5)
FIN-00014 University of Helsinki
Finland
Telephone: +358-9-191 23743
Mobile: +358 50 599 0540
Fax:  +358-9-191 22 779
WWW:  http://www.RNI.Helsinki.FI/~boh/
Journal of Negative Results - EEB: http://www.jnr-eeb.org
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