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DNA vs amino acid sequences

Christopher L. Schardl clscha00 at ukcc.uky.edu
Thu Jun 15 10:14:26 EST 1995

ttha at uhura.cc.rochester.edu (Tom Thatcher) wrote:
>I used the amino acid sequences,
>for the following reasons:
>3) INTRONS:  A DNA sequence comparison should only include coding sequences.

This seems a circular argument, if I am following it

>>5) PROTEIN IS THE UNIT OF SELECTION: For protein-encoding genes, the object
>   on which natural selection acts is the protein itself.  The underlying
>   DNA sequence reflects this process in combination with species-specific
>   pressures on DNA sequence (like the need for thermophiles to have DNA
>   that is resistant to melting).  If function demands that a protein
>   maintain a specific sequence, there still is room for the DNA sequence
>   to change. (see #1).

Do your tree-building algorithms assume neutral theory, or can you weight 
specific sites in the protein for their likelihood of change. Some would consider 
this point a good reason NOT to use the protein sequences. However, it is 
difficult to conceive of how any sequence that evolves at less than maximal rate 
can be assumed to follow the neutral theory. Any sequence that evolves at maximal 
rate is really only good at low taxonomic levels because saturation is quickly 

>My recommendation is, if you can, do the trees both ways 

Sounds like excellent advice!

>You can give a PC to a Homo habilis,

I am still unconvince that I or anyone I know is anything BUT Homo habilis. As 
Mayr points out, it is not possible to apply biological species concepts to 
fossils (untill Jurasic Park becomes a reality).

Chris Schardl
Plant Pathology
University of Kentucky

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