High rate of transition to transversion ??

[Rasmus Nielsen]

In article <3kbn07$5ht at montespan.pasteur.fr> Hassan Badrane  
<hbadrane at pasteur.fr> writes:
> Hello evolusionnists,
> 
> I have many non-coding sequences. I have compared each one to the others  
and 
> between the results that I've got, there is the ratio of the transitions  
to 
> the transvertions. This number was almost similar between the most pairs  
of
> sequences but between few pairs this ratio was so high (X3 to X11).
> In this last pairs the sequences was coming from isolates with a close  
> relationship (close geographic origine).
> My question is why and how we can explane this event ? does it mean  
some-
> thing ?
> 
> I thank you very much for your help
> 
> Hassan
> hbadrane at pasteur.fr

It may indicate that you are approaching saturation in the number of  
substitutions in the other pairwise comparisons.

If the ratio of the rate of transition to transversions is high in your  
data set, the inferred ratio of the number of transitions to transversions  
(based on the number of nucleotide differences between pairs of sequences)  
will level of, as the level of divergence increases.  This is due to the  
simple fact that transitions will be masked by transversions when the  
level of divergence is sufficiently high (enough transversions have  
occured).

Therefore, in your case, you would observe a high ts/tv ratio between the  
closely related sequences (x3 and x11) but not between the other  
sequences.

However, the effect could of course also be due to stochastic factors.  It  
is an entirely different story how to distinguish these two alternatives  
statistically.