High rate of transition to transversion ??

[David Pollock]

In response to <3kbn07$5ht at montespan.pasteur.fr> Hassan Badrane, 
rasmus at mws4.biol.berkeley.edu
writes:

	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).

If the transition to transversion rate ratio is high, however, the 
observed transition
to transversion ratio will level off much faster due to the fact that 
transitions will
saturate (counted numbers will level off) long before transversions.  The 
effect of 
transversions masking transitions is going to be smaller.  Another way of 
looking at it
would be that if the transition rate is much higher than the transversion 
rate, then it
is more likely for an existing transition to be masked by another 
transition simply
because another transition is more likely than a transversion.

David Pollock