[Mesquitelist] S-value

[Monica Guerrini]

Hi!
Thank you very much for your answers to my 
question some days ago! Now I have resolved my 
first problem, that is importing and using a gene 
tree reconstructed with other programs! It is very easy!!!!
But now I have another two questions.
First of all if I measure the distributions of 
test statistics (Slatkin & Maddison's S) on a 
simulated population tree, when I reject or 
accept this model drawn? I know that if the 
observed S.-value of my gene tree falls outside 
of the 95% confidence interval, that model are 
not supported by the data. On the contrary, if I 
have a case similar to the example of Mesquite's 
manual I don't reject the model (S = 9, observed 
values within the 95% confidence interval, that is 4 and 10).
But now I suppose this example:
I measure the observed S-value for my first gene 
tree and that is 9 (for example...!).
Now I draw some population trees corresponding to 
the evolution models I want to test. I measure 
the distribution of S-values for each model.
model n° 1: the S-value distribution has only one 
value, for example 2, so I reject the model (outside the boundary)
model n°2: the S-value distribution has two 
limits: 5 and 15, so I accept the model (inside the boundary)
model n°3: the S-value distribution has only one 
value, that is 9 (exactly my observed S-value)      ??????
model n°4: the S-value distribution has two 
limits: 9 and 15 (lower tail exactly my observed S-value)      ??????
What happen for models n° 3 and 4? I'm not sure 
to accept or reject these hypothesis.......

The second question is:
For use a gene tree (reconstructed with other 
software) and to measure S-value it is better to 
use a sequences tree or an haplotypes tree?

Thank you very very much again for your help!!!!!


Monica