I conducted Mratio analysis on my data set using M_P_Val.exe . It gave me following result;

Average M = 0.110098

Please wait...

0% of the time you expect a smaller ratio at equilibrium.

Using conventional criteria, there is evidence of a significant reduction in population size if less than 5% of the replicates are below the observed value. What I understand from the above results is that I have 0% replicates below thresh hold, so indication of bottleneck in this population.

I also calculated Mc using Critical_M.exe . It gave me following results for the same dataset:

Please wait...

Mean M = 0.791774

95% of equilibrium values of M should be above

Mc = 0.71504

where M = number of alleles / range in allele size

and range = (size of largest allele - size of smallest allele + 1)

I have a confusion here. While calculating Mc, the mean M = 0.791774. However, in the above step, the average M = 0.110098.

Why this difference?

When comparing M to Mc which M do I need to consider? If I take the M calculated by M_P_Val.exe (0.110098) with Mc (0.71504), there is bottle neck. However if I compare Mean M = 0.791774 calculated from Critical_M.exe, then there is no bvottleneck.

I have used Bottleneck and Msvar tools which show bottleneck in this data set.

Can anyone suggest why there occurs difference in M calculated by two Mratio executables/ Which one to consider when comparing it with Mc?

Thanks