In the attached file, I have demographic statistics (Fu's Fs; Tajimas D; and Ramos-Onsins and Rozas's R2 neutrality tests), mismatch distributions (MMD) and related goodness-of-fit statistics for Pooled samples, Clad 1, and Clade 2. For Pooled samples as well as Clade 1, I have significant negative Tajimas D, negative but non-significant Fu's Fs, and positive but non-significant R2 values. For Clade 2, I have non-significant negative Tajimas D, negative and significant Fu's Fs, and negative and significant R2 values. On the other hand, MMD only for Clade 2 is uni-modal. The interpretation of data in each case seems to be complicated. What is the most reasonable demographic explanations for Pooled samples, Clade 1, and Clade 2 based on these evidence?
Hi Fatah,
Tajimas D, Fu's Fs and Ramos-Onsins and Rozas's R2 use different information contents of DNA sequences. Tajima's D test is based on the number of segregating sites; Fu’s Fs test use information from the haplotype distribution, while Ramos-Onsins and Rozas’s R2 test use information of the mutation frequency. The sample sizes and number of segregating sites affect these statistics in different ways. You should give report these two parameters in the table. Read Ramos-Onsins & Rozas, 2002 and a later following up paper by the same author (in MBE 2005?) will help you make a judgement.
BTY. Maybe you can try Bayesian skyline plot to see changes of population size through time.
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