I have used 454 GFLX to (de-novo) sequence two plant ecotypes (two divergent populations which adapted to each of their own habitats) by polling 16 individuals from each ecotype. To date, i have finished assembling, SNPs and Indel detection. And i also calculate population parameters like Watterson's Theta (θ = 4Neμ), Pi (which is expected to be equal to theta under neutral equilibrium). However, i am not sure whether it is possible to inferring some other parameters like Ne (effective population size), divergence time of the two ecotypes.
By the way, i would like to know how do you identify SNP outliers for you data if you have done or doing the same thing. Is it good to use a Fst based approach or Fisher exact test?