Does anybody have a reference to a paper where sequence data was used to estimate theta (rather than microsatellites) for the purpose of controlling for effective population when looking at selection in different populations and species.
It seems that when looking at selection in multiple species, msats may not offer the best way to subtract out the effects of Ne. This is basically because you are assuming that the differences in theta (variability) are related to differences in effective population size, but when looking across several different species… the differences in theta could not only be attributed to differences in Ne, but also to differences inherent to variability at the particular msat loci… How many times have you tried to use a msat that you know to be hypervariable in one species on another, only to find that it monomorphic in the other.
It might be the case that estimating theta from nuclear (or mt?) sequence data might be the better way to do this.