estimating selection and theta

4 Replies

HELP!

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.

4 thoughts on “estimating selection and theta”

  1. KC

    You’re not thinking of something of along the lines of Otto 2000, are you?

    Clues to our evolutionary history lie hidden within DNA sequence data. One of the great challenges facing population geneticists is to identify and accurately interpret these clues. This task is made especially difficult by the fact that many different evolutionary processes can lead to similar observations. For example, low levels of polymorphism within a region can be explained by a low local mutation rate, by selection having eliminated deleterious mutations, or by the recent spread to fixation of a beneficial allele. Theoretical advances improve our ability to distinguish signals left by different evolutionary processes. In particular, a new test might better detect the footprint of selection having favored the spread of a beneficial allele.

    Otherwise, I’m not terribly sure what you’re looking for.