Dear All,
I got the following comment from a reviewer "As some of the markers used are novel and derived from genes putatively involved in the infection process I would like to see a test of neutrality in order to be sure that they should be kept in the analysis. Markers that deviate from neutrality should not be kept to study the population structure in any given species." I have the following puzzles needing your help.
1) When performing genetic diversity or population genetic analyses, do we have to perform neutrality test for each marker we used (I use DNA fragments as markers)? Such analysis, if being performed, can only be performed when we got sequences from all individuals. If I finally find a marker deviates from neutrality, deleting this marker in following analyses may be a waste since I also lost sequence diversity information present in the marker.
2) How to perform a neutrality test? Which programs, and what indices to choose? How to understand the output? That is, when I get the Tajima’s D value (or other indices) for a DNA fragment, how to determine if my DNA fragment conforms to neutrality or not?
3) Is neutrality test only applicable to protein-encoding genes? Can ribosomal RNA genes be used for neutrality test?
4) Is neutrality test the same to selection pressure test? If no, what's their difference?
Thanks for your comments to any of my questions.
Yongjie
