Interpreting results

[glaudelrio]

Hi, Any help from anyone who understands xpclr would be appreciated.

I am trying to use xpclr to detect selective sweeps on the genomic landscape of individuals in a hybrid zone. Here phenotype A, represents one parental population, and phenotype B represents the other parental population.

When I set population A as individuals with a certain phenotype (let's call it phenotype A), and the object population as individuals in with phenotype B, I detect a strong signal of selection (xpclr = 200) in a genomic region containing genes which I know are associated with the production of phenotype A.

On the other hand, when I set population A as individuals with phenotype B, the signal for selection disappear. In other words, when the reference population is population B (with phenotype B), and the object population is population A (with phenotype A), xpclr results for that genomic region, which I know is defining phenotype here, are below 10.

What is the interpretation in this case? Does that mean that xpclr is detecting a signal of positive selection for the allele defining phenotype A?

Thank you for any help you can provide!
cheers