There are usually multiple solutions for the same problem – such as here for instance. Same is true with adaptation – fitness landscapes can have multiple peaks, each corresponding to – say – mutations in different genes. In other words, same fitness can be achieved by convergence using different pathways.
Genomescans have become a popular tool for identifying genomic regions under selection. They could be also used to probe whether different populations have adapted to same selection pressure by gaining mutations in same or different genes. Yet, despite of their increasing popularity, the methods have been also taking some fire as described here.
And more has been just fired. In a well versed comment-piece, Pritchard and Di Rienzo point out that genomescans might not be the tool-of-trade in identifying adaptations (or genes responsible for them) which have a polygenic basis. That is, perhaps most of those traits that people study using classical quantitative genetic methods.
Read more about this from the link below – and hold on to your QST-data for time being.
Pritchard JK & A Di Rienzo (2010) Adaptation – not by sweeps alone. Nature Reviews Genetics 11: 665-667. doi:10.1038/nrg2880