Uninformative polymorphisms bias genome scans for signatures of selection.

ABSTRACT:

Background

With the establishment of high-throughput sequencing technologies and new methods for rapid and extensive single nucleotide (SNP) discovery, marker-based genome scans in search of signatures of divergent selection between populations occupying ecologically distinct environments are becoming increasingly popular.

Methods and results

On the basis of genome-wide SNP marker data generated by RAD sequencing of lake and stream stickleback populations, we show that the outcome of such studies can be systematically biased if markers with a low minor allele frequency are included in the analysis. The reason is that these 'uninformative' polymorphisms lack the adequate potential to capture signatures of drift and hitchhiking, the focal processes in ecological genome scans.

SUBMITTER: Roesti M 

PROVIDER: S-EPMC3426483 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature