Mapping signatures of positive selection in the genome of livestock

Human driven selection during domestication and subsequent breed formation and breeding has left detectable signatures within the genome of livestock breeds. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology and for identifying selected genes that ultimately may help to further genetically improve these economically important species. Genome-wide screenings based on population techniques provide analytical tools to detect these signatures in relation to the act of selection. This review outlines a nonmathematical treatment of the theories and approaches available to scan the genome for evidence of positive selection and is intended for readers who are little or not familiar with population genetics theory. We discuss the genetics underlying phenotypic variation and adaptation and highlight molecular pattern that positive selection leaves behind along with the statistical approaches that are developed to detect such signatures. We describe some of the relative strengths and weaknesses of different strategies and also the challenges with identifying signatures of selection. Ascertainment bias with widely used SNP arrays is also a topic of interest. Finally we review approaches to assess the statistical significance of a signal at a particular locus or window and discuss factors affecting the statistical power to detect selective sweeps.