A statistical test for lineage-specific natural selection on quantitative traits based on multiple-line crosses
Nico Riedel, Bhavin S. Khatri, Michael Lässig, Johannes Berg
Comments: 21 pages, 11 figures
Subjects: Populations and Evolution (q-bio.PE)

Phenotypic differences between species may be attributable to natural selection. However, it is a difficult task to quantify the strength of evidence for selection acting on a particular trait. Here we develop a population-genetic test for selection acting on a quantitative trait, which is based on multiple-line crosses. We show that using multiple lines increases both the power and the scope of selection inference. First, a test based on three or more lines detects selection on a quantitative trait with strongly increased statistical significance, which is quantified by our analysis. Second, a multiple-line test allows to distinguish selection from neutral evolution as well as lineage-specific selection from selection under uniform selection strength. This is in contrast to tests based on two lines, where only differences in selection coefficients can be inferred. Our analytical results are complemented by extensive numerical simulations. We apply the multiple-line test to QTL data on floral character traits in plant species of the Mimulus genus and on photoperiodic traits in different maize strains. In both cases, we find a signature of lineage-specific selection that is not seen in a two-line test. We also extend the multiple-line test to short divergence times.