Fig. 6
From: Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae
Widespread apparent multiple emergence of natural variation. a Plots of sequence identity (500-variant sliding window) of Y55 (top) and SK1 (bottom) to DBVPG6044 (blue) and wine/European clade modal genotype or Y12, respectively (red). Neighbor-joining trees for all strains in the SGRP collection based on 500-variant sliding windows centered about b chrII position 202,724 and c chrII position 750,709. Scale bars show neighbor-joining distance. Fraction of variants segregating within all strains of the SGRP d S. cerevisiae and e S. paradoxus collections that are (left) unique (green) or shared with another isolate (purple) and (right) inferred by phylogeny to have emerged only once (gray) or more than once (pink). The neutral expectation in the absence of selection was calculated separately for each strain collection by ten independent simulations; the bars show the mean across ten simulations and the results of each of the ten simulations are shown; *p < 10−16 by permutation test. f True extent of homoplasy (blue) as compared to inferred apparent multiple emergence (orange) as a function of the fraction of polymorphisms that are subject to balancing selection (fancestral). MAFbalanced is set to 2−1. g True extent of homoplasy (blue) as compared to inferred apparent multiple emergence (orange) as a function of the strength of balancing selection (MAFbalanced). fancestral is set to 10−2. h Inferred apparent multiple emergence as a function of both fancestral (as indicated; shaded lines) and MAFbalanced (abscissa). Results shown are mean ± s.e.m. Source data are provided as a Source Data file
