tion bottleneck as the null distribution, we evaluated the probability of the observed loss of genetic diversity in maize relative to teosinte based on 10,000 coalescent simulations. The CLR test proposed by Kim and Stephan (2002) was used to test the hitchhiking effect and estimate the selection coefficient. We focused this analysis on the ZmETR2 region (loci 7–18) containing ≈7 kb of contiguous sequence. Ancestral and derived alleles at polymorphic sites were identified by comparing to the Tripsacum sequence. If the derived state of a segregating site could not be determined because of unavailable Tripsacum sequence, we assumed the base with the higher frequency to be ancestral. This assumption is conservative and has little effect in detecting selection (Kim and Stephan, 2002; DuMont and Aquadro, 2005). In those loci with a missing state for particular lines, we assumed the segregating sites at these missing sequences had the ancestral state, which is a conservative assumption as shown by the study of Orengo and Aguadé (2007). We did not provide a selection target estimation for 2 reasons: (i) a partially sequenced region will give a less reliable estimate of the selection target (Jensen et al., 2005; Pool et al., 2006); (ii) this selective sweep affected so many regions that estimating the selection target based on a single region is not meaningful. The basic analysis strategy of the CLR test is the same as that described by Wang et al. (2005) with minor modifications. Instead of estimating θ from local teosinte data as Wang et al. (2005) did for tga1, we used a more conservative estimate of θ = 0.0064, estimated from a genomewide value (Wright et al., 2005) as the expected nucleotide diversity in maize. The scaled per-nucleotide recombination parameter Rn = 0.0414 (Hudson, 1987) is the length-weighted mean of Rn across the ZmETR2 region (loci 7–18) estimated from teosinte data. The significance of the resulting likelihood ratio was evaluated by 1,000 simulations of neutral datasets. The GOF test (Jensen et al., 2005) was further used to distinguish between selective sweep and demographic forces. The significance of the GOF value for the observed data was evaluated by 1,000 simulations under the selection scenario produced by the above CLR test.
We thank Carlyn Buckler, Peter Bradbury, Jason Peiffer, Pat Brown, Rob Elshire, Elhan Ersoz, Sean Myles, Michelle Denton, Joan Zhao, and Linda Rigamer Lirette for excellent comments and editorial assistance. This work was supported by the U.S. Department of Agriculture Agricultural Research Service and National Science Foundation Grants DBI-0321467 and DBI-0820619.