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1.
Figure 3

Figure 3. FZF1 gene region and chimeric alleles.. From: Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance.

The FZF1 gene region is shown along with the breakpoints used to generate reciprocal chimeric alleles. Regions with non-neutral evolution are indicated by gray boxes and the predicted zinc fingers are indicated by black boxes [73]. Region lengths between chimera junctions are given for S. cerevisiae. One set of chimeric alleles between S. cerevisiae and S. paradoxus are shown below. The reciprocal set is not shown.

Elizabeth K. Engle, et al. PLoS Genet. 2012 June;8(6):e1002763.
2.
Figure 1

Figure 1. Variation in noncoding substitution rates upstream of FZF1.. From: Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance.

The ratio of the noncoding substitution rate upstream of FZF1 relative to genome-wide substitution rates at fourfold degenerate sites, dNC/dS, is shown above each lineage for the original alignment. The mean and standard deviation of dNC/dS from 18 different alignments (Table S1) is shown below each lineage. dNC/dS was estimated for each lineage using an unconstrained model by maximum likelihood methods implemented in HyPhy. The tree is scaled to the fourfold synonymous substitution rate.

Elizabeth K. Engle, et al. PLoS Genet. 2012 June;8(6):e1002763.
3.
Figure 4

Figure 4. Multiple noncoding and coding changes contribute to sulfite resistance.. From: Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance.

Sulfite resistance is shown for chimeric alleles of FZF1 from S. cerevisiae and S. paradoxus. Chimera breakpoints are shown in Figure 3 and are labeled 5′ to 3′ based on the origin of each region: S. cerevisiae (red, “C”) and S. paradoxus (yellow, “P”). Error bars show the 95% confidence interval of the mean.

Elizabeth K. Engle, et al. PLoS Genet. 2012 June;8(6):e1002763.
4.
Figure 2

Figure 2. FZF1 alleles from different species have diverged in function.. From: Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance.

The left side of the figure shows sulfite resistance of FZF1 alleles from four different species: S. cerevisiae (red), S. paradoxus (yellow), S. mikatae (blue), and S. bayanus (green) in an S. cerevisiae strain background. The right side of the figure shows sulfite resistance of chimeric alleles of FZF1 composed of the 5′ noncoding region from S. paradoxus, S. mikatae and S. bayanus combined with the S. cerevisiae coding region. Error bars show the 95% confidence interval of the mean.

Elizabeth K. Engle, et al. PLoS Genet. 2012 June;8(6):e1002763.
5.
Figure 6

Figure 6. Changes in gene expression caused by FZF1 divergence.. From: Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance.

A Venn diagram of the number of genes with expression differences that depended on the FZF1 allele or an interaction between the FZF1 allele and time. An example of a gene with expression differences due to the FZF1 allele alone (SSU1) or an interaction between the FZF1 allele and time (MET7) are shown above the Venn diagram: S. cerevisiae (S. cer, red), S. paradoxus (S. par, blue), S. cerevisiae 5′ noncoding with S. paradoxus coding (C.P., gold), S. paradoxus 5′ noncoding and S. cerevisiae coding (P.C., green). The number of genes with expression differences that can be attributed to the coding region, upstream noncoding region or an interaction between the two regions is shown below the Venn diagram.

Elizabeth K. Engle, et al. PLoS Genet. 2012 June;8(6):e1002763.
6.
Figure 5

Figure 5. FZF1 alleles affect the expression of both FZF1 and SSU1 subsequent to sulfite treatment.. From: Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance.

Expression of FZF1 (A) and SSU1 (B) was measured prior to and at three time-points after sulfite treatment for strains carrying four FZF1 alleles: S. cerevisiae (S. cer, red), S. paradoxus (S. par, blue), S. cerevisiae 5′ noncoding with S. paradoxus coding (C.P., gold), S. paradoxus 5′ noncoding and S. cerevisiae coding (P.C., green). Expression levels were normalized to the 0 time-point. Each point is the mean of 3–4 individual observations. Error bars represent the 95% confidence interval of the mean.

Elizabeth K. Engle, et al. PLoS Genet. 2012 June;8(6):e1002763.

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