Fig. 2. DoFE for WGD retained genes of two subgenomes.

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Fig. 2. DoFE for WGD retained genes of two subgenomes. From: Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize Mol Biol Evol. 2015;32(12):3226-3235. doi:10.1093/molbev/msv191 Mol Biol Evol | © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Fig. 1. Left: Correlation plot of logarithm of nucleotide diversity for introns for duplicated gene pairs. Right: Correlation plot for nucleotide diversity of upstream (2 kb) regions of duplicated gene pairs. From: Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize Mol Biol Evol. 2015;32(12):3226-3235. doi:10.1093/molbev/msv191 Mol Biol Evol | © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Fig. 3. Median of ratio of nonsynonymous to synonymous diversity Πn/Πs compared between different data sets. Increase in strength of purifying selection from UED-repressed to tissuewise subfunctionalized (BED) to UED-dominant genes. P values were calculated using Wilcoxon rank-sum test: ****P < 2.2 × 10<sup>−16</sup>; ***P = 1.9 × 10<sup>−15</sup>; **P = 2 × 10<sup>−6</sup>; *P = 3 × 10<sup>−4</sup>. From: Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize Mol Biol Evol. 2015;32(12):3226-3235. doi:10.1093/molbev/msv191 Mol Biol Evol | © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Fig. 4. Ratio of nonsynonymous to synonymous nucleotide diversity (Πn/Πs) for maize subgenome 1 and 2 genes for different expression classifications. UED-D, UED-dominant; UED-R, UED-repressed. P values were calculated using Wilcoxon rank-sum test: *P = 2.9 × 10<sup>−4</sup>; ns, not significant. From: Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize Mol Biol Evol. 2015;32(12):3226-3235. doi:10.1093/molbev/msv191 Mol Biol Evol | © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Fig. 5. Number of maize1 and maize2 BED genes dominantly expressed in each tissue. A complete plot with 22 tissues is available in supplementary fig. S10, Supplementary Material online. From: Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize Mol Biol Evol. 2015;32(12):3226-3235. doi:10.1093/molbev/msv191 Mol Biol Evol | © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Fig. 6. Median of the nearest upstream distance to a TE for different expression categories. P values were calculated using Wilcoxon rank-sum test: *P < 1 × 10<sup>−7</sup>; ns, not significant. From: Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize Mol Biol Evol. 2015;32(12):3226-3235. doi:10.1093/molbev/msv191 Mol Biol Evol | © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com