Gene Expression Evolution Figure 6. Optimum mRNA abundance model. (A) Time development of average pairwise variance. (B) Steady-state distributions of mRNA abundance. Model parameters are: L = 1.0, M = 300,000, N = 20,000, sk = 0.01, and n = 20,000. Population size (Ne) is 100. t = 50,000. The selection intensity is 1.67. doi:10.1371/journal.pone.0007943.g006 known categories, housekeeping genes and tissue-specific genes, which are expressed in a small number of cell types. This suggests that the distribution of mRNA abundance among different types of cells is not independent, but rather that the mRNA abundance of housekeeping genes in one cell type evolves to be larger, and would therefore become larger in other cell types in most cases. On the other hand, in the case of tissue-specific genes, the evolution of the mRNA abundance in the cell type where the gene is expressed would not affect the mRNA abundance of other cell types, because by definition it would be confined to the smallest expression level. The evolutionary change of the anatomical pattern of gene expression [63–67] is another interesting area to investigate, although for this purpose our model should be expanded for evaluation of the effects of gene duplication. Figure 7. Relative abundance model. (A) Time development of average pairwise variance. Each point is mean value over 25 repetitions of the simulation. (B) Steady-state distributions of mRNA abundance. Red points represent genes undergoing natural selection. Blue points are neutral genes. Model parameters are: L = 1.0, M = 300,000, N = 20,000, sk = 0.01, and n = 500. Population size (Ne) is 100. t = 50,000. The selection intensity is 5.0. doi:10.1371/journal.pone.0007943.g007 PLoS ONE | www.plosone.org 8 November 2009 | Volume 4 | Issue 11 | e7943