The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

Abstract

The evolutionary rates of protein-coding genes in an organism span, approximately, 3 orders of magnitude and show a universal, approximately log-normal distribution in a broad variety of species from prokaryotes to mammals. This universal distribution implies a steady-state process, with identical distributions of evolutionary rates among genes that are gained and genes that are lost. A mathematical model of such process is developed under the single assumption of the constancy of the distributions of the propensities for gene loss (PGL). This model predicts that genes of different ages, that is, genes with homologs detectable at different phylogenetic depths, substantially differ in those variables that correlate with PGL. We computationally partition protein-coding genes from humans, flies, and Aspergillus fungus into age classes, and show that genes of different ages retain the universal log-normal distribution of evolutionary rates, with a shift toward higher rates in ''younger'' classes but also with a substantial overlap. The only exception involves human primate-specific genes that show a heavy tail of rapidly evolving genes, probably owing to gene annotation artifacts. As predicted, the gene age classes differ in characteristics correlated with PGL. Compared with ''young'' genes (e.g., mammal-specific human ones), ''old'' genes (e.g., eukaryotespecific), on average, are longer, are expressed at a higher level, possess a higher intron density, evolve slower on the short time scale, and are subject to stronger purifying selection. Thus, genome evolution fits a simple model with approximately uniform rates of gene gain and loss, without major bursts of genomic innovation.gene age ͉ gene expression ͉ genome evolution ͉ intron density

Slow protein evolutionary rates are dictated by surface–core association

“…S7A), but the distributions of per protein rates we obtained (Fig. 1) resemble those obtained with dN/dS (18), and so do the correlations of evolutionary rates and expression levels (SI Appendix, Fig. S5) and of ordered versus disordered domains (Table 1).…”

“…The complexity of the determinants of protein sequence implies a variety of independent properties that correlate with slow evolution (1, 7), including multiple interaction partners (3), essentiality (7,8), evolutionary age (18), and high expression levels (2). Nonetheless, we suggest that the underlining reason for slow evolutionary rates is a highly constrained surface.…”

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

“…A key prediction is that properties such as coding length, expression, substitution rate and evolutionary stability change in an age-dependent manner 58,61 . Coding length showed clear age dependence, with the median length increasing several fold from the youngest to the oldest group (Wilcoxon rank-sum test, P < 2.2 × 10 −16 ) ( Supplementary Fig.…”

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

“…Indeed, stronger purifying selection has been reported on old genes (Supplemental Fig. S26; Castresana 2005, 2007;Wolf et al 2009). This suggests that the acquisition of splice forms in younger genes might be under relaxed selection and that purifying selection gets increasingly efficient at preventing the acquisition of new splice variants as genes get older.…”