Constraints and plasticity in genome and molecular-phenome evolution

Abstract

Multiple constraints variously affect different parts of the genomes of diverse life forms. The selective pressures that shape the evolution of viral, archaeal, bacterial and eukaryotic genomes differ markedly, even among relatively closely related animal and bacterial lineages; by contrast, constraints affecting protein evolution seem to be more universal. The constraints that shape the evolution of genomes and phenomes are complemented by the plasticity and robustness of genome architecture, expression and regulation. Taken together, these findings are starting to reveal complex networks of evolutionary processes that must be integrated to attain a new synthesis of evolutionary biology.

Figure 1. Approximate distribution of evolutionary constraints across genomes with different architectures

The fractions of different classes of sequences that are subject to constraints of varying strength are shown as rough approximations of the values that are typical of the respective class of genomes. The data are from REFS ,,,, as discussed in the main text.

Figure 2. The universal distribution of evolutionary rates across orthologous gene sets

The evolutionary rates for five pairs of closely related organisms from different branches of life were calculated as nucleotide distances for the complete sets of orthologous genes. The shapes of the rate distributions are very similar from bacteria to humans. The relative evolution rate for each gene was obtained by dividing its evolution rate by the median rate for the respective pair of organisms. ‘Model’ refers to estimated transition rates in 134 mutationally connected networks for simulated, robustly folding 18-mer protein-like molecules. Original model rates were normalized by their median value and scaled to a standard deviation of 0.25 to match the width of the distributions derived from biological data.

Figure 3. Genomic and phenomic constraints on different levels of biological organization

The degree of constraint and plasticity experienced by genomic and phenomic properties across different levels of biological organization are shown. The arrows should be perceived as indicating the midpoints of the respective intervals, with at least the adjacent intervals overlapping. The relationships between some of the constraints on some classes of sites — for example, synonymous sites and disordered segments in proteins — are ‘educated guesses’ based on current data, and could change with further accumulation of the relevant data and advances in methods for quantifying selective pressures. The scales are rough approximations.