Although sequences containing regulatory elements located
close to protein-coding genes are often only weakly conserved during evolution,
comparisons of rodent genomes have implied that these sequences are subject to
some selective constraints. Evolutionary conservation is particularly apparent
upstream of coding sequences and in first introns, regions that are enriched for
regulatory elements. By comparing the human and chimpanzee genomes, we show here
that there is almost no evidence for conservation in these regions in hominids.
Furthermore, we show that gene expression is diverging more rapidly in hominids
than in murids per unit of neutral sequence divergence. By combining data on
polymorphism levels in human noncoding DNA and the corresponding
human–chimpanzee divergence, we show that the proportion of adaptive
substitutions in these regions in hominids is very low. It therefore seems
likely that the lack of conservation and increased rate of gene expression
divergence are caused by a reduction in the effectiveness of natural selection
against deleterious mutations because of the low effective population sizes of
hominids. This has resulted in the accumulation of a large number of deleterious
mutations in sequences containing gene control elements and hence a widespread
degradation of the genome during the evolution of humans and chimpanzees.