Purifying selection and birth-and-death evolution in the ubiquitin gene family

Ubiquitin is a highly conserved protein that is encoded by a multigene fami ly. It is generally believed that this gene family is subject to concerted evolution, which homogenizes the member genes of the family. However, prote in homogeneity can be attained also by strong purifying selection. We there fore studied the proportion (p(s)) Of synonymous nucleotide differences bet ween members of the ubiquitin gene family from 28 species of fungi, plants, and animals. The results have shown that p(s) is generally very high and i s often close to the saturation level, although the protein sequence is vir tually identical for all ubiquitins from fungi. plants, and animals. A smal l proportion of species showed a low level of P-s values, but these values appeared to be caused by recent gene duplication. It was also found that th e number of repeat copies of the gene family varies considerably with speci es, and some species harbor pseudogenes. These observations suggest that th e members of this gene family evolve almost independently by silent nucleot ide substitution and are subjected to birth-and-death evolution at the DNA level.