Origins and impact of constraints in evolution of gene families * Boris E. Shakhnovich^1 ^,3 and Eugene V. Koonin^2 * / ^1 Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA; , ^2 National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA / Recent investigations of high-throughput genomic and phenomic^ data have uncovered a variety of significant but relatively^ weak correlations between a gene’s functional and evolutionary^ characteristics. In particular, essential genes and genes with^ paralogs have a slight propensity to evolve more slowly than^ nonessential genes and singletons, respectively. However, given^ the weakness and multiplicity of these associations, their biological^ relevance remains uncertain. Here, we show that existence of^ an essential paralog can be used as a specific and strong gauge^ of selection. We partition gene families in several genomes^ into two classes: those that include at least one essential^ gene (E-families) and those without essential genes (N-families).^ We find that weaker purifying selection causes N-families to^ evolve in a more dynamic regime with higher rates both of duplicate^ fixation and pseudogenization. Because genes in E-families are^ subject to significantly stronger purifying selection than those^ in N-families, they survive longer and exhibit greater sequence^ divergence. Longer average survival time also allows for divergence^ of upstream regulatory regions, resulting in change of transcriptional^ context among paralogs in E-families. These findings are compatible^ with differential division of ancestral functions (subfunctionalization)^ or emergence of novel functions (neofunctionalization) being^ the prevalent modes of evolution of paralogs in E-families as^ opposed to pseudogenization (nonfunctionalization), which is^ the typical fate of paralogs in N-families. Unlike other characteristics^ of genes, such as essentiality, existence of paralogs, or expression^ level, membership in an E-family or an N-family strongly correlates^ with the level of selection and appears to be a major determinant^ of a gene’s evolutionary fate. -- ------------------------------------------------------------------ Klaas Vandepoele, PhD Tel. 32 (0)9 3313822 DEPARTMENT OF PLANT SYSTEMS BIOLOGY VIB/GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium E-mail: Klaas.Vandepoele@psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ------------------------------------------------------------------