Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements

@article{nikolaev07rates, abstract = {A comprehensive phylogenetic framework is indispensable for investigating the evolution of genomic features in mammals as a whole, and particularly in humans. Using the ENCODE sequence data, we estimated mammalian neutral evolutionary rates and selective pressures acting on conserved coding and noncoding elements. We show that neutral evolutionary rates can be explained by the generation time (GT) hypothesis. Accordingly, primates (especially humans), having longer GTs than other mammals, display slower rates of neutral evolution. The evolution of constrained elements, particularly of nonsynonymous sites, is in agreement with the expectations of the nearly neutral theory of molecular evolution. We show that rates of nonsynonymous substitutions (dN) depend on the population size of a species. The results are robust to the exclusion of hypermutable CpG prone sites. The average rate of evolution in conserved noncoding sequences (CNCs) is 1.7 times higher than in nonsynonymous sites. Despite this, CNCs evolve at similar or even lower rates than nonsynonymous sites in the majority of basal branches of the eutherian tree. This observation could be the result of an overall gradual or, alternatively, lineage-specific relaxation of CNCs. The latter hypothesis was supported by the finding that 3 of the 20 longest CNCs displayed significant relaxation of individual branches. This observation may explain why the evolution of CNCs fits the expectations of the nearly neutral theory less well than the evolution of nonsynonymous sites. 10.1073/pnas.0705658104}, author = {Nikolaev, Sergey I. and Juan and Popadin, Konstantin and Parand, Leila and Margulies, Elliott H. and Nisc and Antonarakis, Stylianos E. }, citeulike-article-id = {2097684}, doi = {http://dx.doi.org/10.1073/pnas.0705658104}, journal = {Proceedings of the National Academy of Sciences}, keywords = {cns, coding, evolution, substitution\_rate}, month = {December}, pages = {0705658104+}, posted-at = {2008-05-22 20:05:25}, priority = {2}, title = {Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements}, url = {http://dx.doi.org/10.1073/pnas.0705658104}, year = {2007} }

TY - JOUR ID - nikolaev07rates L3 - citeulike-article-id:2097684 N2 - A comprehensive phylogenetic framework is indispensable for investigating the evolution of genomic features in mammals as a whole, and particularly in humans. Using the ENCODE sequence data, we estimated mammalian neutral evolutionary rates and selective pressures acting on conserved coding and noncoding elements. We show that neutral evolutionary rates can be explained by the generation time (GT) hypothesis. Accordingly, primates (especially humans), having longer GTs than other mammals, display slower rates of neutral evolution. The evolution of constrained elements, particularly of nonsynonymous sites, is in agreement with the expectations of the nearly neutral theory of molecular evolution. We show that rates of nonsynonymous substitutions (dN) depend on the population size of a species. The results are robust to the exclusion of hypermutable CpG prone sites. The average rate of evolution in conserved noncoding sequences (CNCs) is 1.7 times higher than in nonsynonymous sites. Despite this, CNCs evolve at similar or even lower rates than nonsynonymous sites in the majority of basal branches of the eutherian tree. This observation could be the result of an overall gradual or, alternatively, lineage-specific relaxation of CNCs. The latter hypothesis was supported by the finding that 3 of the 20 longest CNCs displayed significant relaxation of individual branches. This observation may explain why the evolution of CNCs fits the expectations of the nearly neutral theory less well than the evolution of nonsynonymous sites. 10.1073/pnas.0705658104 JF - Proceedings of the National Academy of Sciences TI - Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements SP - 0705658104 KW - cns KW - coding KW - evolution KW - substitution_rate AU - Nikolaev, Sergey AU - Juan AU - Popadin, Konstantin AU - Parand, Leila AU - Margulies, Elliott AU - Nisc AU - Antonarakis, Stylianos PY - 2007/December/11/ UR - http://dx.doi.org/10.1073/pnas.0705658104 ER -