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

Nikolaev, S. I.; Montoya Burgos, Juan Ignacio; Popadin, Konstantin; Parand, Leila; Margulies, E. H.; Antonarakis, Stylianos

doi:10.1073/pnas.0705658104

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Title		Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
Authors		Nikolaev, S. I. Montoya Burgos, Juan Ignacio Popadin, Konstantin Parand, Leila Margulies, E. H. Antonarakis, Stylianos
Published in		Proceedings of the National Academy of Sciences. 2007, vol. 104, no. 51, p. 20443-20448
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.
Keywords		Animals — Conserved Sequence — DNA, Intergenic/ genetics — Databases, Genetic — Evolution, Molecular — Genetic Code — Genome/ genetics — Genome, Human/genetics — Humans — Selection, Genetic — Sequence Analysis, DNA
Identifiers		DOI: 10.1073/pnas.0705658104 PMID: 18077382
Full text		Article - Limited access to UNIGE Other version: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2154450/pdf/zpq20443.pdf
Structures		Faculté de médecine / Section de médecine clinique / Département de médecine
Citation (ISO format)		NIKOLAEV, S. I. et al. Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. In: Proceedings of the National Academy of Sciences of the United States of America, 2007, vol. 104, n° 51, p. 20443-20448. doi: 10.1073/pnas.0705658104 https://archive-ouverte.unige.ch/unige:8942