TY - JOUR
T1 - Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
AU - Nikolaev, Sergey I.
AU - Montoya-Burgos, Juan I.
AU - Popadin, Konstantin
AU - Parand, Leila
AU - Margulies, Elliott H.
AU - Antonarakis, Stylianos E.
AU - Bouffard, Gerard G.
AU - Idol, Jacquelyn R.
AU - Maduro, Valerie V.B.
AU - Blakesley, Robert W.
AU - Guan, Xiaobin
AU - Hansen, Nancy F.
AU - Maskeri, Baishali
AU - McDowell, Jennifer C.
AU - Park, Morgan
AU - Thomas, Pamela J.
AU - Young, Alice C.
PY - 2007/12/18
Y1 - 2007/12/18
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.
AB - 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.
KW - Constrains
KW - Generation time
KW - Genome
KW - Population size
UR - http://www.scopus.com/inward/record.url?scp=38049174461&partnerID=8YFLogxK
U2 - 10.1073/pnas.0705658104
DO - 10.1073/pnas.0705658104
M3 - Article
C2 - 18077382
AN - SCOPUS:38049174461
SN - 0027-8424
VL - 104
SP - 20443
EP - 20448
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 51
ER -