Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
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 nonc...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2007-12, Vol.104 (51), p.20443-20448 |
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| container_title | Proceedings of the National Academy of Sciences - PNAS |
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| creator | Nikolaev, Sergey I Montoya-Burgos, Juan I Popadin, Konstantin Parand, Leila Margulies, Elliott H Antonarakis, Stylianos E |
| description | 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. |
| doi_str_mv | 10.1073/pnas.0705658104 |
| format | Article |
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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.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.0705658104</identifier><identifier>PMID: 18077382</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Animals ; Biological Sciences ; Chimpanzees ; Conserved Sequence ; Databases, Genetic ; Deoxyribonucleic acid ; DNA ; DNA, Intergenic - genetics ; Evolution ; Evolution, Molecular ; Evolutionary biology ; Genetic Code ; Genetic mutation ; Genome - genetics ; Genome, Human - genetics ; Genomes ; Genomics ; Humans ; Linear regression ; Mammals ; Phylogenetics ; Population size ; Primates ; Selection, Genetic ; Sequence Analysis, DNA</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2007-12, Vol.104 (51), p.20443-20448</ispartof><rights>Copyright 2007 The National Academy of Sciences of the United States of America</rights><rights>Copyright National Academy of Sciences Dec 18, 2007</rights><rights>2007 by The National Academy of Sciences of the USA</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c620t-414a95c7101b0112cf81e93ae13e76c62b876f637fe1f9ee4600e55dd10905b63</citedby><cites>FETCH-LOGICAL-c620t-414a95c7101b0112cf81e93ae13e76c62b876f637fe1f9ee4600e55dd10905b63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/104/51.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/25450911$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/25450911$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,727,780,784,803,885,27924,27925,53791,53793,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18077382$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nikolaev, Sergey I</creatorcontrib><creatorcontrib>Montoya-Burgos, Juan I</creatorcontrib><creatorcontrib>Popadin, Konstantin</creatorcontrib><creatorcontrib>Parand, Leila</creatorcontrib><creatorcontrib>Margulies, Elliott H</creatorcontrib><creatorcontrib>Antonarakis, Stylianos E</creatorcontrib><creatorcontrib>National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program</creatorcontrib><creatorcontrib>National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program</creatorcontrib><title>Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>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.</description><subject>Animals</subject><subject>Biological Sciences</subject><subject>Chimpanzees</subject><subject>Conserved Sequence</subject><subject>Databases, Genetic</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Intergenic - genetics</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Evolutionary biology</subject><subject>Genetic Code</subject><subject>Genetic mutation</subject><subject>Genome - genetics</subject><subject>Genome, Human - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Humans</subject><subject>Linear regression</subject><subject>Mammals</subject><subject>Phylogenetics</subject><subject>Population size</subject><subject>Primates</subject><subject>Selection, Genetic</subject><subject>Sequence Analysis, DNA</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFks2P0zAQxSMEYsvCmRNgcUDikN2ZxI6Ty0poxZdUiQPs2XKTSesqsYvtVPDf46jRFrjsybLmN88z7znLXiJcIcjy-mB1uAIJohI1An-UrRAazCvewONsBVDIvOYFv8iehbAHgEbU8DS7wBqkLOtilbVr01O-MyE6_5tFr00MrPPmSCzuiNHRDVM0zupU9TpSYK5nox5HPRhtWes6Y7dM245ZZ5fblqwbTctooJFsDM-zJ70eAr1Yzsvs7tPHH7df8vW3z19vP6zztiog5hy5bkQrEXADiEXb10hNqQlLklViNrWs-qqUPWHfEPEKgITourQyiE1VXmY3J93DtBmpa9PbXg_q4M2YxldOG_VvxZqd2rqjKlBwLiAJvFsEvPs5UYhqNKGlYdCW3BRU1YCc7XwQLIBLLKoigW__A_du8ja5kBgs-RxCgq5PUOtdCJ76-5ER1ByzmmNW55hTx-u_Nz3zS64JYAswd57luBI4T8fLhLx_AFH9NAyRfsXEvjqx-_mf3MOFSK41iKn-5lTvtVN6601Qd9_nBQHqspHJsT-Cs8_c</recordid><startdate>20071218</startdate><enddate>20071218</enddate><creator>Nikolaev, Sergey I</creator><creator>Montoya-Burgos, Juan I</creator><creator>Popadin, Konstantin</creator><creator>Parand, Leila</creator><creator>Margulies, Elliott H</creator><creator>Antonarakis, Stylianos E</creator><general>National Academy of Sciences</general><general>National Acad Sciences</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20071218</creationdate><title>Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements</title><author>Nikolaev, Sergey I ; 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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.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>18077382</pmid><doi>10.1073/pnas.0705658104</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Biological Sciences Chimpanzees Conserved Sequence Databases, Genetic Deoxyribonucleic acid DNA DNA, Intergenic - genetics Evolution Evolution, Molecular Evolutionary biology Genetic Code Genetic mutation Genome - genetics Genome, Human - genetics Genomes Genomics Humans Linear regression Mammals Phylogenetics Population size Primates Selection, Genetic Sequence Analysis, DNA |
| title | Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements |
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