• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of pnasPNASInfo for AuthorsSubscriptionsAboutThis Article
Proc Natl Acad Sci U S A. Nov 15, 1993; 90(22): 10676–10680.
PMCID: PMC47840

An examination of the generation-time effect on molecular evolution.

Abstract

By using DNA sequences of 17 mammalian genes, the generation-time effect is estimated separately for synonymous substitutions and nonsynonymous substitutions. Star phylogenies composed of rodentia, artiodactyla, and primates are examined. The generation-time effect is found to be more conspicuous for synonymous substitutions than for non-synonymous substitutions, by using the methods of (i) Nei and Gojobori, (ii) Li, and (iii) Ina. The proportion of accepted amino acid substitutions in evolution is estimated to be about twice as large in the primate lineage as in the rodent lineage. This result is in accord with the nearly neutral theory of molecular evolution.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (875K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Easteal S. The pattern of mammalian evolution and the relative rate of molecular evolution. Genetics. 1990 Jan;124(1):165–173. [PMC free article] [PubMed]
  • Sargent TD, Yang M, Bonner J. Nucleotide sequence of cloned rat serum albumin messenger RNA. Proc Natl Acad Sci U S A. 1981 Jan;78(1):243–246. [PMC free article] [PubMed]
  • Dugaiczyk A, Law SW, Dennison OE. Nucleotide sequence and the encoded amino acids of human serum albumin mRNA. Proc Natl Acad Sci U S A. 1982 Jan;79(1):71–75. [PMC free article] [PubMed]
  • Tsujibo H, Tiano HF, Li SS. Nucleotide sequences of the cDNA and an intronless pseudogene for human lactate dehydrogenase-A isozyme. Eur J Biochem. 1985 Feb 15;147(1):9–15. [PubMed]
  • Ishiguro N, Osame S, Kagiya R, Ichijo S, Shinagawa M. Primary structure of bovine lactate dehydrogenase-A isozyme and its synthesis in Escherichia coli. Gene. 1990 Jul 16;91(2):281–285. [PubMed]
  • Fukasawa KM, Li SS. Complete nucleotide sequence of the mouse lactate dehydrogenase-A functional gene: comparison of the exon-intron organization of dehydrogenase genes. Genetics. 1987 May;116(1):99–105. [PMC free article] [PubMed]
  • Morgan JG, Holbrook NJ, Crabtree GR. Nucleotide sequence of the gamma chain gene of rat fibrinogen: conserved intronic sequences. Nucleic Acids Res. 1987 Mar 25;15(6):2774–2776. [PMC free article] [PubMed]
  • Rixon MW, Chung DW, Davie EW. Nucleotide sequence of the gene for the gamma chain of human fibrinogen. Biochemistry. 1985 Apr 9;24(8):2077–2086. [PubMed]
  • Brown WM, Dziegielewska KM, Foreman RC, Saunders NR. Nucleotide and deduced amino acid sequence of a gamma subunit of bovine fibrinogen. Nucleic Acids Res. 1989 Aug 11;17(15):6397–6397. [PMC free article] [PubMed]
  • Noda M, Furutani Y, Takahashi H, Toyosato M, Tanabe T, Shimizu S, Kikyotani S, Kayano T, Hirose T, Inayama S, et al. Cloning and sequence analysis of calf cDNA and human genomic DNA encoding alpha-subunit precursor of muscle acetylcholine receptor. Nature. 305(5937):818–823. [PubMed]
  • Isenberg KE, Mudd J, Shah V, Merlie JP. Nucleotide sequence of the mouse muscle nicotinic acetylcholine receptor alpha subunit. Nucleic Acids Res. 1986 Jun 25;14(12):5111–5111. [PMC free article] [PubMed]
  • Schoepfer R, Luther M, Lindstrom J. The human medulloblastoma cell line TE671 expresses a muscle-like acetylcholine receptor. Cloning of the alpha-subunit cDNA. FEBS Lett. 1988 Jan 4;226(2):235–240. [PubMed]
  • Tanabe T, Noda M, Furutani Y, Takai T, Takahashi H, Tanaka K, Hirose T, Inayama S, Numa S. Primary structure of beta subunit precursor of calf muscle acetylcholine receptor deduced from cDNA sequence. Eur J Biochem. 1984 Oct 1;144(1):11–17. [PubMed]
  • Buonanno A, Mudd J, Shah V, Merlie JP. A universal oligonucleotide probe for acetylcholine receptor genes. Selection and sequencing of cDNA clones for the mouse muscle beta subunit. J Biol Chem. 1986 Dec 15;261(35):16451–16458. [PubMed]
  • Beeson D, Brydson M, Newsom-Davis J. Nucleotide sequence of human muscle acetylcholine receptor beta-subunit. Nucleic Acids Res. 1989 Jun 12;17(11):4391–4391. [PMC free article] [PubMed]
  • Seeburg PH, Sias S, Adelman J, de Boer HA, Hayflick J, Jhurani P, Goeddel DV, Heyneker HL. Efficient bacterial expression of bovine and porcine growth hormones. DNA. 1983;2(1):37–45. [PubMed]
  • Linzer DI, Talamantes F. Nucleotide sequence of mouse prolactin and growth hormone mRNAs and expression of these mRNAs during pregnancy. J Biol Chem. 1985 Aug 15;260(17):9574–9579. [PubMed]
  • Goeddel DV, Heyneker HL, Hozumi T, Arentzen R, Itakura K, Yansura DG, Ross MJ, Miozzari G, Crea R, Seeburg PH. Direct expression in Escherichia coli of a DNA sequence coding for human growth hormone. Nature. 1979 Oct 18;281(5732):544–548. [PubMed]
  • Leung DW, Spencer SA, Cachianes G, Hammonds RG, Collins C, Henzel WJ, Barnard R, Waters MJ, Wood WI. Growth hormone receptor and serum binding protein: purification, cloning and expression. Nature. 1987 Dec 10;330(6148):537–543. [PubMed]
  • Smith WC, Kuniyoshi J, Talamantes F. Mouse serum growth hormone (GH) binding protein has GH receptor extracellular and substituted transmembrane domains. Mol Endocrinol. 1989 Jun;3(6):984–990. [PubMed]
  • Cioffi JA, Wang X, Kopchick JJ. Porcine growth hormone receptor cDNA sequence. Nucleic Acids Res. 1990 Nov 11;18(21):6451–6451. [PMC free article] [PubMed]
  • Miller WL, Thirion JP, Martial JA. Cloning of DNA complementary to bovine prolactin mRNA. Endocrinology. 1980 Sep;107(3):851–853. [PubMed]
  • Linzer DI, Talamantes F. Nucleotide sequence of mouse prolactin and growth hormone mRNAs and expression of these mRNAs during pregnancy. J Biol Chem. 1985 Aug 15;260(17):9574–9579. [PubMed]
  • Cooke NE, Coit D, Shine J, Baxter JD, Martial JA. Human prolactin. cDNA structural analysis and evolutionary comparisons. J Biol Chem. 1981 Apr 25;256(8):4007–4016. [PubMed]
  • Fotsis T, Murphy C, Gannon F. Nucleotide sequence of the bovine insulin-like growth factor 1 (IGF-1) and its IGF-1A precursor. Nucleic Acids Res. 1990 Feb 11;18(3):676–676. [PMC free article] [PubMed]
  • Tobin G, Yee D, Brünner N, Rotwein P. A novel human insulin-like growth factor I messenger RNA is expressed in normal and tumor cells. Mol Endocrinol. 1990 Dec;4(12):1914–1920. [PubMed]
  • Shimatsu A, Rotwein P. Sequence of two rat insulin-like growth factor I mRNAs differing within the 5' untranslated region. Nucleic Acids Res. 1987 Sep 11;15(17):7196–7196. [PMC free article] [PubMed]
  • Brown WM, Dziegielewska KM, Foreman RC, Saunders NR. The nucleotide and deduced amino acid sequences of insulin-like growth factor II cDNAs from adult bovine and fetal sheep liver. Nucleic Acids Res. 1990 Aug 11;18(15):4614–4614. [PMC free article] [PubMed]
  • Jansen M, van Schaik FM, van Tol H, Van den Brande JL, Sussenbach JS. Nucleotide sequences of cDNAs encoding precursors of human insulin-like growth factor II (IGF-II) and an IGF-II variant. FEBS Lett. 1985 Jan 7;179(2):243–246. [PubMed]
  • Stempien MM, Fong NM, Rall LB, Bell GI. Sequence of a placental cDNA encoding the mouse insulin-like growth factor II precursor. DNA. 1986 Oct;5(5):357–361. [PubMed]
  • Sneyers M, Kettmann R, Massart S, Renaville R, Burny A, Portetelle D. Cloning and characterization of a cDNA encoding the bovine insulin-like growth factor binding protein 1 (bIGFBP-1). DNA Seq. 1991;1(6):407–408. [PubMed]
  • Brinkman A, Groffen C, Kortleve DJ, Geurts van Kessel A, Drop SL. Isolation and characterization of a cDNA encoding the low molecular weight insulin-like growth factor binding protein (IBP-1). EMBO J. 1988 Aug;7(8):2417–2423. [PMC free article] [PubMed]
  • Spratt SK, Tatsuno GP, Sommer A. Cloning and characterization of bovine insulin-like growth factor binding protein-3 (bIGFBP-3). Biochem Biophys Res Commun. 1991 Jun 28;177(3):1025–1032. [PubMed]
  • Cubbage ML, Suwanichkul A, Powell DR. Insulin-like growth factor binding protein-3. Organization of the human chromosomal gene and demonstration of promoter activity. J Biol Chem. 1990 Jul 25;265(21):12642–12649. [PubMed]
  • Albiston AL, Herington AC. Cloning and characterization of the growth hormone-dependent insulin-like growth factor binding protein (IGFBP-3) in the rat. Biochem Biophys Res Commun. 1990 Jan 30;166(2):892–897. [PubMed]
  • Maliszewski CR, Baker PE, Schoenborn MA, Davis BS, Cosman D, Gillis S, Cerretti DP. Cloning, sequence and expression of bovine interleukin 1 alpha and interleukin 1 beta complementary DNAs. Mol Immunol. 1988 May;25(5):429–437. [PubMed]
  • Nishida T, Nishino N, Takano M, Kawai K, Bando K, Masui Y, Nakai S, Hirai Y. cDNA cloning of IL-1 alpha and IL-1 beta from mRNA of U937 cell line. Biochem Biophys Res Commun. 1987 Feb 27;143(1):345–352. [PubMed]
  • Nishida T, Nishino N, Takano M, Sekiguchi Y, Kawai K, Mizuno K, Nakai S, Masui Y, Hirai Y. Molecular cloning and expression of rat interleukin-1 alpha cDNA. J Biochem. 1989 Mar;105(3):351–357. [PubMed]
  • Gray PW, Glaister D, Chen E, Goeddel DV, Pennica D. Two interleukin 1 genes in the mouse: cloning and expression of the cDNA for murine interleukin 1 beta. J Immunol. 1986 Dec 1;137(11):3644–3648. [PubMed]
  • Bensi G, Raugei G, Palla E, Carinci V, Tornese Buonamassa D, Melli M. Human interleukin-1 beta gene. Gene. 1987;52(1):95–101. [PubMed]
  • Devos R, Plaetinck G, Cheroutre H, Simons G, Degrave W, Tavernier J, Remaut E, Fiers W. Molecular cloning of human interleukin 2 cDNA and its expression in E. coli. Nucleic Acids Res. 1983 Jul 11;11(13):4307–4323. [PMC free article] [PubMed]
  • Cerretti DP, McKereghan K, Larsen A, Cantrell MA, Anderson D, Gillis S, Cosman D, Baker PE. Cloning, sequence, and expression of bovine interleukin 2. Proc Natl Acad Sci U S A. 1986 May;83(10):3223–3227. [PMC free article] [PubMed]
  • Kashima N, Nishi-Takaoka C, Fujita T, Taki S, Yamada G, Hamuro J, Taniguchi T. Unique structure of murine interleukin-2 as deduced from cloned cDNAs. Nature. 313(6001):402–404. [PubMed]
  • Tonouchi N, Miwa K, Karasuyama H, Matsui H. Deletion of 3' untranslated region of human BSF-2 mRNA causes stabilization of the mRNA and high-level expression in mouse NIH3T3 cells. Biochem Biophys Res Commun. 1989 Sep 15;163(2):1056–1062. [PubMed]
  • Chiu CP, Moulds C, Coffman RL, Rennick D, Lee F. Multiple biological activities are expressed by a mouse interleukin 6 cDNA clone isolated from bone marrow stromal cells. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7099–7103. [PMC free article] [PubMed]
  • Goodwin RG, Lupton S, Schmierer A, Hjerrild KJ, Jerzy R, Clevenger W, Gillis S, Cosman D, Namen AE. Human interleukin 7: molecular cloning and growth factor activity on human and murine B-lineage cells. Proc Natl Acad Sci U S A. 1989 Jan;86(1):302–306. [PMC free article] [PubMed]
  • Droogmans L, Cludts I, Cleuter Y, Kettmann R, Burny A. Nucleotide sequence of bovine interleukin-6 cDNA. DNA Seq. 1992;2(6):411–413. [PubMed]
  • Namen AE, Lupton S, Hjerrild K, Wignall J, Mochizuki DY, Schmierer A, Mosley B, March CJ, Urdal D, Gillis S. Stimulation of B-cell progenitors by cloned murine interleukin-7. Nature. 1988 Jun 9;333(6173):571–573. [PubMed]
  • Irwin DM, Wilson AC. Concerted evolution of ruminant stomach lysozymes. Characterization of lysozyme cDNA clones from sheep and deer. J Biol Chem. 1990 Mar 25;265(9):4944–4952. [PubMed]
  • Ohta T. Multigene families and the evolution of complexity. J Mol Evol. 1991 Jul;33(1):34–41. [PubMed]
  • Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986 Sep;3(5):418–426. [PubMed]
  • Pamilo P, Bianchi NO. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol. 1993 Mar;10(2):271–281. [PubMed]
  • Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111–120. [PubMed]
  • Kimura M. Molecular evolutionary clock and the neutral theory. J Mol Evol. 1987;26(1-2):24–33. [PubMed]
  • Li WH, Wu CI, Luo CC. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol. 1985 Mar;2(2):150–174. [PubMed]
  • Li WH, Tanimura M, Sharp PM. An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J Mol Evol. 1987;25(4):330–342. [PubMed]
  • Ohta T. Slightly deleterious mutant substitutions in evolution. Nature. 1973 Nov 9;246(5428):96–98. [PubMed]
  • Ohta T, Tachida H. Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution. Genetics. 1990 Sep;126(1):219–229. [PMC free article] [PubMed]
  • Tachida H. A study on a nearly neutral mutation model in finite populations. Genetics. 1991 May;128(1):183–192. [PMC free article] [PubMed]
  • Gotoh O. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J Biol Chem. 1992 Jan 5;267(1):83–90. [PubMed]
  • Muse SV, Weir BS. Testing for equality of evolutionary rates. Genetics. 1992 Sep;132(1):269–276. [PMC free article] [PubMed]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...