Accelerated Evolution of Genes of Recent Origin

  • Macarena Toll-Riera
  • Jose Castresana
  • M. Mar Albà


The gene content of any genome is a rich mosaic of genes that have originated at different times during evolution. Among the most interesting properties related to gene age is the fact that younger genes tend to show accelerated evolutionary rates with respect to older genes. Here, we use a large number of closely related mammalian genomes to gain further insights into the relationship between gene age and evolutionary rate. We define a group of primate-specific genes that are absent from 11 non-primate mammalian genomes as well as from other eukaryotic genomes. These genes, of very recent origin, show the highest evolutionary rate and the shortest protein length. We discuss how these results may shed light on understanding the proposed mechanisms for the origin of lineage-specific, novel genes.


Gene Ontology Evolutionary Rate Recent Origin Accelerate Evolution Short Protein 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Abeln S, Deane CM (2005) Fold usage on genomes and protein fold evolution. Proteins 60:690–700PubMedCrossRefGoogle Scholar
  2. 2.
    Albà MM, Castresana J (2005) Inverse relationship between evolutionary rate and age of mammalian genes. Mol Biol Evol 22:598–606PubMedCrossRefGoogle Scholar
  3. 3.
    Albà MM, Castresana J (2007) On homology searches by protein Blast and the characterization of the age of genes. BMC Evol Biol 7:53PubMedCrossRefGoogle Scholar
  4. 4.
    Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  5. 5.
    Begun DJ, Lindfors HA, Thompson ME, Holloway AK (2006) Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics 172:1675–1681PubMedCrossRefGoogle Scholar
  6. 6.
    Birney E et al (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816PubMedCrossRefGoogle Scholar
  7. 7.
    Cai JJ, Woo PC, Lau SK, Smith DK, Yuen KY (2006) Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J Mol Evol 63:1–11PubMedCrossRefGoogle Scholar
  8. 8.
    Chen L, DeVries AL, Cheng CH (1997) Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. Proc Natl Acad Sci USA 94:3811–3816PubMedCrossRefGoogle Scholar
  9. 9.
    Choi IG, Kim SH (2006) Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci USA 103:14056–14061PubMedCrossRefGoogle Scholar
  10. 10.
    Clamp M et al (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 04:19428–33CrossRefGoogle Scholar
  11. 11.
    Clark AG et al (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203–218PubMedCrossRefGoogle Scholar
  12. 12.
    Daubin V, Ochman H (2004) Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res 14:1036–1042PubMedCrossRefGoogle Scholar
  13. 13.
    Dolstra H et al (1999) A human minor histocompatibility antigen specific for B cell acute lymphoblastic leukemia. J Exp Med 189:301–308PubMedCrossRefGoogle Scholar
  14. 14.
    Domazet-Loso T, Tautz D (2003) An evolutionary analysis of orphan genes in Drosophila. Genome Res 13:2213–2219PubMedCrossRefGoogle Scholar
  15. 15.
    Domazet-Loso T, Brajkovic J, Tautz D (2007) A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet 23:533–9PubMedCrossRefGoogle Scholar
  16. 16.
    Duan Z, Feller AJ, Toh HC, Makastorsis T, Seiden MV (1999) TRAG-3, a novel gene, isolated from a taxol-resistant ovarian carcinoma cell line. Gene 229:75–81PubMedCrossRefGoogle Scholar
  17. 17.
    Elhaik E, Sabath N, Graur D (2006) The “inverse relationship between evolutionary rate and age of mammalian genes” is an artifact of increased genetic distance with rate of evolution and time of divergence. Mol Biol Evol 23:1–3PubMedCrossRefGoogle Scholar
  18. 18.
    Flicek P et al (2007) Ensembl 2008. Nucleic Acids Res 36:0707–14CrossRefGoogle Scholar
  19. 19.
    Frith MC et al (2006) The abundance of short proteins in the mammalian proteome. PLoS Genet 2:e52PubMedCrossRefGoogle Scholar
  20. 20.
    Furney SJ, Alba MM, Lopez-Bigas N (2006) Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genomics 7:165PubMedCrossRefGoogle Scholar
  21. 21.
    Gibbs RA et al (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222–234PubMedCrossRefGoogle Scholar
  22. 22.
    Goldovsky L et al (2005) CoGenT + +: an extensive and extensible data environment for computational genomics. Bioinformatics 21:3806–3810PubMedCrossRefGoogle Scholar
  23. 23.
    Harris MA et al (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258–261PubMedCrossRefGoogle Scholar
  24. 24.
    Hurst LD, Smith NG (1999) Do essential genes evolve slowly? Curr Biol 9:747–750PubMedCrossRefGoogle Scholar
  25. 25.
    Iwabe N, Kuma K, Miyata T (1996) Evolution of gene families and relationship with organismal evolution: rapid divergence of tissue-specific genes in the early evolution of chordates. Mol Biol Evol 13:483–493PubMedGoogle Scholar
  26. 26.
    Johnson ME et al (2001) Positive selection of a gene family during the emergence of humans and African apes. Nature 413:514–519PubMedCrossRefGoogle Scholar
  27. 27.
    Kouprina N et al (2004) The SPANX gene family of cancer/testis-specific antigens: rapid evolution and amplification in African great apes and hominids. Proc Natl Acad Sci USA 101:3077–3082PubMedCrossRefGoogle Scholar
  28. 28.
    Lander ES et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921PubMedCrossRefGoogle Scholar
  29. 29.
    Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ (2006) Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci USA 103:9935–9939PubMedCrossRefGoogle Scholar
  30. 30.
    Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151–1155PubMedCrossRefGoogle Scholar
  31. 31.
    Martinez-Morales JR, Henrich T, Ramialison M, Wittbrodt J (2007) New genes in the evolution of the neural crest differentiation program. Genome Biol 8:R36PubMedCrossRefGoogle Scholar
  32. 32.
    Miyata T, Suga H (2001) Divergence pattern of animal gene families and relationship with the Cambrian explosion. BioEssays 23:1018–1027PubMedCrossRefGoogle Scholar
  33. 33.
    Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL (1998) Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396:572–575PubMedCrossRefGoogle Scholar
  34. 34.
    Ohno S (1984) Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence. Proc Natl Acad Sci USA 81:2421–2425PubMedCrossRefGoogle Scholar
  35. 35.
    Okamura K, Feuk L, Marques-Bonet T, Navarro A, Scherer SW (2006) Frequent appearance of novel protein-coding sequences by frameshift translation. Genomics 88:690–697PubMedCrossRefGoogle Scholar
  36. 36.
    Pal C, Papp B, Lercher MJ (2006) An integrated view of protein evolution. Nat Rev Genet 7:337–348PubMedCrossRefGoogle Scholar
  37. 37.
    Schittek B et al (2001) Dermcidin: a novel human antibiotic peptide secreted by sweat glands. Nat Immunol 2:1133–1137PubMedCrossRefGoogle Scholar
  38. 38.
    Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502–504PubMedCrossRefGoogle Scholar
  39. 39.
    Seo TK, Kishino H, Thorne JL (2004) Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Mol Biol Evol 21:1201–1213PubMedCrossRefGoogle Scholar
  40. 40.
    Stoye J, Evers D, Meyer F (1998) Rose: generating sequence families. Bioinformatics 14:157–163PubMedCrossRefGoogle Scholar
  41. 41.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  42. 42.
    Waterston RH et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562PubMedCrossRefGoogle Scholar
  43. 43.
    Wootton JC, Federhen S (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266:554–571PubMedCrossRefGoogle Scholar
  44. 44.
    Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586–1591PubMedCrossRefGoogle Scholar
  45. 45.
    Zhang G et al (2007) Identification and characterization of insect-specific proteins by genome data analysis. BMC Genomics 8:93PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Macarena Toll-Riera
    • 1
  • Jose Castresana
    • 2
  • M. Mar Albà
    • 3
  1. 1.Research Unit on Biomedical Informatics, Institut Municipal d’Investigació MèdicaUniversitat Pompeu FabraBarcelonaSpain
  2. 2.Institute of Molecular Biology of BarcelonaCSICBarcelonaSpain
  3. 3.Catalan Institution for Research and Advanced StudiesBarcelonaSpain

Personalised recommendations