The origin of new genes: glimpses from the young and old (original) (raw)

• Gilbert, W. Why genes in pieces? Nature 271, 44 (1978).
  Article Google Scholar
• van Rijk, A. & Bloemendal, H. Molecular mechanisms of exon shuffling: illegitimate recombination. Genetica 118, 245–249 (2003).
  Article CAS PubMed Google Scholar
• van Rijk, A. A., de Jong, W. W. & Bloemendal, H. Exon shuffling mimicked in cell culture. Proc. Natl Acad. Sci. USA 96, 8074–8079 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Moran, J. V., DeBerardinis, R. J. & Kazazian, H. H. Jr. Exon shuffling by L1 retrotransposition. Science 283, 1530–1534 (1999).
  Article CAS PubMed Google Scholar
• Esnault, C., Maestre, J. & Heidmann, T. Human LINE retrotransposons generate processed pseudogenes. Nature Genet. 24, 363–367 (2000).
  Article CAS PubMed Google Scholar
• Kaessmann, H., Zollner, S., Nekrutenko, A. & Li, W. H. Signatures of domain shuffling in the human genome. Genome Res. 12, 1642–1650 (2002). Based on analysis of human and C. elegans genomes, this paper provides new evidence that intron-phase correlation is a sign of exon shuffling that recombines protein-coding domains to form a new gene.
  Article CAS PubMed PubMed Central Google Scholar
• de Souza, S. J., Long, M., Schoenbach, L., Roy, S. W. & Gilbert, W. Intron positions correlate with module boundaries in ancient proteins. Proc. Natl Acad. Sci. USA 93, 14632–14636 (1996).
  Article CAS PubMed PubMed Central Google Scholar
• Patthy, L. Exon shuffling and other ways of module exchange. Matrix Biol. 15, 301–310, 311–312 (1996).
  Article CAS PubMed Google Scholar
• Ohno, S. Evolution by Gene Duplication (Springer, Berlin, 1970).
  Book Google Scholar
• Kimura, M. The Neutral Theory of Molecular Evolution (Cambridge Univ. Press, Cambridge, 1983).
  Book Google Scholar
• Prince, V. E. & Pickett, F. B. Splitting pairs: the diverging fates of duplicated genes. Nature Rev. Genet. 3, 827–837 (2002).
  Article CAS PubMed Google Scholar
• Bailey, J. A. et al. Recent segmental duplications in the human genome. Science 297, 1003–1007 (2002).
  Article CAS PubMed Google Scholar
• Samonte, R. V. & Eichler, E. E. Segmental duplications and the evolution of the primate genome. Nature Rev. Genet. 3, 65–72 (2002).
  Article CAS PubMed Google Scholar
• Makalowski, W., Mitchell, G. A. & Labuda, D. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet. 10, 188–193 (1994).
  Article CAS PubMed Google Scholar
• Makalowski, W. in The Impact of Short Interspersed Elements (SINEs) on the Host Genome (ed. Maraia, R. J.) 86–104 (Landes Company, Austin, 1995).
  Google Scholar
• Nekrutenko, A. & Li, W. H. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17, 619–621 (2001).
  Article CAS PubMed Google Scholar
• Lorenc, A. & Makalowski, W. Transposable elements and vertebrate protein diversity. Genetica 118, 467–477 (2003).
  Article Google Scholar
• Ochman, H. Lateral and oblique gene transfer. Curr. Opin. Genet. Dev. 11, 616–619 (2001).
  Article CAS PubMed Google Scholar
• de Koning, A. P., Brinkman, F. S., Jones, S. J. & Keeling, P. J. Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis. Mol. Biol. Evol. 17, 1769–1773 (2000).
  Article CAS PubMed Google Scholar
• Bergthorsson, U., Adams, K. L., Thomason, B. & Palmer, J. D. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424, 197–201 (2003).
  Article CAS PubMed Google Scholar
• Thomson, T. M. et al. Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene. Genome Res. 10, 1743–1756 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Nurminsky, D. I., Nurminskaya, M. V., De Aguiar, D. & Hartl, D. L. Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396, 572–575 (1998). In this study, a young D. melanogaster gene showed unusually rapid changes in its structure, from seemingly unrelated resources, which led to unexpected new functions of the gene in sperm tails.
  Article CAS PubMed Google Scholar
• Wang, W., Brunet, F. G., Nevo, E. & Long, M. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 99, 4448–4453 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, W., Thornton, K., Berry, A. & Long, M. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295, 134–137 (2002).
  Article CAS PubMed Google Scholar
• Haldane, J. B. S. The part played by recurrent mutation in evolution. Am. Nat. 67, 5–19 (1933).
  Article Google Scholar
• Fisher, R. A. The sheltering of lethals. Am. Nat. 69, 446–455 (1935).
  Article Google Scholar
• Hughes, A. L. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B 256, 119–124 (1994).
  Article CAS Google Scholar
• Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1545 (1999).
  CAS PubMed PubMed Central Google Scholar
• Walsh, J. B. How often do duplicated genes evolve new functions? Genetics 139, 421–428 (1995).
  CAS PubMed PubMed Central Google Scholar
• Walsh, B. Population-genetic model of the fates of duplicate genes. Genetica 118, 279–294 (2003).
  Article CAS PubMed Google Scholar
• Gu, X. Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18, 453–464 (2001).
  Article CAS PubMed Google Scholar
• Long, M. & Langley, C. H. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260, 91–95 (1993).
  Article CAS PubMed Google Scholar
• Messier, W. & Stewart, C. B. Episodic adaptive evolution of primate lysozymes. Nature 385, 151–154 (1997).
  Article CAS PubMed Google Scholar
• Zhang, J., Rosenberg, H. F. & Nei, M. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl Acad. Sci. USA 95, 3708–3713 (1998).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, J., Zhang, Y. P. & Rosenberg, H. F. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nature Genet. 30, 411–415 (2002). In this study, the authors combine sequence analysis and recombination protein technology to detect positive selection in the adaptive evolution of a new gene duplicate to the changed digestive system in the leaf-eating colobine monkey.
  Article CAS PubMed Google Scholar
• Ohta, T. Further examples of evolution by gene duplication revealed through DNA sequence comparisons. Genetics 138, 1331–1337 (1994).
  CAS PubMed PubMed Central Google Scholar
• Johnson, M. E. et al. Positive selection of a gene family during the emergence of humans and African apes. Nature 413, 514–519 (2001).
  Article CAS PubMed Google Scholar
• Begun, D. J. Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila. Genetics 145, 375–382 (1997).
  CAS PubMed PubMed Central Google Scholar
• Maston, G. A. & Ruvolo, M. Chorionic gonadotropin has a recent origin within primates and an evolutionary history of selection. Mol. Biol. Evol. 19, 320–335 (2002). This paper discusses how an important function (involving pregnancy establishment in human and other primates) arose by gene duplication, supported by ample biological data.
  Article CAS PubMed Google Scholar
• Paulding, C. A., Ruvolo, M. & Haber, D. A. The Tre2 (USP6) oncogene is a hominoid-specific gene. Proc. Natl Acad. Sci. USA 100, 2507–2511 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Long, M., de Souza, S. J., Rosenberg, C. & Gilbert, W. Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor. Proc. Natl Acad. Sci. USA 93, 7727–7731 (1996).
  Article CAS PubMed PubMed Central Google Scholar
• Ranz, J. M., Ponce, A. R., Hartl, D. L. & Nurminsky, D. Origin and evolution of a new gene expressed in the Drosophila sperm axoneme. Genetica 118, 233–244 (2003).
  Article CAS PubMed Google Scholar
• Betrán, E., Wang, W., Jin, L. & Long, M. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Mol. Biol. Evol. 19, 654–663 (2002).
  Article PubMed Google Scholar
• Brown, C. J., Todd, K. M. & Rosenzweig, R. F. Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol. Biol. Evol. 15, 931–942 (1998). This study of experimental evolution shows that a new gene function can arise rapidly as a response to a changed environment.
  Article CAS PubMed Google Scholar
• Hall, B. G. The EBG system of E. coli: origin and evolution of a novel β-galactosidase for the metabolism of lactose. Genetica 118, 143–156 (2003).
  Article CAS PubMed Google Scholar
• McDonald, J. H. & Kreitman, M. Adaptative protein evolution at the Adh locus in. Drosophila. Nature 351, 652–654 (1991).
  CAS PubMed Google Scholar
• Henikoff, S., Ahmad, K. & Malik, H. S. The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293, 1098–1102 (2001).
  Article CAS PubMed Google Scholar
• Malik, H. S. & Henikoff, S. Adaptive evolution of Cid, a centromere-specific histone in Drosophila. Genetics 157, 1293–1298 (2001).
  CAS PubMed PubMed Central Google Scholar
• Betrán, E. & Long, M. Dntf-2r: a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 164, 977–988 (2003).
  PubMed PubMed Central Google Scholar
• Llopart, A., Comeron, J. M., Brunet, F. G., Lachaise, D. & Long, M. Intron presence–absence polymorphism in Drosophila driven by positive Darwinian selection. Proc. Natl Acad. Sci. USA 99, 8121–8126 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Cheng, C. H., Chen, L., Near, T. J. & Jin, Y. Functional antifreeze glycoprotein genes in temperate-water New Zealand nototheniid fish infer an Antarctic evolutionary origin. Mol. Biol. Evol. 28 July 2003 (doi:10.1093/molbev/msg004).
  Article CAS PubMed Google Scholar
• Chen, L., DeVries, A. L. & Cheng, C. H. Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod. Proc. Natl Acad. Sci. USA 94, 3817–3822 (1997). This study clearly showed how a similar environmental challenge in two different geographic locations created similar genes with the same function from different DNA materials.
  Article CAS PubMed PubMed Central Google Scholar
• Chen, L., DeVries, A. L. & Cheng, C. H. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. Proc. Natl Acad. Sci. USA 94, 3811–3816 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Cheng, C. H. & Chen, L. Evolution of an antifreeze glycoprotein. Nature 401, 443–444 (1999).
  Article CAS PubMed Google Scholar
• Thornton, K. & Long, M. Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome. Mol. Biol. Evol. 19, 918–925 (2002).
  Article CAS PubMed Google Scholar
• Charlesworth, B., Coyne, J. A. & Barton N. H. The relatives rates of evolution of sex chromosomes and autosomes. Am. Nat. 130, 113–146 (1987).
  Article Google Scholar
• Orr, H. A. & Betancourt, A. J. Haldane's sieve and adaptation from the standing genetic variation. Genetics 157, 875–884 (2001).
  CAS PubMed PubMed Central Google Scholar
• Betancourt, A. J., Presgraves, D. C. & Swanson, W. J. A test for faster X evolution in Drosophila. Mol. Biol. Evol. 19, 1816–1819 (2002).
  Article CAS PubMed Google Scholar
• The Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
• Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002).
  Article CAS PubMed Google Scholar
• Betrán, E. & Long, M. Expansion of genome coding regions by acquisition of new genes. Genetica 115, 65–80 (2002).
  Article PubMed Google Scholar
• Patthy, L. Protein Evolution by Exon-shuffling (Springer, New York, 1995).
  Google Scholar
• Todd, A. E., Orengo, C. A. & Thornton, J. M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307, 1113–1143 (2001). A detailed structural and sequence analysis of 31 enzyme superfamilies for which structural data are available. Interestingly, almost all of the families were subject to domain shuffling, which highlights the generality of the mechanism in new gene origination.
  Article CAS PubMed Google Scholar
• Long, M., de Souza, S. J. & Gilbert, W. Evolution of the intron–exon structure of eukaryotic genes. Curr. Opin. Genet. Dev. 5, 774–778 (1995).
  Article CAS PubMed Google Scholar
• Long, M., Rosenberg, C. & Gilbert, W. Intron phase correlations and the evolution of the intron/exon structure of genes. Proc. Natl Acad. Sci. USA 92, 12495–12499 (1995).
  Article CAS PubMed PubMed Central Google Scholar
• Gilbert, W., de Souza, S. J. & Long, M. Origin of genes. Proc. Natl Acad. Sci. USA 94, 7698–7703 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Long, M. Evolution of novel genes. Curr. Opin. Genet. Dev. 11, 673–680 (2001).
  Article CAS PubMed Google Scholar
• Long, M., de Souza, S. J., Rosenberg, C. & Gilbert, W. Relationship between “proto-splice sites” and intron phases: evidence from dicodon analysis. Proc. Natl Acad. Sci. USA 95, 219–223 (1998).
  Article CAS PubMed PubMed Central Google Scholar
• Patthy, L. Intron-dependent evolution: preferred types of exons and introns. FEBS Lett. 214, 1–7 (1987).
  Article CAS PubMed Google Scholar
• Roy, S. W., Lewis, B. P., Fedorov, A. & Gilbert, W. Footprints of primordial introns on the eukaryotic genome. Trends Genet. 17, 496–501 (2001). The authors described an unexpectedly significant correlation between the distribution of intron phases and the age of the host genes, which supported a model of ancient exon–intron structure with gradual intron addition.
  Article CAS PubMed Google Scholar
• Fedorov, A., Roy, S., Cao, X. & Gilbert, W. Phylogenetically older introns strongly correlate with module boundaries in ancient proteins. Genome Res. 13, 1155–1157 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).
  Article CAS PubMed Google Scholar
• Deutsch, M. & Long, M. Intron–exon structures of eukaryotic model organisms. Nucleic Acids Res. 27, 3219–3228 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Long, M. & de Souza, S. J. Intron–exon structures: from molecular to population biology. Adv. Genome Biol. 5A, 143–178 (1998).
  Article CAS Google Scholar
• Kazazian, H. H. J. L1 retrotransposons shape the mammalian genome. Science 289, 1152–1153 (2000).
  Article CAS PubMed Google Scholar
• Pickeral, O. K., Makalowski, W., Boguski, M. S. & Boeke, J. D. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res. 10, 411–415 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Harrison, P. M. et al. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res. 12, 272–280 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Sorek, R., Ast, G. & Graur, D. Alu-containing exons are alternatively spliced. Genome Res. 12, 1060–1067 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Lifschytz, E. & Lindsley, D. L. The role of X-chromosome inactivation during spermatogenesis (_Drosophila_-allocycly-chromosome evolution-male sterility-dosage compensation). Proc. Natl Acad. Sci. USA 69, 182–186 (1972).
  Article CAS PubMed PubMed Central Google Scholar
• McCarrey, J. R. Nucleotide sequence of the promoter region of a tissue-specific human retroposon: comparison with its housekeeping progenitor. Gene 61, 291–298 (1987).
  Article CAS PubMed Google Scholar
• McCarrey, J. R. Molecular evolution of the human Pgk-2 retroposon. Nucleic Acids Res. 18, 949–955 (1990).
  Article CAS PubMed PubMed Central Google Scholar
• McCarrey, J. R. Evolution of tissue-specific gene expression in mammals: how a new phosphoglycerate kinase was formed and refined. BioScience 44, 20–27 (1994).
  Article Google Scholar
• Pan, Y., Decker, W. K., Huq, A. H. & Craigen, W. J. Retrotransposition of glycerol kinase-related genes from the X chromosome to autosomes: functional and evolutionary aspects. Genomics 59, 282–290 (1999).
  Article CAS PubMed Google Scholar
• Elliott, D. J. et al. An evolutionarily conserved germ cell-specific hnRNP is encoded by a retrotransposed gene. Hum. Mol. Genet. 9, 2117–2124 (2000).
  Article CAS PubMed Google Scholar
• Betrán, E., Thornton, K. & Long, M. Retroposed new genes out of the X in Drosophila. Genome Res. 12, 1854–1859 (2002).
  Article PubMed PubMed Central CAS Google Scholar
• Kaminker, J. S. et al. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3, 0084 (2002).
  Article Google Scholar
• Swanson, W. J., Clark, A. G., Waldrip-Dail, H. M., Wolfner, M. F. & Aquadro, C. F. Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc. Natl Acad. Sci. USA 98, 7375–7379 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Avner, P. & Heard, E. X-chromosome inactivation: counting, choice and initiation. Nature Rev. Genet. 2, 59–67 (2001).
  Article CAS PubMed Google Scholar
• Franke, A. & Baker, B. S. Dosage compensation rox! Curr. Opin. Cell Biol. 12, 351–354 (2000).
  Article CAS PubMed Google Scholar
• Richler, C. et al. Splicing components are excluded from the transcriptionally inactive XY body in male meiotic nuclei. Mol. Biol. Cell 5, 1341–1352 (1994).
  Article CAS PubMed PubMed Central Google Scholar
• Wu, C -I. & Xu, E. Y. Sexual antagonism and X inactivation — the SAXI hypothesis. Trends Genet. 19, 243–247 (2003).
  Article CAS PubMed Google Scholar
• Wang, P. J., McCarrey, J. R., Yang, F. & Page, D. C. An abundance of X-linked genes expressed in spermatogonia. Nature Genet. 27, 422–426 (2001).
  Article PubMed CAS Google Scholar
• Rice, W. R. Sex chromosomes and the evolution of sexual dimorphism. Evolution 38, 735–742 (1984).
  Article PubMed Google Scholar
• Parisi, M. et al. Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 299, 697–700 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Ranz, J. M., Castillo-Davis, C. I., Meiklejohn, C. D. & Hartl, D. L. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300, 1742–1745 (2003).
  Article CAS PubMed Google Scholar
• Reinke, V. et al. A global profile of germline gene expression in C. elegans. Mol. Cell 6, 605–616 (2000).
  Article CAS PubMed Google Scholar
• Kelly, W. G. et al. X-chromosome silencing in the germline of C. elegans. Development 129, 479–492 (2002).
  CAS PubMed Google Scholar
• Langley, C. H., Montgomery, E. & Quattlebaum, W. F. Restriction map variation in the Adh region of Drosophila. Proc. Natl Acad. Sci. USA 79, 5631–5635 (1982).
  Article CAS PubMed PubMed Central Google Scholar
• Jeffs, P. & Ashburner, M. Processed pseudogenes in Drosophila. Proc. R. Soc. Lond. B 244, 151–159 (1991).
  Article CAS Google Scholar
• Wang, W., Zhang, J., Alvarez, C., Llopart, A. & Long, M. The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster. Mol. Biol. Evol. 17, 1294–1301 (2000).
  Article CAS PubMed Google Scholar
• Long, M., Wang, W. & Zhang, J. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene 238, 135–141 (1999).
  Article CAS PubMed Google Scholar
• Petrov, D. A., Lozovskaya, E. R. & Hartl, D. L. High intrinsic rate of DNA loss in Drosophila. Nature 384, 346–349 (1996).
  Article CAS PubMed Google Scholar
• Weiner, A. M., Deininger, P. L. & Efstratiadis, A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55, 631–661 (1986).
  Article CAS PubMed Google Scholar
• Brosius, J. Retroposons — seeds of evolution. Science 251, 753 (1991).
  Article CAS PubMed Google Scholar
• Javaud, C., Dupuy, F., Maftah, A., Julien, R. & Petit, J -M. The fucosyltransferase gene family: an amazing summary of the underlying mechanisms of gene evolution. Genetica 118, 157–170 (2003).
  Article CAS PubMed Google Scholar
• Hughes, A. Adaptive Evolution of Genes and Genomes, (Oxford Univ. Press, Oxford, 2000).
  Google Scholar
• Courseaux, A. & Nahon, J. L. Birth of two chimeric genes in the Hominidae lineage. Science 291, 1293–1297 (2001). This paper reported two chimeric genes — PMCHL1 and very young PMCHL2 — in Hominidae, which showed that an intron-containing gene structure can be retroposed to another genomic location.
  Article CAS PubMed Google Scholar
• Goodier, J. L., Ostertag, E. M. & Kazazian, H. H. Jr. Transduction of 3′-flanking sequences is common in L1 retrotransposition. Hum. Mol. Genet. 9, 653–657 (2000).
  Article CAS PubMed Google Scholar
• Brosius, J. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238, 115–134 (1999).
  Article CAS PubMed Google Scholar
• Brosius, J. The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118, 99–116 (2003).
  Article CAS PubMed Google Scholar
• Makalowski, W. Genomic scrap yard: how genomes utilize all that junk. Gene 259, 61–67 (2000).
  Article CAS PubMed Google Scholar
• Lorenc, A. & Makalowski, W. Transposable elements and vertebrate protein diversity. Genetica 118, 183–191 (2003).
  Article CAS PubMed Google Scholar
• Ragan, M. A. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201, 187–191 (2001).
  Article CAS PubMed Google Scholar
• McCarthy, A. D. & Hardie, D. G. Fatty acid synthase — an example of protein evolution by gene fusion. Trends Biochem. Sci. 4, 60–63 (1984).
  Article Google Scholar
• Snel, B., Bork, P. & Huynen, M. Gene fusion versus gene fission. Trends Genet. 16, 9–11 (2000).
  Article CAS PubMed Google Scholar
• Martignetti, J. A. & Brosius, J. Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent. Proc. Natl Acad. Sci. USA 90, 9698–9702 (1993).
  Article CAS PubMed PubMed Central Google Scholar
• Martignetti, J. A. & Brosius, J. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. Proc. Natl Acad. Sci. USA 90, 11563–11567 (1993).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, J., Webb, D. M. & Podlaha, O. Accelerated protein evolution and origins of human-specific features: Foxp2 as an example. Genetics 162, 1825–1835 (2002).
  CAS PubMed PubMed Central Google Scholar
• Enard, W. et al. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418, 869–872 (2002).
  Article CAS PubMed Google Scholar
• Brosius, J. & Gould, S. J. On “genomenclature”: a comprehensive (and respectful) taxonomy for pseudogenes and other “junk DNA”. Proc. Natl Acad. Sci. USA 89, 10706–10710 (1992).
  Article CAS PubMed PubMed Central Google Scholar
• Gogolevskaya, I. K. & Kramerov, D. A. Evolutionary history of 4.5SI RNA and indication that it is functional. J. Mol. Evol. 54, 354–364 (2002).
  Article CAS PubMed Google Scholar
• Long, M. Protein-coding segments: evolution of exon–intron gene structure. Nature Encyclopedia of Life Sciences [online], <http://www.els.net> (doi:10.1038/npg.els.0000887) (2000).