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Disparity, adaptation, exaptation, bookkeeping, and contingency at the genome level

Published online by Cambridge University Press:  08 April 2016

Jürgen Brosius*
Affiliation:
Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Strasse 56, Münster, Germany. E-mail: RNA.world@uni-muenster.de

Abstract

The application of molecular genetics, in particular comparative genomics, to the field of evolutionary biology is paving the way to an enhanced “New Synthesis.” Apart from their power to establish and refine phylogenies, understanding such genomic processes as the dynamics of change in genomes, even in hypothetical RNA-based genomes and the in vitro evolution of RNA molecules, helps to clarify evolutionary principles that are otherwise hidden among the nested hierarchies of evolutionary units. To this end, I outline the course of hereditary material and examine several issues including disparity, causation, or bookkeeping of genes, adaptation, and exaptation, as well as evolutionary contingency at the genomic level–issues at the heart of some of Stephen Jay Gould's intellectual battlegrounds. Interestingly, where relevant, the genomic perspective is consistent with Gould's agenda. Extensive documentation makes it particularly clear that exaptation plays a role in evolutionary processes that is at least as significant as–and perhaps more significant than–that played by adaptation.

Type
Generating Disparity
Copyright
Copyright © The Paleontological Society 

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References

Literature Cited

Arendt, D., and Wittbrodt, J. 2001. Reconstructing the eyes of Urbilateria. Philosophical Transactions of the Royal Society of London B 356:15451563.Google Scholar
Arnason, U., Adegoke, J. A., Bodin, K., Born, E. W., Esa, Y. B., Gullberg, A., Nilsson, M., Short, R. V., Xu, X., and Janke, A. 2002. Mammalian mitogenomic relationships and the root of the eutherian tree. Proceedings of the National Academy of Sciences USA 99:81518156.CrossRefGoogle ScholarPubMed
Bailey, J. A., Liu, G., and Eichler, E. E. 2003. An Alu transposition model for the origin and expansion of human segmental duplications. American Journal of Human Genetics 73:823834.Google Scholar
Balakirev, E. S., and Ayala, F. J. 2003. Pseudogenes: are they “junk” or functional DNA? Annual Review of Genetics 37:123151.Google Scholar
Barrel, D. P., and Unrau, P. J. 1999. Constructing an RNA world. Trends in Cell Biology 9:M9M13.Google Scholar
Batzer, M. A., and Deininger, P. L. 2002. Alu repeats and human genomic diversity. Nature Reviews Genetics 3:370379.Google Scholar
Bernardi, G. 2004. Structural and evolutionary genomics: natural selection in genome evolution. Elsevier, Amsterdam.Google Scholar
Bingham, P. M., Kidwell, M. G., and Rubin, G. M. 1982. The molecular basis of P-M hybrid dysgenesis: the role of the P element, a P-strain-specific transposon family. Cell 29:9951004.Google Scholar
Blackburn, E. H. 1991. Telomeres. Trends in Biochemical Sciences 16:378381.Google Scholar
Blackmore, S. 1999. The meme machine. Oxford University Press, Oxford.Google Scholar
Boeke, J. D. 2003. The unusual phylogenetic distribution of retrotransposons: a hypothesis. Genome Research 13:19751983.CrossRefGoogle ScholarPubMed
Brenner, S. 1998. Refuge of spandrels. Current Biology 8:R669.CrossRefGoogle ScholarPubMed
Britten, R. J. 1996. DNA sequence insertion and evolutionary variation in gene regulation. Proceedings of the National Academy of Sciences USA 93:93749377.Google Scholar
Britten, R. J. 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205:177182.Google Scholar
Britten, R. J., and Davidson, E. H. 1969. Gene regulation for higher cells: a theory. Science 165:349357.CrossRefGoogle ScholarPubMed
Britten, R. J., and Davidson, E. H. 1971. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Quarterly Review of Biology 46:111138.Google Scholar
Brosius, J. 1991. Retroposons—seeds of evolution. Science 251:753.Google Scholar
Brosius, J. 1999a. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107:209238.Google Scholar
Brosius, J. 1999b. Many G-protein-coupled receptors are encoded by retrogenes. Trends in Genetics 15:304305.Google Scholar
Brosius, J. 1999c. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115134.Google Scholar
Brosius, J. 1999d. Transmutation of tRNA over time. Nature Genetics 22:89.Google Scholar
Brosius, J. 2001. tRNAs in the spotlight during protein biosynthesis. Trends in Biochemical Sciences 26:653656.Google Scholar
Brosius, J. 2003a. The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118:99116.Google Scholar
Brosius, J. 2003b. From Eden to a hell of uniformity? Directed evolution in humans. Bioessays 25:815821.Google Scholar
Brosius, J. 2003c. Gene duplication and other evolutionary strategies: from the RNA world to the future. Journal of Structural and Functional Genomics 3:117.Google Scholar
Brosius, J. 2003d. How significant is 98.5% ‘junk’ in mammalian genomes? Bioinformatics 19(Suppl. 2):35.Google Scholar
Brosius, J. 2005a. Echoes from the past—are we still in an RNP world? Cytogenetic and Genome Research (in press).Google Scholar
Brosius, J. 2005b. Waste not, want not—transcript excess in multicellular Eukaryotes. Trends in Genetics 21:287288.Google Scholar
Brosius, J., and Gould, S. J. 1992. On “genomenclature”: a comprehensive (and respectful) taxonomy for pseudogenes and other “junk DNA.” Proceedings of the National Academy of Sciences USA 89:1070610710.Google Scholar
Brosius, J., and Kreitman, M. 2000. Eugenics—evolutionary nonsense? Nature Genetics 25:253.Google Scholar
Brosius, J., and Tiedge, H. 1995. Reverse transcriptase: mediator of genomic plasticity. Virus Genes 11:163179.Google Scholar
Brosius, J., and Tiedge, H. 2004. RNomenclature. RNA Biology 1:8183.Google Scholar
Cairns-Smith, A. G. 1982. Genetic takeover and the mineral origins of life. Cambridge University Press, Cambridge.Google Scholar
Cold Spring Harbor Laboratory Press. 1987. Cold Spring Harbor symposia on quantitative biology, Vol. 52. Evolution of catalytic function. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.Google Scholar
Morris, S. Conway 1998. The crucible of creation. Oxford University Press, Oxford.Google Scholar
Morris, S. Conway 2003. Life, the universe and everything: inevitable humans in a lonely universe. Cambridge University Press, Cambridge.Google Scholar
Dagan, T., Sorek, R., Sharon, E., Ast, G., and Graur, D. 2004. AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Research 32 (Database issue):D489492.Google Scholar
Dahl, H. H., Brown, R. M., Hutchison, W. M., Maragos, C., and Brown, G. K. 1990. A testis-specific form of the human pyruvate dehydrogenase E1 alpha subunit is coded for by an intronless gene on chromosome 4. Genomics 8:225232.Google Scholar
Darnell, J. E., and Doolittle, W. F. 1986. Speculations on the early course of evolution. Proceedings of the National Academy of Sciences USA 83:12711275.Google Scholar
Darwin, C. 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, London.Google Scholar
Dawkins, R. 1976. The selfish gene. Oxford University Press, Oxford.Google Scholar
Dawkins, R. 1982. The extended phenotype. W. H. Freeman, San Francisco.Google Scholar
Dawkins, R. 2003. A devil's chaplain. Weidenfeld and Nicolson, London.Google Scholar
DeChiara, T. M., and Brosius, J. 1987. Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proceedings of the National Academy of Sciences USA 84:26242628.Google Scholar
Deininger, P. L., Moran, J. V., Batzer, M. A., and Kazazian, H. H. Jr. 2003. Mobile elements and mammalian genome evolution. Current Opinion in Genetics and Development 13:651658.Google Scholar
D'Erchia, A. M., Gissi, C., Pesole, G., Saccone, C., and Arnason, U. 1996. The guinea-pig is not a rodent. Nature 381:597600.Google Scholar
Dermitzakis, E. T., Reymond, A., Scamuffa, N., Ucla, C., Kirkness, E., Rossier, C., and Antonarakis, S. E. 2003. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science 302:10331035.Google Scholar
Devos, K. M., Brown, J. K. M., and Bennetzen, J. L. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Research 12:10751079.Google Scholar
Dewannieux, M., Esnault, C., and Heidmann, T. 2003. LINE-mediated retrotransposition of marked Alu sequences. Nature Genetics 35:4148.CrossRefGoogle ScholarPubMed
Dietrich, M. R. 2003. Richard Goldschmidt: hopeful monsters and other ‘heresies.’ Nature Reviews Genetics 4:6874.CrossRefGoogle Scholar
Dobzhansky, T. G. 1937. Genetics and the origin of species. Columbia University Press, New York.Google Scholar
Doolittle, W. F., and Sapienza, C. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601603.Google Scholar
Dworkin, J. P., Lazcano, A., and Miller, S. L. 2003. The roads to and from the RNA world. Journal of Theoretical Biology 222:127134.Google Scholar
Ellington, A. D., and Szostak, J. W. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346:818822.Google Scholar
Famulok, M., Mayer, G., and Blind, M. 2000. Nucleic acid aptamers-from selection in vitro to applications in vivo. Accounts of Chemical Research 33:591599.Google Scholar
Franchini, L. F., Ganko, E. W., and McDonald, J. F. 2004. Retro-transposon-gene associations are widespread among D. melanogaster populations. Molecular Biology and Evolution 21:13231331.Google Scholar
Gehring, W. J., and Ikeo, K. 1999. Pax 6: mastering eye morphogenesis and eye evolution. Trends in Genetics 15:371377.Google Scholar
Gesteland, R. F., Cech, T. R., and Atkins, J. F. 1999. The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.Google Scholar
Ghiselin, M. T. 1974. A radical solution to the species problem. Systematic Zoology 23:554556.Google Scholar
Gilbert, W. 1978. Why genes in pieces? Nature 271:501.Google Scholar
Ginzburg, L. R., Bingham, P. M., and Yoo, S. 1984. On the theory of speciation induced by transposable elements. Genetics 107:331341.Google Scholar
Goldschmidt, R. B. 1940. Material basis of evolution. Yale University Press, New Haven, Conn.Google Scholar
Gould, S. J. 1977a. Ever since Darwin: reflections in natural history. Norton, New York.Google Scholar
Gould, S. J. 1977b. Ontogeny and phylogeny. Belknap Press of Harvard University Press, Cambridge.Google Scholar
Gould, S. J. 1980. The panda's thumb. Norton, New York.Google Scholar
Gould, S. J. 1981. What happens to bodies if genes act for themselves? Natural History. November.Google Scholar
Gould, S. J. 1983. Hen's teeth and horse's toes. Norton, New York.Google Scholar
Gould, S. J. 1989. Wonderful life: the Burgess Shale and the nature of history. Norton, New York.Google Scholar
Gould, S. J. 2002. The structure of evolutionary theory. Belknap Press of Harvard University Press, Cambridge.Google Scholar
Gould, S. J., and Lloyd, E. A. 1999. Individuality and adaptation across levels of selection: how shall we name and generalize the unit of Darwinism? Proceedings of the National Academy of Sciences USA 96:1190411909.Google Scholar
Gould, S. J., and Vrba, E. S. 1982. Exaptation—a missing term in the science of form. Paleobiology 8:415.Google Scholar
Graur, D. 1993. Molecular deconstructivism. Nature 363:490.CrossRefGoogle ScholarPubMed
Graur, D., Hide, W. A., and Li, W. H. 1991. Is the guinea-pig a rodent? Nature 351:649652.Google Scholar
Gregory, T. R. 2001. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biological Reviews of the Cambridge Philosophical Society 76:65101.Google Scholar
Gregory, T. R., and Hebert, P. D. 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Research 9:317324.Google Scholar
Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., and Altman, S. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849857.CrossRefGoogle ScholarPubMed
Hagan, C. R., Sheffield, R. F., and Rudin, C. M. 2003. Human Alu element retrotransposition induced by genotoxic stress. Nature Genetics 35:219220.Google Scholar
Hanczyc, M. M., and Dorit, R. L. 1998. Experimental evolution of complexity: in vitro emergence of intermolecular ribozyme interactions. RNA 4:268275.Google Scholar
Herbert, A. 2004. The four Rs of RNA-directed evolution. Nature Genetics 36:1925.Google Scholar
Hurst, G. D., and Werren, J. H. 2001. The role of selfish genetic elements in eukaryotic evolution. Nature Reviews Genetics 2:597606.Google Scholar
Hüttenhofer, A., Kiefmann, M., Meier-Ewert, S., O'Brien, J., Lehrach, H., Bachellerie, J.-P., and Brosius, J. 2001. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO Journal 20:29432953.Google Scholar
Huxley, J. S. 1942. Evolution: the modern synthesis. Allen and Unwin, London.Google Scholar
Jaanusson, V. 1981. Functional thresholds in evolutionary progress. Lethaia 14:251260.Google Scholar
Jepsen, G. L., Simpson, G. G., and Mayr, E., eds. 1949. Genetics, paleontology, and evolution. Princeton University Press, Princeton, N.J.Google Scholar
Jordan, I. K., Rogozin, I. B., Glazko, G. V., and Koonin, E. V. 2003. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends in Genetics 19:6872.Google Scholar
Jurka, J. 1998. Repeats in genomic DNA: mining and meaning. Current Opinion in Structural Biology 8:333337.Google Scholar
Kajikawa, M., and Okada, N. 2002. LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111:433444.Google Scholar
Keller, L., ed. 1999. Levels of selection in evolution. Princeton University Press, Princeton, N.J.Google Scholar
Kidwell, M. G., and Lisch, D. 1997. Transposable elements as sources of variation in animals and plants. Proceedings of the National Academy of Sciences USA 94:77047711.Google Scholar
King, M. C., and Wilson, A. C. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107116.Google Scholar
Kirkness, E. F., Bafna, V., Halpern, A. L., Levy, S., Remington, K., Rusch, D. B., Delcher, A. L., Pop, M., Wang, W., Fraser, C. M., and Venter, J. C. 2003. The dog genome: survey sequencing and comparative analysis. Science 301:18981903.Google Scholar
Kreahling, J., and Graveley, B. R. 2004. The origins and implications of Aluternative splicing. Trends in Genetics 20:14.Google Scholar
Kruger, K., Grabowski, P. J., Zaug, A. J., Sands, J., Gottschling, D. E., and Cech, T. R. 1982. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31:147157.Google Scholar
Kurychev, V. Y., Skryabin, B. V., Kremerskothen, J., Jurka, J., and Brosius, J. 2001. Birth of a gene: locus of neuronal BC200 snmRNA in three prosimians and human BC200 pseudogenes as archives of change in the Anthropoidea lineage. Journal of Molecular Biology 309:10491066.Google Scholar
Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860921.Google Scholar
Lev-Maor, G., Sorek, R., Shomron, N., and Ast, G. 2003. The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science 300:12881291.Google Scholar
Li, T., Spearow, J., Rubin, C. M., and Schmid, C. W. 1999. Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 239:367372.Google Scholar
Makalowski, W. 2000. Genomic scrap yard: how genomes utilize all that junk. Gene 259:6167.Google Scholar
Makalowski, W. 2003. Genomics: not junk after all. Science 300:12461247.Google Scholar
Makalowski, W., Mitchell, G. A., and Labuda, D. 1994. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends in Genetics 10:188193.Google Scholar
Margulies, E. H., Blanchette, M., Program, N. C. S., Haussler, D., and Green, E. D. 2003. Identification and characterization of multi-species conserved sequences. Genome Research 13:25072518.Google Scholar
Martignetti, J. A., and Brosius, J. 1993. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. Proceedings of the National Academy of Sciences USA 90:1156311567.Google Scholar
Mattick, J. S. 2003. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25:930939.Google Scholar
Maxam, A. M., and Gilbert, W. 1977. A new method for sequencing DNA. Proceedings of the National Academy of Sciences USA 74:560564.CrossRefGoogle ScholarPubMed
Smith, J. Maynard 1989. Did Darwin get it right? Essays on games, sex and evolution. Chapman and Hall, New York.Google Scholar
Smith, J. Maynard, and Szathmáry, E. 1995. The major transitions in evolution. Oxford University Press, Oxford.Google Scholar
Mayr, E. 1942. Systematics and the origin of species from the viewpoint of a zoologist. Columbia University Press, New York.Google Scholar
Mayr, E. 2001. What evolution is. Basic Books, New York.Google Scholar
Mazlish, B. 1993. The fourth discontinuity: the co-evolution of humans and machines. Yale University Press, New Haven, Conn.Google Scholar
McCarrey, J. R., and Thomas, K. 1987. Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 326:501505.Google Scholar
McDonald, J. F. 1990. Macroevolution and retroviral elements. Bioscience 40:183191.Google Scholar
McLaughlin, P. J., and Dayhoff, M. O. 1973. Eukaryote evolution: a view based on cytochrome c sequence data. Journal of Molecular Evolution 2:99116.Google Scholar
Mendel, G. 1866. Versuche über Pflanzenhybriden. Verhandlungen des Naturforschenden Vereins in Brünn 4:347.Google Scholar
Mendel, G. 1870. Über einige aus künstlicher Befruchtung gewonnene Hieraciumbastarde. Verhandlungen des naturforschenden Vereins in Brünn 8:2631.Google Scholar
Murphy, W. J., Eizirik, E., Johnson, W. E., Zhang, Y. P., Ryder, O. A., and O'Brien, S. J. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614618.Google Scholar
Nekrutenko, A., and Li, W. H. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends in Genetics 17:619621.Google Scholar
Nelson, K. E., Levy, M., and Miller, S. L. 2000. Peptide nucleic acids rather than RNA may have been the first genetic molecule. Proceedings of the National Academy of Sciences USA 97:38683871.CrossRefGoogle ScholarPubMed
Nelson, P., Kiriakidou, M., Sharma, A., Maniataki, E., and Mourelatos, Z. 2003. The microRNA world: small is mighty. Trends in Biochemical Sciences 28:534540.Google Scholar
Nevo, E. 2001. Evolution of genome-phenome diversity under environmental stress. Proceedings of the National Academy of Sciences USA 98:62336240.Google Scholar
Novina, C. D., and Sharp, P. A. 2004. The RNAi revolution. Nature 430:161164.Google Scholar
Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L. G., Hume, D. A., Hayashizaki, Y., and Tomita, M. 2003. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Research 13:13011306.Google Scholar
O'Brien, S. J., and Murphy, W. J. 2003. Genomics: a dog's breakfast? Science 301:18541855.Google Scholar
Oei, S. L., Babich, V. S., Kazakov, V. I., Usmanova, N. M., Kropotov, A. V., and Tomilin, N. V. 2004. Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters. Genomics 83:873882.Google Scholar
Okada, N. 1991. SINEs. Current Opinion in Genetics and Development 1:498504.Google Scholar
Orgel, L. E., and Crick, F. H. C. 1980. Selfish DNA: the ultimate parasite. Nature 284:604607.Google Scholar
Pasquinelli, A. E., and Ruvkun, G. 2002. Control of developmental timing by micro RNAs and their targets. Annual Review of Cell and Developmental Biology 18:495513.Google Scholar
Piatigorsky, J. 1998. Gene sharing in lens and cornea: facts and implications. Progress in Retinal and Eye Research 17:145174.Google Scholar
Raup, D. M. 1991. Extinction: bad genes or bad luck? Norton, New York.Google Scholar
Rensch, B. 1947. Neuere Probleme der Abstammungslehre (Die Transspezifische Evolution). Ferdinand Enke, Stuttgart.Google Scholar
Rokas, A., and Holland, P. W. 2000. Rare genomic changes as a tool for phylogenetics. Trends in Ecology and Evolution 15:454459.Google Scholar
Ronshaugen, M., McGinnis, N., and McGinnis, W. 2002. Hox protein mutation and macroevolution of the insect body plan. Nature 415:914917.Google Scholar
Rose, M. R., and Doolittle, W. F. 1983. Molecular biological mechanisms of speciation. Science 220:157162.Google Scholar
Runnegar, B. 1987. Rates and modes of evolution in the Mollusca. Pp. 3960in Campbell, K. S. W. and Day, M. F., eds. Rates of evolution. Allen and Unwin, London.Google Scholar
Ryan, S. C., and Dugaiczyk, A. 1989. Newly arisen DNA repeats in primate phylogeny. Proceedings of the National Academy of Sciences USA 86:93609364.Google Scholar
Sadegh-Zadeh, K. 2000. Als der Mensch das Denken Verlernte. Die Entstehung der Machina sapiens. [When man forgot thinking: the emergence of Machina sapiens.]Burgverlag, Tecklenburg, Germany.Google Scholar
Sakharkar, M. K., Kangueane, P., Petrov, D. A., Kolaskar, A. S., and Subbiah, S. 2002. SEGE: a database on ‘intron less/single exonic’ genes from eukaryotes. Bioinformatics 18:12661267.Google Scholar
Sanger, F., and Coulson, A. R. 1975. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology 94:441448.Google Scholar
Sanger, F., Nicklen, S., and Coulson, A. R. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences USA 74:54635467.Google Scholar
Schmalhausen, I. I. 1949. Factors of evolution: the theory of stabilizing selection. Blakiston, Philadelphia.Google Scholar
Schmitz, J., Ohme, M., and Zischler, H. 2001. SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics 157:777784.Google Scholar
Schmitz, J., Ohme, M., Suryobroto, B., and Zischler, H. 2002. The colugo (Cynocephalus variegatus, Dermoptera): the primates' gliding sister? Molecular Biology and Evolution 19:23082312.Google Scholar
Shedlock, A., Takahashi, K., and Okada, N. 2004. SINEs of speciation: tracking lineages with retroposons. Trends in Ecology and Evolution 19:545553.Google Scholar
Shimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I., and Okada, N. 1997. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388:666670.Google Scholar
Shippen-Lentz, D., and Blackburn, E. H. 1990. Functional evidence for an RNA template in telomerase. Science 247:546552.Google Scholar
Simpson, G. G. 1944. Tempo and mode in evolution. Columbia University Press, New York.Google Scholar
Singer, M. F. 1982. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell 28:433434.Google Scholar
Singer, S. S., Männel, D. N., Hehlgans, T., Brosius, J., and Schmitz, J. 2004. From “junk” to gene: curriculum vitae of a primate receptor isoform gene. Journal of Molecular Biology 341:883886.Google Scholar
Sober, E. 1984. The nature of selection: evolutionary theory in philosophical focus. MIT Press, Cambridge.Google Scholar
Sober, E., and Steel, M. 2002. Testing the hypothesis of common ancestry. Journal of Theoretical Biology 218:395408.Google Scholar
Sorek, R., Ast, G., and Graur, D. 2002. Alu-containing exons are alternatively spliced. Genome Research 12:10601067.Google Scholar
Stebbins, G. L. 1950. Variation and evolution in plants. Columbia University Press, New York.Google Scholar
Sterelny, K. 2001. Dawkins vs. Gould: survival of the fittest. Icon Books, Cambridge, U.K.Google Scholar
Stock, G. 1993. Metaman. The merging of humans and machines into a global superorganism. Simon and Schuster, New York.Google Scholar
Sturtevant, A. H., and Dobzhansky, T. 1936. Inversions in the third chromosome of wild races of drosophila pseudoobscura, and their use in the study of the history of the species. Proceedings of the National Academy of Sciences USA 22:448450.Google Scholar
Szathmáry, E. 1990. Towards the evolution of ribozymes. Nature 344:115.Google Scholar
Szathmáry, E., and Smith, J. M. 1995. The major evolutionary transitions. Nature 374:227232.Google Scholar
Szostak, J. W., Bartel, D. P., and Luisi, P. L. 2001. Synthesizing life. Nature 409 (Suppl.):387390.Google Scholar
Thomas, J. W., Touchman, J. W., Blakesley, R. W., Bouffard, G. G., Beckstrom-Sternberg, S. M., Margulies, E. H., Blanchette, M., Siepel, A. C., Thomas, P. J., McDowell, J. C., et al. 2003. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424:788793.CrossRefGoogle ScholarPubMed
Tiedge, H., Chen, W., and Brosius, J. 1993. Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. Journal of Neuroscience 13:23822390.Google Scholar
Tuerk, C., and Gold, L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505510.Google Scholar
van de Lagemaat, L. N., Landry, J. R., Mager, D. L., and Med-strand, P. 2003. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends in Genetics 19:530536.Google Scholar
Wächtershauser, G. 1992. Groundworks for an evolutionary biochemistry: the iron-sulphur world. Progress in Biophysics and Molecular Biology 58:85201.Google Scholar
Wagner, G. P., Amemiya, C., and Ruddle, F. 2003. Hox cluster duplications and the opportunity for evolutionary novelties. Proceedings of the National Academy of Sciences USA 100:1460314606.Google Scholar
Ware, T. L., Wang, H., and Blackburn, E. H. 2000. Three telomerases with completely non-telomeric template replacements are catalytically active. EMBO Journal 19:31193131.Google Scholar
Watson, J. D., and Crick, F. H. C. 1953. Molecular structure of nucleic acids. Nature 171:737738.Google Scholar
Weiner, A. M., Deininger, P. L., and Efstratiadis, A. 1986. Non-viral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annual Review of Biochemistry 55:631661.Google Scholar
Williams, G. C. 1966. Adaptation and natural selection: a critique of some current evolutionary thought. Princeton University Press, Princeton, N.J.Google Scholar
Wilson, D. S. 1975. A theory of group selection. Proceedings of the National Academy of Sciences USA 72:143146.Google Scholar
Wilson, D. S. 1980. The natural selection of populations and communities. Benjamin/Cummings, Menlo Park, Calif.Google Scholar
Wilson, D. S., and Sober, E. 1989. Reviving the superorganism. Journal of Theoretical Biology 136:337356.Google Scholar
Wilson, D. S., and Szostak, J. W. 1999. In vitro selection of functional nucleic acids. Annual Review of Biochemistry 68:611647.Google Scholar
Wilson, E. O. 1971. The insect societies. Belknap Press of Harvard University Press, Cambridge.Google Scholar
Woese, C. R. 2001. Translation: in retrospect and prospect. RNA 7:10551067.Google Scholar
Woese, C. R., and Fox, G. E. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences USA 74:50885090.Google Scholar
Wolfe, K. H., and Li, W. H. 2003. Molecular evolution meets the genomics revolution. Nature Genetics 33 (Suppl.):5265.Google Scholar
Zuckerkandl, E. 1975. The appearance of new structures and functions in proteins during evolution. Journal of Molecular Evolution 7:157.Google Scholar