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12 - Next generation apomorphy: the ubiquity of taxonomically restricted genes

from Part III - Next Generation Challenges and Questions

Published online by Cambridge University Press:  05 June 2016

By
Paul A. Nelson  and
Richard J. A. Buggs
Edited by
Peter D. Olson ,
Joseph Hughes  and
James A. Cotton
Paul A. Nelson
Affiliation:
Biola University, La Mirada, California, USA
Richard J. A. Buggs
Affiliation:
Queen Mary University of London, UK
Peter D. Olson
Affiliation:
Natural History Museum, London
Joseph Hughes
Affiliation:
University of Glasgow
James A. Cotton
Affiliation:
Wellcome Trust Sanger Institute, Cambridge
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Summary

Introduction

The ability to sequence whole genomes at ever-increasing rates has led to the discovery of vast numbers of genes that are unique to each taxon (i.e. apomorphic genes). Before the advent of automated DNA sequencing in the early 1990s, genetic comparison of organisms was only feasible through the targeted amplification of homologous genes shared among divergent taxa, and reliable identification of taxon-specific genes was almost impossible. Shortly after the publication of the first whole genome in 1995, it became clear that species possessed many more taxonomically unique, or restricted, gene sequences than expected. When seven whole genomes had been published, R. F. Doolittle, a molecular biologist of many decades’ experience, commented: ‘I am surprised that so many open reading frames remain as unidentified [i.e. unique] reading frames’ (Doolittle 1997, p. 516). Five years later, when 60 whole genomes had been sequenced, he called taxonomically unique sequences ‘the biggest surprise in genome sequencing’ (Doolittle 2002, p. 698).

Today, with whole-genome sequencing further facilitated by next generation technologies, these taxonomically restricted genes (TRGs; Khalturin et al. 2009), also known as orphan genes (Dujon 1996), or ‘ORFans’ (Fischer and Eisenberg 1999) continue to be discovered in every newly sequenced species genome (Figs 12.1 and 12.2). These genes represent one of the most intriguing aspects of systematics, lying at the intersection of genomics, genetics, comparative and structural biology, phylogenetics and evolution. Yet, by their very nature, they are difficult to study using conventional comparative approaches and attract little research funding.

In this chapter, we review the current status of this conundrum in the light of rapid advances in genomics. Section 12.2 examines the definition of TRGs/ORFans, noting that this is an inherently comparative concept and the status of any gene as a TRG/ORFan is therefore highly contingent. Section 12.3 emphasizes their ubiquity. Section 12.4 discusses the biological significance of some TRGs in terms of putative functions. Section 12.5 discusses hypotheses for the origins and evolution of TRGs, and finally Section 12.6 examines the relevance of TRGs to systematics.

The contingent nature of TRG classification

Assigning any gene the status of ‘taxonomically restricted’ or ‘orphan’ is necessarily a relative judgement; an ‘orphan’ gene always holds its status provisionally.

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Next Generation Systematics , pp. 237 - 263
Publisher: Cambridge University Press
Print publication year: 2016

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References

Abroi, A. and Gough, J. (2011). Are viruses a source of new protein folds for organisms? Virosphere structure space and evolution. BioEssays, 33, 626–35.CrossRefGoogle ScholarPubMed
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403–10.CrossRefGoogle ScholarPubMed
Altschul, S. F., Madden, T. L., Schäffer, A. A., et al. (1997). Gapped BLAST and PSI-BLAST, a new generation of protein database search programs. Nucleic Acids Research, 25, 3389–402.CrossRefGoogle ScholarPubMed
Ang, D. and Georgopoulos, C. (2012). An ORFan no more, the bacteriophage T4 39.2 gene product, NwgI, modulates GroEL chaperone function. Genetics, 190, 989–1000.CrossRefGoogle ScholarPubMed
Armengaud, J., Bland, C., Christie-Oleza, J. and Miotello, G. (2011). Microbial proteogenomics, gaining ground with the avalanche of genome sequences. Journal of Bacteriology and Parasitology, S3–001 [published online]. doi: 10.4172/2155-9597.S3-001.Google Scholar
Baumdicker, F., Hess, W. R. and Pfaffelhuber, P. (2010). The diversity of a distributed genome in bacterial populations. Annals of Applied Probability, 20, 1567–606.CrossRefGoogle Scholar
Baumdicker, F., Hess, W. R. and Pfaffelhuber, P. (2012). The infinitely many genes model for the distributed genome of bacteria. Genome Biology and Evolution, 4, 443–56.CrossRefGoogle Scholar
Begun, D. J., Lindfors, H. A., Kern, A. D. and Jones, C. D. (2007). Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics, 176, 1131–7.Google Scholar
Beiko, R. G. (2011). Telling the whole story in a 10,000-genome world. Biology Direct, 6, 34.CrossRefGoogle Scholar
Bench, S. R., Hanson, T. E., Williamson, K. E., et al. (2007). Metagenomic characterization of Chesapeake Bay virioplankton. Applied and Environmental Microbiology, 73, 7629–41.CrossRefGoogle ScholarPubMed
Boissy, R., Ahmed, A., Janto, B., et al. (2011). Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model. BMC Genomics, 12, 187.CrossRefGoogle ScholarPubMed
Boore, J. L. (2006). The use of genome-level characters for phylogenetic reconstruction. Trends in Ecology & Evolution, 21, 439–46.CrossRefGoogle ScholarPubMed
Boore, J. L. and Fuerstenberg, S. I. (2008). Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction. Philosophical Transactions of the Royal Society B-Biological Sciences, 363, 1445–51.CrossRefGoogle ScholarPubMed
Boto, L. (2010). Horizontal gene transfer in evolution: facts and challenges. Proceedings of the Royal Society B-Biological Sciences, 277, 819–27.CrossRefGoogle ScholarPubMed
Boyer, M., Gimenez, G., Suzan-Monti, M. and Raoult, D. (2010). Classification and determination of possible origins of ORFans through analysis of nucleocytoplasmic large DNA viruses. Intervirology, 53, 310–20.CrossRefGoogle ScholarPubMed
Breitbart, M. (2012). Marine viruses: truth or dare. Annual Review of Marine Science, 4, 425–48.CrossRefGoogle ScholarPubMed
Campbell, M. A., Zhu, W., Jiang, N., et al. (2007). Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiology, 145, 1311–22.CrossRefGoogle ScholarPubMed
Cardoso-Moreira, M. and Long, M. (2012). The origin and evolution of new genes. Methods in Molecular Biology, 856, 161–86.Google ScholarPubMed
Carvunis, A-R., Rolland, T., Wapinski, I., et al. (2012). Proto-genes and de novo gene birth. Nature, 487, 370–4.CrossRefGoogle ScholarPubMed
Chan, C. X., Darling, A. E., Beiko, R. G. and Ragan, M. A. (2009). Are protein domains modules of lateral genetic transfer?PLoS One, 4, e4524.CrossRefGoogle ScholarPubMed
Clamp, M., Fry, B., Kamal, M., et al. (2007). Distinguishing protein-coding and noncoding genes in the human genome. Proceedings of the National Academy of Sciences of the United States of America, 104, 19428–33.CrossRefGoogle ScholarPubMed
Dai, D., Chen, Y., Chen, S., et al. (2008). The evolution of courtship behaviors through the origination of a new gene in Drosophila.Proceedings of the National Academy of Sciences of the United States of America, 105, 7478–83.CrossRefGoogle ScholarPubMed
Daubin, V. and Ochman, H. (2004). Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Research, 14, 1036–42.CrossRefGoogle ScholarPubMed
de Pinna, M. G. G. (1991). Concepts and tests of homology in the cladistic paradigm. Cladistics, 7, 367–94.CrossRefGoogle Scholar
Ding, Y., Zhou, Q. and Wang, W. (2012). Origins of new genes and evolution of their novel functions. Annual Review of Ecology, Evolution, and Systematics, 43, 345–63.CrossRefGoogle Scholar
Djebali, S., Davis, C. A., Merkel, A., et al. (2012). Landscape of transcription in human cells. Nature, 489, 101–8.CrossRefGoogle ScholarPubMed
Domazet-Lošo, T. and Tautz, D. (2003). An evolutionary analysis of orphan genes in Drosophila. Genome Research, 13, 2213–19.CrossRefGoogle ScholarPubMed
Domazet-Lošo, T. and Tautz, D. (2007). A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends in Genetics, 23, 533–9.CrossRefGoogle ScholarPubMed
Domazet-Lošo, T. and Tautz, D. (2008). An ancient evolutionary origin of genes associated with human genetic diseases. Molecular Biology and Evolution, 25, 2699–707.CrossRefGoogle ScholarPubMed
Domazet-Lošo, T. and Tautz, D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature, 468, 815–8.CrossRefGoogle ScholarPubMed
Donoghue, M., Keshavaiah, C., Swamidatta, S. and Spillane, C. (2011). Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. BMC Evolutionary Biology, 11, 47.CrossRefGoogle ScholarPubMed
Doolittle, R. F. (1997). A bug with excess gastric activity. Nature, 388, 515–16.CrossRefGoogle Scholar
Doolittle, R. F. (2002). Biodiversity: microbial genomes multiply. Nature, 416, 697–700.CrossRefGoogle ScholarPubMed
Doolittle, W. (1999). Phylogenetic classification and the universal tree. Science, 284, 2124–9.CrossRefGoogle ScholarPubMed
Dujon, B. (1996). The yeast genome project: what did we learn?Trends in Genetics, 12, 263–70.CrossRefGoogle ScholarPubMed
Dunn, B., Richter, C., Kvitek, D. J., Pugh, T. and Sherlock, G. (2012). Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Research, 22, 908–24.CrossRefGoogle ScholarPubMed
Edwards, A. M., Isserlin, R., Bader, G. D., Frye, S. V., Willson, T. M. and Yu, F. H. (2011). Too many roads not taken. Nature, 470, 163–5.CrossRefGoogle Scholar
Edwards, R. A. and Rohwer, F. (2005). Viral metagenomics. Nature Reviews Microbiology, 3, 504–10.CrossRefGoogle ScholarPubMed
Eisen, J. A. (1998). Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Research, 8, 163–7.CrossRefGoogle ScholarPubMed
Extavour, C. G. (2011). Long-lost relative claims orphan gene, oskar in a wasp. PLoS Genetics, 7, e1002045.CrossRefGoogle Scholar
Fischer, D. and Eisenberg, D. (1999). Finding families for genomic ORFansBioinformatics, 15, 759–62.Google ScholarPubMed
Fisher, R. A. (1930). The Genetical Theory of Natural Selection. Oxford, Oxford University Press.CrossRefGoogle Scholar
Forterre, P. (2006). DNA topoisomerase V: a new fold of mysterious origin. Trends in Biotechnology, 24, 245–7.CrossRefGoogle ScholarPubMed
Forterre, P. and Prangishvili, D. (2009). The origin of viruses. Research in Microbiology 160, 466–72.CrossRefGoogle ScholarPubMed
Fraune, S., Augustin, R., Anton-Erxleben, F., et al. (2010). An early branching metazoan: bacterial colonization of the embryo is controlled by maternal antimicrobial peptides. Proceedings of the National Academy of Sciences of the United States of America, 107, 18067–72.CrossRefGoogle ScholarPubMed
Garza-Garcia, A. A., Driscoll, P. C. and Brockes, J. P. (2010). Evidence for the local evolution of mechanisms underlying limb regeneration in salamanders. Integrative and Comparative Biology. 50, 528–35.CrossRefGoogle ScholarPubMed
Golub, T. (2010). Counterpoint: data first. Nature, 464, 679.CrossRefGoogle ScholarPubMed
Graham, D. E., Overbeek, R., Olsen, G. J. and Woese, C. R. (2000). An archaeal genomic signature. Proceedings of the National Academy of Sciences of the United States of America, 97, 3304–8.CrossRefGoogle ScholarPubMed
Hahn, M. W., Han, M. V. and Han, S. G. (2007). Gene family evolution across 12 Drosophila genomes. PLoS Genetics, 3, e197.CrossRefGoogle ScholarPubMed
Harris, J. K., Kelley, S. T., Spiegelman, G. B. and Pace, N. R. (2003). The genetic core of the universal ancestor. Genome Research, 13, 407–12.CrossRefGoogle ScholarPubMed
Heinen, T. J. A. J., Staubach, F., Häming, D. and Tautz, D. (2009). Emergence of a new gene from an intergenic region. Current Biology, 19, 1527–31.CrossRefGoogle ScholarPubMed
Hillis, D. M. (1994). Homology in molecular biology. In Homology: the Hierarchical Basis of Comparative Biology, ed. Hall, B. K.. San Diego, CA, Academic Press; pp. 339–68.Google Scholar
Holland, J. W., Okamura, B., Hartikainen, H. and Secombes, C. J. (2011). A novel minicollagen gene links cnidarians and myxozoans. Proceedings of the Royal Society B-Biological Sciences, 278, 546–53.CrossRefGoogle ScholarPubMed
Hughes, A. L., Ekollu, V., Friedman, R. and Rose, J. R. (2005). Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology. Systematic Biology, 54, 268–76.CrossRefGoogle ScholarPubMed
Jackson, D. J., McDougall, C., Woodcroft, B., et al. (2010). Parallel evolution of nacre building gene sets in molluscs. Molecular Biology and Evolution, 27, 591–608.CrossRefGoogle ScholarPubMed
Jacob, F. (1977). Evolution and tinkering. Science, 196, 1161–6.CrossRefGoogle ScholarPubMed
Johnson, B. and Tsutsui, N. (2011). Taxonomically restricted genes are associated with the evolution of sociality in the honey bee. BMC Genomics, 12, 164.CrossRefGoogle ScholarPubMed
Kaessmann, H. (2010). Origins, evolution, and phenotypic impact of new genes. Genome Research, 20, 1313–26.CrossRefGoogle ScholarPubMed
Keeling, P. J. and Palmer, J. D. (2008). Horizontal gene transfer in eukaryotic evolution. Nature Reviews Genetics, 9, 605–18.CrossRefGoogle ScholarPubMed
Kessler, M. M., Zeng, Q., Hogan, S., Cook, R., Morales, A. J. and Cottarel, G. (2003). Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Research, 13, 264–71.CrossRefGoogle ScholarPubMed
Khalturin, K., Hemmrich, G., Fraune, S., Augustin, R. and Bosch, T. (2009). More than just orphans: are taxonomically-restricted genes important in evolution?Trends in Genetics, 25, 404–13.CrossRefGoogle Scholar
Knowles, D. G. and McLysaght, A. (2009). Recent de novo origin of human protein-coding genes. Genome Research, 19, 1752–9.CrossRefGoogle ScholarPubMed
Koonin, E. V. (2009). Darwinian evolution in the light of genomics. Nucleic Acids Research, 37, 1011–34.Google ScholarPubMed
Koonin, E. V. (2011). The Logic of Chance: The Nature and Origin of Biological Evolution. Upper Saddle River, NJ, FT Press Science.Google Scholar
Koonin, E. V. and Wolf, Y. I. (2008). Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Research, 36, 6688–719.CrossRefGoogle ScholarPubMed
Koski, L. B. and Golding, G. B. (2001). The closest BLAST hit is often not the nearest neighbor. Journal of Molecular Evolution, 52, 540–2.CrossRefGoogle Scholar
Lapierre, P. and Gogarten, J. P. (2009). Estimating the size of the bacterial pan-genome. Trends in Genetics, 25, 107–10.CrossRefGoogle ScholarPubMed
Lefébure, T., Bitar, P. D. P., Suzuki, H. and Stanhope, M. J. (2010). Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biology and Evolution, 2, 646–55.CrossRefGoogle ScholarPubMed
Levine, M. T., Jones, C. D., Kern, A. D., Lindfors, H. A. and Begun, D. J. (2006). Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proceedings of the National Academy of Sciences of the United States of America, 103, 9935–9.CrossRefGoogle ScholarPubMed
Li, D., Dong, Y., Jiang, Y., Jiang, H., Cai, J. and Wang, W. (2010a). A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand. Cell Research, 20, 408–20.CrossRefGoogle Scholar
Li, R., Li, Y., Zheng, H., et al. (2010b). Building the sequence map of the human pan-genome. Nature Biotechnology, 28, 57–63.CrossRefGoogle ScholarPubMed
Lienau, E. K., DeSalle, R., Rosenfeld, J. A. and Planet, P. J. (2006). Reciprocal illumination in the gene content tree of life. Systematic Biology, 55, 441–53.CrossRefGoogle ScholarPubMed
Lipman, D., Souvorov, A., Koonin, E., Panchenko, A. and Tatusova, T. (2002). The relationship of protein conservation and sequence length. BMC Evolutionary Biology 2, 20.CrossRefGoogle ScholarPubMed
Long, M. (2001). Evolution of novel genes. Current Opinion in Genetics & Development, 11, 673–80.CrossRefGoogle ScholarPubMed
Long, M., Betran, E., Thornton, K. and Wang, W. (2003). The origin of new genes: glimpses from the young and old. Nature Reviews Genetics, 4, 865–75.CrossRefGoogle Scholar
Lynch, J. A., Özüak, O., Khila, A., Abouheif, E., Desplan, C. and Roth, S. (2011). The phylogenetic origin of oskar coincided with the origin of maternally provisioned germ plasm and pole cells at the base of the Holometabola. PLoS Genetics, 7, e1002029.CrossRefGoogle ScholarPubMed
Merkeev, I., Novichkov, P. and Mironov, A. (2006). PHOG: a database of supergenomes built from proteome complements. BMC Evolutionary Biology, 6, 52.CrossRefGoogle ScholarPubMed
Mira, A., Martín-Cuadrado, A. B., D'Auria, G. and Rodríguez-Valera, F. (2010). The bacterial pan-genome: a new paradigm in microbiology. International Microbiology, 13, 45–57.Google ScholarPubMed
Monsch, K. A. (2003). The use of apomorphies in taxonomic defining. Taxon, 52, 105–107.CrossRefGoogle Scholar
Moore, A. D. and Bornberg-Bauer, E. (2012). The dynamics and evolutionary potential of domain loss and emergence. Molecular Biology and Evolution, 29, 787–96.CrossRefGoogle ScholarPubMed
Moran, N. A. and Jarvik, T. (2010). Lateral transfer of genes from fungi underlies carotenoid production in aphids. Science, 328, 624–7.CrossRefGoogle ScholarPubMed
Morgante, M., De Paoli, E. and Radovic, S. (2007). Transposable elements and the plant pan-genomes. Current Opinion in Plant Biology, 10, 149–55.CrossRefGoogle ScholarPubMed
Neme, R. and Tautz, D. (2013). Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics, 14, 117.CrossRefGoogle ScholarPubMed
Narra, H. P., Cordes, M. H. J. and Ochman, H. (2008). Structural features and the persistence of acquired proteins. Proteomics, 8, 1–10.CrossRefGoogle ScholarPubMed
Nichols, R. J., Sen, S., Choo, Y. J., et al. (2011). Phenotypic landscape of a bacterial cell. Cell, 144, 143–56.CrossRefGoogle ScholarPubMed
Ohno, S. (1970). Evolution by Gene Duplication. New York, Springer-Verlag.CrossRefGoogle Scholar
Ohno, S. (1984). Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence. Proceedings of the National Academy of Sciences of the United States of America, 81, 2421–5.CrossRefGoogle ScholarPubMed
Patterson, C. (1982). Morphological characters and homology. In Problems of Phylogenetic Reconstruction, ed. Joysey, K. A. and Friday, A. E.. London, Academic Press; pp. 21–74.Google Scholar
Patterson, C. (1988). Homology in classical and molecular biology. Molecular Biology and Evolution, 5, 603–25.Google ScholarPubMed
Peña-Castillo, L. and Hughes, T. R. (2007). Why are there still over 1000 uncharacterized yeast genes?Genetics, 176, 7–14.CrossRefGoogle ScholarPubMed
Pilcher, H. (2013). All alone. New Scientist, 217, 40–3.CrossRefGoogle Scholar
Prangishvili, D., Garrett, R. A. and Koonin, E. V. (2006). Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Research, 117, 52–67.CrossRefGoogle ScholarPubMed
Rasko, D. A., Rosovitz, M. J., Myers, G. S., et al. (2008). The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of Bacteriology, 190, 6881–93.CrossRefGoogle ScholarPubMed
Reeck, G. R., de Haën, C., Teller, D. C., et al. (1987) “Homology” in proteins and nucleic acids: a terminology muddle and a way out of it. Cell, 50, 667.CrossRefGoogle Scholar
Rödelsperger, C., Streit, A. and Sommer, R. J. (2013) Structure, function and evolution of the nematode genome. In eLS. Chichester, John Wiley & Sons, Ltd. doi: 10.1002/9780470015902.a0024603.Google Scholar
Rost, B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12, 85–94.Google ScholarPubMed
Rutter, M. T., Cross, K. V. and Van Woert, P. A. (2012). Birth, death and subfunctionalization in the Arabidopsis genome. Trends in Plant Science, 17, 204–12.CrossRefGoogle ScholarPubMed
Sabath, N., Wagner, A. and Karlin, D. (2012). Evolution of viral proteins originated de novo by overprinting. Molecular Biology and Evolution, 29, 3767–80.CrossRefGoogle ScholarPubMed
Shapiro, J. (2011). Evolution: A View from the 21st Century. Upper Saddle River, NJ, FT Press Science.Google Scholar
Siepel, A. (2009). Darwinian alchemy: Human genes from noncoding DNA. Genome Research, 19, 1693–95.CrossRefGoogle ScholarPubMed
Siew, N. and Fischer, D. (2003). Unraveling the ORFan puzzle. Comparative and Functional Genomics, 4, 432–41.CrossRefGoogle Scholar
Skovgaard, M., Jensen, L.J., Brunak, Sr, Ussery, D. and Krogh, A. (2001). On the total number of genes and their length distribution in complete microbial genomes. Trends in Genetics, 17, 425–8.CrossRefGoogle ScholarPubMed
Snel, B., Bork, P. and Huynen, M. A. (1999). Genome phylogeny based on gene content. Nature Genetics, 21, 108–10.CrossRefGoogle ScholarPubMed
Snel, B., Huynen, M. A. and Dutilh, B. E. (2005). Genome trees and the nature of genome evolution. Annual Review of Microbiology, 59, 191–209.CrossRefGoogle ScholarPubMed
Sonea, S. and Panisset, M. (1980). Introduction à la Nouvelle Bactériologie. Boston, MA, Les Presses de l'Université de Montréal.Google Scholar
Tautz, D. and Domazet-Lošo, T. (2011). The evolutionary origin of orphan genes. Nature Reviews Genetics, 12, 692–702.CrossRefGoogle ScholarPubMed
Tettelin, H., Masignani, V., Cieslewicz, M. J., et al. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”. Proceedings of the National Academy of Sciences of the United States of America, 102, 13950–5.CrossRefGoogle ScholarPubMed
Tettelin, H., Riley, D., Cattuto, C. and Medini, D. (2008). Comparative genomics, the bacterial pan-genome. Current Opinion in Microbiology, 12, 472–7.Google Scholar
Toll-Riera, M., Bosch, N., Bellora, N., et al. (2009). Origin of primate orphan genes: a comparative genomics approach. Molecular Biology and Evolution, 26, 603–12.Google ScholarPubMed
Touchon, M., Hoede, C., Tenaillon, O., et al. (2009). Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genetic, 5, e1000344.CrossRefGoogle ScholarPubMed
Trimble, V. (1995). The 1920 Shapley-Curtis discussion: background, issues, and aftermath. Publications of the Astronomical Society of the Pacific, 107, 1133–44.CrossRefGoogle Scholar
Typas, A., Banzhaf, M., van den Berg van Saparoea, B., et al. (2010). Regulation of peptidoglycan synthesis by outer-membrane proteins. Cell, 143, 1097–109.CrossRefGoogle ScholarPubMed
Wägele, J-W. (2005). Foundations of Phylogenetic Systematics. Munich, Pfeil-Verlag.Google Scholar
Wang, X., Wang, H., Wang, J., et al. (2011). The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics, 43, 1035–9.CrossRefGoogle ScholarPubMed
Wasmuth, J., Schmid, R., Hedley, A. and Blaxter, M. (2008). On the extent and origins of genic novelty in the phylum Nematoda. PLoS Neglected Tropical Diseases, 2, e258.CrossRefGoogle ScholarPubMed
Wilson, B. A. and Masel, J. (2011). Putatively noncoding transcripts show extensive association with ribosomes. Genome Biology and Evolution, 3, 1245–52.CrossRefGoogle ScholarPubMed
Wilson, G. A., Bertrand, N., Patel, Y., Hughes, J. B., Feil, E. J. and Field, D. (2005). Orphans as taxonomically restricted and ecologically important genes. Microbiology, 151, 2499–501.CrossRefGoogle ScholarPubMed
Wilson, G. A., Feil, E. J., Lilley, A. K. and Field, D. (2007). Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes. PLoS One, 2, e324.CrossRefGoogle ScholarPubMed
Wissler, L., Gadau, J., Simola, D. F., Helmkampf, M. and Bornberg-Bauer, E. (2013) Mechanisms and dynamics of orphan gene emergence in insect genomes. Genome Biology and Evolution, 5, 439–55.CrossRefGoogle ScholarPubMed
Wolf, Y. I., Novichkov, P. S., Karev, G. P., Koonin, E. V. and Lipman, D. J. (2009). The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proceedings of the National Academy of Sciences of the United States of America, 106, 7273–80.CrossRefGoogle ScholarPubMed
Wright, S. (1931). Evolution in Mendelian populations. Genetics, 16, 97–159.Google ScholarPubMed
Wu, D.-D., Irwin, D. M. and Zhang, Y.-P. (2011). De novo origin of human protein-coding genes. PLoS Genetics, 7, e1002379.CrossRefGoogle ScholarPubMed
Zhaxybayeva, O. and Doolittle, W. (2011). Lateral gene transfer. Current Biology, 21, R242–246.CrossRefGoogle ScholarPubMed
Zhou, Q., Zhang, G., Zhang, Y., et al. (2008). On the origin of new genes in Drosophila.Genome Research, 18, 1446–55.CrossRefGoogle ScholarPubMed
Zuckerkandl, E. and Pauling, L. (1965) Molecules as documents of evolutionary history. Journal of Theoretical Biology 8, 357–366.CrossRefGoogle ScholarPubMed

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