The Tangled Tree
Page 44
____. 1868. Letter to August Weismann, October 22, 1868. In The Correspondence of Charles Darwin. vol. 16. Edited by Frederick Burkhardt et al. Cambridge: Cambridge University Press. 2008.
____. 1872. Letter to August Weismann, April 5, 1872. In The Correspondence of Charles Darwin. vol. 20. Edited by Frederick Burkhardt et al. Cambridge: Cambridge University Press. 2013.
Davies, Julian. 2001. “In a Map for Human Life, Count the Microbes, Too.” Science 291 (5512).
Davies, Julian, and Dorothy Davies. 2010. “Origins and Evolution of Antibiotic Resistance.” Microbiology and Molecular Biology Reviews 74 (3).
Davies, Roy. 2008. The Darwin Conspiracy: Origins of a Scientific Crime. London: Golden Square Books.
Dawes, Heather. 2004. “The Quiet Revolution.” Current Biology 14 (15).
Dawkins, Richard. 2006. The Selfish Gene. 30th anniversary ed. New York: Oxford University Press. First published 1976.
Dawson, Martin H. 1930a. “The Transformation of Pneumococcal Types. I. The Conversion of R Forms of Pneumococcus into S Forms of the Homologous Type.” Journal of Experimental Medicine 51 (1).
____. 1930b. “The Transformation of Pneumococcal Types. II. The Interconvertiblity of Type-Specific S Pneumococci.” Journal of Experimental Medicine 51 (1).
Dayhoff, M. O. 1964. “Computer Aids to Protein Sequence Determination.” Journal of Theoretical Biology 8 (1).
Dayrat, Benoît. 2003. “The Roots of Phylogeny: How Did Haeckel Build His Trees?” Systemic Biology 52 (4).
Desmond, Adrian, and James Moore. 1991. Darwin. New York: Warner Books.
Dethlefsen, Les, Margaret McFall-Ngai, and David A. Relman. 2007. “An Ecological and Evolutionary Perspective on Human-Microbe Mutualism and Disease.” Nature 449 (7164).
Dethlefsen, Les, Sue Huse, Mitchell L. Sogin, and David A. Relman. 2008. “The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing.” PLoS Biology 6 (11).
Dodd, Matthew S., Dominic Papineau, Tor Grenne, John E. Slack, Martin Rittner, Franco Pirajno, Jonathan O’Neil, and Crispin T. S. Little. 2017. “Evidence for Early Life in Earth’s Oldest Hydrothermal Vent Precipitates.” Nature 543 (7643).
Dolan, Michael F., and Lynn Margulis. 2011. “Hans Ris. 1914–2002.” From Biographical Memoirs, published by the National Academy of Sciences, Washington, (DC).
Dombrowski, Nina, John A. Donaho, Tony Gutierrez, Kiley W. Seitz, Andreas P. Teske, and Brett J. Baker. 2016. “Reconstructing Metabolic Pathways of Hydrocarbon-Degrading Bacteria from the Deepwater Horizon Oil Spill.” Nature Microbiology 1 (7).
Doolittle, W. Ford. 1972. “Ribosomal Ribonucleic Acid Synthesis and Maturation in the Blue-Green Alga Anacystis nidulans.” Journal of Bacteriology 111 (2).
____. 1978. “Genes in Pieces: Were They Ever Together?” Nature 272 (5654).
____. 1980. “Revolutionary Concepts in Evolutionary Cell Biology.” Trends in Biochemical Sciences 5 (6).
____. 1996. “At the Core of the Archaea.” Proceedings of the National Academy of Sciences 93 (17).
____. 1996. “Some Aspects of the Biology of Cells and Their Possible Evolutionary Significance.” In Evolution of Microbial Life. Edited by D. McLits Roberts, P. Sharp, G. Alderson, and M.A. Collins. Cambridge: Cambridge University Press.
____. 1998. “You Are What You Eat: A Gene Transfer Ratchet Could Account for Bacterial Genes in Eukaryotic Nuclear Genomes.” Trends in Genetics 14 (8).
____. 1999. “Lateral Genomics.” Trends in Cell Biology 9 (12).
____. 1999. “Phylogenetic Classification and the Universal Tree.” Science 284 (5423).
____. 2000. “Uprooting the Tree of Life.” Scientific American 282 (2).
____. 2004. “Q&A, W. Ford Doolittle,” Current Biology 14 (5).
____. 2009. “The Practice of Classification and the Theory of Evolution, and What the Demise of Charles Darwin’s Tree of Life Hypothesis Means for Both of Them.” Philosophical Transactions of the Royal Society of London (B) 364 (1527).
____. 2010. “The Attempt on the Life of the Tree of Life: Science, Philosophy and Politics.” Biology & Philosophy 25 (4).
____. 2013. “Microbial Neopleomorphism.” Biology & Philosophy 28 (2).
____. 2015. “Is Junk DNA Bunk? A Critique of ENCODE.” Proceedings of the National Academy of Sciences 110 (14).
Doolittle, W. Ford, and Norman R. Pace. 1970. “Synthesis of 5S Ribosomal RNA in Escherichia coli After Rifampicin Treatment.” Nature 228 (5267).
____. 1971. “Transcriptional Organization of the Ribosomal RNA Cistrons in Escherichia coli.” Proceedings of the National Academy of Sciences 68 (8).
Doolittle, W. Ford, C. R. Woese, M. L. Sogin, L. Bonen, and D. Stahl. 1975. “Sequence Studies on 16S Ribosomal RNA from a Blue-Green Alga.” Journal of Molecular Evolution 4 (4).
Doolittle, W. Ford, and Carmen Sapienza. 1980. “Selfish Genes, the Phenotype Paradigm and Genome Evolution.” Nature 284 (5757).
Doolittle, W. Ford, and Linda Bonen. 1981. “Molecular Sequence Data Indicating an Endosymbiotic Origin for Plastids.” Annals of the New York Academy of Sciences 361.
Doolittle, W. Ford., and James R. Brown. 1994. “Tempo, Mode, the Progenote, and the Universal Root.” Proceedings of the National Academy of Sciences 91 (15).
Doolittle, W. Ford, Y. Boucher, C. L. Nesbø, C. J. Douady, J. O. Andersson, and A. J. Roger. 2003. “How Big Is the Iceberg of Which Organellar Genes in Nuclear Genomes Are but the Tip?” Philosophical Transactions of the Royal Society of London (B) 358 (1429).
Doolittle, W. Ford, and Eric Bapteste. 2007. “Pattern Pluralism and the Tree of Life Hypothesis.” Proceedings of the National Academy of Sciences 104 (7).
Doudna, Jennifer A., and Emmanuelle Charpentier. 2014. “The New Frontier of Genome Engineering with CRISPR-Cas9.” Science 346 (6213).
Dover, Gabriel and W. Ford Doolittle. 1980. “Modes of Genome Evolution.” Nature 288 (December 18/25).
Downie, A. W. 1972. “Pneumococcal Transformation—A Backward View.” Journal of General Microbiology 72 (3).
Drews, Gerhart. 1999. “Ferdinand Cohn, a Founder of Modern Microbiology.” ASM News 65 (8).
____. 2000. “The Roots of Microbiology and the Influence of Ferdinand Cohn on Microbiology of the 19th Century.” FEMS Microbiology Reviews 24 (3).
Dubos, R. J. 1956. “Oswald Theodore Avery, 1877–1955.” Biographical Memoirs of the Fellows of the Royal Society 2.
Dubos, René J. 1976. The Professor, the Institute, and DNA. New York: Rockefeller University Press.
Dunn, Casey W. 2005. “Complex Colony-Level Organization of the Deep-Sea Siphonophore Bargmannia elongata (Cnidaria, Hydrozoa) Is Directionally Asymmetric and Arises by the Subdivision of Pro-Buds.” Developmental Dynamics 234 (4).
Dunning Hotopp, Julie C. 2011. “Horizontal Gene Transfer Between Bacteria and Animals.” Trends in Genetics 27 (4).
____. 2013. “Lateral Gene Transfer in Multicellular Organisms.” In Lateral Gene Transfer in Evolution. Edited by Uri Gophna. New York: Springer.
Dunning Hotopp, Julie C., Michael E. Clark, Deodoro C. S. G. Oliveira, Jeremy M. Foster, Peter Fischer, Mónica C. Muñoz Torres, Jonathan D. Giebel, Nikhil Kumar, Nadeeza Ishmael, Shiliang Wang et al. 2007. “Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes.” Science 317 (5845).
Dupressoir, Anne, Geoffroy Marceau, Cécile Vernochet, Laurence Bénit, Colette Kanellopoulos, Vincent Sapin, and Thierry Heidmann. 2005. “Syncytin-A and Syncytin-B, Two Fusogenic Placenta-Specific Murine Envelope Genes of Retroviral Origin Conserved in Muridae.” Proceedings of the National Academy of Sciences 102 (3).
Dupressoir, Anne, Cécile Vernochet, Olivia Bawa, Francis Harper, Gérard Pierron, Paule Opolon, and Thierry Heidmann. 2009. “Syncytin-A Knockout Mice Demonstrate the Critical Role in Placentation of a Fusogenic, Endogenous Retrovirus-Derived, Envelope Gene.” Proceedings of the National Academy of Sciences 106 (29).
E
ck, Richard V., and Margaret O. Dayhoff. 1966. “Evolution of the Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences.” Science 152 (3720).
Ehresmann, C., P. Stiegler, P. Carbon, and J. P. Ebel. 1977. “Recent Progress in the Determination of the Primary Sequence of the 16 S RNA of Escherichia coli.” FEBS Letters 84 (2).
Eisen, Jonathan A. 2007. “Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes.” PLoS Biology 5 (3).
____. 2009. “Genomic Evolvability and the Origin of Novelty: Studying the Past, Interpreting the Present, and Predicting the Future.” In Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg. Washington (DC): National Academies Press. www.nap.edu/read/12586.
Eisen, Jonathan A., and Claire M. Fraser. 2003. “Phylogenomics: Intersection of Evolution and Genomics.” Science 300 (5626).
Elde, Nels. C., Stephanie J. Child, Michael T. Eickbush, Jacob O. Kitzman, Kelsey S. Rogers, Jay Shendure, Adam P. Geballe, and Harmit S. Malik. 2012. “Poxviruses Deploy Genomic Accordions to Adapt Rapidly Against Host Antiviral Defenses.” Cell 150 (4).
Eliot, Theodore S. 1971. “Ivan Emmanuel Wallin. 1883–1969.” Anatomical Record 171 (1).
Embley, T. Martin, and William Martin. 2006. “Eukaryotic Evolution, Changes and Challenges.” Nature 440 (7084).
Embley, T. Martin, and Tom A. Williams. 2015. “Steps on the Road to Eukaryotes.” Nature 521 (7551).
Ernster, Lars, and Gottfried Schatz. 1981. “Mitochondria: A Historical Review.” Journal of Cell Biology 91 (3).
Espinal, P., S. Marti, and J. Vila. 2012. “Effect of Biofilm Formation on the Survival of Acinetobacter baumannii on Dry Surfaces.” Journal of Hospital Infection 80 (1).
Ettema, Thijs J. G. 2016. “Mitochondria in the Second Act.” Nature 531 (7592).
Eyres, Isobel, Chiara Boschetti, Alastair Crisp, Thomas P. Smith, Diego Fontaneto, Alan Tunnacliffe, and Timothy G. Barraclough. 2015. “Horizontal Gene Transfer in Bdelloid Rotifers Is Ancient, Ongoing and More Frequent in Species from Desiccating Habitats.” BMC Biology 13 (90).
Fellner, P., and J. P. Ebel. 2017. “Biological Sciences: Observations on the Primary Structure of the 23S Ribosomal RNA from E. coli.” Nature 225 (5238).
Feschotte, Cedric. 2008. “Transposable Elements and the Evolution of Regulatory Networks.” Nature Reviews Genetics 9 (5).
____. 2010. “Bornavirus Enters the Genome.” Nature 463 (7277).
____. 2015. “Transposable Elements.” In Discoveries in Modern Science: Exploration, Invention, Technology. Edited by James Trefil. Farmington Hills (MI): Macmillan Reference USA.
Feschotte, Cedric, and Ellen J. Pritham. 2007. “DNA Transposons and the Evolution of Eukaryotic Genomes.” Annual Review of Genetics 41.
Fitch, Walter M., and Emanuel Margoliash. 1967. “Construction of Phylogenetic Trees: A Method Based on Mutation Distances as Estimated from Cytochrome C Sequences Is of General Applicability.” Science 155 (3760).
Fleischmann, Robert D., Mark D. Adams, Owen White, Rebecca A. Clayton, Ewen F. Kirkness, Anthony R. Kerlavage, Carol J. Bult, Jean-Francois Tomb, Brian A. Dougherty, Joseph M. Merrick et al. 1995. “Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd.” Science 269 (5223).
Flot, Jean-François, Boris Hespeels, Xiang Li, Benjamin Noel, Irina Arkhipova, Etienne G. J. Danchin, Andreas Hejnol, Bernard Henrissat, Romain Koszul, Jean-Marc Aury et al. 2013. “Genomic Evidence for Ameiotic Evolution in the Bdelloid Rotifer Adineta vaga.” Nature 500 (7463).
Forterre, Patrick, Simonetta Gribaldo, and Celine Brochier-Armanet. 2007. “Natural History of the Archaeal Domain.” In Archaea: Evolution, Physiology, and Molecular Biology. Edited by Roger A. Garnett and Hans-Peter Klenk. Hoboken (NJ): Wiley-Blackwell.
Foster, Peter G., Cymon J. Cox, and T. Martin Embley. 2009. “The Primary Divisions of Life: A Phylogenomic Approach Employing Composition-Heterogeneous Methods.” Philosophical Transactions of the Royal Society of London (B) 364 (1527).
Fournier, Gregory P., and E. J. Alm. 2015. “Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code.” Journal of Molecular Evolution 80 (3–4).
Fournier, Gregory P., Cheryl P. Andam, and Johann Peter Gogarten. 2015. “Ancient Horizontal Gene Transfer and the Last Common Ancestors.” BMC Evolutionary Biology 15 (70).
Fox, G. E., E. Stackebrandt, R. B. Hespell, J. Gibson, J. Maniloff, T. A. Dyer, R. S. Wolfe, W. E. Balch, R. S. Tanner, L. J. Magrum et al. 1980. “The Phylogeny of Prokaryotes.” Science 209 (4455).
Fox, George E., Linda J. Magrum, William E. Balch, Ralph S. Wolfe, and Carl R. Woese. 1977. “Classification of Methanogenic Bacteria by 16S Ribosomal RNA Characterization.” Proceedings of the National Academy of Sciences 74 (10.)
Fox, George E., Kenneth R. Pechman, and Carl R. Woese. 1977. “Comparative Cataloging of 16S Ribosomal Ribonucleic Acid: Molecular Approach to Procaryotic Systematics.” International Journal of Systematic Bacteriology 27 (1).
Fox, George E., Kenneth R. Luehrsen, and Carl R. Woese. 1982. “Archaebacterial 5 S Ribosomal RNA.” Zbl. Bakt. Hyg. C3.
Fredericks, David N., editor. The Human Microbiota: How Microbial Communities Affect Health and Disease. Hoboken (NJ): John Wiley & Sons.
Friend, Tim. 2007. The Third Domain: The Untold Story of Archaea and the Future of Biotechnology. Washington, (DC): Joseph Henry Press.
Gardner, Pierce, David H. Smith, Herman Beer, and Robert C. Moellering Jr. 1969. “Recovery of Resistance (R) Factors from a Drug-Free Community.” Lancet 2 (7624). Now labeled vol. 294.
Garrett, Roger A. 2014. “A Backward View from 16S rRNA to Archaea to the Universal Tree of Life to Progenotes: Reminiscences of Carl Woese.” RNA Biology 11 (3).
Garrett, Roger A., and Hans-Peter Klenk, editors. 2007. Archaea: Evolution, Physiology, and Molecular Biology. Hoboken (NJ): Wiley-Blackwell.
Gatenby, J. Brontë. 1928. “Nature of Cytoplasmic Inclusions.” Nature 121 (3040).
Gil, Estel, Assumpcio Bosch, David Lampe, Jose M. Lizcano, Jose C. Perales, Olivier Danos, and Miguel Chillon. 2013. “Functional Characterization of the Human Mariner Transposon Hsmar2.” PLoS One 8 (9).
Gilbert, Clément, John K. Pace II, and Cedric Feschotte. 2009. “Horizontal SPINing of Transposons.” Communicative & Integrative Biology 2 (2).
Gilbert, Clément, Sarah Schaack, John K. Pace II, Paul J. Brindley, and Cedric Feschotte. 2010. “A Role for Host-Parasite Interactions in the Horizontal Transfer of Transposons Across Phyla.” Nature 464 (7293).
Gilbert, Clément, Sharon S. Hernandez, Jaime Flores-Benabib, Eric N. Smith, and Cedric Feschotte. 2011. “Rampant Horizontal Transfer of SPIN Transposons in Squamate Reptiles.” Molecular Biology and Evolution 29 (2).
Gilbert, Clément, Paul Waters, Cedric Feschotte, and Sarah Schaack. 2013. “Horizontal Transfer of OC1 Transposons in the Tasmanian Devil.” BMC Genomics 14 (134).
Gilbert, Scott F., Jan Sapp, and Alfred I. Tauber. 2012. “A Symbiotic View of Life: We Have Never Been Individuals.” Quarterly Review of Biology 87 (4).
Gilbert, Walter. 1986. “The RNA World.” Nature 319 (6055).
Gladyshev, Eugene A., Matthew Meselson and Irina R. Arkhipova. 2008. “Massive Horizontal Gene Transfer in Bdelloid Rotifers.” Science 320 (5880).
Gliboff, Sander. 2008. H. G. Bronn, Ernst Haeckel, and the Origins of German Darwinism: A Study in Translation and Transformation. Cambridge (MA): MIT Press.
Gitschier, Jane. 2015. “The Philosophical Approach: An Interview with Ford Doolittle.” PLoS Genetics 11 (5).
Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston et al. 1996. “Life with 6000 Genes.” Science 274 (5287).
Gogarten, J. Peter. 1995. “The Early Evolution of Cellular Life.” TREE 10 (4).
____. 2003. “Gene Transfer: Gene Swappi
ng Craze Reaches Eukaryotes.” Current Biology 13 (2).
Gogarten, Johann Peter, Henrik Kibak, Peter Dittrich, Lincoln Taiz, Emma Jean Bowman, Barry J. Bowman, Morris F. Manolson, Ronald J. Poole, Takayasu Date, Tairo Oshima et al. 1989. “Evolution of the Vacuolar H+-ATPase: Implications for the Origin of Eukaryotes.” Proceedings of the National Academy of Sciences 86.
Gogarten, J. Peter, Elena Hilario, and Lorraine Olendzenski. 1996. “Gene Duplications and Horizontal Gene Transfer During Early Evolution.” In Evaluation of Microbial Life. Edited by D. McL. Roberts, P. Sharp, G. Alderson, and M.A. Collins. Cambridge: Cambridge University Press.
Gogarten, J. Peter, W. Ford Doolittle, and Jeffrey G. Lawrence. 2002. “Prokaryotic Evolution in Light of Gene Transfer.” Molecular Biology & Evolution 19 (12).
Gogarten, J. Peter, and Jeffrey P. Townsend. 2005. “Horizontal Gene Transfer, Genome Innovation and Evolution.” Nature Reviews Microbiology 3 (9).
Gogarten, Maria Boekels, Johann Peter Gogarten, and Lorraine Olendzenski, editors. 2009. Horizontal Gene Transfer: Genomes in Flux. New York: Springer/Humana Press.
Gold, Larry. 2013. “The Kingdoms of Carl Woese.” Proceedings of the National Academy of Sciences 110 (9).
____. 2014. “Carl Woese in Schenectady: The Forgotten Years.” RNA Biology 11 (3).
Goldenfeld, Nigel. 2014. “Looking in the Right Direction: Carl Woese and Evolutionary Biology.” RNA Biology 11 (3).
Goldenfeld, Nigel, and Carl Woese. 2007. “Biology’s Next Revolution.” Nature 445 (7126).
Goldman, Jason G. 2012. “Ad Memoriam. Lynn Margulis (May 5, 1938–November 22, 2011).” Studies in the History of Biology 4 (2).
Goldner, Morris. 2007. “The Genius of Roger Stanier.” Canadian Journal of Infectious Diseases and Medical Microbiology 18 (3).
Gontier, Nathalie. 2011. “Depicting the Tree of Life: The Philosophical and Historical Roots of Evolutionary Tree Diagrams.” Evolution: Education and Outreach 4 (3).
Gontier, Nathalie, editor. 2015. Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious Heredity. Switzerland: Springer.