The Tangled Tree

by David Quammen

  Lawrence, Jeffrey G., and Howard Ochman. 1997. “Amelioration of Bacterial Genomes: Rates of Change and Exchange.” Journal of Molecular Evolution 44 (4).

  ____. 1998. “Molecular Archaeology of the Escherichia coli Genome.” Proceedings of the National Academy of Sciences 95 (16).

  Lawrence, Jeffrey G., and Heather Hendrickson. 2003. “Lateral Gene Transfer: When Will Adolescence End?” Molecular Microbiology 50 (3).

  Lawrence, Jeffery G., and Adam C. Retchless. 2009. “The Interplay of Homologous Recombination and Horizontal Gene Transfer in Bacterial Speciation.” In Horizontal Gene Transfer: Genomes in Flux. Edited by Maria Boekels Gogarten, Johann Peter Gogarten, and Lorraine Olendzenski. New York: Springer/Humanz Press.

  Lawrence, Jeffrey G., and Adam C. Retchless. 2010. “The Myth of Bacterial Species and Speciation.” Biology & Philosophy 25 (4).

  Lawrence, Philip J. 1972. “Edward Hitchcock: The Christian Geologist.” Proceedings of the American Philosophical Society 116 (1).

  Leahy, Sinead C., William J. Kelly, Eric Altermann, Ron S. Ronimus, Carl J. Yeoman, Diana M. Pacheco, Dong Li, Zhanhao Kong, Sharla McTavish, Carrie Sang et al. 2010. “The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions.” PLoS ONE 5 (1).

  Lederberg, Joshua. 1952. “Cell Genetics and Hereditary Symbiosis.” Physiological Reviews 32 (4).

  ____. 1987. “Genetic Recombination in Bacteria: A Discovery Account.” Annual Review of Genetics 21.

  ____. 1992. “Bacterial Variation Since Pasteur: Rummaging in the Attic: Antiquarian Ideas of Transmissible Heredity, 1880–1940.” ASM News 58 (5).

  ____. 1994. “The Transformation of Genetics by DNA: An Anniversary Celebration of Avery, MacLeod and McCarty (1944).” Genetics 136 (2).

  Lederberg, Joshua, and E. L. Tatum. 1946a. “Gene Recombination in Escherichia coli.” Nature 158 (4016).

  ____. 1946b. “Novel Genotypes in Mixed Cultures of Biochemical Mutants of Bacteria.” Cold Spring Harbor Symposia on Quantitative Biology 11.

  Lederberg, Joshua, and Norton Zinder. 1948. “Concentration of Biochemical Mutants of Bacteria with Penicillin.” Journal of the American Chemical Society 70 (12).

  Lederberg, Joshua, Luigi L. Cavalli, and Esther M. Lederberg. 1952. “Sex Compatibility in Escherichia coli.” Genetics 37 (6).

  Lederberg, Joshua, and E. L. Tatum. 1953. “Sex in Bacteria: Genetic Studies, 1945–1952.” Science 118 (3059).

  Lederberg, Joshua, and Esther M. Lederberg. 1956. “V. Infection and Heredity.” In Cellular Mechanisms in Differentiation and Growth. Edited by Dorothea Rudnick. Princeton (NJ): Princeton University Press.

  Levine, Donald P. 2006. “Vancomycin: A History.” Clinical Infectious Diseases 42 (Suppl. 1).

  Levy, Stuart B., MD. 2002. The Antibiotic Paradox: How the Misuse of Antibiotics Destroys Their Curative Powers. 2nd ed.: Cambridge (MA): Perseus. First published 2001.

  Levy, Stuart B., and Paula Norman. 1970. “Segregation of Transferable R Factors into Escherichia coli Minicells.” Nature 227 (5258).

  Levy, Stuart B., George B. FitzGerald, and Ann B. Macone. 1976a. “Changes in Intestinal Flora of Farm Personnel After Introduction of a Tetracycline-Supplemented Feed on a Farm.” New England Journal of Medicine 295 (11).

  ____. 1976b. “Spread of Antibiotic-Resistant Plasmids from Chicken to Chicken and from Chicken to Man.” Nature 260 (5546).

  Levy, Stuart B., and Laura McMurry. 1978. “Plasmid-Determined Tetracycline Resistance Involves New Transport Systems for Tetracycline.” Nature 276 (5683).

  Lewin, Harris A. 2014. “Memories of Carl from an Improbable Friend.” RNA Biology 11 (3).

  Lewin, Roger. 1982. “Can Genes Jump Between Eukaryotic Species?” Science 217 (4554).

  Ley, Ruth E., Peter J. Turnbaugh, Samuel Klein, and Jeffrey I. Gordon. 2006. “Human Gut Microbes Associated with Obesity.” Nature 444 (7122).

  Liu, Li, Xiaowei Chen, Geir Skogerbø, Peng Zhang, Runsheng Chen, Shunmin He, and Da-Wei Huang. 2012. “The Human Microbiome: A Hot Spot for Microbial Horizontal Gene Transfer.” Genomics 100 (5).

  Liu, Yi-Yun, Yang Wang, Timothy R. Walsh, Ling-Xian Yi, Rong Zhang, James Spencer, Yohei Doi, Guobao Tian, Baolei Dong, Xianhui Huang et al. 2015. “Emergence of Plasmid-Mediated Colistin Resistance Mechanism MCR-1 in Animals and Human Beings in China: A Microbiological and Molecular Biological Study.” Lancet Infectious Diseases 16 (2).

  Löwer, Roswitha, Johannes Löwer, and Reinhard Kurth. 1996. “The Viruses in All of Us: Characteristics and Biological Significance of Human Endogenous Retrovirus Sequences.” Proceedings of the National Academy of Sciences 93 (11).

  Luehrsen, Kenneth R. 2014. “Remembering Carl Woese.” RNA Biology 11 (3).

  Lynch, Vincent J. 2016. “A Copy-and-Paste Gene Regulatory Network.” Science 351 (6277).

  Lynch, Vincent J., Robert D. Leclerc, Gemma May, and Günter P. Wagner. 2011. “Transposon-Mediated Rewiring of Gene Regulatory Networks Contributed to the Evolution of Pregnancy in Mammals.” Nature Genetics 43 (11).

  Ma, Hong, Nuria Marti-Gutierrez, Sang-Wook Park, Jun Wu, Yeonmi Lee, Keiichiro Suzuki, Amy Koski, Dongmei Ji, Tomonari Hayama, Riffat Ahmed et al. 2017. “Correction of a Pathogenic Gene Mutation in Human Embryos.” Nature 548 (7668).

  Ma, Li-Jun, H. Charlotte van der Does, Katherine A. Borkovich, Jeffrey L. Coleman, Marie-Josée Daboussi, Antonio Di Pietro, Marie Dufresne, Michael Freitag, Manfred Grabherr, Bernard Henrissat et al. 2010. “Comparative Genomics Reveals Mobile Pathogenicity Chromosomes in Fusarium.” Nature 464 (7287).

  Magiorkinis, Gkikas, Robert J. Gifford, Aris Katzourakis, Joris De Ranter, and Robert Belshaw. 2012. “Env-less Endogenous Retroviruses Are Genomic Superspreaders.” Proceedings of the National Academy of Sciences 109 (19).

  Makarova, Kira S., L. Aravind, Nick V. Grishin, Igor B. Rogozin, and Eugene V. Koonin. 2002. “A DNA Repair System Specific for Thermophilic Archaea and Bacteria Predicted by Genomic Context Analysis.” Nucleic Acids Research 30 (2).

  Mallet, James, Nora Besansky, and Matthew W. Hahn. 2016. “How Reticulated Are Species?” BioEssays 37.

  Mangeney, Marianne, Martial Renard, Géraldine Schlecht-Louf, Isabelle Bouallaga, Odile Heidmann, Claire Letzelter, Aurélien Richaud, Bertrand Ducos, and Thierry Heidmann. 2007. “Placental Syncytins: Genetic Disjunction Between the Fusogenic and Immunosuppressive Activity of Retroviral Envelope Proteins.” Proceedings of the National Academy of Sciences 104 (51).

  Margulis, Lynn. 1970. Origin of Eukaryotic Cells: Evidence and Research Implications for a Theory of Origin and Evolution of Microbial, Plant, and Animal Cells on the Precambrian Earth. New Haven (CT): Yale University Press.

  ____. 1980. “Undulipodia, Flagella and Cilia.” BioSystems 12 (1–2).

  ____. 1993. Symbiosis in Cell Evolution: Microbial Communities in the Archean and Proterozoic Eons. 2nd ed.: New York: W. H. Freeman. First published 1981.

  ____. 1998. Symbiotic Planet: A New Look at Evolution. New York: Basic Books.

  Margulis, Lynn, and Dorion Sagan. 1986. Micro-Cosmos: Four Billion Years of Microbial Evolution. Foreword by Dr. Lewis Thomas. New York: Summit Books.

  ____. 2003. Acquiring Genomes: A Theory of the Origins of Species. New York: Basic Books.

  Margulis, Lynn, and Karlene V. Schwartz. 1988. Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth. Foreword by Stephen Jay Gould. 2nd ed. New York: W. H. Freeman. First published 1982.

  Marraffini, Luciano A. 2013. “CRISPR-Cas Immunity Against Phages: Its Effects on the Evolution and Survival of Bacterial Pathogens.” PLOS Pathogens 9 (12).

  Marraffini, Luciano A., and Erik J. Sontheimer. 2008. “CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA.” Science 322 (5909).

  Marshall, K. C., editor. 1986. Advances in Microbial Ecology. vol. 9. New York: Plenum Press.

  Martin, Joseph P., Jr., and Irwin Fridovich. 1981. “Evidence for a Nat
ural Gene Transfer from the Ponyfish to Its Bioluminescent Bacterial Symbiont Photobacter leiognathi.” Journal of Biological Chemistry 256 (12).

  Martin, Mark. 2014. “Casting a Long Shadow in the Classroom: An Educator’s Perspective of the Contributions of Carl Woese.” RNA Biology 11 (3).

  Martin, William. 1999. “Mosaic Bacterial Chromosomes: A Challenge En Route to a Tree of Genomes.” BioEssays 21.

  ____. 2005. “Archaebacteria (Archaea) and the Origin of the Eukaryotic Nucleus.” Current Opinion in Microbiology 8 (6).

  Martin, William F. 1996. “Is Something Wrong with the Tree of Life?” BioEssays 18 (7).

  Martin, William, and Rüdiger Cerff. 1986. “Prokaryotic Features of a Nucleus-Encoded Enzyme: cDNA Sequences for Chloroplast and Cystosolic Glyceraldehyde-3-Phosphate Dehydrogenases from Mustard (Sinapis alba).” European Journal of Biochemistry 159 (2).

  Martin, William, and Reinhold G. Herrmann. 1998. “Gene Transfer from Organelles to the Nucleus: How Much, What Happens, and Why?” Plant Physiology 118 (1).

  Martin, William, and Miklós Müller. 1998. “The Hydrogen Hypothesis for the First Eukaryote.” Nature 392 (6671).

  Martin, William, and Klaus V. Kowallik. 1999. “Annotated English Translation of Mereschkowsky’s 1905 Paper ‘Uber Natur und Ursprung der Chromatophoren im Pflanzenreiche.’ ” European Journal of Phycology, 34.

  Martin, William, and Eugene V. Koonin. 2006. “Introns and the Origin of Nucleus-Cytosol Compartmentalization.” Nature 440 (7080).

  Martin, William, John Baross, Deborah Kelley, and Michael J. Russell. 2008. “Hydrothermal Vents and the Origin of Life.” Nature Reviews Microbiology 6 (11).

  Martin, William, Mayo Roettger, Thorsten Kloesges, Thorsten Thiergart, Christian Woehle, Sven Gould, and Tal Dagan. 2012. “Modern Endosymbiotic Theory: Getting Lateral Gene Transfer into the Equation.” Journal of Endocytobiosis and Cell Research 23.

  Marx, Jean. 2007. “New Bacterial Defense Against Phage Invaders Identified.” Science 315 (5819).

  Mather, Alison E., Kate S. Baker, Hannah McGregor, Paul Coupland, Pamela L. Mather, Ana Deheer-Graham, Julian Parkhill, Philippa Bracegirdle, Julie E. Russell, and Nicholas R. Thomson. 2014. “Bacillary Dysentery from World War 1 and NCTC1, the First Bacterial Isolate in the National Collection.” Lancet 384 (9955).

  Mayr, Ernst. 1982. The Growth of Biological Thought: Diversity, Evolution, and Inheritance. Cambridge (MA): Belknap Press of Harvard University Press.

  McCarroll, Robert, Gary J. Olsen, Yvonne D. Stahl, Carl R. Woese, and Mitchell L. Sogin. 1983. “Nucleotide Sequence of the Dictyostelium discoideum Small-Subunit Ribosomal Ribonucleic Acid Inferred from the Gene Sequence: Evolutionary Implications.” Biochemistry 22 (25).

  McCarty, Maclyn. 1985. The Transforming Principle: Discovering That Genes Are Made of DNA. New York: W. W. Norton.

  McCutcheon, John P. 2013. “Genome Evolution: A Bacterium with a Napoleon Complex.” Current Biology 23 (15).

  McCutcheon, John P., and Nancy A. Moran. 2007. “Parallel Genomic Evolution and Metabolic Interdependence in an Ancient Symbiosis.” Proceedings of the National Academy of Sciences 104 (49).

  ____. 2010. “Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution.” Genome Biology and Evolution 2.

  ____. 2012. “Extreme Genome Reduction in Symbiotic Bacteria.” Nature Reviews Microbiology 10 (1).

  McCutcheon, John P., and Carol D. von Dohlen. 2011. “An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs.” Current Biology 21 (16).

  McCutcheon, John P., and Patrick J. Keeling. 2014. “Endosymbiosis: Protein Targeting Further Erodes the Organelle/Symbiont Distinction.” Current Biology 24 (14).

  McInerney, James O. 2016. “A Four Billion Year Old Metabolism.” Nature Microbiology 1 (9).

  McInerney, James O., Mary J. O’Connell, and Davide Pisani. 2014. “The Hybrid Nature of the Eukaryota and a Consilient View of Life on Earth.” Nature Reviews Microbiology 12 (6).

  McInerney, James O., Davide Pisani, and Mary J. O’Connell. 2015. “The Ring of Life Hypothesis for Eukaryote Origins Is Supported by Multiple Kinds of Data.” Philosophical Transactions of the Royal Society of London (B) 370 (1678).

  McKenna, Maryn. 2010. Superbug: The Fatal Menace of MRSA. New York: Free Press.

  Mérejkovsky, Const. de, Prof. Dr. 1920. “La Plante Considérée Comme Un Complexe Symbiotique.” Bull. Soc. Sc. Nat. Ouest. Series 3 (6).

  Mereschkowsky, M. C. 1878. “On a New Genus of Sponge.” Annals and Magazine of Natural History, Series 5, 1 (1).

  Metcalf, Jason A., Lisa J. Funkhouser-Jones, Kristen Brileya, Anna-Louise Reysenbach, and Seth R. Bordenstein. 2014. “Antibacterial Gene Transfer Across the Tree of Life.” eLife. https://elifesciences.org/articles/04266.

  Mi, Sha, Xinhua Lee, Xiang-ping Li, Geertruida M. Veldman, Heather Finnerty, Lisa Racie, Edward LaVallie, Xiang-Yang Tang, Philippe Edouard, Steve Howes et al. 2000. “Syncytin Is a Captive Retroviral Envelope Protein Involved in Human Placental Morphogenesis.” Nature 403 (6771).

  Miller, D., V. Urdaneta, and A. Weltman. 2002. “Vancomycin-Resistant Staphylococcus aureus—Pennsylvania, 2002.” Morbidity and Mortality Weekly Report 51 (40).

  Mirsky, Alfred E. 1968. “The Discovery of DNA.” Scientific American 218 (6).

  Modi, Sheetal R., James J. Collins, and David A. Relman. 2014. “Antibiotics and the Gut Microbiota.” Journal of Clinical Investigation 124 (10).

  Mojica, Francisco J. M., César Díez-Villaseñor, Elena Soria, and Guadalupe Juez. 2000. “MicroCorrespondence.” Molecular Microbiology 36 (1).

  Mojica, Francisco J. M., César Díez-Villaseñor, Jesús García-Martínez, and Elena Soria. 2005. “Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements.” Journal of Molecular Evolution 60 (2).

  Moore, Peter B. 2014. “Carl Woese: A Structural Biologist’s Perspective.” RNA Biology 11 (3).

  Moran, Nancy A., and Paul Baumann. 2000. “Bacterial Endosymbionts in Animals.” Current Opinion in Microbiology 3 (3).

  Moran, Nancy A., John P. McCutcheon, and Atsushi Nakabachi. 2008. “Genomics and Evolution of Heritable Bacterial Symbionts.” Annual Review of Genetics 42.

  Moran, Nancy A., and Tyler Jarvik. 2010. “Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids.” Science 328 (5978).

  Morange, Michel. 2015. “CRISPR-Cas: The Discovery of an Immune System in Prokaryotes.” Journal of Biosciences 40 (2).

  Morell, Virginia. 1996. “Life’s Last Domain.” Science 273 (5278).

  ____. 1997. “Microbiology’s Scarred Revolutionary.” Science 276 (5313).

  Morens, David M., Jeffery K. Taubenberger, and Anthony S. Fauci. 2008. “Predominant Role of Bacterial Pneumonia as a Cause of Death in Pandemic Influenza: Implications for Pandemic Influenza Preparedness.” Journal of Infectious Diseases 198 (7).

  Morgan, Gregory J. 1998. “Emile Zuckerkandl, Linus Pauling, and the Molecular Evolutionary Clock, 1959–1965.” Journal of the History of Biology 31 (2).

  Morris, J. Gareth. 1983. “Roger Yate Stanier, 1916–1982.” Journal of General Microbiology 129.

  Mukherjee, Siddhartha. 2016. The Gene: An Intimate History. New York: Scribner.

  Nair, Prashant. 2012. “Woese and Fox: Life, Rearranged.” Proceedings of the National Academy of Sciences 109 (4).

  Nelson, Karen E., Rebecca A. Clayton, Steven R. Gill, Michelle L. Gwinn, Robert J. Dodson, Daniel H. Haft, Erin K. Hickey, Jeremy D. Peterson, William C. Nelson, Karen A. Ketchum et al. 1999. “Evidence for Lateral Gene Transfer Between Archaea and Bacteria from Genome Sequence of Thermotoga maritima.” Nature 399 (6734).

  Nelson-Sathi, Shijulal, Filipa L. Sousa, Mayo Roettger, Nabor Lozada-Chávez, Thorsten Thiergart, Arnold Janssen, David Bryant, Giddy Landan, Peter Schönheit, Bettina Siebers, James O. McInerney, and William F. Martin. 2015. “Origins of Major Archaeal Clades Correspond to Gene Acquisitions from Bacteria.”
Nature 517 (7532).

  Ng, Hooi Jun, Mario López-Pérez, Hayden K. Webb, Daniela Gomez, Tomoo Sawabe, Jason Ryan, Mikhail Vyssotski, Chantal Bizet, François Malherbe, Valery V. Mikhailov, Russell J. Crawford, and Elena P. Ivanova. 2014. “Marinobacter salarius sp. nov. and Marinobacter similis sp. nov., Isolated from Sea Water.” PLoS One 9 (9).

  Nikoh, Naruo, Kohjiro Tanaka, Fukashi Shibata, Natsuko Kondo, Masahiro Hizume, Masakazu Shimada, and Takema Fukatsu. 2008. “Wolbachia Genome Integrated in an Insect Chromosome: Evolution and Fate of Laterally Transferred Endosymbiont Genes.” Genome Research 18 (2).

  Noble, W. D., Zarina Virani, and Rosemary G. A. Cree. 1992. “Co-Transfer of Vancomycin and Other Resistance Genes from Enterococcus faecalis NCTC 12201 to Staphylococcus aureus.” FEMS Microbiology Letters 72 (2).

  Noller, Harry F. 2013. “By Ribosome Possessed.” Journal of Biological Chemistry 288 (34).

  ____. 2013. “Carl Woese (1928–2012): Discoverer of Life’s Third Domain, the Archaea.” Nature 493 (7434).

  ____. 2014. “Secondary Structure Adventures with Carl Woese.” RNA Biology 11 (3).

  Nowak, Rachel. 1995. “Bacterial Genome Sequence Bagged.” Science 269 (5223).

  Ochman, Howard, Jeffrey G. Lawrence, and Eduardo A. Groisman. 2000. “Lateral Gene Transfer and the Nature of Bacterial Innovation.” Nature 405 (6784).

  Olby, Robert. 1994. The Path to the Double Helix: The Discovery of DNA. Seattle: University of Washington Press.

  Olby, Robert, and Erich Posner. 1967. “An Early Reference to Genetic Coding.” Nature 215 (5100).

  Olsen, Gary J., David J. Lane, Stephen J. Giovannoni, and Norman R. Pace. 1986. “Microbial Ecology and Evolution: A Ribosomal RNA Approach.” Annual Review of Microbiology 40.

  Olsen, Gary J., Carl R. Woese, and Ross Overbeek. 1994. “The Winds of (Evolutionary) Change: Breathing New Life into Microbiology.” Journal of Bacteriology 176 (1).

  Olsen, Gary J., and Carl R. Woese. 1997. “Archaeal Genomics: An Overview.” Cell 89 (7).

  O’Malley, Maureen A. 2009. “What Did Darwin Say About Microbes, and How Did Microbiology Respond?” Trends in Microbiology 17 (8).