The Tangled Tree

by David Quammen

  Thomas, Christopher M., and Kaare M. Nielsen. 2005. “Mechanisms of, and Barriers to, Horizontal Gene Transfer Between Bacteria.” Nature Reviews Microbiology 3 (9).

  Timmis, Jeremy N., Michael A. Ayliffe, Chun Y. Huang, and William Martin. 2004. “Endosymbiotic Gene Transfer: Organelle Genomes Forge Eukaryotic Chromosomes.” Nature Reviews Genetics 5 (2).

  Tranter, Martyn. 2014. “Microbes Eat Rock Under Ice.” Nature 512 (7514).

  Turnbaugh, Peter J., Ruth E. Ley, Michael A. Mahowald, Vincent Magrini, Elaine R. Mardis, and Jeffrey I. Gordon. 2006. “An Obesity-Associated Gut Microbiome with Increased Capacity for Energy Harvest.” Nature 444 (7122).

  Van Boeckel, Thomas P., Charles Brower, Marius Gilbert, Bryan T. Grenfell, Simon A. Levin, Timothy P. Robinson, Aude Teillant, and Ramanan Laxminarayan. 2015. “Global Trends in Antimicrobial Use in Food Animals.” Proceedings of the National Academy of Sciences 112 (18).

  Van der Oost, John. 2013. “New Tool for Genome Surgery.” Science 339 (6121).

  Van Leuven, James T., Russell C. Meister, Chris Simon, and John P. McCutcheon. 2014. “Sympatric Speciation in a Bacterial Endosymbiont Results in Two Genomes with the Functionality of One.” Cell 158 (6).

  Van Niel, C. B. 1946. “The Classification and Natural Relationships of Bacteria.” Cold Spring Harbor Symposia on Quantitative Biology 11.

  ____. 1949. “The ‘Delft School’ and the Rise of General Microbiology.” Bacteriological Reviews 13 (3).

  Venter, J. Craig. 2008. A Life Decoded, My Genome: My Life. London: Penguin Books.

  Venter, J. Craig, Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith, Mark Yandell, Cheryl A. Evans, Robert A. Holt et al. 2001. “The Sequence of the Human Genome.” Science 291 (5507).

  Vernot, Benjamin, and Joshua M. Akey. 2014. “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes.” Science 343 (6174).

  Vetsigian, Kalin, Carl Woese, and Nigel Goldenfeld. 2006. “Collective Evolution and the Genetic Code.” Proceedings of the National Academy of Sciences 103 (28).

  Vogan, Aaron A., and Paul G. Higgs. 2011. “The Advantages and Disadvantages of Horizontal Gene Transfer and the Emergence of the First Species.” Biology Direct 6 (1).

  Wallace, Alfred Russel. 1969. Natural Selection and Tropical Nature: Essays on Descriptive and Theoretical Biology. Facsimile ed. Westmead (UK): Gregg International. Natural Selection was first published in 1870. Tropical Nature was first published in 1878.

  Wallin, Ivan E. 1917. “The Relationships and Histogenesis of Thymus-like Structures in Ammocoetes.” American Journal of Anatomy 22 (1).

  ____. 1922. “On the Nature of Mitochondria: I. Observations on Mitochondria Staining Methods Applied to Bacteria. II. Reactions of Bacteria to Chemical Treatment.” American Journal of Anatomy 30 (2).

  ____. 1923a. “The Mitochondria Problem.” American Naturalist 57 (650).

  ____. 1923b. “On the Nature of Mitochondria: III. The Demonstration of Mitochondria by Bacteriological Methods. IV. A Comparative Study of the Morphogenesis of Root-Nodule Bacteria and Chloroplasts.” American Journal of Anatomy 30 (4).

  ____. 1923c. “On the Nature of Mitochondria: V. A Critical Analysis of Portier’s ‘Les Symbiotes.’ ” Anatomical Record 25 (1).

  ____. 1923d. “Symbionticism and Prototaxis, Two Fundamental Biological Principles.” Anatomical Record 26 (1).

  ____. 1924. “On the Nature of Mitochondria: VII. The Independent Growth of Mitochondria in Culture Media.” American Journal of Anatomy 33 (1).

  ____. 1925. “On the Nature of Mitochondria: IX. Demonstration of the Bacterial Nature of Mitochondria.” American Journal of Anatomy 36 (1).

  Wallin, Ivan Emmanuel. 1927. Symbionticism and the Origin of Species. Reproduction. Baltimore: Waverly Press for Williams & Wilkins.

  Walsh, Ali Morton, R. Daniel Kortschak, Michael G. Gardner, Terry Bertozzi, and David L. Adelson. 2013. “Widespread Horizontal Transfer of Retrotransposons.” Proceedings of the National Academy of Sciences 110 (3).

  Walsh, David A., and W. Ford Doolittle. 2005. “The Real ‘Domains’ of Life.” Current Biology 15 (7).

  Walsh, David A., Mary Ellen Boudreau, Eric Bapteste, and W. Ford Doolittle. 2007.

  “The Root of the Tree: Lateral Gene Transfer and the Nature of the Domains.” In Archaea: Evolution, Physiology, and Molecular Biology. Edited by Roger A. Garrett and Hans-Peter Klenk. Hoboken (NJ): Wiley-Blackwell.

  Wanger, G., T. C. Onstott, and G. Southam. 2008. “Stars of the Terrestrial Deep Subsurface: A Novel ‘Star-Shaped’ Bacterial Morphotype from a South African Platinum Mine.” Geobiology 6 (3).

  Watanabe, Tsutomu. 1963. “Infective Heredity of Multiple Drug Resistance in Bacteria.” Bacteriological Reviews 27 (1).

  Watanabe, Tsutomu, and Toshio Fukasawa. 1961. “Episome-Mediated Transfer of Drug Resistance in Enterobacteriaceae. I. Transfer of Resistance Factors by Conjugation.” Journal of Bacteriology 81 (5).

  Watanabe, Tsutomu, Chizuko Ogata, and Sachiko Sato. 1964. “Episome-Mediated Transfer of Drug Resistance in Enterobacteriaceae. VIII. Six-Drug-Resistance R Factor.” Journal of Bacteriology 88 (4).

  Watasé, S. 1894. “On the Nature of Cell-Organization.” In Biological Lectures Delivered at the Marine Biological Laboratory of Woods Hole, in the Summer Session of 1893. Boston: Ginn.

  Watson, J. D., and F. H. C. Crick. 1953. “Molecular Structure of Nucleic Acids.” Nature 171 (4356).

  Watson, James D. 1968. The Double Helix: A Personal Account of the Discovery of the Structure of DNA. New York: New American Library.

  Weigel, Robert D., editor. 1970. “On the Tendency of Species to Form Varieties; and On the Perpetuation of Varieties & Species by Natural Means of Selection,” by Charles Darwin and A. R. Wallace. Bloomington (IN): Scarlet Ibis Press.

  Weismann, August. 2014. The Germ-Plasm: A Theory of Heredity. Translated by W. Newton Parker, PhD, and Harriet Rönnfeldt, BSc. Reproduction. San Bernardino (CA): Ulan Press. First published 1893 by New York: Charles Scribner’s Sons.

  Weismann, August. 1883. “On Heredity.” In Essays Upon Heredity. Oxford: Clarendon Press. 1889. Electronic Scholarly Publishing, www.esp.org/books/weismann/essays/facsimile.

  ____. 1885. “The Continuity of the Germ-Plasm as the Foundation of a Theory of Heredity.” In Essays Upon Heredity. Oxford: Clarendon Press. 1889. Electronic Scholarly Publishing, www.esp.org/books/weismann/essays/facsimile.

  ____. 2015. The Effect of External Influences upon Development. Romanes lecture, 1894. Reprint from University of Michigan Library. San Bernardino (CA): Google Books. First published 1894 by London: Oxford.

  Weiss, Madeline C., Filipa L. Sousa, Natalia Mrnjavac, Sinje Neukirchen, Mayo Roettger, Shijulal Nelson-Sathi, and William F. Martin. 2016. “The Physiology and Habitat of the Last Universal Common Ancestor.” Nature Microbiology 1 (9).

  Weiss, Robin A. 2006. “The Discovery of Endogenous Retroviruses.” Retrovirology 3 (67).

  Werren, John H. 1997. “Biology of Wolbachia.” Annual Review of Entomology 42.

  ____. 2005. “Heritable Microorganisms and Reproductive Parasitism.” In Microbial Phylogeny and Evolution: Concepts and Controversies. Edited by Jan Sapp. New York: Oxford University Press.

  Westman, W. E., and R. K. Peet. 1985. “Robert H. Whittaker (1920–1980): The Man and His Work.” In Plant Community Ecology: Papers in Honor of Robert H. Whittaker. Edited by R. K. Peet. Dordrecht, Netherlands: Springer.

  Whittaker, R. H. 1957. “The Kingdoms of the Living World.” Ecology 38 (3).

  ____. 1959. “On The Broad Classification of Organisms.” Quarterly Review of Biology 34.

  ____. 1969. “New Concepts of Kingdoms of Organisms.” Science 163 (3863).

  Whittaker, R. H., and Lynn Margulis. 1978. “Protist Classification and the Kingdoms of Organisms.” BioSystems 10 (1–2).

  White, David G., Michael N. Alekshun, and Patrick F. McDermott, editors. 2006. Frontiers in Antimicrobial Res
istance: A Tribute to Stuart B. Levy. Washington (DC): ASM Press.

  Wiedenheft, Blake, Samuel H. Sternberg, and Jennifer A. Doudna. 2012. “RNA-Guided Genetic Silencing Systems in Bacteria and Archaea.” Nature 482 (7385).

  Wilding, E. Imogen, James R. Brown, Alexander P. Bryant, Alison F. Chalker, David J. Holmes, Karen A. Ingraham, Serban Iordanescu, Chi Y. So, Martin Rosenberg, and Michael N. Gwynn. 2000. “Identification, Evolution, and Essentiality of the Mevalonate Pathway for Isopentenyl Diphosphate Biosynthesis in Gram-Positive Cocci.” Journal of Bacteriology 182 (15).

  Williams, Tom A., Peter G. Foster, Tom M. W. Nye, Cymon J. Cox, and T. Martin Embley. 2012. “A Congruent Phylogenomic Signal Places Eukaryotes Within the Archaea.” Philosophical Transactions of the Royal Society of London (B) 279 (1749).

  Williams, Tom A., and T. Martin Embley. 2014. “Archaeal ‘Dark Matter’ and the Origin of Eukaryotes.” Genome Biology and Evolution 6 (3).

  ____. 2015. “Changing Ideas About Eukaryotic Origins.” Philosophical Transactions of the Royal Society of London (B) 370 (1678).

  Williams, Tom A., Sarah E. Heaps, Svetlana Cherlin, Tom M. W. Nye, Richard J. Boys, and T. Martin Embley. 2015. “New Substitution Models for Rooting Phylogenetic Trees.” Philosophical Transactions of the Royal Society of London (B) 370 (1678).

  Williamson, Donald I. 2009. “Caterpillars Evolved from Onychophorans by Hybridogenesis.” Proceedings of the National Academy of Sciences 106 (47).

  Wilson, Edmund B. 1925. The Cell in Development and Heredity. New York: Macmillan.

  Wilson, Katherine L., and Scott C. Dawson. 2011. “Functional Evolution of Nuclear Structure.” Journal of Cell Biology 195 (2).

  Wilson, Robert A. 2013. “The Biological Notion of Individual.” In The Stanford Encyclopedia of Philosophy. Edited by Edward N. Zalta, https://plato.stanford.edu/entries/biology-individual.

  Winther, Rasmus G. 2001. “August Weismann on Germ-Plasm Variation.” Journal of the History of Biology 34 (3).

  Witzany, Günther. 2009. “Introduction: A Perspective on Natural Genetic Engineering and Natural Genome Editing.” Annals of the New York Academy of Sciences 1178.

  Woese, C. R. 1961. “Coding Ratio for the Ribonucleic Acid Viruses.” Nature 190 (4777).

  Woese, C. R. 1965a. “On the Evolution of the Genetic Code.” Proceedings of the National Academy of Sciences 54 (6).

  ____. 1965b. “Order in the Genetic Code.” Proceedings of the National Academy of Sciences 54 (1).

  Woese, Carl. 1970. “Molecular Mechanics of Translation: A Reciprocating Ratchet Mechanism.” Nature 226 (May 30).

  ____. 1998. “The Universal Ancestor.” Proceedings of the National Academy of Sciences 95 (12).

  Woese, Carl R. 1964. “Universality in the Genetic Code.” Science 144 (22 May).

  ____. 1967. The Genetic Code. New York: Harper & Row.

  ____. 1977. “Endosymbionts and Mitochondrial Origins.” Journal of Molecular Evolution 10 (2).

  ____. 1981. “Archaebacteria.” Scientific American 244 (6).

  ____. 1982. “Archaebacteria and Cellular Origins: An Overview.” In Archaebacteria. Edited by Otto Kandler. Stuttgart (Ger.): Gustav Fischer.

  ____. 1983. “The Primary Lines of Descent and the Universal Ancestor.” In Evolution from Molecules to Man. Edited by D. S. Bendall. Cambridge: Cambridge University Press.

  ____. 1987. “Bacterial Evolution.” Microbiological Reviews 51 (2).

  ____. 1994. “Microbiology in Transition.” Proceedings of the National Academy of Sciences 91 (5).

  ____. 1998. “Default Taxonomy: Ernst Mayr’s View of the Microbial World.” Proceedings of the National Academy of Sciences 95 (19).

  ____. 1998. “A Manifesto for Microbial Genomics.” Current Biology 8 (22).

  ____. 2000. “Interpreting the Universal Phylogenetic Tree.” Proceedings of the National Academy of Sciences 97 (15).

  ____. 2002. “On the Evolution of Cells.” Proceedings of the National Academy of Sciences 99 (13).

  ____. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews 68 (2).

  ____. 2005. “Q&A: Carl R. Woese.” Current Biology 15 (4).

  ____. 2007. “The Birth of the Archaea: A Personal Retrospective.” In Archaea: Evolution, Physiology, and Molecular Biology. Edited by Roger A. Garnett and Hans-Peter Klenk. Hoboken (NJ): Wiley-Blackwell.

  Woese, Dr. Carl R. 1962. “Nature of the Biological Code.” Nature 194 (4834).

  Woese, C. R., D. H. Dugre, W. C. Saxinger, and S. A. Dugre. 1966. “The Molecular Basis for the Genetic Code.” Proceedings of the National Academy of Sciences 55 (4).

  Woese, Carl R., George E. Fox, Lawrence Zablen, Tsuneko Uchida, Linda Bonen, Kenneth Pechman, Bobby J. Lewis, and David Stahl. 1975. “Conservation of Primary Structure in 16S Ribosomal RNA.” Nature 254 (5495).

  Woese, Carl R., and George E. Fox. 1977a. “Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms.” Proceedings of the National Academy of Sciences 74 (11).

  ____. 1977b. “The Concept of Cellular Evolution.” Journal of Molecular Evolution 10 (1).

  Woese, Carl R., Otto Kandler, and Mark L. Wheelis. 1990. “Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya.” Proceedings of the National Academy of Sciences 87 (12).

  Woese, Carl R., and Nigel Goldenfeld. 2009. “How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis.” Microbiology and Molecular Biology Reviews 73 (1).

  Wolf, Yuri I., L. Aravind, Nick V. Grishin, and Eugene V. Koonin. 1999. “Evolution of Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events.” Genome Research 9 (8).

  Wolfe, Ralph. 2014. “Early Days with Carl.” RNA Biology 11 (3).

  Wolfe, Ralph S. 1991. “My Kind of Biology.” Annual Review of Microbiology 45.

  ____. 2006. “The Archaea: A Personal Overview of the Formative Years.” In The Prokaryotes. Edited by E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, and F. Thompson. Berlin/Heidelberg: Springer.

  Wright, H. D. 1941. “Obituary. William McDonald Scott, M.D., B.S.C. Edin., D.T.M.&H.” Lancet 237 (6140).

  Wu, Dongying, Sean C. Daugherty, Susan E. Van Aken, Grace H. Pai, Kisha L. Watkins, Hoda Khouri, Luke J. Tallon, Jennifer M. Zaborsky, Helen E. Dunbar, Phat L. Tran et al. 2006. “Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters.” PLoS Biology 4 (6).

  Xue, Katherine. 2014. “Superbug: An Epidemic Begins.” Harvard (May/June).

  Yang, D., Y. Oyaizu, H. Oyaizu, G. J. Olsen, and C. R. Woese. 1985. “Mitochondrial Origins.” Proceedings of the National Academy of Sciences 82 (13).

  Yarus, Michael. 2010. Life from an RNA World: The Ancestor Within. Cambridge (MA): Harvard University Press.

  Yong, Ed. 2008. “Human Gut Bacteria Linked to Obesity.” Not Exactly Rocket Science (blog), October 6, 2008. http://phenomena.nationalgeographic.com/2008/10/06/human-gut-bacteria-linked-to-obesity.

  ____. “Genes from Chagas Parasite Can Transfer to Humans and Be Passed on to Children.” Not Exactly Rocket Science (blog). February 14, 2010. http://phenomena.nationalgeographic.com/2010/02/14/genes-from-chagas-parasite-can-transfer-to-humans-and-be-passed-on-to-children.

  ____. “Meet Your Viral Ancestors—How Bornaviruses Have Been Infiltrating Our Genomes for 40 Million Years.” Not Exactly Rocket Science (blog). January 6, 2010. http://blogs.discovermagazine.com/notrocketscience/2010/01/06/meet-your-viral-ancestors-how-bornaviruses-have-been-infiltrating-our-genomes-for-40-million-years/#.WirPW7aZM0o.

  ____. “Dormant Viruses Can Hide in Our DNA and Be Passed from Parent to Child.” Not Exactly Rocket Science (blog). March 27, 2010. http://blogs.discovermagazine.com/notrocketscience/2010/03/27/dormant-viruses-can-hide-in-our-dna-and-be-passed-from-parent-to-child/#.WirZdLaZM0o.

  ____. “Tree or Ring: The Or
igin of Complex Cells.” Not Exactly Rocket Science (blog). September 13, 2010. http://blogs.discovermagazine.com/notrocketscience/2010/09/13/tree-or-ring-the-origin-of-complex-cells/#.WiraN7aZM0o.

  ____. (2016). I Contain Multitudes: The Microbes Within Us and a Grander View of Life. New York: HarperCollins.

  Yoshida, Shosuke, Kazumi Hiraga, Toshihiko Takehana, Ikuo Taniguchi, Hironao Yamaji, Yasuhito Maeda, Kiyotsuna Toyohara, Kenji Miyamoto, Yoshiharu Kimura, and Kohei Oda. 2016. “A Bacterium That Degrades and Assimilates Poly(ethylene terephthalate).” Science 351 (6278).

  Zablen, L. B., M. S. Kissil, C. R. Woese, and D. E. Buetow. 1975. “Phylogenetic Origin of the Chloroplast and Prokaryotic Nature of Its Ribosomal RNA.” Proceedings of the National Academy of Sciences 72 (6).

  Zambryski, P., J. Tempe, and J. Schell. 1989. “Transfer and Function of T-DNA Genes from Agrobacterium Ti and Ri Plasmids in Plants.” Cell 56 (2).

  Zamecnik, P. C., E. B. Keller, J. W. Littlefield, M. B. Hoagland, and R. B. Loftfield. 1956. “Mechanism of Incorporation of Labeled Amino Acids into Protein.” Journal of Cellular and Comparative Physiology 47 (Suppl. 1).

  Zaremba-Niedzwiedzka, Katarzyna, Eva F. Caceres, Jimmy H. Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Kiley W. Seitz, Karthik Anantharaman, Piotr Starnawski, Kasper U. Kjeldsen et al. 2017. “Asgard Archaea Illuminate the Origin of Eukaryotic Cellular Complexity.” Nature 541 (7637).

  Zhaxybayeva, Olga, and J. Peter Gogarten. 2004. “Cladogenesis, Coalescence, and the Evolution of the Three Domains of Life.” Trends in Genetics 20 (4).

  Zhaxybayeva, Olga, and W. Ford Doolittle. 2011. “Lateral Gene Transfer.” Current Biology 21 (7).

  Zhuo, Xiaoyu, Cedric Feschotte. 2015. “Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages.” PLoS Pathogens 11 (11).

  Zimmer, Carl. 2008. Microcosm: E. Coli and the New Science of Life. New York: Pantheon Books.

  ____. 2010. “Hunting Fossil Viruses in Human DNA.” New York Times (January 12).

  Zinder, Norton D. 1953. “Infective Heredity in Bacteria.” Cold Spring Harbor Symposia in Quantitative Biology 18.