The Tangled Tree

by David Quammen

  O’Malley, Maureen A., and John Dupré. 2007. “Size Doesn’t Matter: Towards a More Inclusive Philosophy of Biology.” Biology & Philosophy 22 (2).

  O’Malley, Maureen A., William Martin, and John Dupré. 2010. “The Tree of Life: Introduction to an Evolutionary Debate.” Biology & Philosophy 25 (4).

  O’Malley, Maureen A., and Eugene V. Koonin. 2011. “How Stands the Tree of Life a Century and a Half After The Origin?” Biology Direct 6 (32).

  Orgel, L. E., and F. H. C. Crick. 1980. “Selfish DNA: The Ultimate Parasite.” Nature 284 (5757).

  Orgel, L. E., F. H. C. Crick, and C. Sapienza. 1980. “Selfish DNA.” Nature 288 (5792).

  Pääbo, Svante. 2003. “The Mosaic That Is Our Genome.” Nature 421 (6921).

  ____. 2014. Neanderthal Man: In Search of Lost Genomes. New York: Basic Books.

  Pace, John K., II, and Cedric Feschotte. 2007. “The Evolutionary History of Human DNA Transposons: Evidence for Intense Activity in the Primate Lineage.” Genome Research 17 (4).

  Pace, John K., II, Clément Gilbert, Marlene S. Clark, and Cedric Feschotte. 2008. “Repeated Horizontal Transfer of a DNA Transposon in Mammals and Other Tetrapods.” Proceedings of the National Academy of Sciences 105 (44).

  Pace, N. R., D. H. L. Bishop, and S. Spiegelman. 1967. “The Kinetics of Product Appearance and Template Involvement in the In Vitro Replication of Viral RNA.” Proceedings of the National Academy of Sciences 58 (2).

  Pace, Norman R. 1997. “A Molecular View of Microbial Diversity and the Biosphere.” Science 276 (5313).

  ____. 2006. “Time For a Change.” Nature 441 (7091).

  ____. 2008. “The Molecular Tree of Life Changes How We See, Teach Microbial Diversity.” Microbe (1).

  ____. 2009. “Mapping the Tree of Life: Progress and Prospects.” Microbiology and Molecular Biology Reviews 73 (4).

  Pace, Norman R., Gary J. Olsen, and Carl R. Woese. 1986. “Ribosomal RNA Phylogeny and the Primary Lines of Evolutionary Descent.” Cell 45 (3).

  Pace, Norman R., David A. Stahl, David J. Lane, and Gary J. Olsen. 1986. “The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences.” In Advances of Microbial Ecology. Vol. 9. Edited by K. C. Marshall. New York: Plenum Press.

  Pace, Norman, Jan Sapp, and Nigel Goldenfeld. 2012. “Phylogeny and Beyond: Scientific, Historical, and Conceptual Significance of the First Tree of Life.” Proceedings of the National Academy of Sciences 109 (4).

  Packard, Alpheus S., M.S., LL.D. 2009. Lamarck, the Founder of Evolution: His Life and Work. With translations of his writings on Organic Evolution. Repr. ed. LaVergne (TN): Kessinger. First published in 1901 by London: Longmans, Green.

  Palmer, Kelli L., and Michael S. Gilmore. 2010. “Multidrug-Resistant Enterococci Lack CRISPR-cas.” mBio 1 (4).

  Panchen, Alec L. 1992. Classification, Evolution, and the Nature of Biology. Cambridge: Cambridge University Press.

  Papagianni, Dimitra, and Michael A. Morse. 2013. The Neanderthals Rediscovered: How Modern Science Is Rewriting Their Story. London: Thames & Hudson.

  Parker, Philip M., editor. 2009. Bacteriology: Webster’s Timeline History 1812–2006. San Diego: ICON Group International.

  Patterson, Nick, Daniel J. Richter, Sante Gnerre, Eric S. Lander, and David Reich. 2006. “Genetic Evidence for Complex Speciation of Humans and Chimpanzees.” Nature 441 (7097).

  Pedersen, Rolf B., Hans Tore Rapp, Ingunn H. Thorseth, Marvin D. Lilley, Fernando J. A. S. Barriga, Tamara Baumberger, Kristin Flesland, Rita Fonseca, Gretchen L. Früh-Green, and Steffen L. Jorgensen. 2010. “Discovery of a Black Smoker Vent Field and Vent Fauna at the Arctic Mid-Ocean Ridge.” Nature Communications 1 (126).

  Pennings, Jeroen L. A., Jan T. Keltjens, and Godfried D. Vogels. 1998. “Isolation and Characterization of Methanobacterium thermoautotrohpicum ΔH Mutants Unable to Grow Under Hydrogen-Deprived Conditions.” Journal of Bacteriology 180 (10).

  Pennisi, Elizabeth. 1998. “Genome Data Shake Tree of Life.” Science 280 (5364).

  ____. 1999. “Is It Time to Uproot the Tree of Life?” Science 284 (5418).

  ____. 2002. “Bacteria Shared Photosynthesis Genes.” Science 298 (5598).

  ____. 2004. “The Birth of the Nucleus.” Science 305 (5685).

  Peterson, Jane, Susan Garges, Maria Giovanni, Pamela McInnes, Lu Wang, Jeffrey A. Schloss, Vivien Bonazzi, Jean E. McEwen, Kris A. Wetterstrand, Carolyn Deal et al. 2009. “The NIH Human Microbiome Project.” Genome Research 19 (12).

  Pietsch, Theodore W. 2012. Trees of Life: A Visual History of Evolution. Baltimore: Johns Hopkins University Press.

  Pisani, Davide, James A. Cotton, and James O. McInerney. 2007. “Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes.” Molecular Biology and Evolution 24 (8).

  Piskurek, Oliver, and Norihiro Okada. 2007. “Poxviruses as Possible Vectors for Horizontal Transfer of Retroposons from Reptiles to Mammals.” Proceedings of the National Academy of Sciences 104 (29).

  Pittis, Alexandros A., and Toni Gabaldón. 2016. “Late Acquisition of Mitochondria by a Host with Chimaeric Prokaryotic Ancestry.” Nature 531 (7592).

  Pollock, M. R. 1970. “The Discovery of DNA: An Ironic Tale of Chance, Prejudice and Insight.” Journal of General Microbiology 63.

  Pollock, Robert. 2015. “Eugenics Lurk in the Shadow of CRISPR.” Science 348 (6237).

  Poundstone, William. 1999. Carl Sagan: A Life in the Cosmos. New York: Henry Holt.

  Pourcel, C., G. Salvignol, and G. Vergnaud. 2005. “CRISPR Elements in Yersinia pestis Acquire New Repeats by Preferential Uptake of Bacteriophage DNA, and Provide Additional Tools for Evolutionary Studies.” Microbiology 151 (Pt. 3).

  Proctor, Lita M., Shaila Chhibba, Jean McEwen, Jane Peterson, Chris Wellington, Carl Baker, Maria Giovanni, Pamela McInnes, and R. Dwayne Lunsford. 2013. “The NIH Human Microbiome Project.” In The Human Microbiota: How Microbial Communities Affect Health and Disease. Edited by David N. Fredricks. Hoboken (NJ): John Wiley & Sons.

  Ragan, Mark A. 2009. “Trees and Networks Before and After Darwin.” Biology Direct 4 (43).

  Ragan, Mark A., James O. McInerney, and James A. Lake. 2009. “The Network of Life: Genome Beginnings and Evolution.” Philosophical Transactions of the Royal Society of London (B) 364 (1527).

  Raoult, Didier, and Eugene V. Koonin. 2012. “Microbial Genomics Challenge Darwin.” Frontiers in Cellular and Infection Microbiology 2 (127).

  Raven, Peter H. 1970. “A Multiple Origin for Plastids and Mitochondria.” Science 169 (3946).

  Reames, Richard. 2007. Arborsculpture: Solutions for a Small Planet. Williams (OR): Arborsmith Studios.

  Reames, Richard, and Barbara Hahn Delbol. 1995. How to Grow a Chair: The Art of Tree Trunk Topiary. Williams (OR): Arborsmith Studios.

  Reanney, Darryl. 1976. “Extrachromosomal Elements as Possible Agents of Adaptation and Development.” Bacteriological Reviews 40 (3).

  Redelsperger, François, Guillaume Cornelis, Cécile Vernochet, Bud C. Tennant, François Catzeflis, Baptiste Mulot, Odile Heidmann, Thierry Heidmann, and Anne Dupressoir. 2014. “Capture of syncytin-Mar1, a Fusogenic Endogenous Retroviral Envelope Gene Involved in Placentation in the Rodentia Squirrel-Related Clade.” Journal of Virology 88 (14).

  Relman, David A., MD. 2011. “Microbial Genomics and Infectious Diseases.” New England Journal of Medicine 365 (4).

  Relman, David A. 2012. “Learning About Who We Are.” Nature 486 (7402).

  ____. 2013. “Metagenomics, Infectious Disease Diagnostics, and Outbreak Investigations: Sequence First, Ask Questions Later?” Journal of the American Medical Association 309 (14).

  ____. 2015. “The Human Microbiome and the Future Practice of Medicine.” Journal of the American Medical Association 314 (11).

  Retchless, Adam C., and Jeffrey G. Lawrence. 2007. “Temporal Fragmentation of Speciation in Bacteria.” Science 317 (5841).

  ____. 2012. “Ecological Adaptation in Bacteria: Speciation Driven by Codon Selection.” Molecular B
iology and Evolution 29 (12).

  Richards, Robert J. 2008. The Tragic Sense of Life: Ernst Haeckel and the Struggle over Evolutionary Thought. Chicago and London: University of Chicago Press.

  Ridley, Matt. 2000. Genome: The Autobiography of a Species in 23 Chapters. New York: HarperCollins. First published 1999.

  ____. 2006. Francis Crick: Discoverer of the Genetic Code. New York: Atlas Books/HarperCollins.

  Riley, David B., Karsten B. Sieber, Kelly M. Robinson, James Robert White, Ashwinkumar Ganesan, Syrus Nourbakhsh and Julie C. Dunning Hotopp. 2013. “Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples.” PLoS Computational Biology 9 (6).

  Ris, Hans, and Walter Plaut. 1962. “Ultrastructure of DNA-Containing Areas in the Chloroplast of Chlamydomonas.” Journal of Cell Biology 13 (3).

  Rivera, Maria C., Ravi Jain, Jonathan E. Moore, and James A. Lake. 1998. “Genomic Evidence for Two Functionally Distinct Gene Classes.” Proceedings of the National Academy of Sciences 95 (11).

  Rivera, Maria C., and James A. Lake. 2004. “The Ring of Life Provides Evidence for a Genome Fusion Origin of Eukaryotes.” Nature 431 (7005).

  Roberts, D. McL., P. Sharp, G. Alderson, and M.A. Collins, editors. 1996. Evolution of Microbial Life. Cambridge: Cambridge University Press.

  Roberts, Elijah, Anurag Sethi, Jonathan Montoya, Carl R. Woese, and Zaida Luthey-Schulten. 2008. “Molecular Signatures of Ribosomal Evolution.” Proceedings of the National Academy of Sciences 105 (37).

  Robinson, Kelly M., Karsten B. Sieber, and Julie C. Dunning Hotopp. 2013. “A Review of Bacteria-Animal Lateral Gene Transfer May Inform Our Understanding of Diseases Like Cancer.” PLOS Genetics 9 (10).

  Rogers, Matthew B., Russell F. Watkins, James T. Harper, Dion G. Durnford, Michael W. Gray, and Patrick J. Keeling. 2007. “A Complex and Punctate Distribution of Three Eukaryotic Genes Derived by Lateral Gene Transfer.” BMC Evolutionary Biology 7 (89).

  Rokas, Antonis, and Peter W. H. Holland. 2000. “Rare Genomic Changes as a Tool for Phylogenetics.” Trends in Ecology & Evolution 15 (11).

  Rokas, Antonis, and Sean B. Carroll. 2006. “Bushes in the Tree of Life.” PLoS Biology 4 (11).

  Romer, Alfred Sherwood. 1966. Vertebrate Paleontology. 3rd ed.: Chicago and London: University of Chicago Press. First published 1933.

  Sagan, Dorion, editor. 2012. Lynn Margulis: The Life and Legacy of a Scientific Rebel. White River Junction (VT): Chelsea Green.

  Sagan, Lynn. 1967. “On the Origin of Mitosing Cells.” Journal of Theoretical Biology 14 (3).

  Salzberg, Steven L., Owen White, Jeremy Peterson, and Jonathan A. Eisen. 2001. “Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?” Science 292 (5523).

  Sanger, Fred. 2001. “The Early Days of DNA Sequences.” Nature Medicine 7 (3).

  Sanger, F., G. G. Brownlee, and B. G. Barrell. 1965. “A Two-Dimensional Fractionation Procedure for Radioactive Nucleotides.” Journal of Molecular Biology 13 (2).

  Sankararaman, Sriram, Swapan Mallick, Michael Dannemann, Kay Prüfer, Janet Kelso, Svante Pääbo, Nick Patterson, and David Reich. 2014. “The Genomic Landscape of Neanderthal Ancestry in Present-Day Humans.” Nature 507 (7492).

  Sapp, Jan. 1994. Evolution by Association: A History of Symbiosis. New York: Oxford University Press.

  ____. 2002. “Paul Buchner (1886–1978) and Hereditary Symbiosis in Insects.” International Microbiology 5 (3).

  ____. 2003. Genesis: The Evolution of Biology. New York: Oxford University Press.

  ____. 2005. “The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology.” Microbiology and Molecular Biology Reviews 69 (2).

  ____. 2009. The New Foundations of Evolution: On the Tree of Life. New York: Oxford University Press.

  Sapp, Jan, editor. 2005. Microbial Phylogeny and Evolution: Concepts and Controversies. New York: Oxford University Press.

  Sapp, Jan, Francisco Carrapiço, and Mikhail Zolotonosov. 2002. “Symbiogenesis: The Hidden Face of Constantin Merezhkowsky.” History and Philosophy of the Life Sciences 24 (3–4).

  Sapp, Jan, and George E. Fox. 2013. “The Singular Quest for a Universal Tree of Life.” Microbiology and Molecular Biology Reviews 77 (4).

  Sarkar, Sahotra. 2014. “Woese on the Received View of Evolution.” RNA Biology 11 (3).

  Schaack, Sarah, Clément Gilbert, and Cedric Feschotte. 2010. “Promiscuous DNA: Horizontal Transfer of Transposable Elements and Why It Matters for Eukaryotic Evolution.” Trends in Ecology and Evolution 25 (9).

  Schulz, Heide N., and Bo Barker Jörgensen. 2001. “Big Bacteria.” Annual Review of Microbiology 55.

  Schwartz, Robert M., and Margaret O. Dayhoff. 1978. “Origins of Prokaryotes, Eukaryotes, Mitochondria, and Chloroplasts.” Science 199 (4327).

  Sears, Cynthia L. 2005. “A Dynamic Partnership: Celebrating Our Gut Flora.” Anaerobe 11 (5).

  Sheridan, Cormac. 2015. “CRISPR Germline Editing Reverberates Through Biotech Industry.” Nature Biotechnology 33 (5).

  Shreeve, James. 2004. The Genome War. New York: Alfred A. Knopf.

  Sievert, D. M., M. L. Boulton, G. Stoltman, D. Johnson, M. G. Stobierski, F. P. Downes, P. A. Somsel, J. T. Rudrik, W. Brown, W. Hafeez et al. 2002. “Staphylococcus aureus Resistant to Vancomycin—United States, 2002.” Morbidity and Mortality Weekly Report 51 (26).

  Silva, Joana C., Elgion L. Loreto, and Jonathan B. Clark. 2004. “Factors That Affect the Horizontal Transfer of Transposable Elements.” Current Issues in Molecular Biology 6 (1).

  Smillie, Chris S., Mark B. Smith, Jonathan Friedman, Otto X. Cordero, Lawrence A. David, and Eric J. Alm. 2011. “Ecology Drives a Global Network of Gene Exchange Connecting the Human Microbiome.” Nature 480 (7376).

  Smith, David Roy, and Patrick J. Keeling. 2015. “Mitochondrial and Plastid Genome Architecture: Reoccurring Themes, but Significant Differences at the Extremes.” Proceedings of the National Academy of Sciences 112 (33).

  Smith, Michael, Da-Fei Feng, and Russell F. Doolittle. 1992. “Evolution by Acquisition: The Case for Horizontal Gene Transfers.” Trends in Biochemical Science 17 (12).

  Smith, Myron L., Johann N. Bruhn, and James B. Anderson. 1992. “The Fungus Armillaria bulbosa Is Among the Largest and Oldest Living Organisms.” Nature 356 (6368).

  Sogin, M., B. Pace, N. R. Pace, and C. R. Woese. 1971. “Primary Structural Relationship of p16 to m16 Ribosomal RNA.” Nature New Biology 232 (28).

  Sogin, Mitchell L., Hilary G. Morrison, Julie A. Huber, David Mark Welch, Susan M. Huse, Phillip R. Neal, Jesus M. Arrieta, and Gerhard J. Herndl. 2006. “Microbial Diversity in the Deep Sea and the Underexplored ‘Rare Biosphere.’ ” Proceedings of the National Academy of Sciences 103 (32).

  Sogin, S. J., M. L. Sogin, and C. R. Woese. 1972. “Phylogenetic Measurement in Procaryotes by Primary Structural Characterization.” Journal of Molecular Evolution 1 (1).

  Sonea, Sorin, and Maurice Panisset. 1983. A New Bacteriology. Boston: Jones and Bartlett. First published as Introduction à la Nouvelle Bactériologie in 1980 by Les Presses de L’Université de Montréal.

  Sonea, Sorin. 1988. “The Global Organism: A New View of Bacteria.” Sciences 28 (4).

  Sonnenburg, Justin L. 2010. “Genetic Pot Luck.” Nature 464 (7290).

  Sorek, Rotem, C. Martin Lawrence, and Blake Wiedenheft. 2013. “CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea.” Annual Review of Biochemistry 82.

  Soucy, Shannon M., Jinling Huang, and Johann Peter Gogarten. 2015. “Horizontal Gene Transfer: Building the Web of Life.” Nature Reviews Genetics 16 (8).

  Spang, Anja, Jimmy H. Saw, Steffen L. Jørgensen, Katarzyna Zaremba-Niedzwiedzka, Joran Martijn, Anders E. Lind, Roel van Eijk, Christa Schleper, Lionel Guy, and Thijs J. G. Ettema. 2015. “Complex Archaea That Bridge the Gap Between Prokaryotes and Eukaryotes.” Nature 521 (7551).

  Spangenburg, Ray, and Kit Moser. 2009. Carl Sagan: A Biography. New York: Prometheus Books.

  Specter, Michael. 2007. “Da
rwin’s Surprise.” New Yorker (December 3).

  ____. 2015. “The Gene Hackers.” New Yorker (November 16).

  ____. 2017. “Rewriting the Code of Life.” New Yorker (January 2).

  Stahl, David A., David J. Lane, Gary J. Olsen, and Norman R. Pace. 1984. “Analysis of Hydrothermal Vent-Associated Symbionts by Ribosomal RNA Sequences.” Science 224 (4647).

  Stahl, David A., David J. Lane, Gary J. Olsen, and Norman R. Pace. 1985. “Characterization of a Yellowstone Hot Spring Microbial Community by 5S rRNA Sequences.” Applied and Environmental Microbiology 49 (6).

  Stanier, Roger Y., and C. B. van Niel. 1941. “The Main Outlines of Bacterial Classification.” Journal of Bacteriology 42 (4).

  Stanier, Roger Y., and C. B. van Niel. 1962. “The Concept of a Bacterium.” Archiv. für Mikrobiologie, 42.

  Stanier, Roger Y. 1980. “The Journey, Not the Arrival, Matters.” Annual Review of Microbiology 34.

  Stanier, Roger Y., John L. Ingraham, Mark L. Wheelis, and Paige R. Painter. 1986. The Microbial World. 5th ed.: Englewood Cliffs (NJ): Prentice-Hall.

  Stevens, P. F. 1983. “Augustin Augier’s ‘Arbre Botanique’ (1801), a Remarkable Early Botanical Representation of the Natural System.” Taxon 32 (2).

  Stoye, Jonathan P. 2012. “Studies of Endogenous Retroviruses Reveal a Continuing Evolutionary Saga.” Nature Reviews Microbiology 10 (6).

  Stringer, Chris. 2012. Lone Survivors: How We Came to Be the Only Humans on Earth. New York: St. Martin’s Press.

  Swithers, Kristen S., Shannon M. Soucy, and J. Peter Gogarten. 2012. “The Role of Reticulate Evolution in Creating Innovation and Complexity.” International Journal of Evolutionary Biology 2012 (418964).

  Syvanen, Michael, and Clarence I. Kado, editors. 2002. Horizontal Gene Transfer. 2nd ed. San Diego: Academic Press, a Division of Harcourt.

  Syvanen, Michael, and Jonathan Ducore. 2010. “Whole Genome Comparisons Reveals a Possible Chimeric Origin for a Major Metazoan Assemblage.” Journal of Biological Systems 18 (2).

  Taylor, F. J. R. “Max.” 2003. “The Collapse of the Two-Kingdom System, the Rise of Protistology and the Founding of the International Society for Evolutionary Protistology (ISEP).” International Journal of Systematic and Evolutionary Biology 53 (Pt. 6).