Reticulate Evolution pp 121-178 | Cite as
Historical and Epistemological Perspectives on What Horizontal Gene Transfer Mechanisms Contribute to Our Understanding of Evolution
- 784 Downloads
Abstract
Since the 1990s, results coming in from molecular phylogenetics necessitate us to recognize that Horizontal Gene Transfer (HGT) occurs massively across all three domains of life. Nonetheless, many of the mechanisms whereby genes can become transferred laterally have been known from the early twentieth century onward. The temporal discrepancy between the first historical observations of the processes, and the rather recent general acceptance of the documented data, poses an interesting epistemological conundrum: Why have incoming results on HGT been widely neglected by the general evolutionary community and what causes for a more favorable reception today? Five reasons are given: (1) HGT was first observed in the biomedical sciences and these sciences did not endorse an evolutionary epistemic stance because of the ontogeny/phylogeny divide adhered to by the founders of the Modern Synthesis. (2) Those who did entertain an evolutionary outlook associated research on HGT with a symbiotic epistemic framework. (3) That HGT occurs across all three domains of life was demonstrated by modern techniques developed in molecular biology, a field that itself awaits full integration into the general evolutionary synthesis. (4) Molecular phylogenetic studies of prokaryote evolution were originally associated with exobiology and abiogenesis, and both fields developed outside the framework provided by the Modern Synthesis. (5) Because HGT brings forth a pattern of reticulation, it contrasts the standard idea that evolution occurs solely by natural selection that brings forth a vertical, bifurcating pattern in the “tree” of life. Divided into two parts, this chapter first reviews current neo-Darwinian “tree of life” versus reticulate “web of life” polemics as they have been debated in high-profile academic journals, and secondly, the historical context of discovery of the various means whereby genes are transferred laterally is sketched. Along the way, the reader is introduced to how HGT contradicts some of the basic tenets of the neo-Darwinian paradigm.
Keywords
Tree of life Web of life Horizontal Gene Transfer Transformation Transduction Conjugation Gene transfer agents Modern Synthesis Extended Synthesis Biomedical sciencesNotes
Acknowledgments
This work was written with the support of the Portuguese Fund for Scientific Research (grant ID SFRH/BPD/89195/2012 and project number UID/FIL/00678/2013) and the John Templeton Foundation (grant ID 36288).
References
- Adams JW, Kaufman RE, Kretschmer PJ, Harrison M, Nienhuis AW (1980) A family of long reiterated DNA sequences, one copy of which is next to the human beta globin gene. Nucleic Acids Res 8(24):6113. doi: 10.1093/nar/8.24.6113 PubMedCentralPubMedGoogle Scholar
- Akamatsu T, Taguchi H (2001) Incorporation of the whole chromosomal DNA in protoplast lysates into competent cells of Bacillus subtilis. Biosci Biotechnol Biochem 65(4):823–829. doi: 10.1271/bbb.65.823 PubMedGoogle Scholar
- Akiba T, Koyama K, Ishiki Y, Kimura S, Fukushima T (1960) On the mechanism of the development of multiple-drug-resistant clones of Shigella. Jpn J Microbiol 4(2):219–227. doi: 10.1111/j.1348-0421.1960.tb00170.x PubMedGoogle Scholar
- Ambler P, Meyer T, Kamen MD (1979) Anomalies in amino acid sequences of small cytochromes c and cytochromes c′ from two species of purple photosynthetic bacteria. Nature 278:661–662PubMedGoogle Scholar
- Andam CP, Williams D, Gogarten JP (2010) Natural taxonomy in light of horizontal gene transfer. Biol Phil 25(4):589–602Google Scholar
- Anderson ES (1968) The ecology of transferable drug resistance in the enterobacteria. Annu Rev Microbiol 22:131–180PubMedGoogle Scholar
- Andersson DI, Hughes D (2010) Antibiotic resistance and its cost: is it possible to reverse resistance? Nat Rev Microbiol 8:260–271. doi: 10.1038/nrmicro2319 PubMedGoogle Scholar
- Arnold ML (2008) Reticulate evolution and humans: origins and ecology. Oxford University Press, New YorkGoogle Scholar
- Avery OT, Macleod CM, McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumonococcal types. Induction of transformation by a deoxyribo-nucleic acid fraction isolated from pnuemococcus type III. J Exp Med 79:137–157PubMedCentralPubMedGoogle Scholar
- Bachmann BJ (1972) Pedigrees of some mutant strains of Escherichia coli K-12. Bacteriological Rev 36(4):525–557Google Scholar
- Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF (2005) Do orthologous gene phylogenies really support tree-thinking? Evol Biol 5:33Google Scholar
- Bapteste E et al (2009) Prokaryotic evolution and the tree of life are two different things. Biology Direct 4:34PubMedCentralPubMedGoogle Scholar
- Bardaji L, Añorga M, Jackson RW, Martínez-Bilbao A, Yanguas N, Murillo J (2011) Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae. PLoS ONE 6(10):e25773PubMedCentralPubMedGoogle Scholar
- Barker A, Clark CA, Manning PA (1994) Identification of VCR, a repeated sequence associated with a locus encoding a hemag glutinin in Vibrio cholerae O1. J Bacteriol 176:5450–5458PubMedCentralPubMedGoogle Scholar
- Behring E, Kitasato S (1890) Ueber das Zustandekommen der Diphtherie-Immunitat und der Tetanus-Immunitat bei Thieren. Deutsche medizinsche Wochenschrift 16:1113–1114Google Scholar
- Beijerinck MW (1898) Über ein Contagium vivum fluidum als Ursache der Fleckenkrankheit der Tabaksblätter. Verhandelingen der Koninklijke academie van Wetenschappen te Amsterdam 65:1–22Google Scholar
- Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, Burt A, Tristem M (2004) Long-term reinfection of the human genome by endogenous retroviruses. PNAS 101(14):4894–4899. doi: 10.1073/pnas.0307800101 PubMedCentralPubMedGoogle Scholar
- Berg DE, Howe MM (eds) (1989) Mobile DNA. American Society for Microbiology, Washington DCGoogle Scholar
- Boeke JD (2003) The unusual phylogenetic distribution of retrotransposons: A hypothesis. Genome Res 13:1975–1983Google Scholar
- Buchner P (1921) Tier und Pflanze in intrazellularer Symbiose. BerlinGoogle Scholar
- Bukhari AI, Shapiro JA, Adhya SL (1977) DNA insertion elements, plasmids, and episomes. Cold Spring Harbor Laboratory: Cold Spring, Harbor NYGoogle Scholar
- Burnet FM (1934) The bacteriophages. Biol Revs Cambridge Phil Soc 9:332–350Google Scholar
- Busslinger M, Rusconi S, Birnstiel ML (1982) An unusual evolutionary behavior of a sea urchin histone gene cluster. EMBO J 1(1):27PubMedCentralPubMedGoogle Scholar
- Case CL, Chung K (1997) Montagu and Jenner: the campaign against smallpox. SIM News 47(2):58–60Google Scholar
- Cavalli Sforza LL (1950) La sessualita new batteri. Boll Ist Sierotera Milano 29:281–289Google Scholar
- Champion AB et al (1980) Evolution in Pseudomonas fluorescens. J Gen Microbiol 120(2):485–511PubMedGoogle Scholar
- Chen I, Dubnau D (2004) DNA uptake during bacterial transformation. Nat Rev Microbiol 2(3):241–249. doi: 10.1038/nrmicro844 PubMedGoogle Scholar
- Chen K, Pachter L (2005) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 1(2):e24. doi: 10.1371/journal.pcbi.0010024 PubMedCentralGoogle Scholar
- Chiura HX, Kogure K, Hagemann S, Ellinger A, Velimirov B (2011) Evidence for particle-induced horizontal gene transfer and serial transduction between bacteria. FEMS Microbiol Ecol 76:576–591PubMedGoogle Scholar
- Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287PubMedGoogle Scholar
- Cohen SN (1976) Transposable genetic elements and plasmid evolution. Nature 263:731–738. doi: 10.1038/263731a0 PubMedGoogle Scholar
- Cohen SN, Miller CA (1969) Multiple molecular species of circular R-factor DNA isolated from Escherichia coli. Nature 224:1273–1277PubMedGoogle Scholar
- Cohen SN, Miller CA (1970) Molecular nature of R-factors isolated from Proteus mirabilis and Escherichia coli. J Mol Biol 50(3):671–687PubMedGoogle Scholar
- Cohen S, Chang A, Hsu L (1972) Nonchromosomal antibiotic resistance in bacteria: genetic transformation of Escherichia coli by R-factor DNA. PNAS 69(8):2110–2114. doi: 10.1073/pnas.69.8.2110 PubMedCentralPubMedGoogle Scholar
- Cohn FJ (1875) Untersuchungen über Bakterien. Beitraege zur Biologie der Planzen 1:127–222Google Scholar
- Campbell A et al (1977) Nomenclature of transposable elements in prokaryotes, DNA insertion elements, plasmids, and episomes. Cold Spring Harbor Laboratories, New York pp 15–22; also, 1979, Gene, 5, pp 197–206Google Scholar
- Cornelissen JH, Cornwell WK (2014) The tree of life in ecosystems: evolution of plant effects on carbon and nutrient cycling. J Ecol 269–274 doi: 10.1111/1365-2745.12217
- Cotton J (2001) Retroviruses from retrotransposons. Genome Biol 2(2):6Google Scholar
- Coughter JP, Stewart GJ (1989) Genetic exchange in the environment. Antonie Van Leeuwenhoek 55(1):15–22PubMedGoogle Scholar
- Cowles HC (1915) Hereditary symbiosis. Bot Gaz 59(1):61–63Google Scholar
- Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) (2002) Mobile DNA II. ASM Press, WashingtonGoogle Scholar
- Crick F (1968) The origin of the genetic code. J Mol Biol 38:367–379PubMedGoogle Scholar
- Dagan T, Martin W (2006) The tree of one percent. Genome Biol 7:118. doi: 10.1186/gb-2006-7-10-118 PubMedCentralPubMedGoogle Scholar
- Dagan T, Martin W (2009) Getting a better picture of microbial evolution en route to a network of genomes. Phil Trans R Soc B 364:2187–2196Google Scholar
- Daniels SP et al (1990) Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics 124:339–335Google Scholar
- Darwin C (1837–1838) Notebook B: [Transmutation of species (1837–1838)]. CUL-DAR121—transcribed by Kees Rookmaaker. Darwin Online. http://darwin-online.org.uk
- Darwin C (1859) On the origin of species. Murray, LondonGoogle Scholar
- Dawkins R (1976) The selfish gene. Oxford Univ Press, LondonGoogle Scholar
- De Bary HA (1861) Die gegenwärtig herrschende Kartoffelkrankheit, ihre Ursache und ihre Verhütung: Eine pflanzenphysiologische Untersuchung in allgemein verständlicher Form dargestellt. Leipzig: A. Förstersche BuchhandlungGoogle Scholar
- de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD (2011) Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet 7:e1002384. doi: 10.1371/journal.pgen.1002384 PubMedCentralPubMedGoogle Scholar
- de Magalhães J, Finch C, Janssens G (2010) Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions. Ageing Res Rev 9(3):315–323. doi: 10.1016/j.arr.2009.10.006 PubMedCentralPubMedGoogle Scholar
- Deininger PL, Batzer MA (2002) Mammalian retroelements. Genome Res 12(10):1455–1465. doi: 10.1101/gr.282402 PubMedGoogle Scholar
- Dennett D, Coyne J, Dawkins R, Myers P (2009) Darwin was right. New Sci 201(2696):25Google Scholar
- D'Herelle F (1917) Sur un microbe invisible antagoniste des bacilles dysentériques. CR Acad Sci Paris 165:373–375. doi: 10.1098/rstb.2009.0040 Google Scholar
- Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124–2128. doi: 10.1126/science.284.5423.2124 PubMedGoogle Scholar
- Doolittle FW (2005) If the tree of life fell, would we recognize the sound? In: Sapp J (ed) Microbial phylogeny and evolution: concepts and controversies. Oxford University Press, New York, pp 119–133Google Scholar
- Doolittle WF (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. Proc Natl Acad Sci USA. doi: 10.1098/rstb.2009.0032 PubMedCentralPubMedGoogle Scholar
- Doolittle WF, Bapteste E (2007) Pattern pluralism and the tree of life hypothesis. Proc Natl Acad Sci USA 104:2043–2049. doi: 10.1073/pnas.0610699104 PubMedCentralPubMedGoogle Scholar
- Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284(5757):601–603. doi: 10.1038/284601a0 PubMedGoogle Scholar
- Doolittle WF et al (1990) A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote. J Mol Evol 31:383–388PubMedGoogle Scholar
- Downie AW (1972) Pneumococcal transformation—a backward view: fourth Griffith memorial lecture. J Gen Microbiol 73(1):1–11. doi: 10.1099/00221287-73-1-1 PubMedGoogle Scholar
- Dubey GP, Ben-Yehuda S (2011) Intercellular nanotubes mediate bacterial communication. Cell 144:590–600PubMedGoogle Scholar
- Dubnau D (1999) DNA uptake in bacteria. Annu Rev Microbiol 53(1):217–244. doi: 10.1146/annurev.micro.53.1.217 PubMedGoogle Scholar
- Ehrlich P (1877) Beiträge zur Kenntniss der Anilinfärbungen und ihren Verwendung in der mikroskopischen Technik.In: Schultze M (ed) Archiv für Mikroskopische Anatomie Bd 13. Valetta St. George, Bonn & W. Waldeyer, Strassburg, pp 263–277Google Scholar
- Ehrlich P (1879a) Beiträge zur Kenntniss der granulirten Bindegewebszellen und der eosinophilen Leukocythen. Archiv fuer Anatomie und Physiologie, Physiologische Abteilung, pp 166–169Google Scholar
- Ehrlich P (1879b) Ueber die specifischen Granulationen des Blutes. Archiv fuer Anatomie und Physiologie, Physiologische Abteilung, pp 571–579Google Scholar
- Ehrlich P (1892a) Bemerkungen über die Immunität durch Vererbung und Säugung. Dtsch Med Wochenschr 18:511Google Scholar
- Ehrlich P (1892b) Ueber Immunität durch Vererbung und Säugung. Zeitschrift für Hygiene und Infektionskrankheiten, medizinische Mikrobiologie, Immunologie und Virologie 12:183–203Google Scholar
- Ehrlich P (1898) Ueber den Zusammenhang von chemischer Constitution und Wirkung. Münchener medizinische Wochenschrift 1654–1655Google Scholar
- Ehrlich P (1900) Cellularbiologische Betrachtungen über Immunität. Bericht der Senckenbergischen Naturforschenden Gesellschaft in Frankfurt am Main 147–150Google Scholar
- Ehrlich P, Morgenroth J (1902) Die Seitenkettentheorie der Immunität. Anleitung zu hygienischen Untersuchungen: nach den im Hygienischen Institut der königl. Ludwig-Maximilians-Universität zu München üblichen Methoden zusammengestellt 3. Aufl 381–394Google Scholar
- Eisen JA (2007) Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol 5(3):e82. doi: 10.1371/journal.pbio.0050082 PubMedCentralPubMedGoogle Scholar
- Eldredge N, Gould SJ (1972) Punctuated equilibria: an alternative to phyletic gradualism. In Schopf TJM (ed) Models in paleobiology. Freeman. Cooper and Co, New York, pp 82–115Google Scholar
- Engelmoer DJ, Rozen DE (2011) Competence increases survival during stress in Streptococcus pneumoniae. Evolution 65(12):3475–3485. doi: 10.1111/j.1558-5646.2011.01402.x PubMedGoogle Scholar
- Finkel SE, Kolter R (2001) DNA as a nutrient: novel role for bacterial competence gene homologs. J Bacteriol 183(21):6288–6293. doi: 10.1128/JB.183.21.6288-6293.2001 PubMedCentralPubMedGoogle Scholar
- Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5:103–107PubMedGoogle Scholar
- Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811PubMedGoogle Scholar
- Flavell AJ (1981) Did retroviruses evolve from transposable elements? Nature 289:10–11PubMedGoogle Scholar
- Fournier GP, Dick AA, Williams D, Gogarten JP (2011) Evolution of the Archaea: emerging views on origins and phylogeny. Res Microbiol 162(1):92–98PubMedGoogle Scholar
- Fox GCA et al (1980) The phylogeny of prokaryotes. Science 209(4455):457–463. doi: 10.1126/science.6771870 PubMedGoogle Scholar
- Freeman VJ (1951) Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae. J Bacter 61(6):675–688Google Scholar
- Galun E 2003 Transposable elements: a guide to the perplexed and the novice. With appendices on RNAi, chromatin remodeling and gene tagging. Kluwer Academic Publishers, Dordrecht NLGoogle Scholar
- Ge F, Wang LS, Kim J (2005) The cobweb of life revealed by genome scale estimates of horizontal gene transfer. PLoS Biol 3:e316. doi: 10.1371/journal.pbio.0030316 PubMedCentralPubMedGoogle Scholar
- Gil R, Amparo L (2012) Factors behind JUNK DNA in Bacteria. Genes 3:634–650. doi: 10.3390/genes3040634
- Gogarten JP, Kibak H, Dittrich P et al (1989) Evolution of the vacuolar H + -ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA 86(17):6661–6665PubMedCentralPubMedGoogle Scholar
- Goldenfeld N, Woese C (2007) Biology’s next revolution. Nature 445:369PubMedGoogle Scholar
- Golding G, Gupta RS (1995) Protein based phylogenies support a chimeric origin of the eukaryotic genome. Mol Biol Evol 12:1–6PubMedGoogle Scholar
- Goldschmitdt R (1940) The material basis of evolution. Yale University Press, New HavenGoogle Scholar
- Gontier N (2007) Universal symbiogenesis: a genuine alternative to universal selectionist accounts. Symbiosis 44:167–181Google Scholar
- Gontier N (2011) Depicting the tree of life: the philosophical and historical roots of evolutionary tree diagrams. Evol Educ Outreach 4(3):515–538Google Scholar
- Gray M et al (1989) On the evolutionary origin of the plant mitochondrion and its genome. PNAS 86:2267–2271PubMedCentralPubMedGoogle Scholar
- Gregory RT 2007 A word about ‘Junk DNA’. Evolver Zone Genomicron http://www.genomicron.evolverzone.com/2007/04/word-about-junk-dna/
- Gribaldo S, Forterre P, Brochier-Armanet C (2011) Editorial: Archaea and the tree of life. Res Microbiol 162:11–14Google Scholar
- Griffith F (1928) The significance of pneumococcal types. J Hyg 27:113–159PubMedCentralPubMedGoogle Scholar
- Griffiths AJF, Miller JH, Suzuki DT, et al (2000) Bacterial conjugation and bacterial transduction. In: An introduction to genetic analysis, 7th edn. WH Freeman, New York. http://www.ncbi.nlm.nih.gov/books/
- Grohmann E, Muth G, Espinosa M (2003) Conjugative plasmid transfer in gram-positive bacteria. Microbiol Mol Biol Reviews 67(2):277–301. doi: 10.1128/MMBR.67.2.277-301.2003 Google Scholar
- Gupta RS, Singh B (1994) Phylogenetic analysis of 70kD heat-shock protein sequences suggest a chimeric origin for the eukaryotic nucleus. Curr Biol 4:1104–1114PubMedGoogle Scholar
- Guttman B, Griffiths A, Suzuki D, Cullis T (2002) Genetics. Oneworld, OxfordGoogle Scholar
- Haeckel E (1866) Generelle Morphologie der Organismen: allgemeine Grundzüge der organischen Formen-Wissenschaft, mechanisch begründet durch die von Charles Darwin reformirte Descendenz-Theorie. Fisher, JenaGoogle Scholar
- Hall RM, Stokes HW (2004) Integrons or super integrons? Microbiology 150(Pt 1):3–4. doi: 10.1099/mic.0.26854-0 PubMedGoogle Scholar
- Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5(10):R245–R249. doi: 10.1016/S1074-5521(98)90108-9 PubMedGoogle Scholar
- Hartley RW (1980) Homology between prokaryotic and eukaryotic ribonucleases. J Mol Evol 15(4):355–358PubMedGoogle Scholar
- Hayes W (1952) Recombination in Bact. coli K 12: unidirectional transfer of genetic material. Nature 169:118–119PubMedGoogle Scholar
- Hayes W (1953) Observations on a transmissible agent determining sexual differentiation in Bacterium coli. J Gen Microbiol 8:72–88PubMedGoogle Scholar
- Hebert P et al (2003) Biological identifications through DNA barcodes. Proc R Soc B 270:313–321. doi: 10.1098/rspb.2002.2218 PubMedCentralPubMedGoogle Scholar
- Heinemann JA, Sprague GF Jr (1989) Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 340:205–209. doi: 10.1038/340205a0 PubMedGoogle Scholar
- Hershey AD, Chase M (1952) Independent functions of viral protein and nucleic acid in growth of bacteriophage. J Gen Physiol 36(1):39–56PubMedCentralPubMedGoogle Scholar
- Hilario E, Gogarten JP (1993) Horizontal transfer of ATPase genes—the tree of life becomes a net of life. Biosystems 31:111–119. doi: 10.1016/0303-2647(93)90038-E PubMedGoogle Scholar
- Hoelzer MA, Michod RE (1991) DNA repair and the evolution of transformation in Bacillus subtilis. III. Sex with damaged DNA. Genetics 128(2):215–223PubMedCentralPubMedGoogle Scholar
- Holloway B, Broda P (1996) William Hayes 1918–1994. Hist Rec Aust Sci 11(2):213–228Google Scholar
- Hong D-Y, Chen Z-D, Qiu Y-L, Donoghue MJ (2008) Patterns of evolution and the tree of life (a symposium volume). J Syst Evol 46(3)Google Scholar
- Hugenholz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18):4765–4774Google Scholar
- Huxley J (1942) Evolution: the Modern Synthesis. Allen & Unwin, LondonGoogle Scholar
- Iwanowski D (1892) Über die Mosaikkrankheit der Tabakspflanze. Bulletin Scientifique publié par l'Académie Impériale des Sciences de Saint-Pétersbourg/Nouvelle Serie III (St. Petersburg) 35:67–70Google Scholar
- Iwasaki W, Takagi T (2009) Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages. PLoS Genet 5(3):e1000402PubMedCentralPubMedGoogle Scholar
- Jacob F (1955) Transduction of lysogeny in Eschercia coli. Virology 1:207–220PubMedGoogle Scholar
- Jacob F, Wollman EL (1958) Les épisomes, elements génétiques ajoutés. Comptes Rendus des Académie des Sciences, Paris 247:154–156Google Scholar
- Jacob F, Schaeffer P, Wollman EL (1960) Microbial genetics. Symposium Soc Gen Microbial 10(67):352Google Scholar
- Jenner E (1798) An inquiry into the causes and effects of the Vaccinæ, Or Cow-Pox. The Harvard ClassicsGoogle Scholar
- Johnsborg O, Eldholm V, Håvarstein LS (2007) Natural genetic transformation: prevalence, mechanisms and function. Res Microbiol 158(10):767–778. doi: 10.1016/j.resmic.2007.09.004 PubMedGoogle Scholar
- Jones D, Sneath HA (1970) Genetic transfer and bacterial taxonomy. Bacteriological Rev 34:40431Google Scholar
- Karnovsky ML (1981) Metchnikoff in Messina: a century of studies on phagocytosis. N Engl J Med 304(19):1178–1180. doi: 10.1056/NEJM198105073041923 PubMedGoogle Scholar
- Keeling PJ, Palmer JD (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Gen 9:605–618. doi: 10.1038/nrg2386 Google Scholar
- Kellis M et al (2014) Defining functional DNA elements in the human genome. PNAS 111(17):6131–6138. doi: 10.1073/pnas.1318948111 PubMedCentralPubMedGoogle Scholar
- Khodosevich K, Lebedev L, Sverdolv E (2002) Endogenous retroviruses and human evolution. Comp Funct Genomics 3:494–498. doi: 10.1002/cfg.216 PubMedCentralPubMedGoogle Scholar
- Kidwell MG, Novy JB (1979) Hybrid dysgenesis in Drosophila melanogaster: sterility resulting from gonodal dysgenesis in the P-M system. Genetics 92:1127–1140PubMedCentralPubMedGoogle Scholar
- Koch R (1876) Untersuchungen ueber Bakterien V. Die Aetiologie der Milzbrand-Krankheit, begruendent auf die Entwicklungsgeschichte des Bacillus Anthracis. Beitr z Biol D Pflanzen 2:277–310Google Scholar
- Koch R (1882) Die Aetiologie der Tuberculose. Berliner Klinische Wochenschrift 19:221–230Google Scholar
- Kovalevskaia NP (2002) Mobile gene cassettes and DNA integration elements. Mol Biol 36(2):261–267Google Scholar
- Kunin V, Goldovsky L, Darzentas N, Ouzounis CA (2005) The net of life: reconstructing the microbial phylogenetic network. Genome Res 15:954–959. doi: 10.1101/gr.3666505 PubMedCentralPubMedGoogle Scholar
- Lang AS, Beatty JT (2000) Genetic analysis of a bacterial genetic exchange element: the Gene Transfer Agent of Rhodobacter capsulatus. PNAS 97(2):859–864. doi: 10.1073/pnas.97.2.859 PubMedCentralPubMedGoogle Scholar
- Lang AS, Zhaxybayeva O, Beatty TJ (2012) Gene transfer agents: phage-like elements of genetic exchange. Nature Rev Mircobiol 10:472–482Google Scholar
- Laveran A (1880) A new parasite found in the blood of malarial patients: parasitic origin of malarial attacks. Bull mem soc med hosp Paris 17:158–164Google Scholar
- Lawton G (2009) Axing Darwin’s tree: the tree of life is an iconic image, but it could be time to fell it. New Scientist 201(2692):34–39Google Scholar
- Lederberg J (1952) Cell genetics and hereditary symbiosis. Physiol Rev 32(4):403–430PubMedGoogle Scholar
- Lederberg J (1955) Recombination mechanisms in bacteria. J Cell Comp Physiol 45(Suppl 2):75Google Scholar
- Lederberg J (1956) Genetic transduction. Am Sci 14(3):264–280Google Scholar
- Lederberg EM (1981) Plasmid reference center registry of transposon (Tn) allocations through. Gene 16:59–61PubMedGoogle Scholar
- Lederberg J (2003) Infectious history. Science 288(5464):27Google Scholar
- Lederberg EM, Lederberg J (1953) Genetic studies of lysogenicity in Escherchia coli. Genetics 38:51–64PubMedCentralPubMedGoogle Scholar
- Lederberg J, Tatum EL (1946) Gene recombination in E coli. Nature 158(4016):558. doi: 10.1038/158558a0 PubMedGoogle Scholar
- Lederberg J, Lederberg EM, Zinder ND, Lively ER (1951) Recombination analysis of bacterial heredity. Cold Spring Harbor Symp Quant Biol 16:413–441PubMedGoogle Scholar
- Lederberg J, Cavalli LL, Lederberg EM (1952) Sex compatibility in Escherichia coli. Genetics 37(6):720–730PubMedCentralPubMedGoogle Scholar
- Lennox ES (1955) Transduction of linked genetic characters of the host by bacteriophage P1. Virology 1:190–206PubMedGoogle Scholar
- Lodish H, Berk A, Zipursky SL et al (2000) Molecular cell biology, 4th edn. Freeman, New YorkGoogle Scholar
- Lopez P, Bapteste E (2009) Molecular phylogeny: reconstructing the forest. Curr Biol 332:171Google Scholar
- Lwoff A (1953) Lysogeny. Bact Rev 17:269–337PubMedCentralPubMedGoogle Scholar
- Lwoff A (1965) Nobel lecture: interaction among virus, cell, and organism. Nobelprizeorg Nobel Media AB http://www.nobelprize.org/nobel_prizes/medicine/laureates/1965/lwoff-lecture.html
- Lwoff A, Gutmann A (1950) Recherches sur un bacillus megatherium lysogène. Ann Inst Pasteur (Paris) 78(6):711–739Google Scholar
- Mahillon J, Chandler M (1998) Insertion sequences. Microbiol Mol Biol Rev 62(3):725–774PubMedCentralPubMedGoogle Scholar
- Mandel M, Higa A (1970) Calcium-dependent bacteriophage DNA infection. J Mol Biol 53(1):159–162. doi: 10.1016/0022-2836(70)90051-3 PubMedGoogle Scholar
- Margulis L (1970) Origin of eukaryotic cells. Yale University Press, New HavenGoogle Scholar
- Margulis L (ed) (1991) Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. The MIT Press, BostonGoogle Scholar
- Margulis L (1998) The symbiotic planet: a new look at evolution. Weidenfeld & Nicolson, LondonGoogle Scholar
- Margulis L, Schwartz KV (1997) Five kingdoms: an illustrated guide to the phyla of life on earth. W.H. Freeman & CompanyGoogle Scholar
- Marrs BL (1974) Genetic recombination in Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 71:971–973PubMedCentralPubMedGoogle Scholar
- Martin W (1999) Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. BioEssays 21:99–104PubMedGoogle Scholar
- Martinez E, de la Cruz F (1988) Transposon Tn21 encodes a RecA-independent site-specific integration system. Mol Gen Genet 211:320–325PubMedGoogle Scholar
- Mashburn-Warren LM, Whiteley M (2006) Special delivery: vesicle trafficking in prokaryotes. Mol Microbiol 61:839–846PubMedGoogle Scholar
- Mattick JS (2002) Type IV pili and twitching motility. Annu Rev Microbiol 56(1):289–314. doi: 10.1146/annurev.micro.56.012302.160938 PubMedGoogle Scholar
- Mayer A (1886) Über die Mosaikkrankheit des Tabaks. Die Landwirtschaftliche Versuchs-stationen 32:451–467Google Scholar
- Mazel D (2006) Integrons: agents of bacterial evolution. Nature Rev Microbiol 4:608–620. doi: 10.1038/nrmicro1462 Google Scholar
- Mazel D, Dychinco B, Webb VA, Davies J (1998) A distinctive class of integron in the Vibrio cholerae genome. Science 280(5363):605–608. doi: 10.1126/science.280.5363.605 PubMedGoogle Scholar
- McClintock B (1941) The stability of broken ends of chromosomes in Zea Mays. Genetics 26(2):234–282PubMedCentralPubMedGoogle Scholar
- McClintock B (1950) The origin and behavior of mutable loci in maize. PNAS 36(6):344–355PubMedCentralPubMedGoogle Scholar
- McClintock B (1953) Induction of instability at selected loci in maize. Genetics 38(6):579–599PubMedCentralPubMedGoogle Scholar
- Merezhkowsky C (1905) Über natur und ursprung der chromatophoren im pflanzenreiche. Biol Centralbl 25(593–604):689–691Google Scholar
- Merezhkowsky C (1910) Theorie der zwei Plasmaarten als Grundlage der Symbiogenese, einer neuen Lehre von der Entstehung der Organismen, Biologisches Centralblatt 30: 278–288, 289–303, 321–347, 353–367Google Scholar
- Messing J, Crea R, Seeburg PH (1981) A system for shotgun DNA sequencing. Nucleic Acids Res 9(2):309–321. doi: 10.1093/nar/9.2.309 PubMedCentralPubMedGoogle Scholar
- Mindell DP, Villarreal LP (2003) Don’t forget about viruses. Science 5:1677Google Scholar
- Mitsuhashi S, Harada K, Hashimoto H, Egawa R (1961) On the drug-resistance of enteric bacteria. Jpn J Exp Med 31:47–52PubMedGoogle Scholar
- Moran NA, Jarvik T (2010) Lateral transfer of genes from fungi underlies carotenoid production in Aphids. Science 328:624–627PubMedGoogle Scholar
- Morange M (2000) A history of molecular biology. Harvard University Press, Cambridge (New Edited edition)Google Scholar
- Morgan GJ (1998) Emile Zuckerkandl, Linus Pauling, and the molecular evolutionary clock, 1959–1965. J Hist Biol 31(2):155–178. doi: 10.1023/A:1004394418084 PubMedGoogle Scholar
- Morse ML, Lederberg EM, Lederberg J (1956) Transduction in Eschercia coli K-12. Genetics 41:142–156PubMedCentralPubMedGoogle Scholar
- Nelson PN, Hooley P, Molecular Immunology Research Group (2004) Human endogenous retroviruses: transposable elements with potential? Clin Exp Immunol 138(1):1–9 doi: 10.1111/j.1365-2249.2004.02592.x
- Neufeld F (1902) Über die agglutination der pneumokokken und über die theorieen der agglutination. Z Hyg Infektionskr 40:54–72Google Scholar
- Neufeld F, Händel L (1910) Weitere Untersuchungen über Pneumokokken Heilsera. III Mitteilung. Über Vorkommen und Bedeutung atypischer Varietäten des Pneumokokkus. Arbeit a.d. Kaiserlichen Gesundheitsamte 34:293–304Google Scholar
- O’Malley M, Martin W, Dupré J (2010) The tree of life: introduction to an evolutionary debate. Biol Philos 25(4):441–453Google Scholar
- Ochia K, Yamanaka T, Kimura K, Sawada O (1959) Inheritance of drug resistance (and its transfer) between Shigella strains and between Shigella and E. coli strains. Nihon Iji Shimpo 1861:34Google Scholar
- Ohno S (1972) So much junk DNA in our genome. In: Smith HH (ed) Evolution of genetic systems. Gordon and Breach, New York, pp 366–370Google Scholar
- Ohshima K, Okada N (2005) SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet Genome Res 110(1–4):475–490. doi: 10.1159/000084981 PubMedGoogle Scholar
- O'Malley MA, Koonin EV (2011) How stands the tree of life a century and a half after the origin? Biology Direct 6:32PubMedCentralPubMedGoogle Scholar
- Palmer JD, Soltis DE, Chase MW (2004) The plant tree of life: an overview of some points of view. Am J Bot 91(10):1437–1445PubMedGoogle Scholar
- Pardee AB, Jacob F, Monod J (1959) The genetic control and cytoplasmic expression of inducibility in the synthesis of beta-galactosidase by E. coli. J Mol Biol 1:165–178Google Scholar
- Pasteur L (1880) De l’attenuation du virus cholera des poules. CR Acad Sci 91:673–680Google Scholar
- Pettersson E, Lundeberg J, Ahmadian A (2009) Generations of sequencing technologies. Genomics 93(2):105–111. doi: 10.1016/j.ygeno.2008.10.003 PubMedGoogle Scholar
- Proft T, Baker EN (2009) Pili in gram-negative and gram-positive bacteria—structure, assembly and their role in disease. Cell Mol Life Sci 66(4):613–635. doi: 10.1007/s00018-008-8477-4 PubMedGoogle Scholar
- Ragan MA, McInerney JO, Lake J (2009) The network of life: genome beginnings and evolution. Phil Trans R Soc B 364(1527):2169–2175PubMedCentralPubMedGoogle Scholar
- Redfield R, Schrag M, Dead A (1997) The evolution of bacterial transformation: sex with poor relations. Genetics 146(1):27–38PubMedCentralPubMedGoogle Scholar
- Reinheimer H (1915) Symbiogenesis: the universal law of progressive evolution. Knapp, Drewett and Sons Ltd, WestminsterGoogle Scholar
- Rivera MC, Lake JA (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431(2005):152–155. doi: 10.1038/nature02848 PubMedGoogle Scholar
- Ryan F (2004) Human endogenous retroviruses in health and disease: a symbiotic perspective. J Roy Soc Med 97:560–565PubMedCentralPubMedGoogle Scholar
- Ryan F (2009) Virolution. Harper Collins, LondonGoogle Scholar
- Sakai T, Iseki S (1954) Transduction of flagellar antigen in Salmonella E group. Gunma Jour Med Sco 3:195–199Google Scholar
- Salmon DE, Smith T (1886) On a new method of producing immunity from contagious diseases. Proc Biol Soc 3:29–33Google Scholar
- San Mauro D, Agorreta A (2010) Molecular systematics: a synthesis of the common methods and the state of knowledge. Cell Mol Biol Lett 15(2):311–341. doi: 10.2478/s11658-010-0010-8 PubMedGoogle Scholar
- Sanger F, Coulson AR (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94(3):441–448. doi: 10.1016/0022-2836(75)90213-2 PubMedGoogle Scholar
- Sapp J (1994) Evolution by association: a history of symbiosis. Oxford University Press, New YorkGoogle Scholar
- Sapp J (2003) Genesis: the evolution of biology. Oxford University Press, New YorkGoogle Scholar
- Sapp J (2009) The new foundations of evolution: on the tree of life. Oxford Univ. Press, New YorkGoogle Scholar
- Schuster S (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5(1):16–8 doi: 10.1038/nmeth1156 (PMID 18165802)
- Scott JR, Zähner D (2006) Pili with strong attachments: gram-positive bacteria do it differently. Mol Microbiol 62(2):320–330PubMedGoogle Scholar
- Serrelli E, Gontier N (eds) (2015) Macroevolution: explanation, interpretation and evidence. Springer, DordrechtGoogle Scholar
- Shapiro JA (1979) Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc Natl Acad Sci USA 76(4):1933–1937. doi: 10.1073/pnas.76.4.1933 PubMedCentralPubMedGoogle Scholar
- Shapiro JA (ed) (1983) Mobile genetic elements. Academic Press, WalthamGoogle Scholar
- Shine J, Czernilofsky AP, Friedrich R, Bishop JM, Goodman HM (1977) Nucleotide sequence at the 5′ terminus of the avian sarcoma virus genome. Proc Natl Acad Sci USA 74(4):1473–1477. doi: 10.1073/pnas.74.4.1473 PubMedCentralPubMedGoogle Scholar
- Singer MF (1982) SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell 28(3):433–434. doi: 10.1016/0092-8674(82)90194-5 PubMedGoogle Scholar
- Sisco KL, Smith HO (1979) Sequence-specific DNA uptake in Haemophilus transformation. PNAS 76(2):972–976. doi: 10.1073/pnas.76.2.972 PubMedCentralPubMedGoogle Scholar
- Spradling AC, Rubin GM (1982) Transposition of cloned P elements into Drosophila germ line chromosomes. Science 218(4570):341–347. doi: 10.1126/science.6289435 PubMedGoogle Scholar
- Staden R (1979) A strategy of DNA sequencing employing computer programs. Nucleic Acids Res 6(7):2601–2610. doi: 10.1093/nar/6.7.2601 PubMedCentralPubMedGoogle Scholar
- Stanto TB (2007) Prophage-like gene transfer agents-novel mechanisms of gene exchange for Methanococcus, Desulfovibrio, Brachyspira, and Rhodobacter species. Anaerobe 13(2):43–49Google Scholar
- Stokes HW, Hall RM (1989) A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol 3:1669–1683PubMedGoogle Scholar
- Summers WC (2006) Phage and the early development of molecular biology. In: Bacteriophages The (ed) Calendar R. Oxford Univ Press, New YorkGoogle Scholar
- Syvänen M (1984a) Conserved regions in mammalian ß-globins: could they arise by cross-species gene exchange? J Theor Biol 107:685–696PubMedGoogle Scholar
- Syvänen M (1984b) The evolutionary implications of mobile genetic elements. Annu Rev Genet 18:271–293PubMedGoogle Scholar
- Syvänen M (1985) Cross-species gene transfer, implications for a new theory of evolution. J Theor Biol 112(2):333–343. doi: 10.1016/S0022-5193(85)80291-5 PubMedGoogle Scholar
- Syvänen M (1986) Cross-species gene transfer: a major factor in evolution? Trends Genetic 4:1–4Google Scholar
- Syvanen M (1987) Molecular clocks and evolutionary relationships: possible distortions due to horizontal gene flow. J Mol Evol 26(1–2):16–23PubMedGoogle Scholar
- Syvanen M, Kado CI (eds) (1998) Horizontal gene transfer. Chapman & Hall, LondonGoogle Scholar
- Tan SY, Dee MK (2009) Elie Metchnikoff (1845–1916): discoverer of phagocytosis. Signapore Med L 50(5):456Google Scholar
- Tauber AI (2003) Metchnikoff and the phagocytosis theory. Nat Rev Mol Cell Biol 4:897–901PubMedGoogle Scholar
- Temin HM (1980) Origin of retroviruses from cellular movable genetic elements. Cell 21:599–600PubMedGoogle Scholar
- The ENCODE Project Consortium et al (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74. doi: 10.1038/nature11247 Google Scholar
- Thomas CM (2000) Horizontal gene pool: bacterial plasmids and gene spread. CRC Press, Boca RatonGoogle Scholar
- Trevors JT, Barkay T, Bourquin AW (1987) Gene transfer among bacteria in soil and aquatic environments: a review. Canad J Microbiol 33(3):191–198Google Scholar
- Twort F (1915) An investigation on the nature of ultra-microscopic viruses. Lancet 2:1241–1243Google Scholar
- Van Beneden PJ (1873) Un mot sur la vie sociale des animaux inférieurs. Bull Acad R Belgique série 2(36):779–796Google Scholar
- Van Beneden PJ (1875) Les comensaux et les parasites dans le règne animal. Biblio Sci. Int, ParisGoogle Scholar
- Villareal LP, Defilipps V (2000) A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. J Virol 74(15):7079–7084Google Scholar
- Villarreal LP, Witzany G (2010) Viruses are essential agents within the roots and stem of the tree of life. J Theor Biol 262(4):698–710PubMedGoogle Scholar
- Von Faber FC (1912) Das erbliche zusammenleben von bacterien und tropischen pflanzen. Jahrb Wiss Bot 51:285–375Google Scholar
- Wallin IE (1927) Symbionticism and the origin of species. Williams and Wilkins company, BaltimoreGoogle Scholar
- Watanabe T (1971) The problems of drug-resistant pathogenic bacteria: the origin of R factors. Ann NY Acad Sci 182:126–140PubMedGoogle Scholar
- Weickert MJ, Adhya S (1993) The galactose regulon of Escherichia coli. Mol Microbio 10(2):245–251Google Scholar
- Weiner AM (2002) SINEs ans LINEs: the art of biting the hand that feeds you. Curr Opin Cell Biol 14:343–350PubMedGoogle Scholar
- Weismann A (1885) Die Continuität des Keimplasma’s als Grundlage einer Theorie der Vererbung. Fischer, JenaGoogle Scholar
- Whittaker RH, Margulis L (1978) Protist classification and the kingdoms of organisms. Biosystems 10:3–18PubMedGoogle Scholar
- Wicker T, Sabot F, Hua-Van A et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8(12):973–982. doi: 10.1038/nrg2165 PubMedGoogle Scholar
- Williams D, Fournier GP, Lapierre P et al (2011) A rooted net of life. Biology Direct 6:45PubMedCentralPubMedGoogle Scholar
- Woese CR (1967) The genetic code: the molecular basis for genetic expression. Harper & RowGoogle Scholar
- Woese CR (1998) The universal ancestor. PNAS 95(12):6854–6859PubMedCentralPubMedGoogle Scholar
- Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. PNAS 74(11):5088–5090. doi: 10.1073/pnas.74.11.5088 PubMedCentralPubMedGoogle Scholar
- Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579. doi: 10.1073/pnas.87.12.4576 PubMedCentralPubMedGoogle Scholar
- Wolf K, Delgiudice L (1987) Horizontal gene transfer between mitochondrial genomes. Endocytobiosis Cell Res 4(2):103–120Google Scholar
- Wollman EL, Jacob F (1955) Sur le mécanisme du transfer de matériel génétique au cours de la recombination chez E. coli K12. Compt Rend Acad Sci 240:2449–2451Google Scholar
- Yen HC, Hu NT, Marrs BL (1979) Characterization of the gene transfer agent made by an overproducer mutant of Rhodopseudomonas capsulata. J Mol Biol 131:157–168PubMedGoogle Scholar
- Zhang Q, Arbuckle J, Wessler SR (2000) Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize. Proc Natl Acad Sci USA 97:1160–1165PubMedCentralPubMedGoogle Scholar
- Zhaxybayeva O, Doolittle WF (2011) Lateral gene transfer. Curr Biol 21(7):R242–R246PubMedGoogle Scholar
- Zinder ND (1955) Bacterial transduction. J Comp Physiol 45(Suppl 2):23–49Google Scholar
- Zinder ND (1992) Forty years ago: the discovery of bacterial transduction. Genetics 132(2):291–294PubMedCentralPubMedGoogle Scholar
- Zinder ND, Lederberg J (1952) Genetic exchange in Salmonella. J Bact 64:679–699PubMedCentralPubMedGoogle Scholar
- Zuckerkandl E, Pauling L (1962) Molecular disease, evolution, and genic heterogeneity. In: Kasha M, Pullman B (eds) Horizons in biochemistry. Academic Press, New York, pp 189–225Google Scholar
- Zuckerkandl E, Pauling L (1965a) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New York, pp 97–166Google Scholar
- Zuckerkandl E, Pauling L (1965b) Molecules as documents of evolutionary history. J Theor Biol 8(2):357–366PubMedGoogle Scholar