Biology & Philosophy

, Volume 25, Issue 4, pp 529–552 | Cite as

Ernst Mayr, the tree of life, and philosophy of biology

  • Maureen A. O’MalleyEmail author


Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral events tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes.


Ernst Mayr Philosophy of biology Evolution Tree of life Species Lateral gene transfer Hybridization 



This paper was presented at the Halifax 2009 meeting of the Questioning the Tree of Life Network, sponsored by the Leverhulme Trust. I am grateful to the audience there for comments and also to the B&P referees who helped me sort out several points and avoid a number of errors. I owe many thanks to John Dupré, Sabina Leonelli, the BMBF Study Group for Evolution and Classification in Biology, Linguistics and the History of Science, and the ISHPSSB 2009 audience for discussion of previous versions of this paper. I also gratefully acknowledge the British Academy, which funded the presentation of this paper in Brisbane at ISHPSSB. The research for all these versions was funded by the ESRC as part of its programme at Egenis, University of Exeter.


  1. Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8:135–141CrossRefGoogle Scholar
  2. Adl SM, Simpson AGB, Farmer MA et al (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of prokaryotes. J Eukaryot Microbiol 52:399–451CrossRefGoogle Scholar
  3. Amundson R (1998) Typology reconsidered: two doctrines on the history of evolutionary biology. Biol Philos 13:153–177CrossRefGoogle Scholar
  4. Andam CP, Williams D, Gogarten JP (2010) Natural taxonomy in light of horizontal gene transfer. Biol Philos (this issue). doi: 10.1007/s10539-010-9212-8
  5. Anderson E (1948) Hybridization of the habitat. Evolution 2:1–9CrossRefGoogle Scholar
  6. Anderson E (1949) Introgressive hybridization. Wiley, NYGoogle Scholar
  7. Anderson E (1953) Introgressive hybridization. Biol Rev 28:280–307CrossRefGoogle Scholar
  8. Anderson E, Stebbins GL (1954) Hybridization as an evolutionary stimulus. Evolution 8:378–388CrossRefGoogle Scholar
  9. Andersson JO (2009) Gene transfer and diversification of microbial eukaryotes. Annu Rev Microbiol 63:177–193CrossRefGoogle Scholar
  10. Andersson JO, Doolittle WF, Nesbø CL (2001) Are there bugs in our genome? Science 292:1848–1850CrossRefGoogle Scholar
  11. Andersson JO, Hirt RP, Foster PG, Roger AJ (2006) Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol 13:94–104CrossRefGoogle Scholar
  12. Arnold ML (2000) Anderson’s paradigm: Louisiana irises and the study of evolutionary phenomena. Mol Ecol 9:1687–1698CrossRefGoogle Scholar
  13. Arnold ML (2006) Evolution through genetic exchange. Oxford University Press, OxfordGoogle Scholar
  14. Arnold ML, Bulger MR, Burke JM, Hempel AL, Williams JH (1999) Natural hybridization: how low can you go and still be important? Ecology 80:371–381CrossRefGoogle Scholar
  15. Avise JC (2008) Clonality: the genetics ecology, and evolution of sexual abstinence in vertebrate animals. Oxford University Press, OxfordGoogle Scholar
  16. Bapteste E, O’Malley MA, Beiko RM et al (2009) Prokaryote evolution and the tree of life are two different things. Biol Direct 4:34. doi: 10.1186/1745-6150-4-34 CrossRefGoogle Scholar
  17. Barton NH (2001) The role of hybridization in evolution. Mol Ecol 10:551–568CrossRefGoogle Scholar
  18. Bendel M, Kienast F, Rigling D (2006) Genetic population structure of three Armillaria species at the landscape scale: a case study from Swiss Pinus mugo forests. Mycol Res 110:705–712Google Scholar
  19. Bergthorsson U, Richardson AO, Young GJ, Goertzen LR, Palmer JD (2004) Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci USA 101:17747–17752CrossRefGoogle Scholar
  20. Beurton PJ (2002) Ernst May through time on the biological species concept—a conceptual analysis. Theory Biosci 121:81–98CrossRefGoogle Scholar
  21. Blaxter M (2007) Symbiont genes in host genomes: fragments with a future? Cell Host Microbe 2:211–213CrossRefGoogle Scholar
  22. Bock WJ (1994) Ernst Mayr, naturalist: his contributions to systematics and evolution. Biol Philos 9:267–327CrossRefGoogle Scholar
  23. Bromham L, Penny D (2003) The modern molecular clock. Nat Rev Genet 4:216–224CrossRefGoogle Scholar
  24. Burgess R, Yang Z (2008) Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol 25:1979–1994CrossRefGoogle Scholar
  25. Burkhardt RW Jr (1994) Ernst Mayr: Biologist-historian. Biol Philos 9:359–371CrossRefGoogle Scholar
  26. Cain J (1994) Ernst Mayr as community architect: launching the society for the study of evolution and the journal Evolution. Biol Philos 9:387–427CrossRefGoogle Scholar
  27. Cain J (2009) Rethinking the synthesis period in evolutionary studies. J Hist Biol 42:621–648CrossRefGoogle Scholar
  28. Casteleyn G, Adams NG, Vanormelingen P, Debeer A-E, Sabbe K, Vyverman W (2009) Natural hybrids in the marine diatom Pseudo-nitzschia pungens (Bacillariophyceae): genetic and morphological evidence. Protist 160:343–354CrossRefGoogle Scholar
  29. Chung C (2003) On the origin of the typological/population distinction in Ernst Mayr’s changing views of species, 1942–1959. Stud Hist Philos Biol Biomed Sci 34:277–296CrossRefGoogle Scholar
  30. Cracraft J (2002) The seven great questions of systematic biology: an essential foundation for conservation and the sustainable use of biodiversity. Ann Mo Bot Gard 89:127–144CrossRefGoogle Scholar
  31. D’Alelio D, Amato A, Kooistra WHCF, Procaccini G, Casotti R, Montresor M (2009) Internal transcribed spacer polymorphism in Pseudo-nitzschia multistriata (Bacillariophyceae) in the Gulf of Naples: recent divergence or intraspecific hybridization? Protist 160:9–20CrossRefGoogle Scholar
  32. Dale C, Moran N (2006) Molecular interactions between bacterial symbionts and their hosts. Cell 126:453–465CrossRefGoogle Scholar
  33. Darwin C (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life (1st ed). John Murray, LondonGoogle Scholar
  34. Dawkins R (2003) The devils chaplain: reflections on hope, lies, science, and love. Houghton Mifflin, BostonGoogle Scholar
  35. Derelle E, Ferraz C, Rombauts S et al (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci USA 103:11647–11652CrossRefGoogle Scholar
  36. Dietrich MR (1998) Paradox and persuasion: negotiating the place of molecular evolution within evolutionary biology. J Hist Biol 31:85–111CrossRefGoogle Scholar
  37. Dobzhansky T (1973) Nothing in biology makes sense except in light of evolution. Am Biol Teach 35:125–129Google Scholar
  38. 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. Phil Trans R Soc B 364:2221–2228CrossRefGoogle Scholar
  39. Doolittle WF (2010) The attempt on the life of the Tree of Life: science, philosophy and politics. Biol Philos (this issue). doi: 10.1007/s10539-010-9210-x
  40. Doolittle WF, Bapteste E (2007) Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA 104:2043–2049CrossRefGoogle Scholar
  41. Doolittle WF, Zhaxybayeva O (2010) Metagenomics and the units of biological organization. BioScience 60:102–112Google Scholar
  42. Dowling TE, Secor CL (1997) The role of hybridization and introgression in the diversification of animals. Annu Rev Ecol Syst 28:593–619CrossRefGoogle Scholar
  43. Dupré J (1993) The disorder of things: metaphysical foundations of the disunity of science. Harvard University Press, CambridgeGoogle Scholar
  44. Eldredge N (2005) Darwin: discovering the tree of life. Norton, NYGoogle Scholar
  45. Ereshefsky M (1992) Eliminative pluralism. Philos Sci 59:671–690CrossRefGoogle Scholar
  46. Ereshefsky M (2010) Microbiology and the species problem. Biol Philos (this issue). doi: 10.1007/s10539-010-9211-9
  47. Fernholm B, Bremer K, Jörnvall H (eds) (1989) The hierarchy of life: molecules and morphologies in phylogenetic analysis. Elsevier, AmsterdamGoogle Scholar
  48. Friesen TL, Stukenbrock EH, Liu Z et al (2006) Emergence of a new disease as a result of interspecific virulence transfer. Nat Genet 38:953–956CrossRefGoogle Scholar
  49. Giraud T, Refrégier G, Le Gac M, de Vienne DM, Hood ME (2008) Speciation in fungi. Fungal Genet Biol 45:791–802CrossRefGoogle Scholar
  50. Gladyshev EA, Meselson M, Arkhipova IR (2008) Massive horizontal gene transfer in bdelloid rotifers. Science 320:1210–1213CrossRefGoogle Scholar
  51. Glass NL, Dementhon K (2006) Non-self recognition and programmed cell death in filamentous fungi. Curr Opin Microbiol 9:553–558CrossRefGoogle Scholar
  52. Glass NL, Kaneko I (2003) Fatal attraction: nonself recognition and heterokaryon incompatibility in filamentous fungi. Eukaryot Cell 2:1–8CrossRefGoogle Scholar
  53. Goremykin VV, Salamini F, Velasco R, Viola R (2008) Mitochondrial DNA of Vitis vinifera and the issue or rampant horizontal gene transfer. Mol Biol Evol 26:99–110CrossRefGoogle Scholar
  54. Grene M, Depew D (2004) The philosophy of biology: an episodic history. Cambridge University Press, CambridgeGoogle Scholar
  55. Guljamow A, Jenke-Kodama H, Saumweber H et al (2007) Horizontal gene transfer of two cytoskeletal elements from a eukaryote to a cyanobacterium. Curr Biol 17:R757–R759CrossRefGoogle Scholar
  56. Haffer J (2007) Ornithology, evolution, and philosophy: the life and science of Ernst Mayr 1904–2005. Springer, BerlinGoogle Scholar
  57. Hagan JB (1999) Naturalists, molecular biologists, and the challenges of molecular evolution. J Hist Biol 32:321–341CrossRefGoogle Scholar
  58. Hart MW, Grosberg RK (2009) Caterpillars did not evolve from onychophorans by hybridogenesis. Proc Nat Acad Sci USA 106:19906–19909CrossRefGoogle Scholar
  59. Hart MC, Green DH, Bresnan E, Bolch CJ (2007) Large subunit ribosomal RNA gene variation and sequence heterogeneity of Dinophysis (Dinophyceae) species from Scottish coastal waters. Harmful Algae 6:271–287CrossRefGoogle Scholar
  60. Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 12:1422–1423CrossRefGoogle Scholar
  61. Heiser CB (1973) Introgression re-examined. Bot Rev 39:347–366CrossRefGoogle Scholar
  62. Hotopp JCD, Clark ME, Oliveira DCSG et al (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317:1753–1756CrossRefGoogle Scholar
  63. Hull DL (1994) Ernst Mayr’s influence on the history and philosophy of biology: a personal memoir. Biol Philos 9:375–386CrossRefGoogle Scholar
  64. Jenkins C, Samudrala R, Anderson I et al (2002) Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter. Proc Natl Acad Sci USA 99:17049–17054CrossRefGoogle Scholar
  65. Keeling PJ, Palmer JD (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9:605–618CrossRefGoogle Scholar
  66. Kitcher P (1987) Ghostly whispers: Mayr, Ghiselin, and the ‘philosophers’ on the ontological status of species. Biol Philos 2:184–192CrossRefGoogle Scholar
  67. Koblmüller S, Duftner N, Sefc KM et al (2007) Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika – the result of repeated introgressive hybridization. BMC Evol Biol 7:7. doi: 10.1186/1471-2148-7-7
  68. Kohn LM (2005) Mechanisms of fungal speciation. Annu Rev Phytopathol 43:279–308CrossRefGoogle Scholar
  69. Kondrashov FA, Koonin EV, Morgunmov IG, Ginogenova TV, Kondrashova MN (2006) Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. Biol Direct 1:31. doi: 101186/1745-6150-1-31 CrossRefGoogle Scholar
  70. Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8:396–401CrossRefGoogle Scholar
  71. Lane CE, Archibald JM (2008) The eukaryotic tree of life: Endosymbiosis takes its TOL. Trends Ecol Evol 23:268–275CrossRefGoogle Scholar
  72. Lapierre P, Gogarten JP (2008) Estimating the size of the bacteria pan-genome. Trends Genet 25:107–110CrossRefGoogle Scholar
  73. Lawrence JG (2002) Gene transfer in bacteria: speciation without species. Theor Popul Biol 61:449–460CrossRefGoogle Scholar
  74. Legendre P (2000) Reticulate evolution: from bacteria to philosopher. J Classif 17:153–157CrossRefGoogle Scholar
  75. Lewens T (2009) Evo-devo and ‘typological thinking’: an exculpation. J Exp Zool (Mol Dev Evol) 312B:1–8CrossRefGoogle Scholar
  76. Lewontin RC, Birch LC (1966) Hybridization as a source of variation for adaptation to new environments. Evolution 20:315–336CrossRefGoogle Scholar
  77. Loftus B, Anderson I, Davies R et al (2005) The genome of the protist parasite Entamoeba histolytica. Nature 433:865–868CrossRefGoogle Scholar
  78. Mallet J (1995) A species definition for the modern synthesis. Trends Ecol Evol 10:294–299CrossRefGoogle Scholar
  79. Mallet J (2005) Hybridization as invasion of the genome. Trends Ecol Evol 20:229–237CrossRefGoogle Scholar
  80. Mallet J (2007) Hybrid speciation. Nature 446:279–283CrossRefGoogle Scholar
  81. Mallet J (2008) Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Phil Trans R Soc B 363:2971–2986CrossRefGoogle Scholar
  82. Mallet J (2010) Why was Darwin’s view of species rejected by twentieth century biologists? Biol Philos (this issue). doi: 10.1007/s10539-010-9213-7
  83. Mallet J, Beltrán M, Neukirchen W, Linares M (2007) Natural hybridization in heliconiine butterflies: the species boundary as continuum. BMC Evol Biol 7:28. doi: 101186/1471-2148-7-28 CrossRefGoogle Scholar
  84. Martin W (2005) Lateral gene transfer and other possibilities. Heredity 94:565–566CrossRefGoogle Scholar
  85. Martin AP, Costello EK, Meyer AF, Nemergut DR, Schmidt SK (2004) The rate and pattern of cladogenesis in microbes. Evolution 58:946–955Google Scholar
  86. Maynard Smith J, Feil EJ, Smith NH (2000) Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays 22:1115–1122CrossRefGoogle Scholar
  87. Mayr E (1942) Systematics and the origin of species from the viewpoint of a zoologist. Columbia University Press, NYGoogle Scholar
  88. Mayr E (1945) Birds of paradise. Nat Hist Mag 54:264–276Google Scholar
  89. Mayr E (1946) History of the North American bird fauna. Wilson Bull 58:3–41Google Scholar
  90. Mayr E (1952a) Introduction. In: Mayr E (ed) The problem of land connections across the South Atlantic, with special reference to the Mesozoic. Bull Am Mus Nat Hist 99:85Google Scholar
  91. Mayr E (1952b) Conclusion. In: Mayr E (ed), The problem of land connections across the South Atlantic, with special reference to the Mesozoic. Bull Am Mus Nat Hist 99:255–258Google Scholar
  92. Mayr E (1953) Comments on evolutionary literature. Evolution 7:273–281CrossRefGoogle Scholar
  93. Mayr E (1959) Trends in avian systematics. Ibis 101:293–302Google Scholar
  94. Mayr E (1961) Cause and effect in biology. Science 134:1501–1506CrossRefGoogle Scholar
  95. Mayr E (1963) Animal species and evolution. Harvard University Press, CambridgeGoogle Scholar
  96. Mayr E (1964) The evolution of living systems. Proc Natl Acad Sci USA 51:934–941CrossRefGoogle Scholar
  97. Mayr E (1965) Classification and phylogeny. Am Zool 5:165–174Google Scholar
  98. Mayr E (1968) Illiger and the biological species concept. J Hist Biol 1:163–178CrossRefGoogle Scholar
  99. Mayr E (1969) Footnotes on the philosophy of biology. Philos Sci 36:197–202CrossRefGoogle Scholar
  100. Mayr E (1972) Continental drift and the history of the Australian bird fauna. Emu 72:26–28CrossRefGoogle Scholar
  101. Mayr E (1981) Biological classification: toward a synthesis of opposing methodologies. Science 214:510–516CrossRefGoogle Scholar
  102. Mayr E (1982) The growth of biological thought: diversity, evolution, and inheritance. Harvard University Press, CambridgeGoogle Scholar
  103. Mayr E (1984) The contributions of ornithology to biology. Bioscience 34:250–255CrossRefGoogle Scholar
  104. Mayr E (1987) The ontological status of species: scientific progress and philosophical terminology. Biol Philos 2:145–166CrossRefGoogle Scholar
  105. Mayr E (1988) Toward a new philosophy of biology: observations of an evolutionist. Harvard University Press, CambridgeGoogle Scholar
  106. Mayr E (1989) A new classification of the living birds of the world. Auk 106:508–512Google Scholar
  107. Mayr E (1990) A natural system of organisms. Nature 348:491CrossRefGoogle Scholar
  108. Mayr E (1991) More natural classification. Nature 353:122CrossRefGoogle Scholar
  109. Mayr E (1992) Darwin’s principle of divergence. J Hist Biol 25:343–359CrossRefGoogle Scholar
  110. Mayr E (1994) Reasons for the failures of theories. Philos Sci 61:529–533CrossRefGoogle Scholar
  111. Mayr E (1995) Darwin’s impact on modern thought. Proc Am Philos Soc 139:317–325Google Scholar
  112. Mayr E (1996) What is a species, and what is not? Philos Sci 63:262–277CrossRefGoogle Scholar
  113. Mayr E (1998a) Two empires or three? Proc Natl Acad Sci USA 95:9720–9723CrossRefGoogle Scholar
  114. Mayr E (1998b) This is biology. Harvard University Press, CambridgeGoogle Scholar
  115. Mayr E (2001a) What evolution is. Basic Books, NYGoogle Scholar
  116. Mayr E (2001b) What evolution is. Interview with Ernst Mayr.
  117. Mayr E (2001c) The philosophical foundations of Darwinism. Proc Am Philos Soc 145:488–495Google Scholar
  118. Mayr E (2002) Interview with Ernst Mayr. BioEssays 24:960–973CrossRefGoogle Scholar
  119. Mayr E (2004a) What makes biology unique? Considerations on the autonomy of a scientific discipline. Harvard University Press, CambridgeCrossRefGoogle Scholar
  120. Mayr E (2004b) The evolution of Ernst: interview with Ernst Mayr. Scientific American, July 6th.
  121. Mayr E (2004c [2000]) The grand old man of evolution (interview conducted by Shermer M, Sulloway FJ). Sceptic 8:76–82. Reprinted online at:
  122. Mayr E, Bock WJ (1994) Provisional classifications v standard avian sequences: Heuristics and communication in ornithology. Ibis 136:12–18CrossRefGoogle Scholar
  123. Mayr E, Gilliard ET (1952) Altitudinal hybridization in New Guinea honeyeaters. Condor 54:325–337CrossRefGoogle Scholar
  124. McBreen K, Lockhart PJ (2006) Reconstructing reticulate evolutionary histories of plants. Trends Plant Sci 11:398–404CrossRefGoogle Scholar
  125. McLaughlin DJ, Hibbett DS, Lutzoni F, Spatafora JW, Vilgalys R (2009) The search for the fungal tree of life. Trends Microbiol 17:488–497CrossRefGoogle Scholar
  126. Mishler BD, Donaghue MJ (1982) Species concepts: a case for pluralism. Syst Zool 31:491–503CrossRefGoogle Scholar
  127. Moran NA (2006) Symbiosis. Curr Biol 16:R866–R871CrossRefGoogle Scholar
  128. Nakashima K, Yamada L, Satou Y, Azuma J, Satoh N (2004) The evolutionary origin of animal cellulose synthase. Dev Genes Evol 214:81–88CrossRefGoogle Scholar
  129. Novo M, Bigey F, Beyne E et al (2009) Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC118. Proc Natl Acad Sci USA 106:16333–16338CrossRefGoogle Scholar
  130. Parfrey LW, Barbero E, Lasser E et al (2006) Evaluating support for the current classification of eukaryotic diversity. PLoS Genet 2(12):e220CrossRefGoogle Scholar
  131. Patterson N, Richter DJ, Gnerre S et al (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441:1103–1108CrossRefGoogle Scholar
  132. Petersen RH, Hughes KW (1999) Species and speciation in mushrooms: development of a species concept poses difficulties. Bioscience 49:440–452CrossRefGoogle Scholar
  133. Presgraves DC, Yi SV (2009) Doubts about complex speciation between humans and chimpanzees. Trends Ecol Evol 24:533–540CrossRefGoogle Scholar
  134. Provine WB (1981) Epilogue (excerpt). In: Mayr E, Provine WB (eds) The evolutionary synthesis. Bull Am Acad Arts Sci 34:17–32 (pp. 25–32)Google Scholar
  135. Raper JR, Baxter MG, Ellingboe AH (1960) The genetic structure of the incompatibility factors of Schizophyllum commune: the A-factor. Proc Natl Acad Sci USA 46:833–842CrossRefGoogle Scholar
  136. Ricard G, McEwan NR, Dutilh BE et al (2006) Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genom 7:22. doi: 10186/1471-2164-7-22 CrossRefGoogle Scholar
  137. Richards TA, Dacks JB, Jenkinson JM et al (2006) Evolution of filamentous plant pathogens: gene exchange across kingdoms. Curr Biol 16:1857–1864CrossRefGoogle Scholar
  138. Richards TA, Soanes DM, Foster PG et al (2009) Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell 21:1897–1911CrossRefGoogle Scholar
  139. Richardson AO, Palmer JD (2007) Horizontal gene transfer in plants. J Exp Bot 58:1–9Google Scholar
  140. Rieppel O (2010) The series, the network, and the tree: changing metaphors of order in nature. Biol Philos (this issue). doi: 10.1007/s10539-010-9216-4
  141. Rieseberg LH (1997) Hybrid origins of plant species. Annu Rev Ecol Syst 28:359–389CrossRefGoogle Scholar
  142. Rieseberg LH, Willis JH (2007) Plant speciation. Science 317:910–914CrossRefGoogle Scholar
  143. Rieseberg LH, Raymond O, Rosenthal DM et al (2003) Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301:1211–1216CrossRefGoogle Scholar
  144. Ros VID, Hurst GDD (2009) Lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant? BMC Biol 7:20. doi: 10.1186/1741-7007-7-20 CrossRefGoogle Scholar
  145. Rosewich UL, Kistler HC (2000) Role of horizontal gene transfer in the evolution of fungi. Annu Rev Phytopathol 38:325–363CrossRefGoogle Scholar
  146. Salzberg SL, White O, Peterson J, Eisen JA (2001) Microbial genes in the human genome: lateral transfer or gene loss? Science 292:1903–1906CrossRefGoogle Scholar
  147. Sanders IR (2006) Rapid disease emergence through horizontal gene transfer between eukaryotes. Trends Ecol Evol 21:656–658CrossRefGoogle Scholar
  148. Sapp J (2009) The new foundations of evolution: on the tree of life. Oxford University Press, OxfordGoogle Scholar
  149. Schardl CL, Craven KD (2003) Interspecific hybridization in plant-associated fungi and oomycetes: a review. Mol Ecol 12:2861–2873CrossRefGoogle Scholar
  150. Schluter D (2009) Evidence for ecological speciation and its alternative. Science 323:737–741CrossRefGoogle Scholar
  151. Scholl EH, Thorne JL, McCarter JP, Bird DM (2003) Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biol 4:R39CrossRefGoogle Scholar
  152. Seehausen O (2004) Hybridization and adaptive radiation. Trends Ecol Evol 19:198–207CrossRefGoogle Scholar
  153. Simpson AGB, Roger AJ (2004) The real ‘kingdoms’ of eukaryotes. Curr Biol 14:R693–R696CrossRefGoogle Scholar
  154. Smith ML, Bruhn JN, Anderson JB (1992) The fungus Armillaria bulbosa is among the largest and oldest living organisms. Nature 356:428–431CrossRefGoogle Scholar
  155. Smocovitis VB (1992) Unifying biology: the evolutionary synthesis and evolutionary biology. J Hist Biol 25:1–65CrossRefGoogle Scholar
  156. Smocovitis VB (1997) G. Ledyard Stebbins, Jr. and the evolutionary synthesis (1924–1950) (1997). Am J Bot 84:1625–1637Google Scholar
  157. Sneath PHA (1975) Cladistic representation of reticulate evolution. Syst Zool 24:360–368CrossRefGoogle Scholar
  158. Sneath PHA (2000) Reticulate evolution in bacteria and other organisms: how can we study it? J Classif 17:159–163CrossRefGoogle Scholar
  159. Soltis PS, Soltis DE (2009) The role of hybridization in plant speciation. Annu Rev Plant Biol 60:561–588CrossRefGoogle Scholar
  160. Spratt BG, Hanage WP, Feil EJ (2001) The relative contributions of recombination and point mutation to the diversification of bacterial clones. Curr Opin Microbiol 4:602–606CrossRefGoogle Scholar
  161. Stanhope MJ, Lupas A, Italia MJ et al (2001) Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature 411:940–944CrossRefGoogle Scholar
  162. Stebbins GL (1959) The role of hybridization in evolution. Proc Am Phil Soc 103:231–251Google Scholar
  163. Stebbins GL (1985) Polyploidy, hybridization, and the invasion of new habitats. Ann Mo Bot Gard 72:824–832CrossRefGoogle Scholar
  164. Syvanen M (1984) The evolutionary implications of mobile genetic elements. Annu Rev Genet 18:271–293CrossRefGoogle Scholar
  165. Syvanen M (1987) Molecular clocks and evolutionary relationships: possible distortions due to horizontal gene flow. J Mol Evol 26:16–23CrossRefGoogle Scholar
  166. Taylor JW, Jacobson DJ, Kroken S et al (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21–32CrossRefGoogle Scholar
  167. Walton JD (2000) Horizontal gene transfer and the evolution of secondary metabolite gene clusters in fungi: an hypothesis. Fungal Genet Biol 30:167–171CrossRefGoogle Scholar
  168. Weber M (2005) Philosophy of experimental biology. Cambridge University Press, CambridgeGoogle Scholar
  169. Wertz RE, Goldstone C, Gordon DM, Riley MA (2003) A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol 16:1236–1248CrossRefGoogle Scholar
  170. Whitman WB (2009) The number of prokaryotes on earth (and why we care). In: Presentation given at Dalhousie University, July 24Google Scholar
  171. Williamson DI (2009) Caterpillars evolved from onychophorans by hybridogenesis. Proc Natl Acad Sci USA 106:15786–15790. doi: 10.1073/pnas.0908357106 Google Scholar
  172. Winsor MP (2003) Non-essentialist methods in pre-Darwinian taxonomy. Biol Philos 18:387–400CrossRefGoogle Scholar
  173. Winsor MP (2006) The creation of the essentialism story: an exercise in metahistory. Hist Phil Life Sci 28:149–174Google Scholar
  174. Woese CR (1996) Phylogenetic trees: Whither microbiology? Curr Biol 6:1060–1063CrossRefGoogle Scholar
  175. Won H, Renner SS (2003) Horizontal gene transfer from flowering plants to Gnetum. Proc Natl Acad Sci USA 100:10824–10829CrossRefGoogle Scholar
  176. Zeyl C (2009) The role of sex in fungal evolution. Curr Opin Microbiol 12:592–598CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.EgenisUniversity of ExeterExeterUK

Personalised recommendations