When integration fails: Prokaryote phylogeny and the tree of life

Studies in History and Philosophy of Science Part C :Studies in History and Philosophy of Biological and Biomedical Sciences

Volumn 44, Issue 4, 2013, Pages 551-562

  O'Malley, Maureen A ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Heuristic; Integration; Philosophy of scientific practice; Phylogeny; Tree of life

Indexed keywords

ARCHAEON; BACTERIUM; BIOLOGY; CLASSIFICATION; EVOLUTION; PHYLOGENY; PROCEDURES; STANDARDS;

ARCHAEA; BACTERIA; BIOLOGICAL EVOLUTION; BIOLOGY; PHYLOGENY;

EID: 84908555081     PISSN: 13698486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.shpsc.2012.10.003     Document Type: Article

References (183)

1. Abby S.S., Tannier E., Gouy M., Daubin V. Lateral gene transfer as a support for the tree of life. Proceedings of the National Academy of Sciences USA 2012, 109:4962-4967.
2. Aderem A. Systems biology: Its practice and challenges. Cell 2005, 121:511-513.
3. Adoutte A., Balavoine G., Lartillot N., Lespinet O., Prud'homme B., de Rosa R. The new animal phylogeny: Reliability and implications. Proceedings of the National Academy of Sciences USA 2000, 97:4453-4456.
4. Andam C.P., Williams D., Gogarten J.P. Biased gene transfer mimics patterns created through shared ancestry. Proceedings of the National Academy of Sciences USA 2010, 107:10679-10684.
5. Anderson E.S. The ecology of transferable drug resistance in the enterobacteria. Annual Review of Microbiology 1968, 22:131-180.
6. Andersson J.O. Horizontal gene transfer between microbial eukaryotes. Horizontal gene transfer: Genomes in flux 2009, 473-487. Humana, NY. M.B. Gogarten, J.P. Gogarten, L.C. Olendzenski (Eds.).
7. Archibald J.M. Origin of eukaryotic cells: 40 Years on. Symbiosis 2011, 54:69-86.
8. Archibald J.M. Plastid origins. Organelle genetics 2012, 19-38. Springer, Berlin. C.F. Bullerwell (Ed.).
9. Arnold M.L. Evolution through genetic exchange 2007, Oxford University Press.
10. Assis L.C.S. Coherence, correspondence, and the renaissance of morphology in phylogenetic systematics. Cladistics 2009, 25:528-544.
11. Auffray C., Imbeaud S., Roux-Rouquié M., Hood L. From functional genomics to systems biology: Concepts and practices. Comptes Rendus Biologies 2003, 326:879-892.
12. Bapteste E., Burian R.M. On the need for integrative phylogenomics, and some steps towards its creation. Biology and Philosophy 2010, 25:711-736.
13. Bapteste E., O'Malley M.A., Beiko R.M., Ereshefsky M., Gogarten J.P., Franklin-Hall L., Lapointe F.J., Dupré J., Dagan T., Boucher Y., Martin W. Prokaryote evolution and the tree of life are two different things. Biology Direct 2009, 4:34. 10.1186/1745-6150-4-34.
14. Bapteste E., Susko E., Leigh J., Ruiz-Trillo I., Bucknam J., Doolittle W.F. Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Molecular Biology and Evolution 2008, 25:83-91.
15. Baroni M., Semple C., Steel M. Hybrids in real time. Systematic Biology 2006, 55:46-56.
16. Bateman R.M., Hilton J., Rudall P.J. Morphological and molecular phylogenetic context of the angiosperms: Contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers. Journal of Experimental Botany 2006, 57:3471-3503.
17. Beauregard-Racine J., Bicep C., Schliep K., Lopez P., Lapointe F.-J., Bapteste E. Of woods and webs: Possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biology Direct 2011, 6:39. 10.1186/1745-6150-6-39.
18. Bechtel W. Integrating sciences by creating new disciplines: The case of cell biology. Biology and Philosophy 1993, 8:277-299.
19. Bechtel, W. (this issue). From molecules to behavior and the clinic: Integration in chronobiology. Studies in History and Philosophy of Biological and Biomedical Sciences.
20. Beiko R.G. Gene sharing and genome evolution: Networks in trees and trees in networks. Biology and Philosophy 2010, 25:659-673.
21. Beiko R.G. Telling the whole story in a 10,000-genome world. Biology Direct 2011, 6:34. 10.1186/1745-6150-6-34.
22. Beiko R.G., Harlow T.J., Ragan M.A. Highways of gene sharing in prokaryotes. Proceedings of the National Academy of Sciences USA 2005, 102:14332-14337.
23. Boucher Y., Bapteste E. Revisiting the concept of lineage in prokaryotes: A phylogenetic perspective. BioEssays 2009, 31:526-536.
24. Bourlat S.J., Nielsen C., Economou A.D., Telford M.J. Testing the new animal phylogeny: A phylum level molecular analysis of the animal kingdom. Molecular Phylogenetics and Evolution 2008, 49:23-31.
25. Boussau B., Guéguen L., Gouy M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evolutionary Biology 2008, 8:22. 10.1186/1471-2148-8-272.
26. Brigandt I. Beyond reductionism and pluralism: Toward an epistemology of explanatory integration. Erkenntis 2010, 73:295-311.
27. Brigandt, I. (this issue). Systems biology and the integration of mechanistic explanation and mathematical explanation. Studies in History and Philosophy of Biological and Biomedical Sciences.
28. Brigandt, I. (in press). Intelligent design and the nature of science. Philosophical and pedagogical points. In K. Kampourakis (Ed.), Philosophical issues in biology education. Berlin: Springer.
29. Brigandt, I., & Love, A. C. (2012). Reductionism in biology. In E. N. Zalta (Ed.), The Stanford encyclopedia of philosophy, http://plato.stanford.edu/archives/sum2012/entries/reduction-biology/.
30. Brochier C., Philippe H., Moreira D. The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome. Trends in Genetics 2000, 16:529-533.
31. Budd A.F., Stolarski J. Corallite wall and septal microstructure in scleractinian reef corals: Comparison of molecular clades within the family Faviidae. Journal of Morphology 2010, 272:66-88.
32. Burian R.M. Unification and coherence as methodological objectives in the biological sciences. Biology and Philosophy 1993, 8:301-318.
33. Bybee S.M., Zaspel J.M., Beucke K.A., Scott C.H., Smith B.W., Branham M.A. Are molecular data supplanting morphological data in modern phylogenetic studies?. Systematic Entomology 2010, 35:2-5.
34. Cali A., Calvanese D., de Giacomo G., Lenzerini M. Data integration under integrity constraints. Information Systems 2003, 29:147-163.
35. Caterino M.S., Cho S., Sperling F.A.H. The current state of insect molecular systematics: A thriving tower of Babel. Annual Review of Entomology 2000, 45:1-54.
36. Chuang H.-Y., Hofree M., Ideker T. A decade of systems biology. Annual Review of Cell and Developmental Biology 2010, 26:721-744.
37. Cohen O., Gophna U., Pupko T. The complexity hypothesis revisited: Connectivity rather than function constitutes a barrier to horizontal gene transfer. Molecular Biology and Evolution 2011, 28:1481-1489.
38. Cornelis G., Heidmann O., Bernard-Stoecklin S., Reynaud K., Véron G., Mulot B., Dupressoir A., Heidmann T. Ancestral capture of syncytin-Car1, a fusogenic endogenous retroviral envelope gene involved in placentation and conserved in Carnivora. Proceedings of the National Academy of Sciences USA 2012, 109:E432-E441.
39. Coughter J.P., Stewart G.J. Genetic exchange in the environment. Antonie van Leeuwenhoek 1989, 55:15-22.
40. Dagan T., Artzy-Randrup Y., Martin W.F. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proceedings of the National Academy of Sciences USA 2008, 105:10039-10044.
41. Dagan T., Martin W.F. The tree of one percent. Genome Biology 2006, 7:118. 10.1186/gb-2006-7-10-118.
42. Dagan T., Martin W.F. Getting a better picture of microbial evolution en route to a network of genomes. Philosophical Transactions of the Royal Society London B 2009, 364:2187-2196.
43. Darwin C. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life 1872, John Murray, London. 6th ed.
44. Dawkins R. The devil's chaplain: Reflections on hope, lies, science, and love 2003, Houghton Mifflin, Boston.
45. Dayhoff M.O., Barker W.C., McLaughlin P.J. Inferences from protein and nucleic acid sequences: Early molecular evolution, divergence of kingdoms and rates of change. Origins of Life 1974, 5:311-330.
46. Deppenmeier U., Johann A., Hartsch T., Merkl R., Schmitz R.A., Martinez-Arias R., Henne A., Wiezer A., Bäumer S., Jacobi C., et al. The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea. Journal of Molecular Microbiology and Biotechnology 2002, 4:453-461.
47. DeSalle R., Schierwater B. An even 'newer' animal phylogeny. BioEssays 2008, 30:1043-1047.
48. Didelot X., Maiden M.C.J. Impact of recombination on bacterial evolution. Trends in Microbiology 2010, 18:315-322.
49. Donoghue P.C.J., Benton M.J. Rocks and clocks: Calibrating the Tree of Life using fossils and molecules. Trends in Ecology and Evolution 2007, 22:424-431.
50. Doolittle W.F. Phylogenetic classification and the universal tree. Science 1999, 284:2124-2128.
51. Doolittle W.F., Bapteste E. Pattern pluralism and the Tree of Life hypothesis. Proceedings of the National Academy of Sciences USA 2007, 104:2043-2049.
52. Dunn C.W., Hejnol A., Matus D.Q., Pang K., Browne W.E., Smith S.A., Seaver E., Rouse G.W., Obst M., Edgecombe G.D., et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749.
53. Ebersberger I., de Matos Simoes R., Kupczok A., Gube M., Koteh E., Voigt K., von Haeseler A. A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution 2011, 10.1093/molbev/msr285.
54. Eernisse D.J., Kluge A.G. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Molecular Biology and Evolution 1993, 10:1170-1195.
55. Edgecombe G.D. Arthropod phylogeny: An overview from the perspectives of morphology, molecular data and the fossil record. Arthropod Structure and Development 2010, 39:74-87.
56. Edgecombe G.D., Giribet G., Dunn C.W., Hejnol A., Kristensen R.M., Neves R.C., Rouse G.W., Worsaae K., Sørensen M.V. Higher-level metazoan relationships: Recent progress and remaining questions. Organisms, Diversity & Evolution 2011, 11:151-172.
57. Edwards S.V. Is a new and general theory of molecular systematics emerging?. Evolution 2009, 63:1-19.
58. Feil E.J., Holmes E.C., Bessen D.E., Chan M.S., Day N.P., Enright M.C., Goldstein R., Hood D.W., Kalia A., Moore C.E., Zhou J., Spratt B.G. Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences. Proceedings of the National Academy of Sciences USA 2001, 98:182-187.
59. Field K.G., Olsen G.J., Lane D.J., Giovannoni S.J., Ghiselin M.T., Raff E.C., et al. Molecular phylogeny of the animal kingdom. Science 1988, 239:748-753.
60. Galtier N., Daubin V. Dealing with incongruence in phylogenomic analyses. Philosophical Transactions of the Royal Society London B 2008, 363:4023-4029.
61. Gee H. Ending incongruence. Nature 2003, 425:782.
62. Gerson, E. M. (this issue). Integration of specialties: An institutional and organizational view. Studies in History and Philosophy of Biological and Biomedical Sciences.
63. Giribet G. A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics. Acta Zoologica 2010, 91:11-19.
64. Ghosh S., Matsuoka Y., Asai Y., Hsin K.-Y., Kitano H. Software for systems biology: From tools to integrated platforms. Nature Reviews Genetics 2011, 12:821-832.
65. Gogarten J.P., Doolittle W.F., Lawrence J.G. Prokaryotic evolution in light of gene transfer. Molecular Biology and Evolution 2002, 19:2226-2238.
66. Gophna U., Ofran Y. Lateral acquisition of genes is affected by the friendliness of their products. Proceedings of the National Academy of Sciences USA 2011, 108:343-348.
67. Grantham T.A. Conceptualizing the (dis)unity of science. Philosophy of Science 2004, 71:133-155.
68. Grantham T.A. The role of fossils in phylogeny reconstruction: Why is it so difficult to integrate paleobiological and neontological evolutionary biology?. Biology and Philosophy 2004, 19:687-720.
69. Grantham, T. A. (2011). Integrative pluralism as a regulative ideal? Integrative pluralism and the path to the double helix. Presentation at Integration in contemporary biology: Philosophical perspectives on the dynamics of interdisciplinarity (University of Minnesota, September 23-25, 2011).
70. Griesemer, J. R. (this issue). Integration of approaches in David Wake's model-taxon research platform for evolutionary morphology. Studies in History and Philosophy of Biological and Biomedical Sciences.
71. Haggerty L.S., Martin F.J., Fitzpatrick D.A., McInerney J.O. Gene and genome trees conflict at many levels. Philosophical Transactions of the Royal Society London B 2009, 364:2209-2219.
72. Halanych K.M. The new view of animal phylogeny. Annual Review of Ecology, Evolution, and Systematics 2004, 35:229-256.
73. Hermsen E.J., Hendricks J.R. W(h)ither fossils? Studying morphological character evolution in the age of molecular sequences. Annals of the Missouri Botanical Garden 2008, 95:72-100.
74. Hilario E., Gogarten J.P. Horizontal transfer of ATPase genes-the tree of life becomes a net of life. BioSystems 1993, 31:111-119.
75. Hotopp J.C., Clark M.E., Oliveira D.C., Foster J.M., Fischer P., Torres M.C., Giebel J.D., Kumar N., Ishmael N., Wang S., et al. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 2007, 317:1753-1756.
76. Huang D., Licuanan W.Y., Baird A.H., Fukami H. Cleaning up the 'Bigmessidae': Molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae. BMC Evolutionary Biology 2011, 11:37. 10.1186/1471-2148-11-37.
77. Huang J., Gogarten J.P. Ancient horizontal gene transfer can benefit phylogenetic reconstruction. Trends in Genetics 2006, 22:361-366.
78. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 2006, 23:254-267.
79. Huson D.H., Scornavacca C. A survey of combinatorial methods for phylogenetic networks. Genome Biology and Evolution 2011, 3:23-35.
80. Hyman A.A. Whither systems biology. Philosophical Transactions of the Royal Society London B 2011, 366:3635-3637.
81. Ideker T., Bafna V., Lemberger T. Integrating scientific cultures. Molecular Systems Biology 2007, 3:105. 10.1038/msb4100145.
82. Jeffroy O., Brinkmann H., Delsuc F., Philippe H. Phylogenomics: The beginning of incongruence?. Trends in Genetics 2006, 22:225-231.
83. Jenner R.A. Accepting partnership by submission? Morphological phylogenetics in a molecular millennium. Systematic Biology 2004, 53:333-342.
84. Jenner R.A. When molecules and morphology clash: Reconciling conflicting phylogenies of the Metazoa by considering secondary character loss. Evolution and Development 2004, 6:372-378.
85. Jenner R.A. Use of morphology in criticizing molecular trees. Journal of Crustacean Biology 2011, 31:373-377.
86. Jones D., Sneath P.H.A. Genetic transfer and bacterial taxonomy. Bacteriological Reviews 1970, 34:40-81.
87. Keeling P.J. Functional and ecological impacts of horizontal gene transfer in eukaryotes. Current Opinion in Genetics and Development 2009, 19:613-619.
88. Keeling P.J., Palmer J.D. Horizontal gene transfer in eukaryotic evolution. Nature Reviews Genetics 2008, 9:605-618.
89. Kitcher P. Explanatory unification. Philosophy of Science 1981, 48:507-531.
90. Kitcher P. Unification as a regulative ideal. Perspectives on Science 1999, 7:337-348.
91. Klenk H.-P., Göker M. En route to a genome-based classification of Archaea and Bacteria?. Systematic and Applied Microbiology 2010, 33:175-182.
92. Koonin E.V. The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biology 2010, 11:209. 10.1186/gb-2010-11-5-209.
93. Lapierre P., Gogarten J.P. Estimating the size of the bacteria pan-genome. Trends in Genetics 2008, 25:107-110.
94. Lapointe F.-J., Lopez P., Boucher Y., Koenig J., Bapteste E. Clanistics: A multi-level perspective for harvesting unrooted gene trees. Trends in Microbiology 2010, 18:341-347.
95. Lauffenburger D.A. The multiple dimensions of Integrative Biology. Integrative Biology 2012, 4:9.
96. Lawrence J.G. Gene transfer in bacteria: Speciation without species. Theoretical Population Biology 2002, 61:449-460.
97. Lawrence J.G., Ochman H. Molecular archaeology of the Escherichia coli genome. Proceedings of the National Academy of Sciences USA 1998, 95:9413-9417.
98. Lawrence J.G., Retchless A.C. The myth of bacterial species and speciation. Biology and Philosophy 2009, 25:569-588.
99. Lecointre G., Deleporte P. Total evidence requires exclusion of phylogenetically misleading data. Zoologica Scripta 2005, 34:101-117.
100. Leigh J.W., Lapointe F.-J., Lopez P., Bapteste E. Evaluating phylogenomic congruence in the post-genomic era. Genome Biology and Evolution 2011, 3:571-587.
101. Lenzerini, M. (2002). Data integration: A theoretical perspective. PODS '02, Proceedings of the twenty-first ACM SIGMOD-SIGACT-SIGART symposium on principles of database systems (pp. 233-246). NY: ACA.
102. Leonelli S. Bio-ontologies as tools for integration in biology. Biological Theory 2008, 3:7-11.
103. Leonelli, S. (this issue). Integrating data to acquire new knowledge: Three modes of integration in plant science. Studies in History and Philosophy of Biological and Biomedical Sciences.
104. Leplae, R., Hebrant, A., Wodak, S. J., and Toussaint, A. (2004). ACLAME: A CLAssification of Mobile genetic Elements. Nucleic Acids Research, 32 (Database issue), D45-D49.
105. Linder C.R., Rieseberg L.H. Reconstructing patterns of reticulate evolution in plants. American Journal of Botany 2004, 91:1700-1708.
106. Liu E.T. Systems biology, integrative biology, predictive biology. Cell 2005, 121:505-506.
107. Loftus B., Anderson I., Davies R., Alsmark U.C., Samuelson J., Amedeo P., Roncaglia P., Berriman M., Hirt R.P., Mann B.J., et al. The genome of the protist parasite Entamoeba histolytica. Nature 2005, 433:865-868.
108. Lockhart P.J., Cameron S.A. Trees for bees. Trends in Ecology and Evolution 2001, 16:84-88.
109. Lukjancenko O., Wassenaar T.M., Ussery D.W. Comparison of 61 sequenced Escherichia coli genomes. Microbial Ecology 2010, 60:708-720.
110. Mallet F., Bouton O., Prudhomme S., Cheynet V., Oriol G., Bonnaud B., Lucotte G., Duret L., Mandrand B. The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology. Proceedings of the National Academy of Sciences USA 2004, 101:1731-1736.
111. Mallet J. Hybridization as an invasion of the genome. Trends in Ecology and Evolution 2005, 20:229-237.
112. Martin W.F. Is something wrong with the tree of life?. BioEssays 1996, 18:523-527.
113. Martin W.F. Mosaic bacterial chromosomes: A challenge en route to a tree of genomes. BioEssays 1999, 21:99-104.
114. Martin W.F. Early evolution without a tree of life. Biology Direct 2011, 6:36. 10.1186/1745-6150-6-36.
115. Martin W.F., Herrmann R.G. Gene transfer from organelles to the nucleus: How much, what happens, and why?. Plant Physiology 1998, 118:9-17.
116. Maynard Smith J., Feil E.J., Smith N.H. Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays 2000, 22:1115-1122.
117. Mayr E. The growth of biological thought: Diversity, evolution, and inheritance 1982, Harvard University Press, Cambridge, MA.
118. McInerney J.O., Cotton J.A., Pisani D. The prokaryotic tree of life: Past, present...and future?. Trends in Ecology and Evolution 2008, 23:276-281.
119. McInerney J.O., Pisani D., Bapteste E., O'Connell M.J. The public goods hypothesis for the evolution of life on Earth. Biology Direct 2011, 6:41. 10.1186/1745-6150-6-41.
120. Medini D., Donati C., Tettelin H., Masignani V., Rappuoli R. The microbial pan-genome. Current Opinion in Genetics and Development 2005, 1:589-594.
121. Mitchell S.D. Biological complexity and integrative pluralism 2003, Cambridge University Press, Cambridge.
122. Morrison D.A. Using data-display networks for exploratory data analysis in phylogenetic studies. Molecular Biology and Evolution 2010, 27:1044-1057.
123. Morrison M. Unifying scientific theories: Physical concepts and mathematical structures 2000, Cambridge University Press, Cambridge.
124. Moustafa A., Beszteri B., Maier U.G., Bowler C., Valentin K., Bhattacharya D. Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 2009, 324:1724-1726.
125. Mykles D.L., Ghalambor C.K., Stillman J.H., Tomanek L. Grand challenges in comparative physiology: Integration across disciplines and across levels of biological organization. Integrative and Comparative Biology 2010, 50:6-16.
126. Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399:323-329.
127. O'Malley M.A. Ernst Mayr, the tree of life, and philosophy of biology. Biology and Philosophy 2010, 25:529-552.
128. O'Malley M.A. The first eukaryote cell: An unfinished history of contestation. Studies in the History and Philosophy of Biological and Biomedical Sciences 2010, 41:212-224.
129. O'Malley M.A., Boucher Y. Paradigm change in evolutionary microbiology. Studies in History and Philosophy of Biological and Biomedical Sciences 2005, 36:183-208.
130. O'Malley M.A., Koonin E.V. How stands the Tree of Life a century and a half after The Origin?. Biology Direct 2011, 6:32. 10.1186/1745-6150-6-32.
131. O'Malley M.A., Soyer O.S. The roles of integration in molecular systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences 2012, 43:58-68.
132. Oppenheim P., Putnam H. Unity of science as a working hypothesis. Minnesota Studies in Philosophy of Science 1985, Vol. 2:3-36. Minnesota University Press, Minneapolis.
133. Paps J., Baguñà J., Riutort M. Lophotrochozoa internal phylogeny: New insights from an up-to-date analysis of nuclear ribosomal genes. Proceedings of the Royal Society of London B 2009, 276:1245-1254.
134. Patel M., Nagi S. The role of model integration in complex systems modelling: An example from cancer biology 2010, Springer, Berlin.
135. Pauling L., Zuckerkandl E. Chemical paleogenetics: Molecular 'restoration studies' of extinct forms of life. Acta Chemica Scandinavica 1963, 17:S9-S16.
136. Philippe H., Brinkmann H., Lavrov D.V., Littlewood D.T.J., Manuel M., Wöheide G., Baurain D. Resolving difficult phylogenetic questions: Why more sequences are not enough. PLoS Biology 2011, 9(3):e1000602.
137. Pisani D., Cotton J.A., McInerney J.O. Supertrees disentangle the chimerical origins of eukaryotic genomes. Molecular Biology and Evolution 2007, 24:1752-1760.
138. Powell A., O'Malley M.A., Müller-Wille S.E.W., Calvert J., Dupré J. Disciplinary baptisms: A comparison of the naming stories of genetics, molecular biology, genomics and systems biology. History and Philosophy of the Life Sciences 2007, 29:5-32.
139. Prill R.J., Marbach D., Saez-Rodriguez J., Sorger P.K., Alexopoulos L.G., Xue X., Clarke N.D., Altan-Bonnet G., Stolovitzky G. Towards a rigorous assessment of systems biology models: The DREAM3 challenge. PLoS One 2010, 5(2):e9202.
140. Puigbò P., Wolf Y.I., Koonin E.V. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. Journal of Biology 2009, 8:59. 10.1186/jbiol159.
141. Ragan M.A., Beiko R.G. Lateral genetic transfer: Open issues. Philosophical Transactions of the Royal Society London B 2009, 364:2241-2251.
142. Ragan M.A., Harlow T.J., Beiko R.G. Do different surrogate methods detect lateral genetic transfer events of different relative ages?. Trends in Microbiology 2006, 14:4-8.
143. Reanney D. Gene transfer as a mechanism of microbial evolution. BioScience 1977, 27:340-344.
144. Regier J.C., Shultz J.W., Ganley A.R.D., Hussey A., Shi D., Ball B., Swick A., Stajich J.E., Cummings M.P., Martin J.W., Cunningham C.W. Resolving arthropod phylogeny: Exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Systematic Biology 2008, 57:920-938.
145. Retchless A.C., Lawrence J.G. Phylogenetic incongruence arising from fragmented speciation in enteric bacteria. Proceedings of the National Academy of Sciences USA 2010, 107:11453-11458.
146. Richards T.A., Soanes D.M., Foster P.G., Leonard G., Thornton C.R., Talbot N.J. Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell 2009, 21:1897-1911.
147. Ripoll C., Guespin-Michel J., Norris V., Thellier M. Defining integrative biology. Complexity 1998, 4:19-20.
148. Rokas A., Carroll S.B. Bushes in the tree of life. PLoS Biology 2006, 4(11):e352.
149. Roth, K. J. (1994). Second thoughts about interdisciplinary studies. American Educator, Spring, 44-48.
150. Schaffner K.F. Theory structure, reduction, and disciplinary integration in biology. Biology and Philosophy 1993, 8:319-347.
151. Schilling M., Pfeifer A.C., Bohl S., Klingmüller U. Standardizing experimental protocols. Current Opinion in Biotechnology 2008, 19:354-359.
152. Schwartz R.M., Dayhoff M.O. Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts: A perspective is derived from protein and nucleic acid sequence data. Science 1978, 199:395-403.
153. Scotland R.W., Olmstead R.G., Bennett J.R. Phylogeny reconstruction: The role of morphology. Systematic Biology 2003, 52:539-548.
154. Sidow A., Wilson A.C. Compositional statistics: An improvement of evolutionary parsiomony and its application to deep branches in the tree of life. Journal of Molecular Evolution 1990, 31:51-68.
155. Stanier R.Y., van Niel C.B. The concept of a bacterium. Archiv für Mikrobiologie 1962, 42:17-35.
156. Suárez-Diáz E., Anaya-Muñoz V.H. History, objectivity, and the construction of molecular phylogenies. Studies in History and Philosophy of Biological and Biomedical Sciences 2008, 39:451-468.
157. Sullivan D.E., Gabbard J.L., Shukla M., Sobrai B. Data integration for dynamic and sustainable systems biology resources: Challenges and lessons learned. Chemical Biodiversity 2010, 7:1124-1141.
158. Telford M.J. Resolving animal phylogeny: A sledgehammer for a tough nut?. Developmental Cell 2008, 14:457-459.
159. Telford M.J., Copley R.R. Improving animal phylogenies with genomic data. Trends in Genetics 2011, 27:186-195.
160. Tettelin H., Riley D., Cattuto C., Medini D. Comparative genomics: The bacterial pan-genome. Current Opinion in Microbiology 2008, 12:472-477.
161. Vriesendorp B., Bakker F.T. Reconstructing patterns of reticulate evolution in angiosperms: What can we do?. Taxon 2005, 54:593-604.
162. Wake M.H. What is 'integrative biology'?. Integrative and Comparative Biology 2003, 43:239-241.
163. Wake M.H. Integrative biology: Science for the 21st century. BioScience 2008, 58:349-353.
164. Welch J.J., Bromham L. Molecular dating when rates vary. Trends in Ecology and Evolution 2006, 20:320-327.
165. Welch R.A., Burland V., Plunkett G., Redford P., Roesch P., Rasko D., Buckles E.L., Liou S.R., Boutin A., Hackett J., et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proceedings of the National Academy of Sciences USA 2002, 99:17020-17024.
166. Wheelis M.L., Kandler O., Woese C.R. On the nature of global classification. Proceedings of the National Academy of Sciences USA 1992, 89:2930-2934.
167. Whittaker R.H. New concepts of kingdoms of organisms. Science 1969, 163:150-160.
168. Wiens J.J., Kuczynski C.A., Townsend T., Reeder T.W., Mulcahy D.G., Sites J.W. Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: Molecular data change the placement of fossil taxa. Systematic Biology 2010, 59:674-688.
169. Wilson A.C., Carlson S.S., White T.J. Biochemical evolution. Annual Review of Biochemistry 1977, 46:573-639.
170. Wimsatt W.C. Reductionism and its heuristics: Making methodological reductionism honest. Synthese 2006, 151:445-475.
171. Woese C.R. Bacterial evolution. Microbiological Reviews 1987, 51:221-271.
172. Woese C.R. Phylogenetic trees: Whither microbiology?. Current Biology 1996, 6:1060-1063.
173. Woese C.R. Interpreting the universal phylogenetic tree. Proceedings of the National Academy of Sciences USA 2000, 97:8392-8396.
174. Woese, C. R. (2005). The archaeal concept and the world it lives in: A retrospective. In Govindjee, J. T. Beatty, H. Gest, & J. F. Allen, (Eds.), Discoveries in photosynthesis (pp. 1109-1120). Dordrecht: Springer.
175. Woese C.R., Fox G.E. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences USA 1977, 74:5088-5090.
176. Woese C.R., Kandler O., Wheelis M.L. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences USA 1990, 87:4576-4579.
177. Wolkenhauer O., Hofmeyr J.-H.S. An abstract cell model that describes the self-organization of cell function in living systems. Journal of Theoretical Biology 2007, 246:461-476.
178. Woolley S.M., Posada D., Crandall K.A. A comparison of phylogenetic network methods using simulation. PLoS One 2008, 3(4):e1913. 10.1371/journal.pone.0001913.
179. Wortley A.H., Scotland R.W. The effect of combining molecular and morphological data in published phylogenetic analyses. Systematic Biology 2006, 55:677-685.
180. Wylie A. Rethinking unity as a 'working hypothesis' for philosophy of science. How archaeologists exploit the disunities of science. Perspectives on Science 1999, 7:293-317.
181. Xie J., Fu Y., Jiang D., Li G., Huang J., Li B., Hsiang T., Peng Y. Intergeneric transfer of ribosomal genes between two fungi. BMC Evolutionary Biology 2008, 8:87. 10.1186/1471-2148-8-87.
182. Yap W.H., Zhang Z., Wang Y. Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. Journal of Bacteriology 1999, 181:5201-5209.
183. Zhaxybayeva O., Swithers K.S., Lapierre P., Fournier G.P., Bickhart D.M., DeBoy R.T., Nelson K.E., Nesbø C.L., Doolittle W.F., Gogarten J.P., Noll K.M. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proceedings of the National Academy of Sciences USA 2009, 106:5865-5870.