Testing fundamental evolutionary hypotheses

Journal of Theoretical Biology

Volumn 223, Issue 3, 2003, Pages 377-385

  Penny, David ^a   Hendy, Michael D ^a   Poole, Anthony M ^a,b  

^a MASSEY UNIVERSITY   (New Zealand)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Evolution; Genetic code; Intelligent Design; Origin of life; Phylogeny limits

Indexed keywords

EVOLUTIONARY BIOLOGY; GENETICS; ORIGIN OF LIFE; PHYLOGENY;

ARTICLE; DNA SEQUENCE; GENETIC CODE; HYPOTHESIS; MOLECULAR EVOLUTION; PHYLOGENY; PRIORITY JOURNAL; THEORETICAL MODEL;

EID: 0038354758     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-5193(03)00099-7     Document Type: Note

References (41)

1. Anon, 1981a. How true is the theory of evolution. Nature 290, 75-76.
2. Anon, 1981b. Darwin's death in South Kensington. Nature 290, 135.
3. Bowler P.J. Evolution. The History of an Idea:1984;University of California Press, Berkeley, CA.
4. Bujnicki J.M. Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J. Mol. Evol. 50:2000;39-44.
5. Chor B., Holland B.R., Penny D., Hendy M.D. Multiple maxima of likelihood in phylogenetic trees. an analytic approach Mol. Biol. Evol. 17:2000;1529-1541.
6. Collins L.J., Moulton V., Penny D. Use of RNA secondary structure for evolutionary relationships. the case of RNase P and RNase MRP J. Mol. Evol. 51:2000;194-204.
7. Cieslik D. Steiner Minimal Trees. 1998;Kluwer, Dordrecht.
8. Cieslik D. The Steiner Ratio. 2001;Kluwer, Dordrecht.
9. Doolittle W.F. The nature of the universal ancestor and the evolution of the proteome. Curr. Opin. Struct. Biol. 10:2000;355-358.
10. Farley J. The Spontaneous Generation Controversy from Descartes to Oparin. 1977;The Johns Hopkins University Press, Baltimore, MD.
11. Halstead B. Popper. good philosophy, bad science? New Scientist. 87:1980;215-217.
12. Henderson I.M., Penny D., Hendy M.D. Models for the evolution of influenza viruses. Nature. 326:1987;22.
13. Henderson I.M., Hendy M.D., Penny D. Influenza viruses, comets, and the science of evolutionary trees. J. Theor. Biol. 140:1989;289-303.
14. Hendy M.D., Penny D., Foulds L.R. Identification of phylogenetic trees of minimal length. J. Theor. Biol. 71:1978;441-452.
15. Hoyle F., Wickramasinghe N.C. Living Comets. 1984;Cardiff University Press, Cardiff.
16. Hoyle F., Wickramasinghe N.C. The case for life as a cosmic phenomenon. Nature. 322:1986;509-511.
17. Jain R., Rivera M.C., Lake J.A. Horizontal transfer among genomes. the complexity hypothesis Proc. Natl Acad. Sci. USA. 96:1999;3801-3806.
18. Lee N., Bessho Y., Wei K., Szostak J.W., Suga H. Ribozyme-catalyzed tRNA aminoacylation. Nat. Struct. Biol. 7:2000;28-33.
19. Lenski R.E., Mongold J.A., Sniegowski P.D., Travisano M., Vasi F., Gerrish P.J., Schmidt T.M. Evolution of competitive fitness in experimental populations of E. coli. what makes one genotype a better competitor than another? Antonie Van Leeuwenhoek. 73:1998;35-47.
20. Lin Y.-H., Waddell P.J., Penny D. Pika and Vole mitochondrial genomes add support to both rodent monophyly and glires. Gene. 294:2002;119-129.
21. Lockhart P.J., Huson D.et al. How molecules evolve in bacteria. Mol. Biol. Evol. 17:2000;835-838.
22. Logan D.T., Andersson J., Sjöberg B.-M., Nordlund P. A glycyl radical site in the crystal structure of a class III ribonucleotide reductase. Science. 283:1999;1499-1504.
23. Long M., Thornton K. Gene duplication and evolution. Science. 293:2001;1551a.
24. Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science. 290:2000;1151-1155.
25. Penny D., Foulds L.R., Hendy M.D. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature. 297:1982;197-200.
26. Penny D., McComish B.J., Charleston M.A., Hendy M.D. Mathematical elegance with biochemical realism. the covarion model of molecular evolution J. Mol. Evol. 53:2001;711-723.
27. Poole A.M., Jeffares D.C., Penny D. Prokaryotes, the new kids on the block. Bioessays. 21:1999;880-889.
28. Poole A., Penny D., Sjöberg B.-M. Methyl-RNA. an evolutionary bridge between RNA and DNA? Chem. Biol. 7:2000;R207-R216.
29. Poole A.M., Phillips M.J., Penny D. Prokaryote and eukaryote evolvability. Biosystems. 69:2003;163-185.
30. Pupo G.M., Lan R., Reeves P.R. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl Acad. Sci. USA. 97:2000;10567-10572.
31. Riddiford A., Penny D. The scientific status of evolutionary theory. Pollard J.W. Evolutionary Theory: Paths into the Future. 1984;1-38 Wiley, London and New York.
32. Ronneberg T.A., Freeland S.J., Landweber L.F. Genview and Gencode. a pair of programs to test theories of genetic code evolution Bioinformatics. 17:2001;280-281.
33. Saito H., Watanabe K., Suga H. Concurrent molecular recognition of the amino acid and tRNA by a ribozyme. RNA. 7:2001;1867-1878.
34. Sober E., Steel M. Testing the hypothesis of common ancestry. J. Theor. Biol. 218:2002;395-408.
35. Tuffley C., Steel M.A. Modeling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147:1997;63-91.
36. Turner P.E., Chao L. Prisoner's dilemma in an RNA virus. Nature. 398:1999;441-443.
37. Waddell, P.J., 1995. Statistical methods of phylogenetic analysis: including Hadamard conjugations, LogDet transformations and maximum likelihood. Ph.D. Thesis, Massey University, Palmerston North.
38. Williams B.A.P., Hirt R.P., Lucocq J.M., Embley T.M. A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature. 418:2002;865-869.
39. Woese C.R. Interpreting the universal phylogenetic tree. Proc. Natl Acad. Sci. USA. 97:2000;8392-8396.
40. Wolfe K.H. Yesterday's polyploids and the mystery of diploidization. Nat. Rev. Genet. 2:2001;333-341.
41. Zhang L., Gaut B.S., Vision T.J. Gene duplication and evolution. Science. 293:2001;1551a.