Base Compositional Bias and Phylogenetic Analyses: A Test of the "Flying DNA" Hypothesis

Molecular Phylogenetics and Evolution

Volumn 10, Issue 3, 1998, Pages 408-416

  Van Den Bussche, Ronald A ^a   Baker, Robert J ^a   Huelsenbeck, John P ^b   Hillis, David M ^b  

^a TEXAS TECH UNIVERSITY   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Base compositional bias; phylogenetic analyses; chiropteran; bats.

Indexed keywords

DNA; MITOCHONDRIAL DNA;

ANIMAL; BAT; CELL NUCLEUS; CHEMISTRY; DNA BASE COMPOSITION; GENETICS; HUMAN; MAMMAL; METABOLISM; PHYLOGENY; PRIMATE; REVIEW; STATISTICS;

ANIMALS; BASE COMPOSITION; CELL NUCLEUS; CHIROPTERA; DNA; DNA, MITOCHONDRIAL; HUMANS; MAMMALS; PHYLOGENY; PRIMATES; STATISTICS;

EID: 0032248712     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1998.0531     Document Type: Article

References (61)

1. Adkins R. M., Honeycutt R. L. Molecular phylogeny of the superorder Archonta. Proc. Natl. Acad. Sci. USA. 88:1991;10317-10321.
2. Ammerman L. K., Hillis D. M. A molecular test of bat relationships: Monophyly or diphyly. Syst. Biol. 41:1992;222-232.
3. Bailey W. J., Slightom J. L., Goodman M. Rejection of the "Flying Primate" hypothesis by phylogenetic evidence from the ε-globin gene. Science. 256:1992;86-89.
4. Baker R. J., Honeycutt R. L., Van Den Bussche R. A. Examination of monophyly of bats: Restriction map of the ribosomal DNA cistron. Contributions to Mammalogy in Honor of Karl F. Koopman. 1991a;. p. 42-53.
5. Baker R. J., Longmire J. L., Van Den Bussche R. A. Organization of repetitive elements in the upland cotton genome (Gossypium hirsutum. J. Hered. 86:1995;178-185.
6. Baker R. J., Novacek M. J., Simmons N. On the monophyly of bats. Syst. Zool. 40:1991b;216-231.
7. Bennet S., Alexander L. J., Crozier R. H., Mackinlay A. G. Are megabats flying primates? Contrary evidence from a mitochondrial DNA sequence. Aust. J. Biol. Sci. 41:1988;327-332.
8. Bernardi G. Genome organization and species formation in vertebrates. J. Mol. Evol. 37:1993;331-337.
9. Bernardi G., Mouchiroud D., Gautier C., Bernardi G. Compositional patterns in vertebrate genomes: Conservation and change in evolution. J. Mol. Evol. 28:1988;7-18.
10. Bernardi G., Olofsson B., Filipski J., Zerial M., Salinas J., Cunny G., Meunier-Rotival M., Rodier F. The mosaic genome of warm-blooded vertebrates. Science. 228:1985;953-957.
11. Cacciò S., Perani P., Saccone S., Kadi F., Bernardi G. Single-copy sequence homology among the GC-richest isochores of the genomes from warm-blooded vertebrates. J. Mol. Evol. 39:1994;331-339.
12. Collins T. M., Wimberger P. H., Naylor G. N. P. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Syst. Biol. 43:1994;482-496.
13. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:1981;368-376.
14. Fitch W. M. Toward defining the course of evolution: Minimal change for a specific tree topology. Syst. Zool. 20:1971;406-416.
15. Forterre P., Benachenhou-lafha N., Labedan B. Universal tree of life. Nature. 362:1993;795.
16. Goldman N. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:1993;182-198.
17. Hasegawa M., Hashimoto T. Ribosomal RNA trees misleading. Nature. 361:1993;23.
18. Hasegawa M., Kishino H., Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:1985;160-174.
19. Hillis D. M., Huelsenbeck J. P., Cunningham C. W. Application and accuracy of molecular phylogenies. Science. 264:1994a;671-677.
20. Hillis D. M., Huelsenbeck J. P., Swofford D. L. Hobgoblin of phylogenetics. Nature. 369:1994b;363-364.
21. Hillis D. M., Mable B. K., Moritz C. Applications of molecular systematics: The state of the field and a look to the future. Hillis D. M., Moritz C., Mable B. K. Molecular Systematics. 1996;515-543 Sinauer, Sunderland.
22. Huelsenbeck J. P., Hillis D. M., Jones R. Parametric bootstrapping in molecular phylogenetics: Applications and performance. Ferraris J. D., Palumbi S. R. Molecular Zoology: Strategies and Protocols. 1996a;19-45 Wiley.
23. Huelsenbeck J. P., Hillis D. M., Nielsen R. A likelihood-ratio test of monophyly. Syst. Biol. 45:1996b;546-558.
24. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:1985;13-34.
25. Janacek L. L., Longmire J. L., Wichman H. A., Baker R. J. Genome organization of repetitive elements in the rodent,Peromyscus leucopus. Mamm. Genome. 4:1993;374-381.
26. Jukes T. H., Bhushan V. Silent nucleotide substitutions and G + C content of some mitochondrial and bacterial genes. J. Mol. Evol. 24:1986;39-44.
27. Kidd K. K., Sgaramella-Zonta L. A. Phylogenetic analysis: Concepts and methods. Am. J. Human Genet. 23:1971;235-252.
28. Lake J. A. Reconstructing evolutionary trees from DNA and protein sequences: Paralinear distances. Proc. Natl. Acad. Sci. USA. 91:1994;1455-1459.
29. Linnaeus C. Systema Nature. 1758;Laurentii Salvii, Stockholm.
30. Liu H., Beckenbach A. T. Evolution of the mitochondrial cytochrome oxidase II gene among 10 orders of insects. Mol. Phylogenet. Evol. 1:1992;41-52.
31. Lockhart P. J., Howe C. J., Bryant D. A., Beanland T. J., Larkum A. W. D. Substitutional bias confound inference of cyanelle origins from sequence data. J. Mol. Evol. 34:1992a;153-162.
32. Lockhart P. J., Penny D., Hendy M. D., Howe C. J., Beanland T. J., Larkum A. W. D. Controversy on chloroplast origins. FEBS Lett. 301:1992b;127-131.
33. Lockhart P. J., Steel M. A., Hendy M. D., Penny D. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:1994;605-612.
34. Loomis W. F., Smith D. W. Molecular phylogeny ofDictyostelium discoideum. Proc. Natl. Acad. Sci. USA. 87:1992;9093-9097.
35. Mindell D. P., Dick C. W., Baker R. J. Phylogenetic relationships among megabats, microbats, and primates. Proc. Natl. Acad. Sci. USA. 88:1991;10322-10326.
36. Mouchiroud D., Bernardi G. Compositional properties of coding sequences and mammalian phylogeny. J. Mol. Evol. 37:1993;109-116.
37. Penny D., Hendy M. D., Zimmer E. A., Hambry R. K. Trees from sequences: Panacea or Pandora's box. Aust. Syst. Bot. 3:1990;21-38.
38. Pettigrew J. D. Flying primates? Megabats have the advanced pathway from eye to midbrain. Science. 231:1986;1304-1306.
39. Pettigrew J. D. Wings or brain? Convergent evolution in the origin of bats. Syst. Zool. 40:1991a;199-216.
40. Pettigrew J. D. A fruitful wrong hypothesis? Response to Baker, Novacek, and Simmons. Syst. Zool. 40:1991b;231-239.
41. Pettigrew J. D. Flying DNA. Curr. Biol. 4:1994;277-280.
42. Pettigrew J. D., Jamieson B. G. M., Robson S. K., Hall L. S., McNally K. I., Cooper N. M. Phylogenetic relations between microbats, megabats and primates (Mammalia: Chiroptera and Primates). Philos. Trans. R. Soc. Lond. Ser. B. 325:1989;489-559.
43. Russo C. A. M., Takezaki N., Nei M. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13:1996;525-536.
44. Rzhetsky A., Nei M. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9:1992;945-967.
45. Sabeur G., Macaya G., Kadi F., Bernardi G. The isochore patterns of mammalian genomes and their phylogenetic implications. J. Mol. Evol. 37:1993;93-108.
46. Saccone C., Lanave C., Pesole G., Preparata G. Influence of base composition on quantitative estimates of gene evolution. Methods Enzymol. 183:1990;570-583.
47. Sidow A., Wilson A. C. Compositional statistics: An improvement of evolutionary parsimony and its application to deep branches in the tree of life. J. Mol. Evol. 31:1990;51-68.
48. Sidow A., Wilson A. C. Compositional statistics evaluated by computer simulations. Miyamoto M. M., Cracraft J. Phylogenetic Analysis of DNA Sequences. 1991;129-146 Oxford Univ. Press, New York.
49. Simmons N. B. The case for chiropteran monophyly. Am. Mus. Novit. 3103:1994;1-54.
50. Simmons N. B., Novacek M. J., Baker R. J. Approaches, methods, and the future of the chiropteran monophyly controversy: A reply to J. D. Pettigrew. Syst. Zool. 40:1991;239-243.
51. Smith J. D. Chiropteran evolution. Baker R. J., Jones J. K. Jr., Carter D. C. Biology of Bats of the New World Family Phyllostomatidae, Part I. 1977;49-69 Texas Tech. Univ. Lubbock.
52. Smith J. D., Madkour G. Penial morphology and the question of chiropteran phylogeny. Wilson D. E., Gardner A. L. Proceedings of the Fifth International Bat Research Conference. 1980;347-365 Texas Tech Univ. Press, Lubbock.
53. Sogin M. L., Hinkle G., Lelpe D. D. Universal tree of life. Nature. 362:1993;795.
54. Stanhope M. J., Czelusniak J., Si J.-S., Nickerson J., Goodman M. A molecular perspective on mammalian evolution from the gene encoding Interphotoreceptor Retinoid Binding Protein, with convincing evidence for bat monophyly. Mol. Phylogenet Evol. 1:1992;148-160.
55. Steel M. Recovering a tree from the Markov leaf colourations it generates under a Markov model. Appl. Math. Lett. 7:1994;19-23.
56. Steel M. A., Lockhart P. J., Penny D. Confidence in evolutionary trees from biological sequence data. Nature. 366:1993;440-442.
57. Sueoka N. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA. 85:1988;2653-2657.
58. Swofford D. L., Olsen G. J., Waddell P. J., Hillis D. M. Phylogenetic inference. Hillis D. M., Moritz C., Mable B. K. Molecular Systematics. 1996;407-514 Sinauer, Sunderland.
59. Thewissen J. G. M., Babcock S. K. Distinctive cranial and cervical innervation of wing muscles: New evidence for bat monophyly. Science. 251:1991;934-936.
60. Van Den Bussche R. A., Longmire J. L., Baker R. J. How bats achieve a small C-value: Frequency of repetitive DNA inMacrotus. Mamm. Genome. 6:1995;521-525.
61. Wibble J. R., Novacek M. J. Cranial evidence for the monophyletic origin of bats. Am. Mus. Novit. 2911:1988;1-19.