A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock

Molecular Biology and Evolution

Volumn 23, Issue 9, 2006, Pages 1731-1740

  Pereira, Sergio L ^a   Baker, Allan J ^a,b  

^a DEPARTMENT OF NATURAL HISTORY   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Aves; Divergence times; Fossil; Molecular clock; Rate of DNA evolution; Vertebrates

Indexed keywords

CYTOCHROME B; DNA;

AMPHIBIA; ARTICLE; BAYES THEOREM; BIRD; CRETACEOUS; FOSSIL; GENETIC HETEROGENEITY; LIZARD; MOLECULAR CLOCK; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; VERTEBRATE;

ANIMALS; BAYES THEOREM; BIRDS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FOSSILS; GENES, MITOCHONDRIAL; GENETIC SPECIATION; GENETIC VARIATION; LIKELIHOOD FUNCTIONS; PHYLOGENY; TIME; VARIATION (GENETICS); VERTEBRATES;

AMPHIBIA; ANSER; AVES; BRANTA; IXODIDA; MYA; SQUAMATA; VERTEBRATA;

EID: 33747179098     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl038     Document Type: Article

References (79)

1. Aleixo A. 2004. Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification. Evolution 58:1303-17.
2. Aris-Brosou S, Yang Z. 2002. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst Biol 51:703-14.
3. Baker AJ, Huynen LJ, Haddrath O, Millar CD, Lambert DM. 2005. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: the giant moas of New Zealand. Proc Natl Acad Sci USA 102:8257-62.
4. Barker FK, Cibois A, Schikler P, Feinstein J, Cracraft J. 2004. Phylogeny and diversification of the largest avian radiation. Proc Natl Acad Sci USA 101:11040-5.
5. Benton MJ. 1993. The fossil record 2. London: Chapman and Hall.
6. Benton MJ. 2000. Vertebrate paleontology. New York: Chapman and Hall.
7. Benton MJ, Ayala FJ. 2003. Dating the tree of life. Science 300:1698-700.
8. Bickart KJ. 1990. The birds of the Late Miocene-Early Pliocene big sandy formation, Mohave County, Arizona. Ornithol Monogr 44:1-72.
9. Blair JE, Hedges SB. 2005. Molecular phylogeny and divergence times of deuterostome animals. Mol Biol Evol 22:2275-84.
10. Blair JE, Shah P, Hedges SB. 2005. Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinformatics 6:53.
11. Boles WE. 1992. Revision of Dromaius gidju Patterson and Rich 1987 from Rivesleigh, northwestern Queensland, Australia, with a reassessment of its generic position. Nat Hist Mus Los Angel Cty Sci Ser 36:195-208.
12. Bollmer JL, Kimball RT, Whiteman NK, Sarasola JH, Parker PG. 2006. Phylogeography of the Galapagos hawk (Buteo galapagoensis): a recent arrival to the Galapagos Islands. Mol Phylogenet Evol 39:237-47.
13. Brodkorb P. 1964. Catalogue of fossil birds, part 2 (Anseriformes through Galliformes). Bull Fla State Mus Biol Sci 8:195-335.
14. Bromham L, Phyllips MJ, Penny D. 1999. Growing up with dinosaurs: molecular dates and the mammalian radiation. Trends Ecol Evol 14:113-8.
15. Brown WM, George M, Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 76:1967-71.
16. Cheviron ZA, Hackett SJ, Capparella AP. 2005. Complex evolutionary history of a Neotropical lowland forest bird (Lepidothrix coronata) and its implications for historical hypotheses of the origin of Neotropical avian diversity. Mol Phylogenet Evol 36:338-57.
17. Clarke JA, Tambussi CP, Noriega JI, Erickson GM, Ketcham RA. 2005. Definitive fossil evidence for the extant avian radiation in the Cretaceous. Nature 433:305-8.
18. Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, Ward R. 2001. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409:704-7.
19. Cooper A, Penny D. 1997. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 275:1109-13.
20. Cooper RA, Millener P. 1993. The New Zealand biota: historical background and new research. Trends Ecol Evol 8:429-33.
21. Cracraft J, Barker FK, Braun M, et al. (14 co-authors). 2004. Phylogenetic relationships among modern birds (Neornithes): towards an avian tree of life. In: Cracraft J, Donoghue M, editors. Assembling the tree of life. New York: Oxford University Press. p 468-89.
22. Cracraft J, Donoghue M. 2004. Assembling the tree of life. New York: Oxford University Press.
23. Crowe TM, Short LL. 1992. A new gallinaceous bird from the Oligocene of Nebraska, with comments on the phylogenetic position of the Gallinuloididae. Nat Hist Mus Los Angel Cty Sci Ser 36:179-85.
24. Delsuc F, Vizcaíno SF, Douzery EJP. 2004. Influence of tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans. BMC Evol Biol 4:11.
25. Douzery EJP, Delsuc F, Stanhope MJ, Huchon D. 2003. Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations. J Mol Evol 57:S201-13.
26. Dyke GJ. 2001. The evolutionary radiation of modern birds: systematics and patterns of diversification. Geol J 36:305-15.
27. Eberhard JR, Bermingham E. 2005. Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans. Mol Phylogenet Evol 36:288-304.
28. Ericson PG, Christidis L, Cooper A, Irestedt M, Jackson J, Johansson US, Norman JA. 2002. A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proc Biol Sci 269:235-41.
29. Feduccia A. 1995. Explosive evolution in tertiary birds and mammals. Science 267:637-8.
30. Gaffney ES. 1990. The comparative osteology of the Triassic turtle Proganochelys. Bull Am Mus Nat Hist 194:1-263.
31. Gill FB, Slikas B, Sheldon FH. 2005. Phylogeny of titmice Paridae: II. Species relationships based on sequences of the mitochondrial cytochrome-b gene. Auk 122:121-43.
32. Gillooly JF, Allen AP, West GB, Brown JH. 2005. The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proc Natl Acad Sci USA 102:140-5.
33. Gingerich PD, Uhen MD. 1998. Likelihood estimation of the time of origin of Cetacea and the time of origin of Cetacea and Artiodactyla. Paleontol Electron [serial online] 1:1-47.
34. Golding GB. 1983. Estimates of DNA and protein sequence divergence: an examination of some assumptions. Mol Biol Evol 1:125-42.
35. Gradstein FM, Ogg JG, Smith AG, et al. (39 co-authors). 2004. A geologic time scale 2004. Cambridge: Cambridge University Press.
36. Graur D, Martin W. 2004. Reading the entrails of chickens: molecular timescales of molecular evolution and the illusion of precision. Trends Genet 20:80-6.
37. Haddrath O, Baker AJ. 2001. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc Biol Sci 268:939-45.
38. Hedges SB, Kumar S. 2003. Genomic clocks and evolutionary timescales. Trends Genet 19:200-6.
39. Hedges SB, Kumar S. 2004. Precision of molecular time estimates. Trends Genet 20:242-7.
40. Hedges SB, Parke PH, Sibley CG, Kumar S. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-9.
41. Ho SY, Phillips MJ, Cooper A, Drummond AJ. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 22:1561-8.
42. Jacobs LL, Downs WR. 1994. The evolution of murine rodents in Asia. In: Tomida Y, Li C-K, Setoguchi T, editors. Rodent and lagomorph families of Asian origins and diversification. Tokyo: National Science Museum Monographs. p 149-56.
43. Kessler LG, Avise JC. 1985. A comparative description of mitochondrial DNA differentiation in selected avian and other vertebrate genera. Mol Biol Evol 2:109-25.
44. Kimura M. 1968. Evolutionary rate at the molecular level. Nature 217:624-6.
45. Kishino H, Thorne JL, Bruno WJ. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol 18:352-61.
46. Klicka J, Zink RM. 1997. The importance of recent ice ages in speciation: a failed paradigm. Science 277:1666-9.
47. Kumar S, Hedges SB. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-20.
48. Lovette IJ. 2004. Mitochondrial dating and mixed support for the "2% rule" in birds. Auk 121:1-6.
49. Luo ZX, Ji Q, Wible JR, Yuan CX. 2003. An Early Cretaceous tribosphenic mammal and metatherian evolution. Science 302:1934-40.
50. Maddison DR, Maddison WP. 2000. MacClade 4.0. Sunderland: Sinauer Associates, Inc.
51. Menning W, Weyer D, Drozdzewski G, van Ameron HWJ, Wendt I. 2000. A carboniferous timescale 2000: discussion and use of geological parameters as time indicators from Central and Western Europe. Geol Jahrb A 156:3-44.
52. Meylan PA, Moody RTJ, Walker CA, Chapman SD. 2000. Sandownia harrisi, a highly derived trionychoid turtle (Testudines: Cryptodira) from the Early Cretaceous of the Isle of Wight, England. J Vertebr Paleontol 20:522-32.
53. Mindell DP, Knight A, Baer C, Huddleston CJ. 1996. Slow rates of molecular evolution in birds and the metabolic rate and body temperature hypothesis. Mol Biol Evol 13:422-6.
54. Muller J, Reisz RR. 2005. Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates. Bioessays 27:1069-75.
55. Near TJ. 2005. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am Nat 165:137-46.
56. Nei M, Xu P, Glazko G. 2001. Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organism. Proc Natl Acad Sci USA 98:2497-502.
57. Paton RL, Smithson TR, Clack JA. 1999. An amniote-like skeleton from the Early Carboniferous of Scotland. Nature 398:508-13.
58. Paxinos EE, James HF, Olson SL, Sorenson MD, Jackson J, Fleischer RC. 2002. mtDNA from fossils reveals a radiation of Hawaiian geese recently derived from the Canada goose (Branta canadensis). Proc Natl Acad Sci USA 99:1399-404.
59. Pereira SL, Baker AJ. 2006. A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites. Mol Phylogenet Evol 38:499-509.
60. Pereira SL, Grau ET, Wajntal A. 2004. Molecular architecture and rates of DNA substitutions of the mitochondrial control region of cracid birds. Genome 47:535-45.
61. Reisz RR, Mueller J. 2004. Molecular timescales and the fossil record: a paleontological perspective. Trends Genet 20:237-41.
62. Ruta M, Coates MI. 2004. Bones, molecules and crown-tetrapod origins. In: Donoghue PCJ, Smith MP, editors. Telling the evolutionary time: molecular clocks and the fossil record. New York: CRC Press. p 224-62.
63. Salgado-Labouriau M. 1994. Historia Ecologica da Terra. Sao Paulo, Brazil: Editora Edgard Blücher Ltda.
64. Sanderson MJ. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol 19:1218-31.
65. Sanderson MJ. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol 19:101-9.
66. Shields GF, Wilson AC. 1987. Calibration of mitochondrial DNA evolution in geese. J Mol Evol 24:212-7.
67. Sibley CG, Ahlquist JE. 1990. Phylogeny and classification of birds: a study in molecular evolution. New Haven: Yale University Press.
68. Slack KE, Jones CM, Ando T, Harrison GL, Fordyce RE, Arnason U, Penny D. 2006. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol Biol Evol 23:1144-55.
69. Springer MS, Murphy WJ, Eizirik E, O'Brien SJ. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci USA 100:1056-61.
70. Thorne JL, Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst Biol 51:689-702.
71. Thorne JL, Kishino H. 2005. Estimation of divergence times from molecular sequence data. In: Nielsen R, editor. Statistical methods in molecular evolution. New York: Springer. p 233-56.
72. Thorne JL, Kishino H, Painter IS. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 15:1647-57.
73. van Tuinen M, Hedges SB. 2001. Calibration of avian molecular clocks. Mol Biol Evol 18:206-13.
74. van Tuinen M, Hedges SB. 2004. The effect of external and internal fossil calibrations on the avian evolutionary timescale. J Paleontol 78:45-50.
75. Wilson AC, Cann RL, Carr S, et al. 1985. Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linn Soc 26:375-400.
76. Yang Z, Yoder AD. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst Biol 52:705-16.
77. Zhang P, Zhou H, Chen YQ, Liu YF, Qu LH. 2005. Mitogenomic perspectives on the origin and phylogeny of living amphibians. Syst Biol 54:391-400.
78. Zuckerkandl E, Pauling L. 1962. Molecular disease, evolution, and genetic heterogeneity. In:MarshaM, PullmanB, editors.Horizons in biochemistry. New York: Academic Press. p 189-225.
79. Zuckerkandl E, Pauling L. 1965. Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ, editors. Evolving genes and proteins. New York: Academic Press. p 97-166.