Patterns of calibration age sensitivity with quartet dating methods

Journal of Paleontology

Volumn 78, Issue 1, 2004, Pages 7-30

  Brochu, Christopher A ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALIBRATION; CROCODILIAN; DATING METHOD; DIVERGENCE;

ALLIGATOR; CAIMAN; CROCODYLIDAE (ALL CROCODILES);

EID: 0347093277     PISSN: 00223360     EISSN: None     Source Type: Journal    
DOI: 10.1666/0022-3360(2004)078<0007:POCASW>2.0.CO;2     Document Type: Article

References (106)

1. ADKINS, R. M., A. H. WALTON, AND R. HONEYCUTT. 2003. Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. Molecular Phylogenetics and Evolution, 26: 409-420.
2. ARBOGAST, B. S., S. V. EDWARDS, J. WAKELEY, P. BEERLI, AND J. B. SLOWINSKI. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic time scales. Annual Review of Ecology and Systematics, 33:707-740.
3. ARCHIBALD, J. D., AND D. H. DEUTSCHMAN. 2001. Quantitative analysis of the timing of the origin and diversification of extant placental orders. Journal of Mammalian Evolution, 8:107-124.
4. ARNASON, U., A. GULLBERG, AND A. JANKE. 1998. Molecular timing of primate divergences as estimated by two nonprimate calibration points. Journal of Molecular Evolution, 47:718-727.
5. BENTON, M. J. 1998. Molecular and morphological phylogenies of mammals: congruence with stratigraphic data. Molecular Phylogenetics and Evolution, 9:398-407.
6. BENTON, M. J. 2001. Early origins of modern birds and mammals: molecules vs. morphology. BioEssays, 21:1043-1051.
7. BROCHU, C. A. 1997. Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis. Systematic Biology, 46:479-522.
8. BROCHU, C. A. 1999. Phylogeny, systematics, and historical biogeography of Alligatoroidea. Society of Vertebrate Paleontology Memoir, 6: 9-100.
9. BROCHU, C. A. 2000. Phylogenetic relationships and divergence timing of Crocodylus based on morphology and the fossil record. Copeia, 2000:657-673.
10. BROCHU, C. A. 2001. Congruence between physiology, phylogenetics, and the fossil record on crocodylian historical biogeography, p. 9-28. In G. Grigg, F. Seebacher, and C. E. Franklin (eds.), Crocodilian Biology and Evolution. Surrey Beatty and Sons, Sydney.
11. BROCHU, C. A. 2003. Phylogenetic approaches toward crocodylian history. Annual Review of Earth and Planetary Sciences, 31:357-397.
12. BROCHU, C. A. In press. Alligatorine phylogeny and the status of Allognathosuchus Mook, 1921. Journal of Vertebrate Paleontology.
13. BROCHU, C. A., AND L. D. DENSMORE. 2001. Crocodile phylogenetics: a review of current progress, p. 3-8. In G. Grigg, F. Seebacher, and C. E. Franklin (eds.), Crocodilian Biology and Evolution. Surrey Beatty and Sons, Sydney.
14. BROCHU, C. A., J. M. THEODOR, AND C. D. SUMRALL. In review. When clocks collide: estimating divergence time from molecules and the fossil record. Journal of Paleontology.
15. BROMHAM, L., AND M. D. HENDY. 2000. Can fast early rates reconcile molecular dates with the Cambrian explosion? Proceedings of the Royal Society of London B, 267:1041-1047.
16. BROMHAM, L., M. J. PHILLIPS, AND D. PENNY. 1999. Growing up with dinosaurs: molecular dates and the mammalian radiation. Trends in Ecology and Evolution, 14:113-118.
17. BROMHAM, L., D. PENNY, A. RAMBAUT, AND M. D. HENDY. 2000. The power of relative rate tests depends on the data. Journal of Molecular Evolution, 50:296-301.
18. BROMHAM, L., A. RAMBAUT, R. FORTEY, A. COOPER, AND D. PENNY. 1998. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proceedings of the National Academy of Sciences of the USA, 95:12386-12389.
19. BRYANT, L. J. 1989. Non-dinosaurian lower vertebrates across the Cretaceous-Tertiary Boundary in northeastern Montana. University of California Publications in Geological Sciences, 134:1-107.
20. BUCKLEY, G. A., C. A. BROCHU, D. W. KRAUSE, AND D. POL. 2000. A pug-nosed crocodyliform from the Late Cretaceous of Madagascar. Nature, 405:941-944.
21. BUSCALIONI, A. D., F. ORTEGA, AND D. VASSE. 1997. New crocodiles (Eusuchia: Alligatoroidea) from the Upper Cretaceous of southern Europe. Comptes Rendus de l"Academie des Sciences de Paris, Sciences de la Terre et des Planétes, 325:525-530.
22. BUSCALIONI, A. D., F. ORTEGA, D. B. WEISHAMPEL, AND C. M. JIANU. 2001. A revision of the crocodyliform Allodaposuchus precedens from the Upper Cretaceous of the Hateg Basin, Romania. Its relevance in the phylogeny of Eusuchia. Journal of Vertebrate Paleontology, 21:74-86.
23. CARVALHO, I. S., AND R. J. BERTINI. 1999. Mariliasuchus: um novo Crocodylomorpha (Notosuchia) do Cretáceo da Bacia Bauru, Brasil. Geología Colombiana, 24:83-105.
24. CLARK, J. M. 1994. Patterns of evolution in Mesozoic Crocodyliformes, p. 84-97. In N. C. Fraser and H.-D. Sues (eds.), In the Shadow of the Dinosaurs: Early Mesozoic Tetrapods. Cambridge University Press, New York.
25. CLARK, J. M., AND M. A. NORELL. 1992. The Early Cretaceous crocodylomorph Hylaeochampsa vectiana from the Wealden of the Isle of Wight. American Museum Novitates, 3032:1-19.
26. CONROY, C. J., AND M. VAN TUINEN. 2003. Extracting time from phylogenies: positive interplay between fossil and genetic data. Journal of Mammalogy, 84:444-455.
27. COOPER, A., AND D. PENNY. 1997. Mass survival of birds across the Cretaceous-Tertiary Boundary. Science, 275:1109-1113.
28. CORNELI, P. S. 2003. Complete mitochondrial genomes and eutherian evolution. Journal of Mammalian Evolution, 9:281-305.
29. DELGADO, S., D. CASANE, L. BONNAUD, M. LAURIN, J.-Y. SIRE, AND M. GIRONDOT. 2001. Molecular evidence for Precambrian origin of amelogenin, the major protein of vertebrate enamel. Molecular Biology and Evolution, 18:2146-2153.
30. DENSMORE, L. D. 1983. Biochemical and immunological systematics of the order Crocodilia, p. 397-465. In M. K. Hecht, B. Wallace, and G. H. Prance (eds.), Evolutionary Biology. Volume 16. Plenum Press, New York.
31. DENSMORE, L. D., AND R. D. OWEN. 1989. Molecular systematics of the order Crocodilia. American Zoologist, 29:831-841.
32. DENSMORE, L. D., AND P. S. WHITE. 1991. The systematics and evolution of the Crocodilia as suggested by restriction endonuclease analysis of mitochondrial and nuclear ribosomal DNA. Copeia, 1991:602-615.
33. DYKE, G. J. 2001. The evolutionary radiation of modern birds: systematics and patterns of diversification. Geological Journal, 36:305-315.
34. EASTEAL, S. 2001. Molecular evidence for the early divergence of placental mammals. BioEssays, 21:1052-1058.
35. EIZIRIK, E., W. J. MURPHY, AND S. J. O'BRIEN. 2001. Molecular dating and biogeography of the early placental mammal radiation. Journal of Heredity, 92:212-219.
36. FEDUCCIA. A. 1995. Explosive radiation in Tertiary birds and mammals. Science, 267:637-638.
37. FELSENSTEIN, J. 2003. Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts, 580 p.
38. GASPARINI, Z. 1996. Biogeographic evolution of the South American crocodilians. Münchner Geowissenschaftliche Abhandlungen, 30:159-184.
39. GATESY, J., R. D. SALLE, AND W. WHEELER. 1993. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Molecular Phylogenetics and Evolution, 2:152-157.
40. GATESY, J., G. AMATO, M. NORELL, R. DESALLE, AND C. HAYASHI. 2003. Combined support for wholesale taxic atavism in gavialine crocodylians. Systematic Biology, 52:403-422.
41. GINGERICH, P. D. 1986. Temporal scaling of molecular evolution in primates and other mammals. Molecular Biology and Evolution, 3:205-221.
42. GLAZKO, G. V., AND M. NEI. 2003. Estimation of divergence times for major lineages of primate species. Molecular Biology and Evolution, 20:424-434.
43. GRAYBEAL, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Systematic Biology, 47:9-17.
44. HAKING, E., L. KRUCKENHAUSER, A. GAMAUF, M. J. RIESING, AND W. PINSKER. 2001. The complete sequence of the mitochondrial genome of Buteo buteo (Aves, Accipitridae) indicates an early split in the phylogeny of raptors. Molecular Biology and Evolution, 18:1892-1904.
45. HÄRLID, A., A. JANKE, AND U. ARNASON. 1998. The complete mitochondrial genome of Rhea americana and early avian divergences. Journal of Molecular Evolution, 46:669-679.
46. HASEGAWA. M., H. KISHINO, AND T. YANO. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 21:160-174.
47. HASS, C. A., M. A. HOFFMAN, L. D. DENSMORE, AND L. R. MAXSON. 1992. Crocodilian evolution: insights from immunological data. Molecular Phylogenetics and Evolution, 1:193-201.
48. HOLLAND. S. M., AND M. E. PATZKOWSKY. 2002. Stratigraphic variation in the timing of first and last occurrences. Palaios, 17:134-146.
49. HUA, S., AND S. JOUVE. In press. A primitive gavialoid from the Paleocene of Morocco. Journal of Vertebrate Paleontology.
50. HUCHON, D., F. M. CATZEFLIS, AND E. J. P. DOUZERY. 2000. Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi. Proceedings of the Royal Society of London B, 267:393-402.
51. HUCHON, D., O. MADSEN, M. J. J. B. SIBBALD, K. AMENT, M. J. STANHOPE, F. M. CATZEFLIS, W. W. DE JONG, AND E. J. P. DOUZERY. 2002. Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. Molecular Biology and Evolution, 19:1053-1065.
52. HUELSENBECK, J. P., B. LARGET, AND D. L. SWOFFORD. 2000. A compount Poisson process for relaxing the molecular clock. Genetics, 154: 1879-1892.
53. KAWASHITA, S. Y., G. F. O. SANSON, O. FERNANDES, B. ZINGALES, AND M. R. S. BRIONES. 2001. Maximum-likelihood divergence date estimates based on rRNA gene sequences suggest two scenarios of Trypanosoma cruzi intraspecific evolution. Molecular Biology and Evolution, 18:2250-2259.
54. LANGSTON, W. 1965. Fossil crocodilians from Colombia and the Cenozoic history of the Crocodilia in South America. University of California Publications in Geological Sciences, 52:1-152.
55. LEE, M. S. Y. 1999. Molecular clock calibrations and metazoan divergence dates. Journal of Molecular Evolution, 49:385-391.
56. MALONE, B. 1979. The systematics, phylogeny and paleobiology of the genus Alligator. Ph.D. dissertation, City University of New York, 159 p.
57. MARKWICK, P. J. 1998. Crocodilian diversity in space and time: the role of climate in paleoecology and its implication for understanding K/T extinctions. Paleobiology, 24:470-497.
58. MARSHALL, C. R. 1990a. Confidence intervals on stratigraphic ranges. Paleobiology, 16:1-10.
59. MARSHALL, C. R. 1990b. The fossil record and estimating divergence times between lineages: maximum divergence times and the importance of reliable phylogenies. Journal of Molecular Evolution, 30:400-408.
60. MARSHALL, C. R. 1997. Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons. Paleobiology, 23:165-173.
61. MEDINA, C. J. 1976. Crocodilians from the Late Tertiary of northwestern Venezuela: Melanosuchus fisheri sp. nov. Breviora, 438:1-14.
62. NEI, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
63. NEI, M., P. XU, AND G. V. GLAZKO. 2001. Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proceedings of the National Academy of Sciences of the U. S. A., 98:2497-2502.
64. NORELL, M. A. 1989. The higher level relationships of the extant Crocodylia. Journal of Herpetology, 23:325-335.
65. NORMAN, J. E., AND M. V. ASHLEY. 2000. Phylogenetics of Perissodactyla and tests of the molecular clock. Journal of Molecular Evolution, 50:11-21.
66. OWEN, R. 1850. Monograph on the Fossil Reptilia of the London Clay, and of the Bracklesham and Other Tertiary Beds, Part II: Crocodilia (Crocodilus, etc.). Paleontographical Society, London, 50 p.
67. PERSSON, P. O. 1960. Reptiles from the Senonian (U. Cret.) of Scania (S. Sweden). Arkiv for Mineralogi och Geologi, 2:431-478.
68. POE, S. 1997. Data set incongruence and the phylogeny of crocodilians. Systematic Biology, 45:393-414.
69. POL, D. 1999. Basal mesoeucrocodylian relationships: new clues to old conflicts. Journal of Vertebrate Paleontology, 19:69A.
70. RAMBAUT, A., AND L. BROMHAM. 1998. Estimating divergence data from molecular sequences. Molecular Biology and Evolution, 15:442-448.
71. RAY, D. A., AND L. D. DENSMORE. 2002. The crocodilian mitochondrial control region: general structure, conserved sequences, and evolutionary implications. Journal of Experimental Zoology, 294:334-346.
72. RAY, D. A., AND L. D. DENSMORE. 2003. Repetitive sequences in the crocodilian mitochondrial control region: Poly-A sequences and heteroplasmic tandem repeats. Molecular Biology and Evolution, 20: 1006-1013.
73. RAY, D. A., P. S. WHITE, H. V. DUONG, T. CULLEN, AND L. D. DENSMORE. 2001. High levels of genetic variability in West African dwarf crocodiles Osteolaemus tetraspis tetraspis, p. 58-63. In G. Grigg, F. Seebacher, and C. E. Franklin (eds.), Crocodilian Biology and Evolution. Surrey Beatty and Sons, Sydney.
74. RODRIGUEZ-TRELLES, F., R. TARRIO, AND F. J. AYALA. 2002. A methodological bias toward overestimation of molecular evolutionary time scales. Proceedings of the National Academy of Sciences of the U. S. A., 99:8112-8115.
75. SALISBURY, S. W., AND P. M. A. WILLIS. 1996. A new crocodylian from the Early Eocene of southeastern Queensland and a preliminary investigation of the phylogenetic relationships of crocodyloids. Alcheringa, 20:179-227.
76. SANDERSON, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14:1218-1231.
77. SANDERSON, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19:101-109.
78. SCHWIMMER, D. R. 2002. King of the Crocodylians: The Paleobiology of Deinosuchus. Indiana University Press, Bloomington, 220 p.
79. SERENO, P. C., C. A. SIDOR, H. C. E. LARSSON, AND B. GADO. 2003. A new notosuchian from the Early Cretaceous of Niger. Journal of Vertebrate Paleontology, 23:477-482.
80. SMITH, A. B. 2001. Large-scale heterogeneity of the fossil record: implications for Phanerozoic biodiversity studies. Philosophical Transactions of the Royal Society of London, 356:351-367.
81. SMITH, A. B., AND K. J. PETERSON. 2002. Dating the time of origin of major clades: molecular clocks and the fossil record. Annual Review of Earth and Planetary Sciences, 30:65-88.
82. SMITH, A. B., A. S. GALE, AND N. E. A. MONKS. 2001. Sea-level change and rock record bias in the Cretaceous: a problem for extinction and biodiversity studies. Paleobiology, 27:241-253.
83. SNYDER, D. 2003. New Alligator remains from the Miocene of Florida and notes on Alligator phylogeny. Journal of Vertebrate Paleontology, 23:99A.
84. SOLOW, A. R. 2003. Estimation of stratigraphic ranges when fossil finds are not randomly distributed. Paleobiology, 29:181-185.
85. SOLTIS, P. S., D. E. SOLTIS, V. SAVOLAINEN, P. R. CRANE, AND T. G. BARRACLOUGH. 2002. Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. Proceedings of the National Academy of Sciences of the U. S. A., 99:4430-4435.
86. SPRINGER, M. S. 1995. Molecular clocks and the incompleteness of the fossil record. Journal of Molecular Evolution, 41:531-538.
87. SPRINGER, M. S. 1997. Molecular clocks and the timing of the placental and marsupial radiations in relation to the Cretaceous-Tertiary boundary. Journal of Mammalian Evolution, 4:285-302.
88. SPRINGER, M. S., W. J. MURPHY, E. EIZIRIK, AND S. J. O'BRIEN. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proceedings of the National Academy of Sciences of the U. S. A., 100:1056-1061.
89. SPRINGER, M. S., R. W. DEBRY, C. DOUADY, H. M. AMRINE, O. MADSEN, W. W. DE JONG, AND M. J. STANHOPE. 2001. Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Molecular Biology and Evolution, 18:132-143.
90. STEEL, M. A., A. C. COOPER, AND D. PENNY. 1996. Confidence intervals for the divergence time of two clades. Systematic Biology, 45:127-134.
91. STRAUSS, D., AND P. M. SADLER. 1989. Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology, 21:411-427.
92. STROMER, E. 1925. Ergebnisse der Forschungsreisen Prof. E. Stromers in den Wüsten Ägyptens, II: Wirbeltier-Reste der Baharije-Stufe (Unterestes Cenoman), 7: Stomatosuchus inermis Stromer, ein schwach bezahnter Krokodilier. Abhandlungen der Bayerischen Akademie der Wissenshaften Mathematisch-naturvissenschaftliche Abteilung, 30:1-9.
93. STROMER, E. 1933. Ergebnisse der Forschungsreisen Prof. E. Stromers in den Wüsten Ägyptens. 12: Die Procölen Crocodilia. Abhandlungen der Bayerischen Akademie der Wissenshaften Mathematisch-naturvissenschaftliche Abteilung, N. F., 15:1-55.
94. SWINTON, W. E. 1937. The crocodile of Maransart (Dollosuchus dixoni [Owen]). Mémoires du Musée Royal d'Histoire Naturelle de Belgique, 80:1-46.
95. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference, p. 407-514. In D. M. Hillis, C. Moritz, and B. K. Mable (eds.), Molecular Systematics (second edition). Sinauer Associates, Sunderland, Massachusetts.
96. THORNE, J. L., AND H. KISHINO. 2002. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology, 51:689-702.
97. THORNE, J. L., H. KISHINO, AND I. S. PAINTER. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution, 15:1647-1657.
98. VAN TUINEN, M., C. G. SIBLEY, AND S. B. HEDGES. 2000. The early history of modern birds inferred from DNA sequences of nuclear and mitochondrial ribosomal genes. Molecular Biology and Evolution, 17: 451-457.
99. WADDELL, P. J., Y. CAO, M. HASEGAWA, AND D. P. MINDELL. 1999. Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework. Systematic Biology, 48:119-137.
100. WAYNE, R. K., B. VAN VALKENBURGH, AND S. J. O'BRIEN. 1991. Molecular distance and divergence time in carnivores and primates. Molecular Biology and Evolution, 8:297-319.
101. WHITE, P. S., AND L. D. DENSMORE. 2001. DNA sequence alignments and data analysis methods: their effect on the recovery of crocodylian relationships, p. 29-37. In G. Grigg, F. Seebacher, and C. E. Franklin (eds.), Crocodilian Biology and Evolution. Surrey Beatty and Sons, Sydney.
102. WILLIAMSON, T. E. 1996. ?Brachychampsa sealeyi, sp. nov., (Crocodylia, Alligatoroidea) from the Upper Cretaceous (lower Campanian) Menefee Formation, northwestern New Mexico. Journal of Vertebrate Paleontology, 16:421-431.
103. WILLIS, P. M. A., R. E. MOLNAR, AND J. D. SCANLON. 1993. An early Eocene crocodilian from Murgon, southeastern Queensland. Kaupia, 3: 27-33.
104. WRAY, G. A. 2001. Dating branches on the Tree of Life using DNA. Genome Biology, 3:1-7.
105. WU, X.-C., A. P. RUSSELL, AND D. B. BRINKMAN. 2001. A review of Leidyosuchus canadensis Lambe, 1907 (Archosauria: Crocodylia) and an assessment of cranial variation based upon new material. Canadian Journal of Earth Sciences, 38:1665-1687.
106. YODER, A. D., AND Z. YANG. 2000. Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution, 17:1081-1090.