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When clocks (and communities) collide: Estimating divergence time from molecules and the fossil record

Published online by Cambridge University Press:  20 May 2016

Christopher A. Brochu
Affiliation:
1Department of Geoscience, University of Iowa, Iowa City 52242
Colin D. Sumrall
Affiliation:
2Department of Geological Sciences, University of Tennessee, Knoxville 37996
Jessica M. Theodor
Affiliation:
3Department of Geology, Illinois State Museum, Springfield 62703

Extract

Traditionally, deep time was the domain of paleontology. Origination time could be assessed only through reference to first appearance data in the rock record. This changed almost from the beginnings of modern molecular biology, when it was realized that molecules could be used to calculate divergence times between living species. Early studies relied on immunological distance information, and the underlying rationale was simple: because evolution involves changes to the genetic code, and because these changes accumulate over time, we should expect the number of accumulated changes (the molecular distance) between living taxa to increase as their time of divergence becomes older (Zuckerkandl and Pauling, 1962). By inferring a rate of evolution of the genetic code, we can place absolute time estimates on divergence points.

Type
Selected Papers from the Sixth North American Paleontological Convention
Copyright
Copyright © The Paleontological Society 

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References

Alroy, J. 1999. The fossil record of North American mammals: evidence for a Paleocene evolutionary radiation. Systematic Biology, 48:107118.Google Scholar
Arbogast, B. S., Edwards, S. V., Wakeley, J., Beerli, P., and Slowinski, J. B. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic time scales. Annual Review of Ecology and Systematics, 33:707740.CrossRefGoogle Scholar
Archibald, J. D., and Deutschman, D. H. 2001. Quantitative analysis of the timing of the origin and diversification of extant placental orders. Journal of Mammalian Evolution, 8:107124.CrossRefGoogle Scholar
Barraclough, T. G., and Savolainen, V. 2001. Evolutionary rates and species diversity in flowering plants. Evolution, 55:677683.Google Scholar
Benton, M. J. 2001. Early origins of modern birds and mammals: molecules vs. morphology. BioEssays, 21:10431051.Google Scholar
Brochu, C. A. 1997. Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis. Systematic Biology, 46:479522.Google Scholar
Brochu, C. A. 2000. Phylogenetic relationships and divergence timing of Crocodylus based on morphology and the fossil record. Copeia, 2000:657673.Google Scholar
Bromham, L. 2002. Molecular clocks in reptiles: life history influences rate of molecular evolution. Molecular Biology and Evolution, 19:302309.Google Scholar
Bromham, L. 2003. What can DNA tell us about the Cambrian explosion? Integrative and Comparative Biology, 43:148156.Google Scholar
Bromham, L., Penny, D., and Phillips, M. 1999. Molecular dates and the mammalian radiation: reply. Trends in Ecology and Evolution, 14:278.Google Scholar
Bromham, L., Phillips, M. J., and Penny, D. 1999. Growing up with dinosaurs: molecular dates and the mammalian radiation. Trends in Ecology and Evolution, 14:113118.Google Scholar
Bromham, L., Woolftt, M., Lee, M. S. Y., and Rambaut, A. 2002. Testing the relationship between morphological and molecular rates of change along phylogenies. Evolution, 56:19211930.Google Scholar
Budd, G. E. 2003. The Cambrian fossil record and the origin of the phyla. Integrative and Comparative Biology, 43:157165.Google Scholar
Burke, A. C., and Feduccia, A. 1997. Developmental patterns and the identification of homologies in the avian hand. Science, 278:666668.CrossRefGoogle Scholar
Cooper, A., and Penny, D. 1997. Mass survival of birds across the Cretaceous-Tertiary Boundary. Science, 275:11091113.Google Scholar
Corneli, P. S. 2003. Complete mitochondrial genomes and eutherian evolution. Journal of Mammalian Evolution, 9:281305.Google Scholar
Cracraft, J. 2001. Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proceedings of the Royal Society of London B, 268:459469.Google Scholar
Densmore, L. D. 1983. Biochemical and immunological systematics of the order Crocodilia, p. 397465. In Hecht, M. K., Wallace, B., and Prance, G. H. (eds.), Evolutionary Biology. Volume 16. Plenum Press, New York.CrossRefGoogle Scholar
Douady, C., Chatelier, P. I., Madsen, O., de Jong, W. W., Catzeflis, F. M., Springer, M. S., and Stanhope, M. J. 2002. Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews. Molecular Phylogenetics and Evolution, 25:200209.Google Scholar
Doyle, J. A. 1998. Molecules, morphology, fossils, and the relationship of angiosperms and Gnetales. Molecular Phylogenetics and Evolution, 9:448462.CrossRefGoogle ScholarPubMed
Easteal, S. 2001. Molecular evidence for the early divergence of placental mammals. BioEssays, 21:10521058.Google Scholar
Feduccia, A. 1995. Explosive radiation in Tertiary birds and mammals. Science, 267:637638.Google Scholar
Felsenstein, J. 2003. Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts, 580 p.Google Scholar
Fleagle, J. G. 1998. Primate Adaptation and Evolution (second edition). Academic Press, San Diego, 608 p.Google Scholar
Foote, M., Hunter, J. P., Janis, C. M., and Sepkoski, J. J. 1999. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science, 283:13101314.CrossRefGoogle ScholarPubMed
Gauthier, J., and Wagner, G. 1998. I, II, II or II, III, IV or both? A solution to the problem of avian digit homology. Journal of Vertebrate Paleontology, 18:45A46A.Google Scholar
Givnish, T. J., and Sytsma, K. J. 1997. Homoplasy in molecular s. morphological data: the likelihood of correct phylogenetic inference, p. 55101. In Givnish, T. J. and Sytsma, K. J. (eds.), Molecular Evolution and Adaptive Radiation. Cambridge University Press, New York.Google Scholar
Goodman, M. 1989. Emerging alliance o phylogenetic systematics and molecular biology: a new age of exploration, p. 4361. In Fernholm, B., Bremer, K., and Jörnwell, H. (eds.), The Hierarchy of Life. Elsevier Science Publishers, Amsterdam.Google Scholar
Hadly, E. A. 2003. The interface of paleontology and mammalogy: past, present, and future. Journal of Mammalogy, 84:347353.Google Scholar
Harshman, J., Huddleston, C. J., Bollback, J. P., Parsons, T. J., and Braun, M. J. 2003. True and false gharials: a nuclear gene phylogeny of Crocodylia. Systematic Biology, 52:386402.Google Scholar
Hasegawa, M., Kishino, H., and Yano, T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 21:160174.Google Scholar
Hedges, S. B., and Sibley, C. G. 1994. Molecules vs. morphology in avian evolution: the case of the “pelicaniform” birds. Proceedings of the National Academy of Sciences of the U. S. A., 91:98619865.Google Scholar
Holland, S. M., and Patzkowsky, M. E. 2002. Stratigraphic variation in the timing of first and last occurrences. Palaios, 17:134146.2.0.CO;2>CrossRefGoogle Scholar
Hope, S. 2002. The Mesozoic radiation of Neornithes, p. 339388. In Chiappe, L. and Witmer, L. M. (eds.), Mesozoic Birds: Above the Heads of Dinosaurs. University of California Press, Berkeley.Google Scholar
Huelsenbeck, J. P., and Rannala, B. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science, 276:227232.Google Scholar
Kimura, M. 1968. Evolutionary rate at the molecular level. Nature, 217:624626.Google Scholar
Kirchman, J. J., Hackett, S. J., Goodman, S. M., and Bates, J. M. 2001. Phylogeny and systematics of ground rollers (Brachypteraciidae) of Madagascar. The Auk, 118:849863.Google Scholar
Krieger, J., and Fuerst, P. A. 2002. Evidence for a slowed rate of molecular evolution in the Order Acipenseriformes. Molecular Biology and Evolution, 19:891897.Google Scholar
Kumar, S., and Hedges, S. B. 1998. A molecular timescale for vertebrate evolution. Nature, 392:917920.CrossRefGoogle ScholarPubMed
Kundrát, M., Seichert, V., Russell, A. P., and Smetana, K. 2002. Pentadactyl pattern of the avian wing autopodium and pyramid reduction hypothesis. Journal of Experimental Zoology, 294:152159.CrossRefGoogle ScholarPubMed
Larsson, H. C. E., and Wagner, G. P. 2002. Pentadactyl ground state of the avian wing. Journal of Experimental Zoology, 294:146151.Google Scholar
Lee, M. S. Y. 1999. Molecular clock calibrations and metazoan divergence dates. Journal of Molecular Evolution, 49:385391.Google Scholar
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, 24:470497.Google Scholar
Marshall, C. R. 1990. The fossil record and estimating divergence times between lineages: maximum divergence times and the importance of reliable phylogenies. Journal of Molecular Evolution, 30:400408.Google Scholar
Marshall, C. R. 1997. Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons. Paleobiology, 23:165173.Google Scholar
Marshall, C. R. 1999. Fossil gap analysis supports early Tertiary origin of trophically diverse avian orders: Comment. Geology, 27:95.Google Scholar
Mayr, G., and Mourer-Chauvire, C. 2003. Phylogeny and fossil record of the Brachypteraciidae: a Comment on Kirchman et al. (2001). The Auk, 120:202203.CrossRefGoogle Scholar
Mindell, D. P., Knight, A., Baer, C., and Huddleston, C. J. 1996. Slow rates of molecular evolution in birds and the metabolic rate and body temperature hypothesis. Molecular Biology and Evolution, 13:422426.Google Scholar
Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.Google Scholar
Omland, K. E. 1997. Correlated rates of molecular and morphological evolution. Evolution, 51:13811393.Google Scholar
Patterson, C. 1987. Molecules and Morphology in Evolution: Conflict or Compromise? Cambridge University Press, New York, 229 p.Google Scholar
Pilbeam, D. R. 1968. The earliest hominids. Nature, 219:13351338.Google Scholar
Sarich, V. M., and Wilson, A. C. 1967. Immunological time scale for hominid evolution. Science, 158:12001203.Google Scholar
Sibley, C. G., and Ahlquist, J. E. 1987. Avian phylogeny reconstructed from comparisons of the genetic material, DNA, p. 95121. In Patterson, C. (ed.), Molecules and Morphology in Evolution: Conflict or Compromise? Cambridge University Press, New York.Google Scholar
Simons, E. L. 1961. The phyletic position of Ramapithecus. Postilla, 54:120.Google Scholar
Smith, A. B., and Peterson, K. J. 2002. Dating the time of origin of major clades: molecular clocks and the fossil record. Annual Review of Earth and Planetary Sciences, 30:6588.Google Scholar
Solow, A. R. 2003. Estimation of stratigraphic ranges when fossil finds are not randomly distributed. Paleobiology, 29:181185.Google Scholar
Springer, M. S. 1995. Molecular clocks and the incompleteness of the fossil record. Journal of Molecular Evolution, 41:531538.Google Scholar
Springer, M. S., Murphy, W. J., Eizirik, E., and O'Brien, S. J. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proceedings of the National Academy of Sciences of the U. S. A., 100:10561061.Google Scholar
Swofford, D. L., Olsen, G. J., Waddell, P. J., and Hillis, D. M. 1996. Phylogenetic inference, p. 407514. In Hillis, D. M., Moritz, C., and Mable, B. K. (eds.), Molecular Systematics (second edition). Sinauer Associates, Sunderland, Massachusetts.Google Scholar
van Tuinen, M., Sibley, C. G., and Hedges, S. B. 2000. The early history of modern birds inferred from DNA sequences of nuclear and mitochondrial ribosomal genes. Molecular Biology and Evolution, 17:451457.Google Scholar
Vignaud, P., Duringer, P., Mackaye, H. T., Likius, A., Blondel, C., Boisserie, J.-R., de Bonis, L., Eisenmann, V., Etienne, M.-E., Geraads, D., Guy, F., Lehmann, T., Lihoreau, F., Lopez-Martinez, N., Mourer-Chauviré, C., Otero, O., Rage, J. C., Schuster, M., Viriot, L., Zazzo, A., and Brunet, M. 2002. Geology and palaeontology of the Upper Miocene Toros-Menalla hominid locality, Chad. Nature, 418:152155.Google Scholar
Webster, A. J., Payne, R. J. H., and Pagel, M. 2003. Molecular phylogenies link rates of evolution and speciation. Science, 301:478.Google Scholar
Whittle, C.-A., and Johnston, M. O. 2003. Broad-scale analysis contradicts the theory that generation time affects molecular evolutionary rates in plants. Journal of Molecular Evolution, 56:223233.Google Scholar
Wikström, N., Savolainen, V., and Chase, M. W. 2001. Evolution of the angiosperms: calibrating the family tree. Proceedings of the Royal Society of London B, 268:22112220.Google Scholar
Wood, B. 2002. Hominid revelations from Chad. Nature, 418:133135.Google Scholar
Wray, G. A., Levinton, J. S., and Shapiro, L. H. 1996. Molecular evidence for deep Precambrian divergences among metazoan phyla. Science, 274:568573.CrossRefGoogle Scholar
Yi, S., Ellsworth, D. L., and Li, W.-H. 2002. Slow molecular clocks in Old World monkeys, apes, and humans. Molecular Biology and Evolution, 19:21912198.Google Scholar
Zuckerkandl, E., and Pauling, L. 1962. Molecular disease, evolution and genic heterogeneity, p. 189225. In Kasha, M. and Pullman, B. (eds.), Horizons in Biochemistry. Academic Press, New York.Google Scholar