Abstract
Rapid evolutionary radiations characterize many higher-level taxa. This pattern of diversification poses a challenge for accurate phylogenetic reconstruction, since the few synapomorphies defining short internal branches are often overwritten over long periods of evolutionary time, making determination of homology difficult and rendering the outgroup method of rooting prone to error for both molecular and morphological systematic investigations (Carroll, 1988; Novacek, 1992; Swofford et al., 1996). These issues can be addressed and hopefully overcome by employing comprehensive taxon sampling, large numbers of characters, multiple data sets (derived from different sources), and diverse inferential techniques. In spite of being limited to samples of only living or recently extinct taxa, molecular data have great potential to help decipher the pattern and timing of rapid and ancient radiations. Specifically, they provide a means to collect larger numbers of phylogenetic characters than most morphological data matrices, and present a simpler and better understood mode of evolution that can be currently modeled within a maximum likelihood (ML) framework (e.g., Goldman et al., 2000; Swofford et al., 1996; Whelan et al., 2001).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Benton, M. J., 1993, The Fossil Record 2, Chapman & Hall, London.
Benton, M. J., 1999, Early origins of modern birds and mammals: molecules vs. morphology, BioEssays 21:1043–1051.
Bromham, L., Phillips, M. J., and Penny, D., 1999, Growing up with dinosaurs: Molecular dates and the mammalian radiation, Tr. Ecol. Evol. 14: 113–118.
Buckley, T. R., 2002, Model misspecification and probabilistic tests of topology: evidence from empirical data sets, Syst. Biol. 51: 509–523.
Carroll, R. L., 1988, Vertebrate Paleontology and Evolution, Freeman and Co, New York.
D’Erchia, A. M., Gissi, C., Pesole, G., Saccone, C., and Arnason, U., 1996, The guinea pig is not a rodent, Nature 381: 597–600.
Easteal, S., 1999, Molecular evidence for the early divergence of placental mammals, BioEssays 21:1052–1058.
Eizirik, E., Murphy, W. J., and O’Brien, S. J., 2001, Molecular dating and biogeography of the early placental mammal radiation, J. Hered. 92: 212–219.
Foote, M., Hunter, J. P., Janis, C. M., and Sepkoski, J. J. Jr., 1999, Evolutionary and preservational constraints on origins of biologic groups: Divergence times of eutherian mammals, Science 283:1310–1314.
Gatesy, J., Milinkovitch, M., Waddell, V., and Stanhope, M., 1999, Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa, Syst. Biol. 48: 6–20.
Goldman, N., Anderson, J. P., and Rodrigo, A. G., 2000, Likelihood-based tests of topologies in phylogenetics, Syst. Biol. 49: 652–670.
Graur, D., Hide, W. A., and Li, W.-H., 1991, Is the guinea-pig a rodent? Nature 351: 649–652.
Graur, D., Duret, L., and Gouy, M., 1996, Phylogenetic position of the order Lagomorpha (rabbits, hares, and allies), Nature 379: 333–335.
Groves, C. P., 1989, A Theory of Human and Primate Evolution, Clarendon Press, Oxford.
Hillis, D. M., 1996, Inferring complex phylogenies, Nature 383: 130–131.
Huelsenbeck, J. P. and Ronquist, F., 2001, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics 17: 754–755.
Huelsenbeck, J. P., Ronquist, F., Nielsen, R, and Bollback, J. P., 2001, Bayesian inference of phylogeny and its impact on evolutionary biology, Science 294: 2310–2314.
Kay, R. F., Ross, C., and Williams, B. A., 1997, Anthropoid origins, Science 275: 797–804.
Kishino, H. and Hasegawa, M., 1989, Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea, J. Mol. Evol. 29: 170–179.
Kishino, H., Thorne, J. L., and Bruno, W. J., 2001, Performance of a divergence time estimation method under a probabilistic model of rate evolution, Mol. Biol. Evol. 18: 352–361.
Kumar, S. and Hedges, S. B., 1998, A molecular timescale for vertebrate evolution, Nature 392: 917–920.
Lavergne, A., Douzery, E., Stichler, T., Catzeflis, F. M., and Springer, M. S., 1996, Interordinal mammalian relationships: Evidence for paenungulate monophyly is provided by complete mitochondrial 12S rRNA sequences, Mol. Phylogenet. Evol. 6: 245–258.
Madsen, O., Scally, M., Douady, C. J., Kao, D. J., DeBry, R. W., Adkins, R., et al., 2001, Parallel adaptive radiations in two major clades of placental mammals, Nature 409: 610–614.
Martin, A. P. and Palumbi, S. R., 1993, Body size, metabolic rate, generation time, and the molecular clock, Proc. Natl. Acad. Sci. USA 90: 4087–4091.
Martin, R. D., 1990, Primate Origins and Evolution: A Phylogenetic Reconstruction, Princeton University Press, Princeton.
Martin, R D., 1993, Primate origins: Plugging the gaps, Nature 363: 223–234.
McKenna, M. C. and Bell, S. K., 1997, Classification of Mammals Above the Species Level, Columbia University Press, New York.
Murphy, W. J., Eizirik, E., Johnson, W. E., Zhang, Y.-P., Ryder, O. A., and O’Brien, S. J., 2001a, Molecular phylogenetics and the origins of placental mammals, Nature 409: 614–618.
Murphy, W. J., Eizirik, E., O’Brien, S. J., Madsen, O., Scally, M., Douady, C. J., et al., 2001b, Resolution of the early placental mammal radiation using Bayesian phylogenetics, Science 294: 2348–2351.
Novacek, M. J., 1992, Mammalian phylogeny: Shaking the tree, Nature 356: 121–125.
Pryer, K. M., Schneider, H., Smith, A. R, Cranfill, R., Wolf, P. G., Hunt, J. S., and Sipes, S. D., 2001, Horsetails and ferns are a monophyletic group and the dosest living relatives to seed plants, Nature 409: 618–622.
Qiu, Y. L., Lee, J., Bernasconi-Quadroni, F., Soltis, D. E., Soltis, P. S., Zanis, M., et al., 1999, The earliest angiosperms: Evidence from mitochondrial, plastid, and nuclear genomes, Nature 402: 404–407.
Rambaut, A. and Grassly, N. C., 1997, Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Comput. Applic. Biosci. 13: 235–238.
Reyes, A., Gissi, C., Pesole, G., Catzeflis, F., and Saccone, C., 2000, Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris, Mol. Biol. Evol. 17: 979–983.
Reyes, A., Pesole, G., and Saccone, C., 1998, Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: Further evidence of rodent paraphyly, Mol. Biol. Evol. 15: 499–505.
Ross, C., Williams, B., and Kay, R. F., 1998, Phylogenetic analysis of anthropoid relationships, J. Human Evol. 35: 221–306.
Schmitz, J., Ohme, M., and Zischler, H., 2001, SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates, Genetics 157: 777–784.
Schmitz, J., Ohme, M., and Zischler, H., 2002, The complete mitochondrial sequence of Tarsius bancanus: Evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA, Mol. Biol. Evol. 19: 544–553.
Seiffert, E. R., Simons, E. L., and Attia, Y., 2003, Fossil evidence for an ancient divergence of lorises and galagos. Nature 422: 421–424.
Seiffert, E. R., Simons, E. L., and Simons, C. V. M, (this volume) Phylogenetic, biogeographic, and adaptive implications of new fossil evidence bearing on crown anthropoid origins and early stem catarrhine evolution.
Shoshani, J. and McKenna, M. C., 1998, Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data, Mol. Phylogenet. Evol. 9: 572–584.
Simpson, G. G., 1945, The principles of classification and a classification of mammals, Bull. Am. Mus. Nat. Hist. 85: 1–350.
Soltis, P. S., Soltis, D. E., and Chase, M. W., 1999, Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology, Nature 402: 402–404.
Springer, M. S., Cleven, G. C., Madsen, O., de Jong, W. W., Waddell, V. G., Armine, H. M., and Stanhope, M. J., 1997, Endemic African mammals shake the phylogenetic tree, Nature 388: 61–64.
Springer, M. S., DeBry, R. W., Douady, C., Amrine, H. M., Madsen, O., de Jong, W. W., and Stanhope, M. J., 2001, Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction, Mol. Biol. Evol. 18:132–143.
Springer, M.S., Murphy, W.J., Eizirik, E., O’Brien, S. J., 2003, Placental mammal diversification and the Cretaceous-Tertiary boundary, Proc. Natl. Acad. Sci. USA 100:1056–1061.
Swofford, D. L., Olsen, G., Waddell, P., and Hillis, D. M., 1996, Phylogenetic inference, in: Moleeular Systematics. D.M. Hillis, C. Moritz, and B. Mable, eds., Sinauer, Sunderland, pp. 407–514.
Swofford D. L., 1998, PAUP*: Phylogenetic Analysis Using Parsimony and Other Methods. Sinauer, Sunderland.
Takezaki, N., Rzhetsky, A., and Nei, M., 1995, Phylogenetic test of the molecular clock and linearized trees, Mol. Biol. Evol. 12: 823–833.
Tavaré, S., Marshall, C. R., Will, O., Soligo, C., and Martin, R. D., 2002, Using the fossil record to estimate the age of the last common ancestor of extant primates, Nature 416: 726–729.
Teeling, E. C., Scally, M., Kao, D. J., Romagnoli, M., Springer, M. S., and Stanhope, M. J., 2000, Molecular evidence regarding the origin of echolocation and flight in bats, Nature 403: 188–192.
Thorne, J. L., Kishino, H., and Painter, I. S., 1998, Estimating the rate of evolution of the rate of molecular evolution, Mol. Biol. Evol. 15: 1647–1657.
Whelan, S., Lio, P., and Goldman, N., 2001, Molecular phylogenetics: State-of-the-art methods for looking into the past, Trends Genet. 17: 262–272.
Yoder, A. D., and Yang, Z., 2000, Estimation of primate speciation dates using local molecular clocks, Mol. Biol. Evol. 17: 1081–1090.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer Science+Business Media New York
About this chapter
Cite this chapter
Eizirik, E., Murphy, W.J., Springer, M.S., O’Brien, S.J. (2004). Molecular Phylogeny and Dating of Early Primate Divergences. In: Ross, C.F., Kay, R.F. (eds) Anthropoid Origins. Developments in Primatology: Progress and Prospects. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-8873-7_2
Download citation
DOI: https://doi.org/10.1007/978-1-4419-8873-7_2
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4613-4700-2
Online ISBN: 978-1-4419-8873-7
eBook Packages: Springer Book Archive