Inferring the historical patterns of biological evolution

Nature - Tập 401 Số 6756 - Trang 877-884 - 1999
Mark Pagel1
1School of Animal and Microbial Sciences, University of Reading, Whiteknights, UK

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Hillis,D. M., Moritz,C. & Mable,B. K. Molecular Systematics, 2nd edn (Sinauer, Sunderland, Massachusetts, 1996).

Pagel,M. Inferring evolutionary processes from phylogenies. Zool. Scripta 26, 331–348 (1997).

Edwards,A. W. F. Likelihood (Cambridge Univ. Press, Cambridge, 1972).

Golding,G. B. & Dean,A. M. The structural basis of molecular adaptation. Mol. Biol. Evol. 15, 355– 369 (1998).

Ivics,Z., Hackett,P. B., Plasterk,R. H. & Izsvak,Z. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91, 501–510 (1997).

Pagel,M. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. B 255, 37–45 (1994).

Schluter,D. Uncertainty in ancient phylogenies. Nature 377, 108–109 (1995).

Schluter,D., Price,T., Mooers,A. Ø. & Ludwig,D. Likelihood of ancestor states in adaptive radiation. Evolution 51, 1699–1711 ( 1997).

Yang,Z., Kumar,S. & Nei,M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141, 1641–1650 (1995).

Koshi,J. M. & Goldstein,R. A. Probabilistic reconstruction of ancestral protein sequences. J. Mol. Evol. 42, 313–320 (1996).

Mooers,A. Ø. & Schluter,D. Support for one and two rate models of discrete trait evolution. Syst. Biol. 48, 623–633 (1999).

Pagel,M. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol. 48, 612–622 (1999).

Hillis,D. M., Bull,J. J., White,M. E., Badgett,M. R. & Molineux, I. J. Experimental phylogenetics: generation of a known phylogeny. Science 255, 589– 592 (1992).

Collins,T. M., Wimberger,P. H. & Naylor, G. J. P. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Syst. Biol. 43, 482–496 (1994).

Maddison,D. R. Phylogenetic methods for inferring the evolutionary history and process of change in discreetly valued characters. Annu. Rev. Entomol. 39, 267–292 (1994).

Tuffley,C. & Steel,M. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bull. Math. Biol. 59, 581–607 (1997).

Johnston,J. Econometric Methods (McGraw Hill, New York, 1963).

Martins,E. P. & Hansen,T. F. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat. 149, 646–667 (1997).

Jermann,T. M., Opitz,J. G., Stackhouse,J. & Benner,S. A. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374, 57–59 (1995).

Li,W.-H. Molecular Evolution (Sinauer, Sunderland, Massachusetts, 1997).

Yeager,M. & Hughes,A. L. Evolution of the mammalian MHC: natural selection, recombination, and convergent evolution. Immunol. Rev. 167, 45–58 ( 1999).

Bull,J. J. et al. Exceptional convergent evolution in a virus. Genetics 147, 1497–1507 ( 1997).

Roux,K. H. et al. Structural analysis of the nurse shark (new) antigen receptor (NAR): Molecular convergence of NAR and unusual mammalian immunoglobulins. Proc. Natl Acad. Sci. USA 95, 11804– 11809 (1998).

Crandall,K. A., Kelsey,C. R., Imamichi,H., Lane,H. C. & Salzman,N. P. Parallel evolution of drug resistance in HIV: Failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol. Biol. Evol. 16, 372– 382 (1999).

Mojzsis,S. J. et al. Evidence for life on earth before 3,800 million years ago. Nature 384, 55–59 (1996).

Woese,C. R. Bacterial evolution. Microbiol. Rev. 51, 221–271 (1987).

Pace,N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734–740 ( 1997).

Brown,J. R. & Doolittle,W. F. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61, 456–504 (1997).

Galtier,N., Tourasse,N. & Gouy,M. A nonhyperthermophilic common ancestor to extant life forms. Science 283, 220– 221 (1999).

Fitch,W. M., Leiter,J. M. E., Li,X. & Palese,P. Positive Darwinian evolution in human influenza A viruses. Proc. Natl Acad. Sci. USA 88, 4270–4274 ( 1991).

Omland,K. Character congruence between a molecular and a morphological phylogeny for dabbling ducks (Anas). Syst. Biol. 43, 369–386 (1994).

Omland,K. Correlated ratest of molecular and morphological evolution. Evolution 51, 1381–1393 ( 1997).

Strauss,E. Can mitochondrial clocks keep time? Science 283, 1435–1438 (1999).

Rambaut,A. & Bromham,L. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15, 442–448 (1998).

Bromham,L., Rambaut,A., Fortey,R., Cooper,A. & Penny,D. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proc. Natl Acad. Sci. USA 95, 12386– 12389 (1998).

Fortey,R. Life: An Unauthorised Biography (HarperCollins, London, 1997).

Valentine,J. W., Erwin,D. H. & Jablonski, D. Developmental evolution of metazoan bodyplans: The fossil evidence. Dev. Biol. 173, 373– 381 (1996).

Bowring,S. A. et al. Calibrating rates of early Cambrian evolution. Science 261, 1293–1298 ( 1993).

Wray,G., Levinton,J. S. & Shapiro, L. H. Molecular evidence for deep precambrian divergences among the metazoan phyla. Science 274, 568 –573 (1996).

Ayala,F. J., Rzhetsky,A. & Ayala,F. J. Origin of the metazoan phyla: molecular clocks confirm paleontological estimates. Proc. Natl Acad. Sci. USA 95, 606–611 (1998).

Kerr,R. A. Earliest animals growing younger? Science 284, 411–412 (1999).

Raup,D. M. Mass Extinctions: Bad Genes or Bad Luck? (Oxford Univ. Press, Oxford, 1991).

Cooper,A. & Penny,D. Mass survival of birds across the Cretaceous–Tertiary boundary: molecular evidence. Science 275, 1109–1113 (1997).

Hedges,S. B., Parker,P. H., Sibley,C. G. & Kumar,S. Continental breakup and the ordinal diversification of birds and mammals. Nature 381, 226–229 ( 1996).

Vilá,C. et al. Multiple and ancient origins of the domestic dog. Science 276, 1687–1689 ( 1997).

Krings,M. et al. Neandertal DNA sequences and the origin of modern humans. Cell 90, 19–30 ( 1997).

Darwin,C. The Origin of Species by Means of Natural Selection, 6th edn (with corrections and additions to 1872) (John Murray, London, 1888).

Bowler,P. J. Charles Darwin: The Man and His Influence (Blackwell, Oxford, 1991).

Gould,S. J. & Eldredge,N. Punctuated equilibria comes of age. Nature 366, 223–227 (1993).

Williams,G. C. Natural Selection (Oxford Univ. Press, Oxford, 1992 ).

Hecht,M. K. & Hoffman,A. Why no neo-Darwinism: a critique of paleobiological challenges. Oxford Surv. Evol. Biol. 3, 1–47 (1986).

Foote,M. & Sepkoski,J. J. Jr Absolute measures of the completeness of the fossil record. Nature 398 , 415–417 (1999).

Mooers,A. Ø., Vamosi,S. M. & Schluter, D. Using phylogenies to test macroevolutionary hypotheses of trait evolution. Am. Nat. 154, 249– 259 (1999).

Harvey,P. H. & Pagel,M. The Comparative Method in Evolutionary Biology (Oxford Univ. Press, Oxford, 1991).

Pagel,M. Seeking the evolutionary regression coefficient: an analysis of what comparative methods measure. J. Theor. Biol. 164, 191 –205 (1993).

Ridley,M. The Explanation of Organic Diversity (Oxford Univ. Press, Oxford, 1981).

Maddison,W. P. A method for testing the correlated evolutionary of two binary characters: are gains and losses concentrated on certain branches of a phylogenetic tree. Evolution 44, 539–557 (1990).

Felsenstein,J. Phylogenies and the comparative method. Am. Nat. 125 , 1–15 (1985).

Pagel,M. A method for the analysis of comparative data. J. Theor. Biol. 156, 431–442 ( 1992).

Garland,T. Jr, Harvey,P. H. & Ives,A. R. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Syst. Biol. 41, 18–32 (1992).

Martins,E. P. & Garland,T. H. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45, 534–557 ( 1991).

Purvis,A., Gittleman,J. L. & Luh, H. K. Truth or consequences—effects of phylogenetic accuracy on two comparative methods. J. Theor. Biol. 167, 293–300 (1994).

Rolland,C., Danchin,E. & de Fraipont, M. The evolution of coloniality in birds in relation to food, habitat, predation, and life-history traits: a comparative analysis. Am. Nat. 151, 514–529 (1998).

Ricklefs,R. E. & Starck,J. M. Applications of phylogenetically independent contrasts: A mixed progress report. Oikos 77, 167–172 ( 1996).

Price,T. Correlated evolution and independent contrasts. Phil. Trans. R. Soc. Lond. B 352, 519–529 (1997).

Harvey,P. H. & Rambaut,A. Phylogenetic extinction rates and comparative methodology. Proc. R. Soc. Lond. B 265, 1691–1696 (1998).

Durham,W. Coevolution: Genes, Culture, and Human Diversity (Stanford Univ. Press, Stanford, 1991).

Holden,C. & Mace,R. A phylogenetic analysis of the evolution of lactose digestion. Hum. Biol. 69, 605 –628 (1997).

Jerison,H. J. Evolution of the Brain and Intelligence (Academic, New York, 1973).

Martin,R. D. Relative brain size and metabolic rate in terrestrial vertebrates. Nature 293, 57–60 ( 1981).

Pagel,M. & Harvey,P. H. Taxonomic differences in the scaling of brain on body weight in mammals. Science 244, 1589–1593 (1989).

Arnason,U., Gullberg,A. & Janke,A. Molecular timing of primate divergences as estimated by two nonprimate calibration points. J. Mol. Evol. 47 , 718–727 (1998).

Purvis,A. A composite estimate of primate phylogeny. Phil. Trans. R. Soc. Lond. B 348, 405–421 ( 1995).

Healy,S. D. & Krebs,J. R. Food storing and the hippocampus in Paridae. Brain Behav. Evol. 47, 195– 199 (1996).

Wilson,I. & Balding,D. Geneaological inference from microsatellite data. Genetics 150, 499– 510 (1998).

Larget,B. & Simon,D. L. Markov chain monte carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750–759 ( 1999).

Ursing,B. M. & Arnason,U. Analyses of mitochondrial genomes strongly support a hippopotamus–whale clade. Proc. R. Soc. Lond. B 265, 2252–2255 ( 1998).