Inferring ancestral states without assuming neutrality or gradualism using a stable model of continuous character evolution

BMC Evolutionary Biology

Volumn 14, Issue 1, 2014, Pages

  Elliot, Michael G ^a   Mooers, Arne Ø ^b  

^a ST JOHN S COLLEGE   (United Kingdom)

^b SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Ancestral state reconstruction; Comparative methods; Evolutionary models

Indexed keywords

ANCESTRY; BODY MASS; BROWNIAN MOTION; DATABASE; GRADUALISM; HYPOTHESIS TESTING; MAMMAL; PHYLOGENETICS; STOCHASTICITY;

MAMMALIA;

ANIMAL; BIOLOGICAL MODEL; CLASSIFICATION; EVOLUTION; GENETICS; MAMMAL; MONTE CARLO METHOD; PHYLOGENY; PHYSIOLOGY; PROBABILITY;

ANIMALS; BIOLOGICAL EVOLUTION; MAMMALS; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PHYLOGENY;

EID: 84965187191     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/s12862-014-0226-8     Document Type: Article

References (84)

1. Harvey P, Pagel M: The Comparative Method in Evolutionary Biology. Oxford Series in Ecology and Evolution. Oxford, UK: Oxford University Press; 1991.
2. Martins E (Ed): Phylogenies and the Comparative Method in Animal Behavior, Oxford, UK: Oxford University Press; 1996.
3. Pagel M, Harvey P: Comparative methods for examining adaptation depend on evolutionary models. Folio Primatol 1989, 53:203-220.
4. Cunninham C: Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses. Syst Biol 1999, 48:665-674.
5. Oakley T, Cunninham C: Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution 2000, 54:397-405.
6. Finarelli J, Flynn J: Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record. Syst Biol 2006, 55:301-313.
7. Slater G, Harmon L, Alfaro M: Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 2012, 66:3931-3944.
8. Cavalli-Sforza L, Edwards A: Phylogenetic analysis models and estimation procedures. Am J Hum Genet 1967, 19:233-257.
9. Maddison W: Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree. Syst Zool 1991, 40(3):304-14.
10. McArdle B, Rodrigo A: Estimating the ancestral state of a continuous-valued character using squared-change parsimony: an analytical solution. Syst Biol 1994, 43:573-578.
11. Schluter D, Price T, Mooers A, Ludwig D: Likelihood of ancestor states in adaptive radiation. Evolution 1997, 51(6):1699-1711.
12. Grafen A: The phylogenetic regression. Phil Trans Roy Soc Lond B 1989, 326:265-292.
13. Harmon L, Schulte J, Larson A, Losos J: Tempo and mode of evolutionary radiation in iguanian lizards. Science 2003, 301:2385-2396.
14. Harmon L, Losos J, Davies T, Gillespie R, Gittleman J, Jennings W, Kozak K, McPeek M, Moreno-Roark F, Near T, Purvis A, Ricklefs R, Schluter D, Schulte J, Seehausen O, Sidlauskas B, Torres-Carvajal O, Weir J, Mooers A: Early bursts of body size and shape evolution are rare in comparative data. Evolution 2010, 64:2385-2396.
15. O'Meara B, Ane C, Sanderson M, Wainwright P: Testing for different rates of continuous trait evolution using likelihood. Evolution 2006, 60:922-933.
16. Gnedenko B, Kolmogorov A: Limit Distributions for Sums of Independent Random Variables. Addison-Wesley Series in Statistics. Reading MA: Addison-Wesley; 1949.
17. Samorodnitsky G, Taqqu M: Stable Non-Gaussian Random Processes. New York: Chapman and Hall; 1994.
18. Uchaikin V, Zolotarev V: Chance and Stability: Stable Distributions and their Applications. Utrecht: VSP; 1999.
19. Nolan J: Numerical calculation of stable densities and distribution functions. Stoch Mod 1997, 13:759-774.
20. Gorenflo R, Mainardi F, Moretti D, Pagnini G, Paradisi P: Fractional diffusion: probability distributions and random walkmodels. Physica A 2002, 305:106-112.
21. Lavallée D: Stochasticmodeling of slip spatial complexities for the 1979 Imperial Valley, California, earthquake. Geophys Res Lett 2003, 30:1-4.
22. Nikias C: Signal Processing with Alpha-Stable Distributions and Applications. New York: Wiley-Blackwell; 1997.
23. Wiswanathan G, Afanasyev V, Buldyrev S, Murphy E, Prince P, Stanley H: Lévy flight search patterns of wandering albatrosses. Nature 1996, 381:413-415.
24. Menabde M, Sivapalan M: Modeling of rainfall time series and extremes, using bounded random cascades and Lévy-stable distributions. Water Resour Res 2000, 36:3293-3300.
25. Weron R: Modeling and forecasting electricity loads and prices: a statistical approach. New York: John Wiley; 2006.
26. Young M: Revisiting non-normal real estate return distributions by property type in the U.S. J Real Estate Financ Econ 2008, 36:233-248.
27. Fofack H, Nolan J: Distribution of parallel exchange rates in African countries. J Int Money Financ 2001, 20:987-1001.
28. Rachev S (Ed): Handbook of Heavy Tailed Distributions in Finance. Handbooks in Finance, Amsterdam: North-Holland; 2003.
29. Arce G: Nonlinear Signal Processing. New York: Wiley; 2005.
30. Mikosch T, Resnick S, Rootzén H, Stegeman A: Is network traffic approximated by stable lévymotion or fractional brownian motion? Ann Appl Probab 2002, 12:23-68.
31. Landis M, Schraiber J, Liang M: Phylogenetic analysis using Lévy processes: finding jumps in the evolution of continuous traits. Syst Biol 2013, 62:193-204.
32. Devroye L: Non-Uniform Random Variate Generation. New York: Springer Verlag; 1986.
33. Matsui M, Takemura A: Improvements in numerical evaluation of symmetric stable density and its derivatives. CIRJE Discuss Papers 2004, F292:1-20.
34. Brorsen B, Yang S: Maximum likelihood estimates of symmetric stable distribution parameters. Commun Stat Simul Comp 1990, 19:1459-1464.
35. McCulloch J: A Practical Guide to Heavy Tails: Statistical Techniques and Applications. Cambridge, MA: Birkhäuser Boston; 1998. chap. Numerical approximation of the symmetric stable distribution and density.
36. Nolan J: Lévy Processes: Theory and Applications. Cambridge, MA: Birkhäuser Boston; 2001. chap. Maximum likelihood estimation and diagnostics for stable distributions.
37. Ciuperca G, Ridolfi A, Idier J: Penalized maximum likelihood estimator for normalmixtures. Scan J Stat 2003, 30:45-59.
38. Metropolis M, Rosenbluth A, Rosenbluth M, Teller A, Teller E: Equation of state calculations by fast computing machines. J Chem Phys 1953, 21:1087-1092.
39. Geyer C: Computing Science and Statistics: Proceedings of the 23rd Symposium of the Interface. New York: American Statistical Association; 1991. chap. Marko chain Monte Carlo maximum likelihood.
40. Neal R: Slice sampling. Ann Stat 2003, 31:705-767.
41. McLachlan G: Finite mixture models. New York: Wiley; 2000.
42. Akaike H: A new look at the statistical model identification. IEEE Trans Automat Contr 1974, 19:716-723.
43. Spiegelhalter D, Best N, Carlin B, van der Linde A: Bayesian measures of model complexity and fit (with discussion). J Roy Stat Soc B 2002, 64:583-616.
44. Ando T, Tsay R: Predictive likelihood for Bayesian model selection and averaging. Int J Forecast 2010, 26:744-763.
45. Rambaut A, Drummond A: Tracer v1.4, Available from. http://beast.bio. ed.ac.uk/Tracer
46. Brooks S, Gelman A: General methods for monitoring convergence of iterative simulation. J Comp Graph Stat 1998, 7:434-455.
47. Maddison W, Maddison D: Mesquite: a modular system for evolutionary analysis, version 2.6. 2011. http://www.mesquiteproject.org.
48. Bininda-Emonds O, Cardillo M, Jones K, MacPhee R, Beck R, Grenyer R, Price S, Vos R, Gittleman J, Purvis A: The delayed rise of present-day mammals. Nature 2007, 446:507-512.
49. Ernest S: Life history characteristics of placental nonvolant mammals. Ecology 2003, 84:3402.
50. Pitnick S, Jones K, Wilkinson G: Mating system and brain size in bats. Proc R Soc Lond B 2006, 273:719-724.
51. Hansen T, Pienaar J, Orzack S: A comparative method for studying adaptation to a randomly evolving environment. Evolution 2008, 62:1965-1977.
52. Blomberg SP, Jr. Garland T, Ives AR: Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 2003, 57:717-745.
53. Eastman J, Alfaro M, Joyce P, Hipp A, Harmon L: A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 2011, 65:3578-3589.
54. Harmon J, Weir JT, Brock C, Glor RE, Challenger W: GEIGER: Investigating evolutionary radiations. Bioinformatics 2008, 24:129-131.
55. Cooper N, Purvis A: Body size evolution inmammals: complexity in tempo and mode. Am Nat 2010, 175:727-738.
56. Alroy J, Crampton J, Erwin D, Kiessling W, Miller A, Peters A, Polly D: The Paleobiology Database. 2011. Published online at http://www.paleodb.org, accessed June 2011.
57. Fleagle J: Primate Adaptation and Evolution. New York: Academic Press; 1999.
58. Goswami A, Friscia A (Eds): Carnivoran Evolution: New Views on Phylogeny, Form and Function, Cambridge, UK: Cambridge University Press; 2010.
59. Ji Q, Luo Z, Yuan C, Wible J, Zhang J, Georgi J: The earliest known eutherian mammal. Nature 2002, 416:816-822.
60. Luo Z, Yuan C, Meng Q, Ji Q: A Jurassic eutherian mammal and divergence of marsupials and placentals. Nature 2011, 476:443-445.
61. Rasmussen D, Pickford M, Mein P, Senut B, Conroy G: Earliest known Procaviid Hyracoid from the late Miocene of Namibia. JMammal 1996, 77:745-754.
62. Rose K: The Beginning of the Age of Mammals. Baltimore: Johns Hopkins University Press; 2006.
63. Rose K, DeLeon V, Missiaen P, Rana R, Sahni A, Singh L, Smith T: Early Eocene lagomorph (Mammalia) from Western India and the early diversification of Lagomorpha. Proc Biol Sci 2008, 275:1203-1208.
64. Rydell J, Speakman J: Evolution of nocturnality in bats: potential competitors and predators during their early history. Biol J Linn Soc Lond 1995, 54:183-191.
65. Wood J: The extinction of the Multituberculates outside North America: a global approach to testing the competition model. Master's thesis. Ohio State University 2010.
66. Coddington J: Cladistic tests of adadaptation hypotheses. Cladistics 1988, 4:3-22.
67. Pagel M: Inferring the historical patterns of biological evolution. Nature 1999, 401:877-884.
68. Martins E: Adaptation and the comparative method. Trends Ecol Evol 2000, 15:296-299.
69. Pagel M, Meade A, Barker D: Bayesian estimation of ancestral character states on phylogenies. Syst Biol 2004, 53:673-684.
70. Donoghue M, Doyle J, Gauthier J, Kluge A, Rowe T: The importance of fossils in phylogeny reconstruction. Ann Rev Ecol Systemat 1989, 20:431-460.
71. Webster A, Purvis A: Testing the accuracy ofmethods for reconstructing ancestral states of continuous characters. Proc Biol Sci 2002, 269:143-149.
72. Polly P: Paleontology and the comparative method: ancestral node reconstructions versus observed node values. Am Nat 2001, 157:596-609.
73. Hansen T: Stabilizing selection and the comparative analysis of adaptation. Evolution 1997, 51:1341-1351.
74. Butler M, King A: Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am Nat 2004, 164:233-257.
75. Beaulieu J, Jhwueng D, Boettiger C, O'Meara B: Modeling stabilizing selection: expanding the Ornstein-Uhlenbeck model of adaptive evolution. Evolution 2012, 66:2369-2383.
76. Gittleman J, Kot M: Adaptation: statistics and a null model for estimating phylogenetic effects. Syst Biol 1990, 39:227-241.
77. Garland T, Harvey P, Ives A: Procedures for the analysis of comparative data using phylogenetically independent contrasts. Sys Biol 1992, 41:18-32.
78. Thorne J, Kishino H, Painter I: Estimating the rate of evolution of the rate of molecular evolution. Bol Biol Evol 1998, 15:1647-1657.
79. Felsenstein J: Phylogenies and the comparative method. Am Nat 1985, 125:1-15.
80. Garland T, Dickerman A, Janis C, Jones J: Phylogenetic analysis of covariance by computer simulation. Syst Biol 1993, 42:265-292.
81. Martins EP, Hansen TF: Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am Nat 149:646-667.
82. McCulloch J: A Practical Guide to Heavy Tails: Statistical Techniques and Applications. Cambridge, MA: Birkhäuser Boston; 1998. chap. Linear regression with stable disturbances.
83. Frain J: Maximum likelihood estimates of regression coefficients with alpha-stable residuals and day of week effects in total returns on equity indices. Trinity Econ Papers 2008, tep0108:1-27.
84. Paulaauskas V, Rachev S: Maximum likelihood estimators in regression models with infinite variance innovations. Stat Pap 2003, 44:47-65.