Potential pitfalls of reconstructing deep time evolutionary history with only extant data, a case study using the canidae (mammalia, carnivora)

Evolution

Volumn 67, Issue 12, 2013, Pages 3678-3685

  Finarelli, John A ^a   Goswami, Anjali ^b  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Ancestral state reconstruction; Body size; Evolutionary rates; Fossils

Indexed keywords

BODY MASS; BODY SIZE; CANID; DATA INTERPRETATION; DATABASE; FOSSIL RECORD; PARAMETERIZATION; PHYLOGENY; RECONSTRUCTION;

CANIDAE; CANIS FAMILIARIS; CARNIVORA; MAMMALIA;

ANCESTRAL STATE RECONSTRUCTION; ANIMAL; ARTICLE; BODY SIZE; CANIDAE; EVOLUTIONARY RATES; FOSSIL; GENETICS; MOLECULAR EVOLUTION; TIME;

ANCESTRAL STATE RECONSTRUCTION; BODY SIZE; EVOLUTIONARY RATES; FOSSILS;

ANIMALS; CANIDAE; EVOLUTION, MOLECULAR; FOSSILS; TIME FACTORS;

EID: 84888843142     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12222     Document Type: Article

References (70)

1. Albert, J. S., D. M. Johnson, and J. H. Knouft . 2009. Fossils provide better estimates of ancestral body size than do extant taxa in fishes. Acta Zoologica 90:357-384.
2. Alroy, J. 1998. Cope's rule and the dynamics of body mass evolution in North American fossil mammals. Science 280:731-734.
3. Alroy, J.. 2000. Understanding the dynamics of trends within evolving lineages. Paleobiology 26:319-329.
4. Bardeleben, C., R. L. Moore, and R. K. Wayne . 2005. A molecular phylogeny of the Canidae based on six nuclear loci. Mol. Phyl. Evol. 37:815-831.
5. Bininda-Emonds, O. R. P., M. Cardillo, K. E. Jones, R. D. E. MacPhee, R. M. D. Beck, R. Grenyer, S. A. Price, R. A. Vos, J. L. Gittleman, and A. Purvis . 2007. The delayed rise of present-day mammals. Nature 446:507-512.
6. Blomberg, S. P., J. T. Garland, and A. R. Ives . 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745.
7. Burnham, K. P., and D. R. Anderson . 2002. Model selection and multimodel inference: a practical information-theoretic approach. Springer, New York.
8. Carbone, C., A. Teacher, and J. M. Rowcliffe . 2007. The cost of carnivory. PLoS Biol. 5:0363-0368.
9. Czaplewski, N. J., G. S. Morgan, and S. A. McCleod . 2008. Chiroptera. Pp. 174-197 in C. M. Janis, G. F. Gunnell, and M. D. Uhen, eds. Evolution of tertiary mammals of North America. Cambridge Univ. Press, New York.
10. Edwards, A. W. F. 1992. Likelihood: expanded edition. The Johns Hopkins Univ. Press, Baltimore, MD.
11. Ernest, S. K. M. 2003. Life history characteristics of placental non-volant mammals. Ecology 84:3402.
12. Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
13. Finarelli, J. A. 2007. Mechanisms behind active trends in body size evolution in the Canidae (Carnivora: Mammalia). Am. Nat. 170:876-885.
14. Finarelli, J. A.. 2008a. Hierarchy and the reconstruction of evolutionary trends: evidence for constraints on the evolution of body size in terrestrial caniform carnivorans (Mammalia). Paleobiology 34:553-562.
15. Finarelli, J. A.. 2008b. Testing hypotheses of the evolution of brain-body size scaling in the Canidae (Carnivora, Mammalia). Paleobiology 34:35-45.
16. Finarelli, J. A.. 2008c. A total evidence phylogeny of the Arctoidea (Carnivora: Mammalia): relationships among basal taxa. J. Mammalian Evol. 15:231-259.
17. Finarelli, J. A., and J. J. Flynn . 2006. Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record. Syst. Biol. 55:301-313.
18. Finarelli, J. A., and J. J. Flynn . 2009. Brain size evolution and sociality in Carnivora. Proc. Natl. Acad. Sci. 106:9345-9349.
19. Flynn, J. J., J. A. Finarelli, S. Zehr, J. Hsu, and M. A. Nedbal . 2005. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst. Biol. 54:317-337.
20. Flynn, L. J., and L. L. Jacobs . 2008. Castoroidea. Pp. 391-405 in C. M. Janis, G. F. Gunnell, and M. D. Uhen, eds. The evolution of tertiary mammals of North America. Cambridge Univ. Press, New York.
21. Garland, T., P. H. Harvey, and A. R. Ives . 1992. Procedures for the analysis of comparative data using phyogenetically independent contrasts. Syst. Biol. 41:18-32.
22. Gaubert, P., and P. Cordeiro-Estrela . 2006. Phylogenetic systematics and tempo of evolution of the Viverrinae (Mammalia, Carnivora, Viverridae) within feliformians: implications for faunal exchanges between Asia and Africa. Mol. Phyl. Evol. 41:266-278.
23. Gittleman, J. L. 1986. Carnivore life history patterns: allometric, phylogenetic, and ecological associations. Am. Nat. 127:744-771.
24. Gould, S. J. 1988. Trends as changes in variance-a new slant on progress and directionality in evolution. Journal of Paleontology 62:319-329.
25. Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
26. Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341-1351.
27. Harmon, L. J., J. B. Losos, T. J. Davies, R. G. Gillespie, J. L. Gittleman, W. B. Jennings, K. H. Kozak, M. A. McPeek, F. Moreno-Roark, T. J. Near, et al. 2010. Early bursts of body size and shape evolution are rare in comparative data. Evolution 64:2385-2396.
28. Huelsenbeck, J. P. 1991. When are fossils better than extant taxa in phylogenetic analysis. Syst. Zool. 40:458-469.
29. Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32:578-601.
30. Hunt, G.. 2007. The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages. Proc. Natl. Acad. Sci. 104:18404-18408.
31. Hunt, G.. 2012. Measuring rates of phenotypic evolution and the inseparability of tempo and mode. Paleobiology 38:351-373.
32. Hurvich, C. M., and C.-L. Tsai . 1989. Regression and time series model selection in small samples. Biometrika 76:297-307.
33. Isaac, N. J. B., K. E. Jones, J. L. Gittleman, and A. Purvis . 2005. Correlates of species richness in mammals: body size, life history, and ecology. Am. Nat. 165:600-607.
34. Jablonski, D. 1997. Body-size evolution in Cretaceous molluscs and the status of Cope's rule. Nature 385:250-252.
35. Jablonski, D.. 2008. Extinction and the spatial dynamics of biodiversity. Proc. Natl. Acad. Sci. 105 (Suppl. 1):11528-11535.
36. Jablonski, D., and D. M. Raup . 1995. Selectivity of End-Cretaceous marine bivalve extinctions. Science 268:389-392.
37. Janis, C. M., M. W. Colbert, M. C. Coombs, W. D. Lambert, B. J. MacFadden, B. J. Mader, D. R. Prothero, R. M. Schoch, J. Shoshani, and W. P. Wall . 1998. Perissodactyla and Probosciedea. Pp. 511-524 in C. M. Janis, K. M. Scott, and L. L. Jacobs, eds. Evolution of tertiary mammals of North America. Cambridge Univ. Press, New York.
38. Kolokotrones, T., S. Van, E. J. Deeds, and W. Fontana . 2010. Curvature in metabolic scaling. Nature 464:753-756.
39. Kuhner, M. K., and J. Felsenstein . 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
40. Lindblad-Toh, K., C. M. Wade, T. S. Mikkelsen, E. K. Karlsson, D. B. Jaffe, M. Kamal, M. Clamp, J. L. Chang, E. J. Kulbokas, M. C. Zody, et al. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803-819.
41. Lyons, S. K., F. A. Smith, and J. H. Brown . 2004. Of mice, mastodons and men: human-mediated extinctions on four continents. Evol. Ecol. Res. 6:339-358.
42. McShea, D. W. 1994. Mechanisms of large-scale evolutionary trends. Evolution 48:1747-1763.
43. McShea, D. W., and R. N. Brandon . 2010. Biology's first law: the tendency for diversity and complexity to increase in evolutionary systems. University of Chicago Press, Chicago.
44. Monroe, M. J., and F. Bokma . 2010. Little evidence for Cope's rule from Bayesian phylogenetic analysis of extant mammals. J. Evol. Biol. 23:2017-2021.
45. Nyakatura, K., and O. R. P. Bininda-Emonds . 2012. Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biol. 10:1-31.
46. Oakley, T. H., and C. W. Cunningham . 2000. Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution 54:397-405.
47. Polly, P. D. 2001. Paleontology and the comparative method: ancestral node reconstructions versus observed node values. Am. Nat. 157:596-609.
48. Roopnarine, P. D. 2001. The description and classification of evolutionary mode: a computational approach. Paleobiology 27:446-465.
49. Royall, R. M. 1997. Statistical evidence: a likelihood paradigm. Chapman and Hall, New York.
50. Ruta, M., P. J. Wagner, and M. I. Coates . 2006. Evolutionary patterns in early tetrapods. I. Rapid initial diversification followed by decrease in rates of character change. Proc. R. Soc. B-Biol. Sci. 273:2107-2111.
51. Sato, J. J., M. Wolsan, S. Minami, T. Hosoda, M. H. Sinaga, K. Hiyama, Y. Yamaguchi, and H. Suzuki . 2009. Deciphering and dating the red panda's ancestry and early adaptive radiation of Musteloidea. Mol. Phyl. Evol. 53:907-922.
52. Slater, G. J., L. J. Harmon, and M. E. Alfaro . 2012. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 66:3931-3944.
53. Smaers, J. B., D. K. N. Dechmann, A. Goswami, C. Soligo, and K. Safi . 2012. Comparative analyses of evolutionary rates reveal different pathways to encephalization in bats, carnivorans, and primates. Proc. Natl. Acad. Sci. 109:18006-18011.
54. Smith, F. A., S. K. Lyons, S. K. M. Ernest, K. E. Jones, D. M. Kaufman, T. Dayan, P. A. Marquet, J. H. Brown, and J. P. Haskell . 2003. Body mass of Late Quaternary mammals. Ecology 84:3403.
55. Solow, A. R., and S. C. Wang . 2008. Some problems with assessing Cope's Rule. Evolution 62:2092-2096.
56. Sookias, R. B., R. J. Butler, and R. B. J. Benson . 2012. Rise of dinosaurs reveals major body-size transitions are driven by passive processes of trait evolution. Proc. R. Soc. B: Biol. Sci. 279:2180-2187.
57. Stanley, S. M. 1973. An explanation for Cope's rule. Evolution 27:1-26.
58. Tedford, R. H., B. E. Taylor, and X. M. Wang . 1995. Phylogeny of the Caninae (Carnivora: Canidae): the living taxa. Am. Mus. Nov. 3146:1-37.
59. Tedford, R. H., X. Wang, and B. E. Taylor . 2009. Phylogenetic systematics of the North American fossil Caninae (Carnivora, Canidae). Bull. Am. Mus. Nat. Hist. 325:1-218.
60. Van Valkenburgh, B., X. M. Wang, and J. Damuth . 2004. Cope 's Rule, hypercarnivory, and extinction in North American canids. Science 306:101-104.
61. Venditti, C., A. Meade, and M. Pagel . 2011. Multiple routes to mammalian diversity. Nature 479:393-396.
62. Wagner, P. J. 1996. Contrasting the underlying patterns of active trends in morphologic evolution. Evolution 50:990-1007.
63. Wagner, P. J.. 1998. A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa. Paleobiology 24:430-449.
64. Wagner, P. J.. 2000. The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity. Syst. Biol. 49:65-86.
65. Wagner, P. J., M. A. Kosnik, and S. Lidgard . 2006. Abundance distributions imply elevated complexity of post-Paleozoic marine ecosystems. Science 314:1289-1292.
66. Wang, S. C. 2005. Accounting for unequal variances in evolutionary trend mechanisms. Paleobiology 31:191-198.
67. Wang, X., and R. H. Tedford . 1996. Canidae. Pp. 433-452 in D. R. Prothero, and R. J. Emry, eds. The terrestrial eocene-oligocene transition in North America. Cambridge Univ. Press, Cambidge, U.K.
68. Wang, X. M. 1994. Phylogenetic systematics of the Hesperocyoninae (Carnivora: Canidae). Bull. Am. Mus. Nat. Hist. 221:1-207.
69. Wang, X. M., R. H. Tedford, and B. E. Taylor . 1999. Phylogenetic systematics of the Borophaginae (Carnivora: Canidae). Bull. Am. Mus. Nat. Hist. 243:1-391.
70. Yu, L., P. T. Luan, W. Jin, O. A. Ryder, L. G. Chemnick, H. A. Davis, and Y. P. Zhang . 2011. Phylogenetic Utility of Nuclear Introns in Interfamilial Relationships of Caniformia (Order Carnivora). Syst. Biol. 60:175-187.