Extant-only comparative methods fail to recover the disparity preserved in the bird fossil record

Evolution

Volumn 69, Issue 9, 2015, Pages 2414-2424

  Mitchell, Jonathan S ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Adaptive radiation; Fossils; Macroevolution; Morphological evolution; Paleobiology

Indexed keywords

ADAPTIVE RADIATION; BIRD; COMPARATIVE STUDY; CRETACEOUS; FOSSIL RECORD; MORPHOLOGY; PALEOBIOLOGY; PHYLOGENETICS;

AVES;

ANATOMY AND HISTOLOGY; ANIMAL; BIOLOGICAL MODEL; BIRD; CLASSIFICATION; ENVIRONMENTAL ASPECTS AND RELATED PHENOMENA; EVOLUTION; FOSSIL; PHYLOGENY; SPECIES EXTINCTION;

ANIMALS; BIOLOGICAL EVOLUTION; BIRDS; ECOLOGICAL AND ENVIRONMENTAL PHENOMENA; EXTINCTION, BIOLOGICAL; FOSSILS; MODELS, BIOLOGICAL; PHYLOGENY;

EID: 84941599643     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12738     Document Type: Article

References (55)

1. Barker, F. K. 2011. Phylogeny and diversification of modern passerines, in Living Dinosaurs: The Evolutionary History of Modern Birds (eds G. Dyke and G. Kaiser). John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9781119990475.ch9
2. Behrensmeyer, A. K., S. M. Kidwell, and R. A. Gastaldo. 2000. Taphonomy and paleobiology. Paleobiology 26:103-147.
3. Behrensmeyer, A. K., C. T. Stayton, and R. E. Chapman. 2003. Taphonomy and ecology of modern avifaunal remains from Amboseli Park, Kenya. Paleobiology 29:52-70.
4. Benson, R. B., and J. N. Choiniere. 2013. Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds. Proc. R. Soc. Lond. B Biol. Sci. 280:20131780. Available at http://dx.doi.org/10.1098/rspb.2013.1780.
5. Boettiger, C., G. Coop, and P. Ralph. 2012. Is your phylogeny informative? Measuring the power of comparative methods. Evolution 66:2240-2251.
6. Brown, J., J. Rest, J. Garcia-Moreno, M. Sorenson, and D. Mindell. 2008. Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biol. 6:6.
7. Brusatte, S. L., G. T. Lloyd, S. C. Wang, and M. A. Norell. 2014. Gradual assembly of avian body plan culminated in rapid rates of evolution across the dinosaur-bird transition. Curr. Biol. 24:2386-2392.
8. Burnham, K. P., and D. R Anderson. 2004. Model selection and multimodel inference: a practical information theoretic approach, 2nd edn. Springer, New York.
9. Butler, M. A., and A. A. King. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164:683-695.
10. Feduccia, A. 1995. Explosive evolution in tertiary birds and mammals. Science 267:637-638.
11. Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
12. 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.
13. Foote, M. 1997. The evolution of morphological diversity. Ann. Rev. Ecol. Evol. 28:129-152.
14. Freckleton, R. P., and P. H. Harvey. 2006. Detecting non-Brownian trait evolution in adaptive radiations. PLoS Biol 4:e373.
15. Gower, J. C. 1971. A general coefficient of similarity and some of its properties. Biometrics 27:857-871.
16. Grande, L. 2013. The lost world of Fossil Lake: snapshots from deep time. Univ. of Chicago Press, Chicago, Illinois.
17. Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M. J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman et al. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320:1763-1768.
18. Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Am. Nat. 51:1341-1353.
19. Harmon, L. J., J. A. Schulte, A. Larson, and J. B. Losos. 2003. Tempo and mode of evolutionary radiation in Iguanian lizards. Science 301:961-964.
20. Harmon, L. J., J. Melville, A. Larson, and J. B. Losos. 2008a. The role of geography and ecological opportunity in the diversification of day geckos (Phelsuma). Syst. Biol. 57:562-573.
21. Harmon, L. J., J. T. Weir, C. D. Brock, R. E. Glor, and W. Challenger. 2008b. GEIGER: investigating evolutionary radiations. Bioinformatics 24:129-131.
22. Harmon, L. J., J. B. Losos, T. Jonathan Davies, R. G. Gillespie, J. L. Gittleman, W. Bryan 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.
23. Hopkins, M. J., and A. B. Smith. 2015. Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution. Proc. Natl. Acad. Sci. USA 112:3758-3763.
24. Ingram, T., L. J. Harmon, and J. B. Shurin. 2012. When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model. J. Evol. Biol. 25:1902-1910.
25. James, H. F. 2005. Paleogene fossils and the radiation of modern birds. Auk 122:1049-1054.
26. Jarvis, E. D., S. Mirarab, A. J. Aberer, B. Li, P. Houde, C. Li, S. Y. W. Ho, B. C. Faircloth, B. Nabholz, J. T. Howard et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320-1331.
27. Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, and A. O. Mooers. 2012. The global diversity of birds in space and time. Nature 491:444-448.
28. Ksepka, D. T., and C. A. Boyd. 2012. Quantifying historical trends in the completeness of the fossil record and the contributing factors: an example using Aves. Paleobiology 38:112-125.
29. Ksepka, D. T., J. A. Clarke, S. J. Nesbitt, F. B. Kulp, and L. Grande. 2013. Fossil evidence of wing shape in a stem relative of swifts and hummingbirds (aves, pan-apodiformes). Proc. R. Soc. Lond. B Biol. Sci. 280:20130580. http://dx.doi.org/10.1098/rspb.2013.0580
30. Legendre, P., and L. Legendre. 1998. Numerical ecology. 2nd English ed. Elsevier, Amsterdam.
31. Lingoes, J. C. 1971. Some boundary conditions for a monotone analysis of symmetric matrices. Psychometrika 36:195-203.
32. Livezey, B. C., and R. L. Zusi. 2007. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. ii. Analysis and discussion. Zool. J. Linn. Soc. 149:1-95.
33. Manegold, A. 2008. Passerine diversity in the late Oligocene of Germany: earliest evidence for the sympatric coexistence of Suboscines and Oscines. Ibis 150:377-387.
34. Mayr, G. 2005. The paleogene fossil record of birds in Europe. Biol Rev. 80:515-542.
35. Mayr, G., and A. Manegold. 2004. The oldest European fossil songbird from the Early Oligocene of Germany. Naturwissenschaften 91:173-177.
36. Mayr, G., and V. Wilde. 2015. Eocene fossil is earliest evidence of flower-visiting by birds. Biol. Lett. 10:20140223
37. Mitchell, J. S. 2015. Preservation is predictable: quantifying the effect of taphonomic biases on ecological disparity in birds. Paleobiology 41:353-367.
38. Mitchell, J. S., and P. J. Makovicky. 2014. Low ecological disparity in Early Cretaceous birds. Proc. R. Soc. B Biol. Sci. 281:20140608. http://dx.doi.org/10.1098/rspb.2014.0608.
39. Morlon, H., T. L. Parsons, and J. B. Plotkin. 2011. Reconciling molecular phylogenies with the fossil record. Proc. Natl. Acad. Sci. USA 108:16327-16332.
40. Martin Hughes, Sylvain Gerber, and Matthew Albion Wills. 2013. Clades reach highest morphological disparity early in their evolution PNAS 110(34):13875-13879. doi:10.1073/pnas.1302642110
41. Naish, D. 2014. The fossil record of bird behaviour. J. Zool. 292:268-280.
42. Nesbitt, S. J., D. T. Ksepka, and J. A. Clarke. 2011. Podargiform affinities of the enigmatic Fluvioviridavis platyrhamphus and the early diversification of Strisores ("Caprimulgiformes" + Apodiformes). PLoS ONE 6:e26350.
43. Pacheco, M. A., F. U. Battistuzzi, M. Lentino, R. F. Aguilar, S. Kumar, and A. A. Escalante. 2011. Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Mol. Biol. Evol. 28:1927-1942.
44. Pant, S. R., A. Goswami, and J. A. Finarelli. 2014. Complex body size trends in the evolution of sloths (Xenarthra: Pilosa). BMC Evol. Biol. 14. Available at dx.doi.org/10.1186/s12862-014-0184-1.
45. R Core Team. 2014. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
46. Schweizer, M., S. T. Hertwig, and O. Seehausen. 2014. Diversity versus disparity and the role of ecological opportunity in a continental bird radiation. J. Biogeogr. 41:1301-1312.
47. Shipley, B., D. Vile, and E. Garnier. 2006. From plant traits to plant communities: a statistical mechanistic approach to biodiversity. Science 314:812-814.
48. Slater, G. J. 2013. Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary. Methods Ecol. Evol. 4(8):734-744.
49. Slater, G. J., and M. W. Pennell. 2013. Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution. Syst. Biol. 63:293-308.
50. 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.
51. Smith, N. D., L. Grande, and J. A. Clarke. 2013. A new species of Threskiornithidae-like bird (Aves, Ciconiiformes) from the Green River Formation (Eocene) of Wyoming. J. Vertebr. Paleontol. 33:363-381.
52. Turvey, S. T., and T. M. Blackburn. 2011. Determinants of species abundance in the Quaternary vertebrate fossil record. Paleobiology 37:537-546.
53. Uyeda, J. C., D. S. Caetano, and M. W. Pennell. 2014. Comparative analysis of principal components can be misleading. Available at http://dx.doi.org/10.1101/007369.
54. Warton, D. I., B. Shipley, and T. Hastie. 2014. CATS regression - a model-based approach to studying trait-based community assembly. Methods Ecol. Evol. 6:389-398.
55. Zanno, L. E., and P. J. Makovicky. 2011. Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution. Proc. Natl. Acad. Sci. USA 108:232-237.