Hostname: page-component-586b7cd67f-vdxz6 Total loading time: 0 Render date: 2024-11-25T06:05:23.210Z Has data issue: false hasContentIssue false
  • English
  • Français

Models and Methods for Analyzing Phenotypic Evolution in Lineages and Clades

Published online by Cambridge University Press:  21 July 2017

Gene Hunt  and
Matthew T. Carrano
Gene Hunt
Affiliation:
Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
Matthew T. Carrano
Affiliation:
Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
Get access

Abstract

In this chapter we discuss methods for analyzing continuous traits, with an emphasis on those approaches that rely on explicit statistical models of evolution and incorporate genealogical information (ancestor–descendant or phylogenetic relationships). After discussing the roles of models and genealogy in evolutionary inference, we summarize the properties of commonly used models including random walks (Brownian motion), directional evolution, and stasis. These models can be used to devise null-hypothesis tests about evolutionary patterns, but it is often better to fit and compare models equally using information criteria and related approaches. We apply these methods to a published data set of dental measurements in a sequence of ancestor–descendant populations in the early primate Cantius, with the particular goal of determining the best-supported mode of evolutionary change in this lineage. We also assess a series of questions about the evolution of femoral dimensions in several clades of dinosaurs, including testing for a trend of increasing body size (Cope's Rule), testing for correlations among characters, and reconstructing ancestral states. Finally, we list briefly some additional models, approaches, and issues that arise in genealogically informed analyses of phenotypic evolution.

Type
Morphological Data
Information
The Paleontological Society Papers , Volume 16: Quantitative Methods in Paleobiology , October 2010 , pp. 245 - 269
Copyright
Copyright © 2010 by the Paleontological Society 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Akaike, H. 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19(6):716–723.Google Scholar
Anderson, D. R., Burnham, K. P., and Thompson, W. L. 2000. Null hypothesis testing: problems, prevalence, and an alternative. Journal of Wildlife Management, 64(4):912–923.CrossRefGoogle Scholar
Arbour, V. M., Burns, M. E., and Sissons, R. L. 2009. A redescription of the ankylosaurid dinosaur Dyoplosaurus acutosquameus Parks, 1924 (Ornithischia: Ankylosauria) and a revision of the genus. Journal of Vertebrate Paleontology, 29(4):1117–1135.Google Scholar
Arnold, S. J., Pfrender, M. E., and Jones, A. G. 2001. The adaptive landscape as a conceptual bridge between micro- and macroevolution. Genetica, 112–113:9–32.CrossRefGoogle Scholar
Averianov, A. O., Voronkevich, A. V., Lechchinskiy, S. V., and Fayngertz, A. 2006. A ceratopsian dinosaur Psittacosaurus sibiricus from the Early Cretaceous of west Siberia, Russia and its phylogenetic relationships. Journal of Systematic Palaeontology, 4(4):359–395.CrossRefGoogle Scholar
Blomberg, S. P., Garland, T., and Ives, A. R. 2003. Testing for phylogenetic signal in comparative data: behavioural traits are more labile. Evolution, 57(4):717–745.Google ScholarPubMed
Bokma, F. 2008. Detection of “Punctuated Equilibrium” by Bayesian Estimation of Speciation and Extinction Rates, Ancestral Character States, and Rates of Anagenetic and Cladogenetic Evolution on a Molecular Phytogeny. Evolution, 62(11):2718–2726.CrossRefGoogle Scholar
Bookstein, F. L. 1987. Random walk and the existence of evolutionary rates. Paleobiology, 13(4):446–464:CrossRefGoogle Scholar
Boyd, C. A., Brown, C. M., Scheetz, R. D., and Clarke, J. A. 2009. Taxonomic revison of the basal neornithischian taxa Thescelosaurus and Bugenasaura . Journal of Vertebrate Paleontology, 29(3):758–770.Google Scholar
Brusatte, S. L., Benton, M. J., Ruta, M., and Floyd, G. T. 2008. Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science, 321(5895):1485–1488.Google Scholar
Burnham, K. P., and Anderson, D. R. 2010. Model Selection and Multimodel Inference. Springer, New York, 516 p.Google Scholar
Butler, M. A., and King, A. A. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist, 164(6):683–695.Google Scholar
Butler, R. J., Galton, P. M., Porro, L. B., Chiappe, L. M., Henderson, D. M., and Erickson, G. M. 2010. Lower limits of ornithischian dinosaur body size inferred from a new Upper Jurassic heterodontosaurid from North America. Proceedings of the Royal Society of London B, 277:375–381.Google ScholarPubMed
Carpenter, K., Bartlett, J., Bird, J., and Barrick, R. 2008. Ankylosaurs from the Price River Quarries, Cedar Mountain Formation (Lower Cretaceous), east-central Utah. Journal of Vertebrate Paleontology, 28(4):1089–1101.CrossRefGoogle Scholar
Carrano, M. T. 2006. Body-size evolution in the Dinosauria, p. 225–268. In Carrano, M. T., Gaudin, T. J., Blob, R. W., and Wible, J. R. (eds.), Amniote Paleobiology. University of Chicago Press, Chicago.Google Scholar
Cleveland, W. S. 1979. Robust locally weighted regression and smoothing scatterplots. Journal of the American Statistical Association, 74(368):829–836.Google Scholar
Clyde, W. C., and Gingerich, P. D. 1994. Rates of evolution in the dentition of early Eocene Cantius: comparison of size and shape. Paleobiology, 20(4):506–522.Google Scholar
Dalla Vecchia, F. M. 2009. Tethyshadros insularis, a new hadrosauroid dinosaur (Ornithischia) from the Upper Cretaceous of Italy. Journal of Vertebrate Paleontology, 29(4):1100–1116.CrossRefGoogle Scholar
Diniz-Filho, J. A. F., Bini, L. M., and Hawkins, B. A. 2003. Spatial autocorrelation and red herrings in geographical ecology. Global Ecology and Biogeography, 12:53–64.CrossRefGoogle Scholar
Drummond, A., Ho, S., Phillips, M., and Rambaut, A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology, 4:e88.Google Scholar
Eldredge, N., and Gould, S. J. 1972. Punctuated equilibria: an alternative to phyletic gradualism, p. 82–115. In Schopf, T. J. M. (ed.), Models in Paleobiology. Freeman, Cooper & Company, San Francisco.Google Scholar
Eldredge, N., Thompson, J. N., Brakffield, P. M., Gavrilets, S., Jablonski, D., Jackson, J. B. C., Lenski, R. E., Lieberman, B. S., McPeek, M. A., and Miller, W. I. 2005. The dynamics of evolutionary stasis. Paleobiology, 31 (Supplement to 2):133–145.CrossRefGoogle Scholar
Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist, 125(1):1–15.Google Scholar
Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Inc., Sunderland, Massachusetts, 664 p.Google Scholar
Finarelli, J. A., and Flynn, J. J. 2006. Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record. Systematic Biology, 55(2):301–313.CrossRefGoogle ScholarPubMed
Fisher, D. C. 1994. Stratocladistics: Morphological and temporal patterns and their relation to phylogenetic process, p. 133–171. In Grande, L. and Rieppel, O. (eds.), Interpreting the Hierarchy of Nature. Academic Press.Google Scholar
Foote, M. 1991. Analysis of morphological data, p. 59–86. In Gilinsky, N. L. and Signor, P. W. (eds.), Analytical Paleobiology. Volume 4. The Paleontological Society.Google Scholar
Foote, M. 1996. On the probability of ancestors in the fossil record. Paleobiology, 22(2):141–151.CrossRefGoogle Scholar
Ford, T. L., and Kirkland, J. I. 2001. Carlsbad ankylosaur(Ornithischia, Ankylosauria): an ankylosaurid and not a nodosaurid, p. 239–260. In Carpenter, K. (ed.), The Armored Dinosaurs. Indiana University Press, Bloomington, IN.Google Scholar
Garland, T., Harvey, P. H., and Ives, A. R. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41(1):18–32.Google Scholar
Garland, T., and Ives, A. R. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist, 155(3):346–364.CrossRefGoogle ScholarPubMed
Geary, D. H., Hunt, G., Magyar, I., and Schultz, H. 2010. The paradox of gradualism: phyletic evolution in two lineages of lymnocardiid bivalves (Lake Pannon, central Europe). Paleobiology, In press.CrossRefGoogle Scholar
Gingerich, P. D. 1983. Rates of evolution: effects of time and temporal scaling. Science, 222(4620):159–161.CrossRefGoogle ScholarPubMed
Gingerich, P. D. 1993. Quantification and comparison of evolutionary rates. American Journal of Science, 293-A:453–478.Google Scholar
Gingerich, P. D. 2000. Arithmetic or geometric normality of biological variation: an empirical test of theory. Journal of Theoretical Biology, 204(2):201–221.CrossRefGoogle ScholarPubMed
Gingerich, P. D. 2009. Rates of evolution. Annual Review of Ecology Evolution and Systematics, 40:657–675.CrossRefGoogle Scholar
Gould, S. J. 2002. The Structure of Evolutionary Theory. Belknap Press, Cambridge, Massachusetts, 1433 p.Google Scholar
Hannisdal, B. 2006. Phenotypic evolution in the fossil record: Numerical experiments. Journal of Geology, 114(2):133–153.CrossRefGoogle Scholar
Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution, 51(5):1341–1351.CrossRefGoogle ScholarPubMed
Hansen, T. F., and Martins, E. P. 1996. Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution, 50(4):1404–1417.CrossRefGoogle ScholarPubMed
Hansen, T. F., Pienaar, J., and Orzack, S. H. 2008. A comparative method for studying adaptation to a randomly evolving environment. Evolution, 62(8):1965–1977.Google ScholarPubMed
Harmon, L. J., Weir, J., Brock, C., Glor, R., Challenger, W., and Hunt, G. 2009. geiger: analysis of evolutionary diversification.Google Scholar
Hone, D. W. E., Keesey, T. M., Pisani, D., and Purvis, A. 2005. Macroevolutionary trends in the Dinosauria: Cope's Rule. Journal of Evolutionary Biology, 18:587–595.CrossRefGoogle ScholarPubMed
Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology, 32(4):578–601.Google Scholar
Hunt, G. 2008a. Evolutionary patterns within fossil lineages: model-based assessment of modes, rates, punctuations and process, p. 117–131. In Bambach, R. K. and Kelley, P. H. (eds.), From Evolution to Geobiology: Research Questions Driving Paleontology at the Start of a New Century. The Paleontological Society.Google Scholar
Hunt, G. 2008b. Gradual or pulsed evolution: when should punctuational explanations be preferred? Paleobiology, 34(3):360–377.Google Scholar
Hunt, G. 2008c. paleoTS: Modeling evolution in paleontological time-series.Google Scholar
Hunt, G., Bell, M. A., and Travis, M. P. 2008. Evolution toward a new adaptive optimum: Phenotypic evolution in a fossil stickleback lineage. Evolution, 62(3):700–710.CrossRefGoogle Scholar
Hunt, G., Cronin, T. M., and Roy, K. 2005. Species-energy relationship in the deep sea: a test using the Quaternary fossil record. Ecology Letters, 8:739–747.Google Scholar
Lande, R. 1976. Natural selection and random genetic drift in phenotypic evolution. Evolution, 30:314–334.Google Scholar
Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. American Naturalist, 136(6):727–741.CrossRefGoogle Scholar
Maddison, W. P. 1991. Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogeny. Systematic Zoology, 40:304–314.CrossRefGoogle Scholar
Maddison, W. P., and Maddison, D. R. 2009. Mesquite: a modular system for evolutionary analysis.Google Scholar
Maidment, S. C. R., Norman, D. B., Barrett, P. M., and Upchurch, P. 2008. Systematics and phylogeny of Stegosauria (Dinosauria: Ornithischia). Journal of Systematic Palaeontology, 6(04):367–407.Google Scholar
Marcot, J. D., and Fox, D. L. 2008. StrataPhy: a new computer program for stratocladistic analysis. Palaeontologia Electronica, 11(1):1–16.Google Scholar
Martins, E. P., and Hansen, T. F. 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist, 149(4):646–667.CrossRefGoogle Scholar
McKinney, M. L. 1990. Classifying and analyzing evolutionary trends, p. 28–58. In McNamara, K. J. (ed.), Evolutionary Trends. University of Arizona Press, Tucson.Google Scholar
McShea, D. W. 1994. Mechanisms of large-scale evolutionary trends. Evolution, 48(6):1747–1763.CrossRefGoogle ScholarPubMed
Novas, F. E., Cambiaso, A. V., and Ambrosio, A. 2004. A new basal iguanodontian (Dinosauria, Ornithischia) from the Upper Cretaceous of Patagonia. Ameghiniana, 41(1):75–82.Google Scholar
O'Meara, B. C., Ané, C., Sanderson, M. J., and Wainwright, P. C. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution, 60(5):922–933.Google ScholarPubMed
Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London Series B-Biological Sciences, 255(1342):37–45.Google Scholar
Pagel, M. 1998. Inferring evolutionary processes from phylogenies. Zoologica Scripta, 26:331–348.CrossRefGoogle Scholar
Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature, 401:877–884.Google Scholar
Pagel, M. 2002. Modelling the evolution of continuously varying characters on phylogenetic trees: the case of hominid cranial capacity, p. 269–286. In MacLeod, N. and Forey, P. L. (eds.), Morphology, Shape and Phylogeny. Taylor & Francis, London.CrossRefGoogle Scholar
Paradis, E., and Claude, J. 2002. Analysis of comparative data using generalized estimating equations. Journal of Theoretical Biology, 218:175–185.Google Scholar
Paradis, E., Claude, J., and Strimmer, K. 2004. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics, 20(2):289–290.CrossRefGoogle ScholarPubMed
R Development Core Team, 2009. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.Google Scholar
Raup, D. M. 1977. Stochastic models in evolutionary paleobiology, p. 59–78. In Hallam, A. (ed.), Patterns of Evolution as Illustrated by the Fossil Record. Elsevier Scientific Publishing Company, Amsterdam.CrossRefGoogle Scholar
Raup, D. M., and Crick, R. E. 1981. Evolution of single characters in the Jurassic ammonite Kosmoceras . Paleobiology, 7(2):200–215.Google Scholar
Raup, D. M., and Gould, S. J. 1974. Stochastic simulation and evolution of morphology: towards a nomothetic paleontology. Systematic Zoology, 23:305–322.CrossRefGoogle Scholar
Revell, L. J., and Collar, D. C. 2009. Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution, 63(4):1090–1100.Google Scholar
Revell, L. J., and Harmon, L. J. 2008. Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters. Evolutionary Ecology Research, 10(3):311–331.Google Scholar
Rohlf, F. J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution, 55(11):2143–2160.Google Scholar
Roopnarine, P. D. 2001. The description and classification of evolutionary mode: a computational approach. Paleobiology, 27(3):446–465.2.0.CO;2>CrossRefGoogle Scholar
Roopnarine, P. D., Byars, G., and Fitzgerald, P. 1999. Anagenetic evolution, stratophenetic patterns, and random walk models. Paleobiology, 25(1):41–57.Google Scholar
Roy, K., and Foote, M. 1997. Morphological approaches to measuring biodiversity. Trends in Ecology and Evolution, 12(7):277–281.Google Scholar
Ruta, M., Wagner, P. J., and Coaxes, M. I. 2006. Evolutionary patterns in early tetrapods. I. Rapid initial diversification followed by decrease in rates of character change. Proceedings of the Royal Society B-Biological Sciences, 273(1598):2107–2111.Google Scholar
Ryan, M. J. 2007. A new basal centrosaurine ceratopsid from the Oldman Formation, southeastern Alberta. Journal of Paleontology, 81(2):376–396.Google Scholar
Sanderson, M. J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19(2):301–302.CrossRefGoogle ScholarPubMed
Schluter, D., Price, T., Mooers, A., and Ludwig, D. 1997. Likelihood of ancestor states in adaptive radiation. Evolution, 51(6):1699–1711.CrossRefGoogle ScholarPubMed
Sheets, H. D., and Mitchell, C. E. 2001. Why the null matters: statistical tests, random walks and evolution. Genetica, 112–113:105–125.CrossRefGoogle Scholar
Sidlauskas, B. 2008. Continuous and Arrested Morphological Diversification in Sister Clades of Characiform Fishes: A Phylomorphospace Approach. Evolution, 62(12):3135–3156.CrossRefGoogle ScholarPubMed
Simpson, G. G. 1944. Tempo and Mode in Evolution. Columbia University Press, New York, 237 p.Google Scholar
Smith, A. 1994. Systematics and the Fossil Record. Blackwell Scientific, Oxford.Google Scholar
Sues, H.-D., and Averianov, A. 2009. A new basal hadrosauroid dinosaur from the Late Cretaceous of Uzbekistan and the early radiation of duck-billed dinosaurs. Proceedings of the Royal Society B: Biological Sciences, 276(1667):2549–2555.Google Scholar
Thomas, G. H., Meiri, S., and Phillimore, A. B. 2009. Body size diversification in Anolis: novel environment and island effects. Evolution, 63(8):2017–2030.Google Scholar
Vickaryous, M. K., Maryanska, T., and Weishampel, D. B. 2004. Ankylosauria, p. 363–392. In Weishampel, D. B., Dodson, P., and Osmólska, H. (eds.), The Dinosauria, second edition. University of California Press, Berkeley.Google Scholar
Walker, J. D., and Geissman, J. W. 2009. 2009 GSA geological time scale. GSA Today, 19(4/5):60–61.CrossRefGoogle Scholar
Webster, A. J., and Purvis, A. 2002a. Ancestral states and evolutionary rates of continuous characters, p. 247–268. In MacLeod, N. and Forey, P. L. (eds.), Morphology, Shape and Phylogeny. Taylor & Francis, London.Google Scholar
Webster, A. J., and Purvis, A. 2002b. Testing the accuracy of methods for reconstructing ancestral states of continuous characters. Proceedings of the Royal Society of London, Series B, 269:143–149.Google Scholar
Weishampel, D. B., Jianu, C.-M., Csiki, Z., and Norman, D. B. 2003. Osteology and phylogeny of Zalmoxes (n. g.), an unusual euornithopod dinosaur from the latest Cretaceous of Romania. Journal of Systematic Palaeontology; 1(2):65–123.Google Scholar
You, H.-L., Tanoue, K., and Dodson, P. 2008. New data on cranial anatomy of the ceratopsian dinosaur Psittacosaurus major . Acta Palaeontologica Polonica, 53(2):183–196.Google Scholar