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Abstract

The phylogenetic comparative method (PCM) has an important place in evolutionary biology. This chapter aims at giving an overview on some selected topics. We first review briefly some important historical milestones including some early contributions and the relationships of comparative methods with phylogenetics. Some fundamental points on statistical inference, adaptation, and causality are then discussed. We also discuss briefly the application of the PCM to anthropology and conclude with some perspectives on its future development and applications.

Notes

Acknowledgments

I am grateful to László Zsolt Garamszegi for inviting me to write this chapter. Many thanks to two anonymous reviewers for their positive comments.

References

  1. Bartoszek K, Pienaar J, Mostad P, Andersson S, Hansen TF (2012) A phylogenetic comparative method for studying multivariate adaptation. J Theor Biol 314:204–215CrossRefGoogle Scholar
  2. Bininda-Emonds ORP, Cardillo M, Jones KE, MacPhee RDE, Beck RMD, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A (2007) The delayed rise of present-day mammals. Nature 446:507–512CrossRefGoogle Scholar
  3. Blomberg SP, Garland T Jr, Ives AR (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717–745CrossRefGoogle Scholar
  4. Blomberg SP, Lefevre JG, Wells JA, Waterhouse M (2012) Independent contrasts and PGLS regression estimators are equivalent. Syst Biol 61:382–391CrossRefGoogle Scholar
  5. Bock KE (1966) The comparative method of anthropology. Comp Stud Soc Hist 8:269–280CrossRefGoogle Scholar
  6. Bock WJ (1959) Preadaptation and multiple evolutionary pathways. Evolution 13:194–211CrossRefGoogle Scholar
  7. Bock WJ (2003) Ecological aspects of the evolutionary processes. Zool Sci 20:279–289CrossRefGoogle Scholar
  8. Borgerhoff Mulder M, Nunn CL, Towner MC (2006) Cultural macroevolution and the transmission of traits. Evol Anthropol 15:52–64CrossRefGoogle Scholar
  9. Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis models and estimation procedures. Am J Hum Genet 19:233–257PubMedPubMedCentralGoogle Scholar
  10. Cheverud JM, Dow MM, Leutenegger W (1985) The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates. Evolution 39:1335–1351CrossRefGoogle Scholar
  11. Cliff AD, Ord JK (1981) Spatial and temporal analysis: autocorrelation in space and time. In: Wrigley EN, Bennett RJ (eds) Quantitative geography: a british view. Routledge & Kegan Paul, London, pp 104–110Google Scholar
  12. Clutton-Brock TH, Harvey PH (1979) Comparison and adaptation. Proc R Soc Lond B 205:547–565CrossRefGoogle Scholar
  13. Cuvier G (1798) Tableau élémentaire de l’histoire naturelle des animaux. Baudouin, ParisGoogle Scholar
  14. Darwin C (1859) On the origin of species by means of natural selection. John Murray, LondonGoogle Scholar
  15. Eastman JM, Harmon LJ, Tank DC (2013) Congruification: support for time scaling large phylogenetic trees. Meth Ecol Evol 4:688–691CrossRefGoogle Scholar
  16. Felsenstein J (1973) Maximum-likelihood estimation of evolutionary trees from continuous characters. Am J Hum Genet 25:471–492PubMedPubMedCentralGoogle Scholar
  17. Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1–15CrossRefGoogle Scholar
  18. Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, SunderlandGoogle Scholar
  19. Felsenstein J (2005) Using the quantitative genetic threshold model for inferences between and within species. Phil Trans R Soc Lond B 360:1427–1434CrossRefGoogle Scholar
  20. Felsenstein J (2008) Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am Nat 171:713–725CrossRefGoogle Scholar
  21. Fisher RA (1930) The genetical theory of natural selection (a complete variorum edition, 1999). Oxford University Press, OxfordGoogle Scholar
  22. Forster P, Toth A, Bandelt HJ (1998) Evolutionary network analysis of word lists: visualising the relationships between Alpine romance languages. J Quant Linguist 5:174–187CrossRefGoogle Scholar
  23. Freedman DA (2009) Statistical models: theory and practice (revised edition). Cambridge University Press, CambridgeGoogle Scholar
  24. Garamszegi LZ, Møller AP (2010) Effects of sample size and intraspecific variation in phylogenetic comparative studies: a meta-analytic review. Biol Rev 85:797–805Google Scholar
  25. Gittleman JL, Kot M (1990) Adaptation: statistics and a null model for estimating phylogenetic effects. Syst Zool 39:227–241CrossRefGoogle Scholar
  26. Grafen A (1989) The phylogenetic regression. Phil Trans R Soc Lond B 326:119–157CrossRefGoogle Scholar
  27. Grafen A, Ridley M (1997) A new model for discrete character evolution. J Theor Biol 184:7–14CrossRefGoogle Scholar
  28. Grandcolas P, Nattier R, Legendre F, Pellens R (2011) Mapping extrinsic traits such as extinction risks or modelled bioclimatic niches on phylogenies: does it make sense at all? Cladistics 27:181–185CrossRefGoogle Scholar
  29. Hadfield JD, Nakagawa S (2010) General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters. J Evol Biol 23:494–508CrossRefGoogle Scholar
  30. Hadjipantelis PZ, Jones NS, Moriarty J, Springate DA, Knight CG (2013) Function-valued traits in evolution. J R Soc Interface 10(20121):032Google Scholar
  31. Haeckel E (1887) Report on the Radiolaria collected by H.M.S. Challenger during the years 1873–1876. Her Majesty’s Stationery Office, LondonGoogle Scholar
  32. Hansen TF, Martins EP (1996) Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 50:1404–1417CrossRefGoogle Scholar
  33. Harvey PH, Pagel MD (1991) The comparative method in evolutionary biology. Oxford University Press, OxfordGoogle Scholar
  34. Houwing-Duistermaat JJ, van Houwelingen HC, Terhell A (1998) Modelling the cause of dependency with application to filaria infection. Statist Med 17:2939–2954CrossRefGoogle Scholar
  35. Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time. Nature 491:444–448CrossRefGoogle Scholar
  36. Jombart T, Pavoine S, Devillard S, Pontier D (2010) Putting phylogeny into the analysis of biological traits: a methodological approach. J Theor Biol 264:693–701CrossRefGoogle Scholar
  37. Kiekbaev DI (2003) Comparative law: method, science or educational discipline? Electronic journal of comparative law 7.3. url http://www.ejcl.org/73/art73-2.html
  38. Kuhn TS, Mooers AO, Thomas GH (2011) A simple polytomy resolver for dated phylogenies. Meth Ecol Evol 2:427–436CrossRefGoogle Scholar
  39. Lamarck JB (1809) Philosophie zoologique. Flammarion (1994 edition), ParisGoogle Scholar
  40. Lapiedra O, Sol D, Carranza S, Beaulieu JM (2013) Behavioural changes and the adaptive diversification of pigeons and doves. Proc R Soc Lond B 280(20122):893Google Scholar
  41. Laurent G (1986) Cuvier et Lamarck: la querelle du catastrophisme. La Recherche 17:1510–1518Google Scholar
  42. Legendre P (1993) Spatial autocorrelation: trouble or new paradigm? Ecology 74:1659–1673CrossRefGoogle Scholar
  43. Leroi AM, Rose MR, Lauder GV (1994) What does the comparative method reveal about adaptation? Am Nat 143:381–402CrossRefGoogle Scholar
  44. Lindenfors P, Jansson F, Sandberg M (2011) The cultural evolution of democracy: saltational changes in a political regime landscape. PLoS ONE 6:e28270CrossRefGoogle Scholar
  45. Losos JB (1994) An approach to the analysis of comparative data when a phylogeny is unavailable or incomplete. Syst Biol 43:117–123CrossRefGoogle Scholar
  46. Losos JB (2011) Convergence, adaptation, and constraint. Evolution 65:1827–1840CrossRefGoogle Scholar
  47. Lynch M (1991) Methods for the analysis of comparative data in evolutionary biology. Evolution 45:1065–1080CrossRefGoogle Scholar
  48. Mace R, Pagel M (1994) The comparative method in anthropology (with discussion). Curr Anthropol 35:549–564CrossRefGoogle Scholar
  49. Martins EP (1996) Conducting phylogenetic comparative studies when the phylogeny is not known. Evolution 50:12–22CrossRefGoogle Scholar
  50. Martins EP (2000) Adaptation and the comparative method. Trends Ecol Evol 15:296–299CrossRefGoogle Scholar
  51. Martins EP, Hansen TF (1997) Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am Nat 149:646–667 erratum vol 153, p 488CrossRefGoogle Scholar
  52. Münkemüller T, Lavergne S, Bzeznik B, Dray S, Jombart T, Schiffers K, Thuiller W (2012) How to measure and test phylogenetic signal. Meth Ecol Evol 3:743–756CrossRefGoogle Scholar
  53. Ollier S, Couteron P, Chessel D (2006) Orthonormal transform to decompose the variance of a life-history trait across a phylogenetic tree. Biometrics 62:471–477CrossRefGoogle Scholar
  54. O’Meara BC, Ané C, Sanderson MJ, Wainwright PC (2006) Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922–933CrossRefGoogle Scholar
  55. Pagel M (1994) Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc R Soc Lond B 255:37–45CrossRefGoogle Scholar
  56. Pagel M, Meade A (2006) Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. Am Nat 167:808–825PubMedGoogle Scholar
  57. Pagel M, Meade A, Barker D (2004) Bayesian estimation of ancestral character states on phylogenies. Syst Biol 53:673–684CrossRefGoogle Scholar
  58. Pagel MD, Harvey PH (1988) Recent developments in the analysis of comparative data. Quart Rev Biol 63:413–440CrossRefGoogle Scholar
  59. Paradis E, Claude J (2002) Analysis of comparative data using generalized estimating equations. J Theor Biol 218:175–185CrossRefGoogle Scholar
  60. Pavoine S, Ollier S, Pontier D, Chessel D (2008) Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities. Theor Pop Biol 73:79–91CrossRefGoogle Scholar
  61. Pavoine S, Baguette M, Bonsall MB (2010) Decomposition of trait diversity among the nodes of a phylogenetic tree. Ecol Monogr 80:485–507CrossRefGoogle Scholar
  62. Pennell MW, Harmon LJ (2013) An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Ann NY Acad Sci 1289:90–105CrossRefGoogle Scholar
  63. Pepin KM, Lass S, Pulliam JRC, Read AF, Lloyd-Smith JO (2010) Identifying genetic markers of adaptation for surveillance of viral host jumps. Nat Rev Microbiol 8:802–813CrossRefGoogle Scholar
  64. Revell LJ (2009) Size-correction and principal components for interspecific comparative studies. Evolution 63:3258–3268CrossRefGoogle Scholar
  65. Rohlf FJ (2006) A comment on phylogenetic correction. Evolution 60:1509–1515CrossRefGoogle Scholar
  66. Santos JC, Cannatella DC (2011) Phenotypic integration emerges from aposematism and scale in poison frogs. Proc Natl Acad Sci USA 108:6175–6180CrossRefGoogle Scholar
  67. Shipley B (2013) The AIC model selection method applied to path analytic models compared using a d-separation test. Ecology 94:560–564CrossRefGoogle Scholar
  68. Simpson GG (1944) Tempo and mode in evolution. Columbia University Press, New YorkGoogle Scholar
  69. Smith SA, Beaulieu JM, Stamatakis A, Donoghue MJ (2011) Understanding angiosperm diversification using small and large phylogenetic trees. Am J Bot 98:404–414CrossRefGoogle Scholar
  70. Spreitzer RJ, Peddi SR, Satagopan S (2005) Phylogenetic engineering at an interface between large and small subunits imparts land-plant kinetic properties to algal Rubisco. Proc Natl Acad Sci USA 102:17225–17230CrossRefGoogle Scholar
  71. Stone GN, Nee S, Felsenstein J (2011) Controlling for non-independence in comparative analysis of patterns across populations within species. Phil Trans R Soc Lond B 366:1410–1424CrossRefGoogle Scholar
  72. Thomas GH, Hartmann K, Jetz W, Joy JB, Mimoto A, Mooers AO (2013) PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences. Meth Ecol Evol 4:1011–1017CrossRefGoogle Scholar
  73. Tiao GC, Reinsel GC, Xu DM, Pedrick JH, Zhu XD, Miller AJ, DeLuisi JJ, Mateer CL, Wuebbles DJ (1990) Effects of autocorrelation and temporal sampling schemes on estimates of trend and spatial correlation. J Geophys Res-Atmos 95:20507–20517CrossRefGoogle Scholar
  74. von Hardenberg A, Gonzalez-Voyer A (2013) Disentangling evolutionary cause-effect relationships with phylogenetic confirmatory path analysis. Evolution 67:378–387CrossRefGoogle Scholar
  75. Watt WB (2013) Causal mechanisms of evolution and the capacity for niche construction. Biol Philos 28:757–766CrossRefGoogle Scholar
  76. Whitney KD, Boussau B, Baack EJ, Garland T (2011) Drift and genome complexity revisited. PLoS Genet 7(e1002):092Google Scholar
  77. Yan XH, Gurtler JB, Fratamico PM, Hu J, Juneja VK (2012) Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food. Cell Biosci 2:39CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Institut de Recherche pour le DéveloppementMontpellierFrance

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