|Original language||English (US)|
|Title of host publication||Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology|
|Publisher||Springer Berlin Heidelberg|
|Number of pages||27|
|State||Published - Jan 1 2014|
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TY - CHAP
T1 - Graphical methods for visualizing comparative data on phylogenies
AU - Revell, L.J.
N1 - Cited By :9 Export Date: 17 April 2018 Correspondence Address: Revell, L.J.; Department of Biology, University of Massachusetts BostonUnited States References: Ackerly, D., Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal (2009) PNAS, 106, pp. 19699-19706; Adler, D., Murdoch, D., Rgl: 3D visualization device system (OpenGL) (2013) R Package Version 0, 93, p. 935; Archie, J., Day, W., Felsenstein, J., Maddison, W., Meacham, C., Rohlf, F.J., Swofford, D., (1986) Newick Tree Format, , http://evolution.genetics.washington.edu/phylip/newicktree.html, More information; Atkinson, Q.D., Gray, R.D., Curious parallels and curious connections: Phylogenetic thinking in biology and historical linguistics (2005) Syst Biol, 54, pp. 513-526; Baum, D.A., Smith, S.D., (2013) Tree thinking: An introduction to phylogenetic biology, , Roberts and Company, Greenwood Village; Beaulieu, J.M., O’meara, B.C., Donoghue, M.J., Identifying hidden rate changes in the evolution of a binary morphological character: The evolution of plant habit in the campanulid angiosperms (2013) Syst Biol, 62, pp. 725-737; Becker, R.A., Wilks, A.R., Brownrigg, R., Minka, T.P., Maps: Draw geographical maps (2013) R Package Version 2, pp. 2-3; Bininda-Emonds, O.R., Cardillo, M., Jones, K.E., Macphee, R., Beck, R., Grenyer, R., Price, S.A., Purvis, A., The delayed rise of present-day mammals (2007) Nature, 446, pp. 508-512; Bokma, F., 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 phylogeny (2008) Evolution, 62, pp. 2718-2726; Bollback, J.P., SIMMAP: Stochastic character mapping of discrete traits on phylogenies (2006) BMC Bioinf, 7, p. 88; Butler, M.A., King, A.A., Phylogenetic comparative analysis: A modeling approach for adaptive evolution (2004) Am Nat, 164, pp. 683-695; Collar, D.C., Wainwright, P.C., Alfaro, M.E., Revell, L.J., Mehta, R.S., (2013) R: A Language and Environment for Statistical Computing, , R Foundation for Statistical Computing, Vienna; Eastman, J.M., Alfaro, M.E., Joyce, P., Hipp, A.L., Harmon, L.J., A novel comparative method for modeling shifts in the rate of character evolution on trees (2011) Evolution, 65, pp. 3578-3589; Edwards, E.J., Osborne, C.P., Strömberg, C., Smith, S.A., The origins of C4 grasslands: Integrating evolutionary and ecosystem science (2010) Science, 328, pp. 587-591; Evans, M., Smith, S.A., Flynn, R.S., Donoghue, M.J., Climate, niche evolution, and diversification of the “bird-cage” evening primroses (Oenothera, sections Anogra and Kleinia) (2009) Am Nat, 173, pp. 225-240; Felsenstein, J., Phylogenies and the comparative method (1985) Am Nat, 125, pp. 1-15; Felsenstein, J., Phylogenies and quantitative characters (1988) Ann Rev Ecol Syst, 19, pp. 445-471; Felsenstein, J., (2004) Inferring Phylogenies, , Sinauer Associates, Sunderland; Felsenstein, J., A comparative method for both discrete and continuous characters using the threshold model (2012) Am Nat, 179, pp. 145-156; Fitzjohn, R.G., Quantitative traits and diversification (2010) Syst Biol, 59, pp. 619-633; Freckleton, R.P., Harvey, P.H., Pagel, M., Phylogenetic analysis and comparative data: A test and review of evidence (2002) Am Nat, 160, pp. 712-726; Glor, R.E., Phylogenetic insights on adaptive radiation (2010) Ann Rev Ecol Evol Syst, 41, pp. 251-270; Harmon, L.J., Schulte, J., Larson, A., Losos, J.B., Tempo and mode of evolutionary radiation in iguanian lizards (2003) Science, 301, pp. 961-964; Harvey, P.H., Pagel, M.D., (1991) The Comparative Method in Evolutionary Biology., , Oxford University Press, Oxford; Huelsenbeck, J.P., Nielsen, R., Bollback, J.P., Stochastic mapping of morphological characters (2003) Syst Biol, 52, pp. 131-158; Lemon, J., (2006) Plotrix: A Package in the Red Light District of R. 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PY - 2014/1/1
Y1 - 2014/1/1
N2 - Phylogenies have emerged as central in evolutionary biology over the past three decades or more, and an extraordinary expansion in the breadth and sophistication of phylogenetic comparative methods has played a large role in this growth. In this chapter, I focus on a somewhat neglected area: The use of graphical methods to simultaneously represent comparative data and trees. As this research area is theoretically very broad, I have concentrated on new methods developed by me, or techniques devised by others and implemented by me as part of my R phylogenetics package, phytools. I describe a variety of methods in this chapter, including approaches that can be used to map reconstructed discrete or continuous character evolution on trees; techniques for projecting phylogenetic trees into morphospace; and methods for visualizing phylogenies in the context of a global or regional geographic map. In this chapter, my intention is not merely to showcase new methods that I have developed. Rather, I have also dedicated considerable attention to detailing the algorithms and computational techniques required for these approaches with the hope that this chapter will become a resource or jumping-off point for researchers interested in building new, more advanced approaches and methods in this area. © Springer-Verlag Berlin Heidelberg 2014.
AB - Phylogenies have emerged as central in evolutionary biology over the past three decades or more, and an extraordinary expansion in the breadth and sophistication of phylogenetic comparative methods has played a large role in this growth. In this chapter, I focus on a somewhat neglected area: The use of graphical methods to simultaneously represent comparative data and trees. As this research area is theoretically very broad, I have concentrated on new methods developed by me, or techniques devised by others and implemented by me as part of my R phylogenetics package, phytools. I describe a variety of methods in this chapter, including approaches that can be used to map reconstructed discrete or continuous character evolution on trees; techniques for projecting phylogenetic trees into morphospace; and methods for visualizing phylogenies in the context of a global or regional geographic map. In this chapter, my intention is not merely to showcase new methods that I have developed. Rather, I have also dedicated considerable attention to detailing the algorithms and computational techniques required for these approaches with the hope that this chapter will become a resource or jumping-off point for researchers interested in building new, more advanced approaches and methods in this area. © Springer-Verlag Berlin Heidelberg 2014.
U2 - 10.1007/978-3-662-43550-2_4
DO - 10.1007/978-3-662-43550-2_4
M3 - Chapter
SN - 9783662435502
SP - 77
EP - 103
BT - Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology
PB - Springer Berlin Heidelberg