|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|
Access to Document
FingerprintDive into the research topics of 'Graphical methods for visualizing comparative data on phylogenies'. Together they form a unique fingerprint.
Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology. Springer Berlin Heidelberg, 2014. p. 77-103.
Research output: Chapter in Book/Report › Chapter
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. R-News, 6, pp. 8-12; Ligges, U., Mächler, M., Scatterplot3d: An R Package for visualizing multivariate data (2003) J Stat Softw, 8, pp. 1-20; Losos, J.B., (2009) Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles., , University of California Press, Berkeley; Losos, J.B., Seeing the forest for the trees: The limitations of phylogenies in comparative biology (2011) Am Nat, 177, pp. 709-727; Mahler, D.L., Revell, L.J., Glor, R.E., Losos, J.B., Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles (2010) Evolution, 64, pp. 2731-2745; Miles, D.B., Dunham, A.E., Historical perspectives in ecology and evolutionary biology: The use of phylogenetic comparative analyses (1993) Ann Rev Ecol Syst, 24, pp. 587-619; Miller, E.T., Zanne, A.E., Ricklefs, R.E., Niche conservatism constrains australian honeyeater assemblages in stressful environments (2013) Ecol Lett, 16, pp. 1186-1194; Near, T.J., Bolnick, D.I., Wainwright, P.C., Fossil calibrations and molecular divergence time estimates in centrarchid fishes (Teleostei: Centrarchidae) (2005) Evolution, 59, pp. 1768-1782; Nielsen, R., Mapping mutations on phylogenies (2002) Syst Biol, 51, pp. 729-739; Nunn, C.L., (2011) The Comparative Approach in Evolutionary Anthropology and Biology, , University of Chicago Press, Chicago; O’meara, B., Evolutionary inferences from phylogenies: A review of methods (2012) Ann Rev Ecol Evol Syst, 43, pp. 267-285; O’meara, B.C., Ané, C., Sanderson, M.J., Wainwright, P.C., Testing for different rates of continuous trait evolution using likelihood (2006) Evolution, 60, pp. 922-933; Pagel, M., Detecting correlated evolution on phylogenies: A general method for comparative analysis of discrete characters (1994) Proc Roy Soc Ser B, 255, pp. 37-45; Paradis, E., (2012) Analysis of Phylogenetics and Evolution with R, 2Nd Edn., , Springer, New York; Paradis, E., Claude, J., Strimmer, K., APE: Analyses of phylogenetics and evolution in R language (2004) Bioinformatics, 20, pp. 289-290; Pennell, M.W., Harmon, L.J., An integrative view of phylogenetic comparative methods: Connections to population genetics, community ecology and paleobiology (2013) Ann NY Acad Sci, 1289, pp. 90-105; Pybus, O.G., Harvey, P.H., Testing macro-evolutionary models using incomplete molecular phylogenies (2000) Proc Roy Soc B, 267, pp. 2267-2272; Ree, R.H., Smith, S.A., Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis (2008) Syst Biol, 57, pp. 4-14; Revell, L.J., Phytools: An R package for phylogenetic comparative biology (and other things) (2012) Methods Ecol Evol, 3, pp. 217-223; Revell, L.J., Two new graphical methods for mapping trait evolution on phylogenies (2013) Methods Ecol Evol, 4, pp. 754-759; Revell, L.J., Ancestral character estimation under the threshold model from quantitative genetics (2014) Evolution, 68, pp. 743-759; Revell, L.J., Mahler, D.L., Peres-Neto, P.R., Redelings, B.D., A new method for identifying exceptional phenotypic diversification (2012) Evolution, 66, pp. 135-146; Rohlf, F.J., Comparative methods for the analysis of continuous variables: Geometric interpretations (2001) Evolution, 55, pp. 2143-2160; Rohlf, F.J., Geometric morphometrics and phylogeny (2002) Morphology, Shape, and Phylogeny, pp. 175-193. , MacLeod N, Forey PL, CRC Press: Boca Raton; Rosindell, J., Harmon, L.J., OneZoom: A fractal explorer for the tree of life (2012) Plos Biol, 10, pp. e1001406; Schliep, K.P., Phangorn: Phylogenetic analysis in R (2011) Bioinformatics, 27, pp. 592-593; Schluter, D., Price, T., Mooers, A., Ludwig, D., Likelihood of ancestor states in adaptive radiation (1997) Evolution, 51, pp. 1699-1711; Sidlauskas, B., Continuous and arrested morphological diversification in sister clades of characiform fishes: A phylomorphospace approach (2008) Evolution, 12, pp. 3135-3156; Smith, S.A., Beaulieu, J.M., Donoghue, M.J., Mega-phylogeny approach for comparative biology: An alternative to supertree and supermatrix approaches (2009) BMC Evol Biol, 9, p. 37; Thornton, J.W., Desalle, R., Gene family evolution and homology: Genomics meets phylogenetics (2000) Ann Rev Genomics Hum Genet, 1, pp. 41-73; Verbruggen, H., (2008) Treegradients, , http://www.phycoweb.net/software/TreeGradients/; Yang, Z., (2006) Computational Molecular Evolution., , Oxford University Press, Oxford
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