3015 The Journal of Experimental Biology 208 3015 3035 Published by The Company of Biologists 2005 doi 10 1242 jeb 01745 Commentary Phylogenetic approaches in comparative physiology Theodore Garland Jr1 Albert F Bennett2 and Enrico L Rezende1 1 Department of Biology University of California Riverside CA 92521 USA and 2Department of Ecology and Evolutionary Biology University of California Irvine CA 92697 USA Author for correspondence e mail abennett uci edu Accepted 13 June 2005 Summary Over the past two decades comparative biological and Monte Carlo computer simulations We discuss when analyses have undergone profound changes with the and how to use phylogenetic information in comparative studies and provide several examples in which it has been incorporation of rigorous evolutionary perspectives and helpful or even crucial to a comparative analysis We also phylogenetic information This change followed in large consider some difficulties with phylogenetically based part from the realization that traditional methods of statistical methods and of comparative approaches in statistical analysis tacitly assumed independence of all observations when in fact biological groups such as general both practical and theoretical It is our personal species are differentially related to each other according to opinion that the incorporation of phylogeny information into comparative studies has been highly beneficial not their evolutionary history New phylogenetically based only because it can improve the reliability of statistical analytical methods were then rapidly developed inferences but also because it continually emphasizes the incorporated into the comparative method and applied potential importance of past evolutionary history in to many physiological biochemical morphological and determining current form and function behavioral investigations We now review the rationale for including phylogenetic information in comparative studies and briefly discuss three methods for doing this Key words allometry comparative method evolutionary physiology model of evolution phylogeny statistical analysis independent contrasts generalized least squares models Introduction Studies of organismal form and function rely on multiple types of scientific investigation including theory description experimentation and comparison Comparing species is an ancient human enterprise done for a variety of reasons Sanford et al 2002 Since Charles Darwin the comparative method comparing populations species or higher taxa has been the most common and productive means of elucidating past evolutionary processes Harvey and Pagel 1991 Brooks and McClennan 2002 Comparative methods have been used extensively to infer evolutionary adaptation that is changes in response to natural selection for alternate physiological meanings of adaptation see Garland and Adolph 1991 Bennett 1997 They are most often promoted and criticized e g Leroi et al 1994 within this context However comparative methods are not used to infer adaptation alone Garland and Adolph 1994 Sanford et al 2002 but are also employed to analyze the effects of sexual selection e g Hosken et al 2001 Nunn 2002 Smith and Cheverud 2002 Aparicio et al 2003 Cox et al 2003 which may be nonadaptive or even maladaptive with respect to natural selection These methods can also be used to compare rates of evolution across clades or the amount of morphospace occupied by clades or by ecologically defined groups Garland 1992 Clobert et al 1998 Ricklefs and Nealen 1998 Garland and Ives 2000 Hutcheon and Garland 2004 McKechnie and Wolf 2004 Of particular interest for the present review they are also widely used to explore trade offs e g Clobert et al 1998 Vanhooydonck and Van Damme 2001 and to examine functional mechanistic relationships among traits e g Lauder 1990 Iwaniuk et al 1999 Mottishaw et al 1999 Autumn et al 2002 Hale et al 2002 Gibbs et al 2003 Johnston et al 2003 Herrel et al 2005 including allometric scaling with body size e g Garland 1994 Reynolds and Lee 1996 Williams 1996 Clobert et al 1998 Garland and Ives 2000 Nunn and Barton 2000 Herrel et al 2002 Perry and Garland 2002 Rezende et al 2002 2004 Schleucher and Withers 2002 McGuire 2003 Al kahtani et al 2004 McKechnie and Wolf 2004 Mu oz Garcia and Williams in press Comparative methods have been radically restructured over the past two decades and now routinely incorporate both phylogenetic information and explicit models of character THE JOURNAL OF EXPERIMENTAL BIOLOGY 3016 T Garland A F Bennett and E L Rezende evolution Indeed Sanford et al 2002 suggest that this new emphasis be termed the comparative phylogenetic method As outlined in Blomberg and Garland 2002 this revolution in comparative phylogenetic methodology followed from several conceptual advances 1 adaptation should not be casually inferred from comparative data 2 the incorporation of phylogenetic information increases both the quality and even the type of inference from comparative data alone 3 because all organisms are differentially related to each other taxa cannot be assumed to be independent of each other for statistical purposes 4 statistical analyses of comparative data must assume some model of character evolution for effective inference 5 taxa used in comparative analyses should be chosen in regard to their phylogenetic affinities as well as the area of functional investigation and 6 even phylogenetically based comparisons are purely correlational and inferences of causation drawn from them can be enhanced by other approaches including experimental manipulations To expand on some of these points quality in point 2 includes the simple fact that adding an independent estimate of phylogenetic relationships to a comparative analysis increases often greatly the amount of basic data that is brought to bear on a given question whereas type refers to analyses that are simply impossible without a phylogenetic perspective such as reconstructing ancestral values or comparing rates of evolution among lineages Although phylogenetic information and a suitable analytical method may allow any comparative data set to be rescued from phylogenetic nonindependence e g avoid inflated Type I error rates point 3 phylogenetically informed choice of species point 5 can accomplish more such as actually increasing statistical power to detect relationships among traits Garland et al 1993 Garland 2001 Finally we note that point 6 was recognized long ago but has been re
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