Commentary Phylogenetic approaches in comparative physiology Theodore Garland , Jr 1 , Albert

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. 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 Of particular interest for the present review, they are also widely used to explore trade-offs (e.g. Comparative methods have been radically restructured over the past two decades, and now routinely incorporate both phylogenetic information and explicit models of character 3015 Over the past two decades, comparative biological analyses have undergone profound changes with the incorporation of rigorous evolutionary perspectives and phylogenetic information. This change followed in large part from the realization that traditional methods of statistical analysis tacitly assumed independence of all observations, when in fact biological groups such as species are differentially related to each other according to their evolutionary history. New phylogenetically based analytical methods were then rapidly developed, incorporated into 'the comparative method', and applied to many physiological, biochemical, morphological and behavioral investigations. We now review the rationale for including phylogenetic information in comparative studies and briefly discuss three methods for doing this (independent contrasts, generalized least-squares models, and Monte Carlo computer simulations). We discuss when and how to use phylogenetic information in comparative studies and provide several examples in which it has been helpful, or even crucial, to a comparative analysis. We also consider some difficulties with phylogenetically based statistical methods, and of comparative approaches in general, both practical and theoretical. It is our personal opinion that the incorporation of phylogeny information into comparative studies has been highly beneficial, not …