An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values

Interspecific comparisons have played a prominent role in evolutionary biol ogy at least since the time of Charles Darwin. Since 1985, the "comparative method" has been revitalized by new analytical techniques that use phyloge netic information and by increased availability of phylogenies (often from molecular data sets), Because species descend from common ancestors in a hi erarchical fashion, related species tend to resemble each other (elephants look like elephants); therefore, cross-species data sets generally do not c omprise Independent and identically distributed data points, Phylogenetical ly based statistical methods attempt to account for this fact, Phylogenetic methods allow traditional topics in comparative and ecological physiology to be addressed with greater rigor, including the form of allometric relati onships and whether physiological phenotypes vary predictably in relation t o behavior, ecology or environmental characteristics, which provides eviden ce about adaptation, They can also address new topics, such as whether rate s of physiological evolution have differed among lineages (clades), and whe re and when a phenotype first evolved, We present brief overviews of three phylogenetically based statistical methods: phylogenetically independent co ntrasts, Monte Carlo computer simulations to obtain null distributions of t est statistics, and phylogenetic autocorrelation, In a new result, we show analytically how to use independent contrasts to estimate ancestral values and confidence intervals about them, These confidence intervals often excee d the range of variation observed among extant species, which points out th e relatively great uncertainty inherent in such inferences, The use of phyl ogenies should become as common as the use of body size and scaling relatio nships in the analysis of physiological diversity.