Fig. 1. Hypothetical evolutionary relationships among 17 species of organisms. Vertical axis represents time in relative units, with the top of the `phylogenetic tree' representing the present. Hence, species 1–7 and 8–13 are alive now (extant), whereas species e1–e4 are extinct. Statements about phylogenetic relationships are based solely on recency of common ancestry. For example, species 1 and 2 are each other's closest relative because they share a more recent common history with each other than with any other species depicted in this figure. The horizontal axis is arbitrary, and note that nodes could be rotated for graphical convenience with no implication for evolutionary relationships. `Clades' are hierarchically arranged, `monophyletic' groups of species, including all species that have descended from a common ancestor as well as that basal ancestor. All species within a given clade are more closely related to each other (they share a more recent common ancestor) than to any species in another clade. In the strict sense, a clade includes all species that have ever existed within it. Thus, Clade B includes species 7 as well as e1–e4. However, as it is impossible to know of all extinct species within a given clade and as physiologists rarely include extinct taxa in their studies, the term `clade' is often used in a relative way with respect to a particular collection of species that are included in a given study. Consider a comparative physiological study of species 1–13. Species 1–6 might be referred to as Clade 1, while species 7–13 might be referred to as Clade 2. However, note that species 7 is relatively distantly related to the other extant species in Clade 2 (i.e. species 8–13 shared a last common ancestor much more recently than the last common ancestor of them with species 7). Hence, a researcher studying species 1–13 might prefer to write in terms of Clades A, B and C in order to highlight the fact that, a priori, she would expect species 7 to be somewhat different from species 8–13. (Importantly, a priori hypotheses about particular single species can be tested with well-established phylogenetically based statistical methods, although they may not be convincing to some regardless of the level of statistical significance; see Garland et al., 1993; Garland and Adolph, 1994; Garland and Ives, 2000.) Branch lengths in this figure are proportional to divergence times. All phylogenetically based statistical methods use branch lengths in their calculations, although some assume (arbitrarily) that each branch segment is equal in length. Alternatively, under the commonly assumed Brownian motion model of character evolution (see Fig. 2), branch lengths are assumed to be in units proportional to (relative) divergence times and hence to the variance of character evolution along each branch segment (i.e. longer branches imply greater variance of character change; see Felsenstein, 1985).