Supporting Information Finarelli and Flynn 10.1073/pnas.0901780106 SI Text comparisons to extant taxa appreciably lower the power of Phylogeny of the Carnivora. Valid statistical analysis of compara- statistical analyses. tive data in biological systems always requires information on the The still imprecise understanding of the evolutionary rela- phylogenetic relationships of the organisms being analyzed to tionships among fossil and extant musteloid taxa (7–11) presents account for the statistical nonindependence of observed char- further challenges in reconstructing character transformations acter values for closely related taxa (1, 2). We constructed a across this clade. We partitioned both nonfelid feliforms and composite cladogram of the Carnivora based on frameworks musteloids into ‘‘archaic’’ and ‘‘modern’’ groups based on first provided by several recent molecular phylogenies of the Car- appearances of taxa in the fossil record. It should be noted that nivora and further augmented by clade-specific phylogenies both of these cutoffs are necessarily arbitrary, and the groupings derived from DNA and morphological data. Recent phyloge- they produce are both highly paraphyletic. Therefore, in contrast netic analyses of the Carnivora using DNA sequence data have to the preceding use of paraphyletic groups, for which observed greatly improved our understanding of the interrelationships change in the allometries can be mapped to a single branch of the among the traditional family-level clades within this clade. In phylogeny, changes between archaic and modern feliforms or addition, morphological and ‘‘total evidence’’ phylogenies, in- musteloids only represent differences between early and late cluding fossil taxa, provide the means to incorporate extinct appearing members of each group. This approach is similar to carnivoran lineages within a molecular framework encompassing previous attempts to document change in relative brain size modern clades. All phylogenetic hypotheses used in this analysis, within a group through time, by partitioning taxa into early/late and references to supporting analyses, are given in Fig. S3. or extant/fossil partitions, and then assessing change in the We identify 2 paraphyletic groups (‘‘Stem Canidae’’ and residual values across these partitions (see, for example, refs. 12, ‘‘Nandinia/Basal Feliforms’’; Fig. S3) that are incorporated as 13, and 14). Although it is always preferable to map evolutionary stem outgroups to 2 monophyletic clades to facilitate the recon- transformations directly onto branches of a phylogeny, given struction of evolutionary transformations between these clades both ambiguity in the fossil record and the phylogeny for these and inferred plesiomorphic conditions of the stem outgroups. groups, the approach presented here represents a conservative Using this approach, a previous analysis of caniforms found analysis and the best potential hypothesis given the presently evidence for a change in the encephalization allometry between available data. a paraphyletic stem canid group and the crown radiation of To determine the cutoffs between archaic and modern taxon Canidae (wolves, foxes, jackals, etc.) (3). In a similar manner, in partitions within Musteloidea and nonfelid Feliformia, we as- this analysis several fossil taxa comprising a paraphyletic stem sessed the residuals for fossil taxa in each clade relative to the group lying just outside crown-clade Feliformia (e.g., Stenogale) brain volume/body mass regression for the extant taxa in each (4–6) were clustered with Nandinia (Asian palm civet) into a respective clade. If a transformation in the encephalization group of stem feliforms. Due to low sample size, this group was allometry between archaic and modern sets of taxa for either further combined with the extinct clade Nimravidae (‘‘false group is to be preferred over a hypothesis proposing one sabretooths’’) into a paraphyletic stem group, ‘‘Basal Feli- allometry for all taxa within the group, then it is most likely to formia’’ (see Fig. S3) (4, 5). be supported if the partition corresponds to a dramatic change Two additional paraphyletic groups were also considered (Fig. in the distribution of observed residuals. Plotting the distribution S3). With the exception of Felidae (cats) and Nimravidae, of residuals against time (12) for each group reveals sharp sample sizes of brain volume estimates for fossil feliforms are increases in both maximum and median residual values for both small, and within the caniforms a similar situation is encountered groups (at 12 Ma for feliforms and 10 Ma for musteloids). 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