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Supporting Information Steiper and Seiffert 10.1073/pnas.1119506109 SI Text trices using Mesquite version 2.72 (11), and supertrees were Primate Phylogeny Reconstruction. Comprehensive, taxon-rich calculated using the heuristic search option in PAUP* 4.0b10 molecular phylogenies are available for extant primates [e.g., across 5,000 replicates. Perelman et al. (1)], but phylogenetic estimates for extinct pri- Tests of trait evolution also require that the phylogeny be time- mates tend to be much more restricted in their taxonomic scaled. A time-scaled phylogeny is easily generated for extant taxa sampling [e.g., living and extinct platyrrhine anthropoids (2) and from molecular clock analyses; however, for this analysis, fossil living and extinct catarrhine anthropoids (3)]. Because a com- taxa were also required to be part of this time-scaled phylogeny. prehensive morphological phylogenetic analysis of the entire Although most fossils have at least an approximate date associ- primate radiation is not available, we used a supertree approach ated with them, there is no simple method for generating the age [using matrix representation with parsimony (MRP) (4)] to ob- for the last common ancestors of fossil taxa. For example, whereas tain a broad estimate of relationships among living and extinct Australopithecus africanus has a last common ancestor with hu- primates. We combined results from four different studies into mans at some point along the hominin branch (12), it is not a composite taxon-rich phylogeny that included 62 extant pri- currently possible to determine precisely when this last common mate genera and 123 extinct primate species. We placed par- ancestor existed, despite having a date for A. africanus fossils. ticular emphasis on sampling members of the early phases of Acknowledging these difficulties and uncertainties, we re- primate evolution, because it is the deepest nodes of primate constructed a time-calibrated phylogeny that included fossil and phylogeny that exhibit the greatest disagreement between mo- extant primates using the following rules: lecular and fossil evidence for divergence times. The molecular i) Divergence dates among extant genera are based on Perel- dating analysis also required that relationships among extant – taxa be the same as those recovered by Perelman et al. (1), so the man et al. (1) from their tables 1 3. only morphology-based trees that could be used in the MRP ii) Internodes along stem lineages were distributed by equally analysis were those that were congruent with their study. Rossie dividing stem-lineage lengths by the number of extinct and MacLatchy’s (3) analysis of Eocene-to-Recent catarrhines clades that branch off from that stem lineage. Similarly, for terminal branches, branch lengths were equally divided (i.e., the tree in their figure 8) recovered relationships among for each extinct clade that connects to it. For example, to extant catarrhines that are consistent with the Perelman et al. (1) connect A. africanus to the Homo lineage, we divided the phylogeny, and so did not require modification. In the remaining Homo lineage (6.6 Ma) into two equal-length branches (3.3 two cases, the trees we included were based on morphological Ma) and connected the A. africanus branch to this midpoint. phylogenetic analyses that were constrained by a molecular iii) Fossil species were placed at their currently estimated age “scaffold” (5). For living and extinct platyrrhines, we included on the geological timescale, with ages rounded to the near- Kay et al.’s (2) analysis that was constrained to fit a molecular est 1 Ma. For example, A. africanus is dated to ∼2 Ma (13). scaffold (i.e., the tree in their figure 20A). For both the Rossie Because A. africanus connects to the Homo stem lineage at and MacLatchy (3) and Kay et al. (2) trees, we used results that 3.3 Ma, this requires a 1.3-Ma–long terminal branch to were derived from runs that included some ordered multistate connect A. africanus to the Homo branch. characters to maintain as much methodological consistency as iv) For extinct clades and extinct species, branch lengths were possible across these disparate datasets. For the remaining living distributed in such a way that terminal species branches and extinct primates (plesiadapiforms, strepsirrhines, adapi- and internodes were assigned, at minimum, a length of 2 forms, omomyiforms, tarsiids, and stem and early crown an- Ma [unless extinct taxa were too ancient, based on the thropoids), we used the matrix of Boyer et al. (6), which was divergence dates calculated for extant taxa by Perelman reanalyzed with a backbone constraint of extant taxa based on et al. (1)] to allow for 2-Ma internodes. One such case is the relationships recovered by Perelman et al. (1). The matrix the parapithecoid-proteopithecid clade, within which some was analyzed with some multistate characters ordered and internodes were assigned lengths shorter than 2 Ma early scaled, and with premolar reacquisition not allowed [see also in their phylogeny to accommodate their placement within Boyer et al. (6)]. The matrix was analyzed with the heuristic crown Anthropoidea as sister taxa of Platyrrhini; another is search option in PAUP* 4.0b10 (7) across 5,000 replicates, with Saharagalago, which is too old for internodes along the a random addition sequence and tree bisection and reconnection galagid stem lineage to be distributed equally. branch swapping. Three highly fragmentary taxa (Loveina min- v) Polytomies were broken up by resolving them with very uta, L. sheai, and L. wapiteinsis) and two more complete taxa short branch lengths (0.01 Ma). (Rooneyia viejaensis and Plesiopithecus teras) were excluded be- cause these species have proven to be particularly unstable given This method generated a time-calibrated phylogeny of extant different assumptions about character evolution and the rela- genera and extinct species (Fig. S2A). tionships of extant taxa [see Boyer et al. (6) and Seiffert et al. (8– This phylogeny was used in the analyses of body size (BS) 10), which are based on the same core character-taxon matrix, evolution. The analyses of absolute endocranial volume (EV) and with minor modifications], and we considered it preferable for relative endocranial volume (REV) required a different tree for these unstable taxa to not have a major influence on the phy- two reasons. First, most primate fossil species do not preserve logeny used for ancestral body mass calculation. The Eocene crania. Second, there are some extinct primates for which EV can sivaladapids Hoanghonius and Wailekia were included in the be reconstructed that have not been placed in a phylogeny using phylogenetic analysis but could not be used in the reconstruction parsimony analysis of character data (e.g., Chilecebus). Because of ancestral states for body mass because m1 measurements are so few fossil primate crania are available, it was nevertheless either not available (Wailekia) or unpublished (Hoanghonius). critical to include as many of these specimens as possible into the Finally, the genus-level phylogeny of Perelman et al. (1) (their time-scaled phylogeny. To generate a time-scaled phylogeny for figure 1) was integrated into the supertree. Strict consensus trees these analyses, the BS tree was pruned of fossil taxa that do not from each of these four studies were converted into MRP ma- preserve crania. Subsequently, the following specimens were Steiper and Seiffert www.pnas.org/cgi/content/short/1119506109 1of15 added to the pruned supertree as follows: A. africanus was linked 29.745, κ; 26.446, λ; 26.534, δλ; 30.008, δκ; 26.885, κλ; 27.935, to the Homo branch (12); Oreopithecus was linked to the great δλκ. A model with no scaling factors was compared with each ape stem (14); Chilecebus was placed halfway along the platyr- scaling factor individually (none vs. λ, none vs. κ, none vs. δ); the rhine stem lineage, based in part on its small relative brain size, BFs showed that both the λ and κ parameters improved the which apparently falls outside the range of all extant platyrrhines model, especially κ, which had the highest harmonic mean (15); Mioeuoticus was placed in a polytomy at the base of crown likelihood and a BF of 10.24 (Table S9). Comparing the κ model Lorisiformes using a very small branch to approximate a tri- with models in which two and three parameters were used (κ vs. chotomy (16) (our method requires bifurcating trees); the no- δλ, κ vs. δκ, κ vs. κλ, κ vs. δκλ) showed that the κ-only model still tharctid adapiforms Smilodectes and Notharctus were linked to had the best fit. Given this analysis of BFs, the preferred model the notharctid Cantius as a sister taxon to Pronycticebus (17). for the regression analysis was a model that included the κ pa- Ignacius was alternatively placed as a sister taxon to Plesiadapis rameter (posterior mean = 0.31). The average values for the (18) or as the most basal taxon in a paraphyletic plesiadapiform phylogenetically corrected regression slope and intercept yielded group (19). The monophyletic plesiadapiform phylogram the equation EV = 0.670 × BS − 1.274. is presented in Fig. S2B, and both tree files are presented in The within-directional model BFs were compared for these SI Appendix. REV data. The directional model with no scaling factors was compared with each scaling factor individually (none vs. λ, none Computation of Bayes Factors. Models were compared using Bayes vs. κ, none vs. δ). Here the BFs showed that the κ and λ pa- factors (BFs) as described in the main text. Note that in our rameters improved the model, with BFs of 11.28 and 11.30, re- reporting of the Bayes factors, for consistency we are reporting spectively (Table S6). Comparing the κ and λ models with negative values where more complex models have lower like- models where two or three parameters were used (κ vs.