Report. Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition

Current Biology 24, 2386 2392, October 20, 2014 ª2014 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.cub.2014.08.034 Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition Report Stephen L. Brusatte, 1, * Graeme T. Lloyd, 2 Steve C. Wang, 3 and Mark A. Norell 4 1 School of GeoSciences, University of Edinburgh, Edinburgh EH9 3JW, UK 2 Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK 3 Department of Mathematics and Statistics, Swarthmore College, Swarthmore, PA 19081, USA 4 Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA Summary The evolution of birds from theropod dinosaurs was one of the great evolutionary transitions in the history of life [1 22]. The macroevolutionary tempo and mode of this transition is poorly studied, which is surprising because it may offer key insight into major questions in evolutionary biology, particularly whether the origins of evolutionary novelties or new ecological opportunities are associated with unusually elevated bursts of evolution [23, 24]. We present a comprehensive phylogeny placing birds within the context of theropod evolution and quantify rates of morphological evolution and changes in overall morphological disparity across the dinosaur-bird transition. Birds evolved significantly faster than other theropods, but they are indistinguishable from their closest relatives in morphospace. Our results demonstrate that the rise of birds was a complex process: birds are a continuum of millions of years of theropod evolution, and there was no great jump between nonbirds and birds in morphospace, but once the avian body plan was gradually assembled, birds experienced an early burst of rapid anatomical evolution. This suggests that high rates of morphological evolution after the development of a novel body plan may be a common feature of macroevolution, as first hypothesized by G.G. Simpson more than 60 years ago [25]. Results The fossil record provides unique insight into major evolutionary transitions: the origins of entirely new body plans and behaviors. In one of the great transitions in the history of life, bipedal carnivorous theropod dinosaurs evolved feathers and wings [1, 2], dramatically reduced their body size [3 6], and gave rise to birds. The dinosaur-bird transition is captured by a rich fossil record that has expanded tremendously in recent years including thousands of feathered dinosaur specimens from northeastern China found over the past two decades [2] providing an unparalleled opportunity to dissect a major morphological, behavioral, and paleobiological transformation in deep time. In particular, the dinosaur-bird transition can provide key insight into major questions in contemporary evolutionary biology, particularly whether the origins of evolutionary novelties or new ecological opportunities are *Correspondence: stephen.brusatte@ed.ac.uk associated with unusually elevated bursts of evolution [23, 24]. This hypothesis was first articulated by George Gaylord Simpson in the 1940s [25] and has been the subject of intense debate ever since. Phylogenetic Analysis Birds are members of the theropod dinosaur subgroup Coelurosauria, a diverse clade that includes tyrannosauroids and dromaeosaurids, among others [7 14]. Our comprehensive, new phylogenetic analysis is a species-level analysis that includes nearly all Mesozoic coelurosaurs that are known from well-preserved and diagnostic fossils available for study. It is the latest iteration of the Theropod Working Group (TWiG) project, a 20-year program centered at the American Museum of Natural History that has been building progressively larger and more inclusive data sets of coelurosaurian phylogeny based on personal study of specimens. Previous TWiG analyses have focused extensively on the most derived paravian coelurosaurs: birds (technically known as avialans) and their very closest relatives, such as dromaeosaurids and troodontids [8, 9]. Here, for the first time, we incorporate a broad range of more basal (nonparavian) coelurosaurs into a TWiG analysis. Our data set includes 150 coelurosaurs scored for 853 characters, approximately twice the size of previous TWiG data sets (Supplemental Experimental Procedures available online). Our phylogenetic analysis places birds within the broader framework of theropod evolution (Figure 1; see also Figures S1 and S2). Tyrannosauroids are the most basal major coelurosaurian subgroup; therizinosauroids and alvarezsauroids form a clade with oviraptorosaurs and paravians exclusive of more basal coelurosaurs; therizinosauroids and oviraptorosaurs are not sister taxa; and, for the first time, a TWiG analysis recovers a polytomy between avialans, dromaeosaurids, and troodontids, meaning that the immediate relative of birds cannot be clearly identified. The recently described Aurornis, Xiaotingia, and Anchiornis comprise a clade of basal troodontids, not avialans, as recently proposed [14]. The iconic Archaeopteryx is positioned as the basal-most avialan taxon, a traditional placement that is in agreement with most previous studies [8 10], not as a closer relative of dromaeosaurids, as was found in a recent series of analyses [11, 12]. Morphological Rates The anatomical characters compiled for the phylogenetic analysis provide a ready source of data for examining trends in anatomical evolution across the dinosaur-bird transition. Because our data set includes features from throughout the skeleton, it can encapsulate changes in overall anatomy and document the evolution of the entire avian body plan. It complements recent analyses focused on more specific features, such as body size [3 6, 22] and limb measurements [19 21]. Maximum-likelihood analyses of rates of character evolution on the phylogeny, which test whether individual branches or entire clades have significantly different rates than the remainder of the tree [26, 27], identify high rates in birds (avialans) and the internal branches leading toward birds (Figure 2; see also Figure S3). High rates in birds are consistently found under a variety of conditions: in different most-parsimonious

Rapid Evolution across Dinosaur-Bird Transition 2387 Figure 1. Phylogenetic Relationships of Coelurosaurian Theropods Based on a Data Set of 152 Taxa Scored for 853 Characters Strict consensus tree of 99,999 most-parsimonious trees (3,360 steps, consistency index = 0.322, retention index = 0.777). Silhouettes are from http://phylopic.org/. See also Figures S1 and S2 for the full strict reduced consensus tree. Experimental Procedures and http:// dx.doi.org/10.5061/dryad.84t75). This provides robust evidence that birds (and their stem lineage) evolved faster than other theropods and that their origin was associated with an early burst of rapid morphological evolution. Previous studies have found significant changes in body size and limb morphology either progressively prior to the origin of birds or within more derived birds [3, 5, 6, 19, 20, 22], but our analysis of the overall phenotype puts the major rate shift at the origin of Avialae itself. High rates are also common among tyrannosauroids, the only major coelurosaurian subgroup to evolve colossal size (5 tons or more in mass). If genuine, this may suggest that dinosaurs developed gigantism by accelerating rates of morphological evolution, perhaps incongruous with a recent finding that large theropods had slower rates of proportional body size evolution than smaller lineages [6]. However, the high tyrannosauroid rates appear to be artifactual, probably caused by an overinflation of taxa and characters in the data set relevant to these iconic and well-studied theropods. First, high tyrannosauroid rates are not seen in all iterations (based on different branch durations) of the primary analysis, and in some iterations, significantly low rates are recovered. Second, the high tyrannosauroid rates disappear in many of our sensitivity analyses (Supplemental Experimental Procedures and http://dx.doi.org/10.5061/dryad. 84t75). This is not the case with the high rates in birds, as these are seen in all branch dating iterations and persist in all sensitivity analyses. trees (MPTs), using different branch dating techniques, when terminal and internal branches are tested separately, and when the phylogeny is subsampled down to a common number of species in each major subgroup (Supplemental Disparity and Morphospace Occupation When the character data set is used to calculate disparity, by ordinating all taxa in a morphospace depicting the spread of morphological variability among coelurosaurs [28], there is no firm evidence that birds group separately from other species or have greater disparity than other coelurosaur groups (Figure 3; Tables S1 S3). Although there is separation

Current Biology Vol 24 No 20 2388 Allosaurus Bicentenaria Zuolong Tanycolagreus Coelurus Kileskus Guanlong Proceratosaurus Sinotyrannus Dilong Juratyrant Eotyrannus Xiongguanlong Dryptosaurus Appalachiosaurus Bistahieversor Tyrannosauroidea Tugulusaurus Ornitholestes Tyrannosauridae Juravenator Sinocalliopteryx Huaxiagnathus Compsognathidae Mirischia Compsognathus Sinosauropteryx Nqwebasaurus Pelecanimimus Shenzhousaurus Beishanlong Harpymimus Garudimimus Sinornithomimus Archaeornithomimus Gallimimus Anserimimus Struthiomimus Qiupalong Ornithomimus Ornithomimosauria Alvarezsauroidea Therizinosauroidea Epidexipteryx Pedopenna Oviraptorosauria Oviraptorosauria (inc. Epidexipteryx + Pedopenna) Archaeopteryx Sapeornis Jeholornis Jixiangornis Confuciusornis Avialae Other avialans Anchiornis clade Troodontidae Other Troodontidae Dromaeosauridae Figure 2. Summary of Results of Two Rate Tests on the First of Ten Randomly Sampled Most-Parsimonious Trees Clades are collapsed as in Figure 1, with the full tree and all per-branch and clade rate results shown at http://dx.doi.org/10.5061/dryad.84t75. Pie charts along individual branches indicate the proportion of significantly high (red), significantly low (blue), and nonsignificant (white) per-branch rates based on 100 replicates to take into account dating uncertainty. Results for the clade test are shown for the nine major subclades, with the larger pie charts indicating the proportion of high, low, and nonsignificant rates across 100 replicates of dating uncertainty, using the same color scheme. Silhouettes are from http:// phylopic.org/. See also Figure S3 for the full clade rate results on our primary tree.

Rapid Evolution across Dinosaur-Bird Transition 2389 PC axis 2-100 -50 0 50 100 150 PC axis 3-100 -50 0 50 100 Tyrannosauroidea Alvarezsauroidea -100-50 0 50 PC axis 1-100 -50 0 50 100 150 PC axis 2 Oviraptorosauria Compsognathidae Troodontidae Ornithomimosauria of birds and other coelurosaurs on the first principal coordinate axis (which explains only a small portion of overall variance), there is wide overlap on all other axes. Permutation tests, which assess whether the morphospace means of two groups significantly differ from each other over all axes, find birds to be indistinct from their closest paravian relatives (Tables S1 and S2; Supplemental Experimental Procedures). Pairwise comparisons between other coelurosaur subgroups are also generally insignificant, but a few are significant. This Dromaeosauridae Therizinosauroidea Avialae Figure 3. Discrete Character Morphospace of Coelurosaurian Theropods, Depicting the Overall Anatomical Variability of Species Bivariate plots of principal coordinate axes 2 versus 1 and 3 versus 2 are shown (axes 1 3 account for 4.25% of total variance). Birds are largely distinct from other coelurosaurs on principal coordinate axis 1, but not on axis 2 or 3 (or all subsequent axes). Permutation tests indicate that there is no clear, significant separation between birds and their closest relatives among theropods (Tables S1 S3; Supplemental Experimental Procedures). demonstrates, for example, that birds and dromaeosaurids are less distinct from each other than are therizinosauroids and oviraptorosaurs, one of the significant comparisons. In other words, birds are not a notable outlier when placed in the context of the entire coelurosaur morphospace. Although birds are clearly distinct compared to all other living vertebrates, the avian bauplan isn t especially distinct relative to other coelurosaurs, particularly their closest relatives. These results are consistent with many recent phylogenetic studies, ours included (see Phylogenetic Analysis in the Results), which find few characters separating Avialae from nonavialan theropods. These results may also help explain why so many alternative phylogenetic analyses have difficulty in placing certain taxa (such as Anchiornis and Archaeopteryx) consistently in either Avialae or among the clades of nonavialan theropods most closely related to birds [7 14]. Discussion The rate and disparity results presented here paint a complex picture of the dinosaur-bird transition and the early evolution of birds. In general anatomical terms, birds are a continuum of millions of years of theropod evolution. There is no great jump between nonbirds and birds in morphospace. Instead, those features that today combine to set birds apart from other vertebrates feathers, wishbones, air sacs, and hundreds more evolved piecemeal in Mesozoic theropods [18]. Therefore, we surmise that a Mesozoic naturalist would make no immediate distinction between a Velociraptor-type animal and an Archaeopteryx-type animal. That said, there is an increased rate of morphological evolution associated with the origin of birds, beginning in the stem lineage leading toward birds and continuing throughout most of the avialan portion of Mesozoic coelurosaur phylogeny. This rate does not correspond to a major shift in morphospace occupation, so it does not reflect

Current Biology Vol 24 No 20 2390 the sudden and simultaneous acquisition of a distinct avian body plan. Instead, it suggests that birds evolved their distinctive features gradually and that once the classic bird-like skeleton was assembled, something was unlocked that allowed birds to evolve rapidly within their fairly indistinct area of morphospace. There is growing evidence that changes in discrete character evolution, body size, and limb anatomy occurred quickly in the vicinity of the origin of birds, either at the node Avialae, in close avialan outgroups, or beginning with slightly more derived birds [3 6, 19 22]. It is likely that different types of data will pinpoint changes at slightly different positions on phylogeny, but in general, recent studies converge in identifying the dinosaur-bird transition as an abnormally rapid period of morphological evolution. We hypothesize that high rates of morphological change after the development of a novel body plan, whether that development is sudden or gradual, may be a common feature of macroevolution. This is generally consistent with Simpson s theory of adaptive radiations and quantum evolution [25] and a recent study that identified high morphological rates in Cambrian arthropods, after their characteristic bauplans were assembled [29]. It is also consistent with recent studies that found high rates of morphological evolution during the early history of lungfish [27], tetrapods [30], and archosaurs (the larger group containing dinosaurs and crocodiles) [31]. Although such early bursts are rarely found in analysis of neontological data [23], improved methods [6, 24, 27] and the deep-time perspective of a good fossil record may show that they are a major driver of evolution and biodiversity. Experimental Procedures Phylogenetic Analysis The phylogenetic analysis includes 152 taxa scored for 853 discrete characters. The analysis is the latest and most inclusive version of the American Museum of Natural History s TWiG data set. This data set has grown iteratively over the past 15 years with the addition of new taxa and characters [8, 9]. The focus of previous TWiG analyses has been paravian theropods (avialans, dromaeosaurids, and troodontids), reflecting long-standing interest in the origin of birds and the relationships of birds and their closest dinosaurian relatives. We added a wealth of new data relevant to nonparavian coelurosaurs, particularly nonmaniraptoran basal coelurosaurs (tyrannosauroids, ornithomimosaurs, compsognathids, and singleton taxa). Compared to the most recent TWiG data set [9], this analysis includes 41 new taxa and 379 new characters. As a result, the analysis presented here includes a nearly complete sample of Mesozoic coelurosaurs that have been available to us for personal study. The new taxa include a nearly complete sample of basal coelurosaurs and the recently described paravians Eosinopteryx [32] and Aurornis [14], which are particularly close relatives of birds. The new characters include a number of novel characters pertinent to basal coelurosaurs, characters relevant to the ingroup relationships of tyrannosauroids that were previously published by our research group [33], and characters from recent phylogenetic analyses of nonparavian coelurosaur subgroups [34 37]. The character list and data set are provided at http:// dx.doi.org/10.5061/dryad.84t75. The phylogenetic data set was analyzed with equally weightedparsimony in TNT v 1.1 [38]. Allosaurus was used as the outgroup to root the tree. The data set was first analyzed under the New Technology search options, using sectorial search, ratchet, tree drift, and tree fuse options with default parameters. The minimum length tree was found in ten replicates, a procedure that aims to initially sample as many tree islands as possible. The generated MPTs were then analyzed under traditional tree bisection and reconnection branch swapping, a procedure that aims to more fully explore each tree island. Clade support was assessed via decay indices and jackknife resampling analysis. Morphological Rates Rates of discrete character morphological evolution in a phylogenetic context were assessed using likelihood tests conducted in R [27]. The first of these asks whether an individual branch has a significantly higher or lower rate of evolution than the rest of the tree, and the second asks whether a particular clade has a significantly higher or lower rate than the remainder of the tree. Only Mesozoic coelurosaurs were included in these analyses, which utilized the 853-character discrete data set from the phylogenetic analysis. For each analysis, the tree was time scaled before characters were optimized, using the equal branch scaling measure based on the absolute ages of the terminal taxa [31, 39]. After time scaling, ancestral character states were estimated using the likelihood-based rerooting function in the R package phytools [40], which in turn allows the total number of changes along each branch to be recorded. Per-branch rates were calculated based on the total number of changes along the branch, with a correction for missing data, divided by the time duration of the branch [27]. Multiple replicates were used to take into account uncertainty in branch durations, based on uncertainty in the ages of the terminal taxa. Likelihood was then used to assess which branches and clades had higher or lower rates than the rest of the tree, following the protocols of [27]. For our primary analysis, we randomly selected a single MPT and applied the per-branch and per-clade tests using 100 replicates. We followed this with a number of sensitivity tests to gauge how robust the recovered patterns were. The first of these involved randomly selecting nine other MPTs to assess how differences in tree topology affect the rate results. The second examined the effects of different time-scaling algorithms by using a different option, the minimum-branch-length method [39]. The third tested for rate heterogeneity on a tree where branches were scaled to a unit length, to gauge how much of the rate results could be explained solely by the amount of character change (not branch duration). The fourth examined the effect of the number of sampled taxa in each major clade by randomly removing taxa from Alvarezsauroidea, Avialae, Compsognathidae, Dromaeosauridae, Ornithomimosauria, Oviraptorosauria, Therizinosauria, Troodontidae, and Tyrannosauroidea until each one was the same sample size (set at six species, based on the smallest clade, the compsognathids). Finally, the fifth tested for potential bias in rate between terminal and internal branches (such as that due to the lack of sampled autapomoprhies) by separating the two branch types and repeating the per-branch and per-clade tests. Disparity and Morphospace Occupation In order the test the morphological distinctiveness of birds relative to other theropods, we plotted all coelurosaurs in our data set into a multivariate morphospace, which represents the spread of anatomical form in a group [28]. This morphospace is nonphylogenetic (phenetic) in nature and only denotes the total spread of morphological variation in coelurosaurs without any indication of the speed at which this variation accumulates, making our morphospace-based tests distinct from our rate-based tests above. The morphospace was constructed by deriving a Euclidean distance matrix from our 853-character discrete data set, which was then subjected to principal coordinates analysis (PCO; equivalent to multidimensional scaling), a multivariate ordination technique that summarizes information from the distance matrix into a smaller and more manageable set of coordinate axes. The first axis represents those character distances contributing most to the overall variability among coelurosaurs, and each additional axis represents distances of progressively less significance. Each coelurosaur has a score on each axis, which together represent aspects of the overall anatomical form for each taxon. The distinctiveness of avialans relative to other coelurosaurs was tested in three ways. First, we used permutation tests to perform pairwise comparisons of group means in R and PAST [41]. These comparisons tested the equality of multivariate means (based on the 125 recovered PCO axes, which comprise 90% of total variance) of two designated groups (for example, avialans versus deinonychosaurs). The Mahalanobis distance between the two group means was calculated and compared with a null distribution of between-group distances obtained by random permutation of the group labels. Second, we compared Euclidean distances between avialans and their closest relatives (dromaeosaurids and troodontids) with Euclidean distances between several control pairs of coelurosaurian groups that are sister taxa or particularly close relatives. This served to assess whether birds are more distant from their closest relatives in morphospace than are various other pairwise groups of close relatives. The means and distributions of distances for the avialans versus close relative comparisons and the various other coelurosaur close relative comparisons were assessed for statistical significance with t tests and Mann-Whitney-Wilcoxon tests. Third, we tested whether avialans occupied a larger volume of morphospace than other coelurosaurs by calculating four disparity metrics for

Rapid Evolution across Dinosaur-Bird Transition 2391 the various coelurosaur subgroups (sum and product of the ranges and variances on the PCO axes). These disparity metrics quantify how much morphospace avialans and the other groups occupy. Differences in the disparity metrics between avialans and other coelurosaur groups were tested for significance with a permutation test. Accession Numbers Data for this paper are available on Dryad at http://dx.doi.org/10.5061/ dryad.84t75. Supplemental Information Supplemental Information includes Supplemental Experimental Procedures, three figures, and three tables and can be found with this article online at http://dx.doi.org/10.1016/j.cub.2014.08.034. Author Contributions S.L.B. led the project, compiled the anatomical data set, ran the phylogenetic analyses, ran some of the disparity analyses, and wrote the manuscript. G.T.L. led the morphological rates component of the project, wrote code in R, ran all rates analyses in R, and contributed to the manuscript. S.C.W. wrote code in R, ran disparity analyses in R, and contributed to the manuscript. M.A.N. is the leader of the TWiG project, collected anatomical data for the TWiG project, oversaw S.L.B. s PhD thesis (on which this manuscript is based), and contributed to the manuscript. Acknowledgments This work is funded by NSF DEB 1110357, Marie Curie Career Integration Grant EC 630652, an NSF GRF, Columbia University, and the American Museum of Natural History (S.L.B.) and by the Swarthmore College Research Fund and James Michener Faculty Fellowship (S.C.W.). We thank R. Benson, A. Dececchi, G. Dyke, H. Larsson, and M. Lee for discussion and three anonymous reviewers for helpful comments. We thank those who have contributed to the TWiG dataset: L. Chiappe, J. Choiniere, J. Clark, J. Clarke, P. Makovicky, A. Turner, and L. Zanno. 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Current Biology, Volume 24 Supplemental Information Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition Stephen L. Brusatte, Graeme T. Lloyd, Steve C. Wang, and Mark A. Norell

Supplemental Data Figure S1, Related to Figure 1. Reduced strict consensus of the 99999 most parsimonious trees recovered by the cladistic analysis (tree length=3360 steps; consistency index=0.322; retention index=0.777). The reduced strict consensus is calculated after the a posteriori removal of five taxa: Kinnareemimus, Epidendrosaurus, Pyroraptor, Hesperonychus, and Limenavis. Numbers next to nodes denote Bremer support value/jackknife percentage. Those nodes without any numbers are characterized by Bremer values of 1 and a jackknife percentage of less than 60%. The Oviraptorosauria + Paraves clade is collapsed here for space reasons but is fully shown in the following figure (Figure S2).

Figure S2, Related to Figure 1. Reduced strict consensus relationships within the Oviraptorosauria + Paraves clade (see the placement of this clade among higher-level coelurosaur phylogeny in Figure S1above). Refer to the caption of Figure S1 for explanation.

Figure S3, Related to Figure 2. Results of 100 dating uncertainty replicates for the clade test on the first sampled tree. For a higher resolution version of the figure please see our Dryad appendix.

Table S1, Related to Disparity and Morphospace Occupation: Morphospace Separation Tests Comparing Avialans vs. Other Coelurosaurs Avialans vs. All Other Coelurosaurs Permutation (2000 replicates, Mesozoic avialans only): Mahalanobis distance=205.91, p=0.02049 Permutation (2000 replicates, all avialans): Mahalanobis distance=168.64, p=0.00049975 Permutation (2000 replicates, Anchiornis, Aurornis, Xiaotingia as avialans): Mahalanobis distance=122.99, p=0.0034983 Additional Comparisons for Context Dromaeosaurids vs. all other coelurosaurs: Mahalanobis distance=124.61, p=0.0195 Troodontids vs. all other coelurosaurs: Mahalanobis distance=104.13, p=0.16542 Oviraptorosaurs vs. all other coelurosaurs: Mahalanobis distance=179.14, p=0.16342 Ornithomimosaurs vs. all other coelurosaurs: Mahalanobis distance=260.96, p=0.011494 Therizinosauroids vs. all other coelurosaurs: Mahalanobis distance=142.8, p=0.13643 Alvarezsauroids vs. all other coelurosaurs: Mahalanobis distance=100.22, p=0.34733 Compsognathids vs. all other coelurosaurs: Mahalanobis distance=396.97, p=0.096452 Tyrannosauroids vs. all other coelurosaurs: Mahalanobis distance=108.64, p=0.084958 Deinonychosaurs vs. all other coelurosaurs: Mahalanobis distance=131.79, p=0.0009995

Table S2, Related to Disparity and Morphospace Occupation: Morphospace Separation Tests Comparing Avialans vs. Sister Taxa/Closest Relatives Deinonychosaurs vs. Avialans Permutation (2000 replicates, Mesozoic avialans only, on only 57 PC axes): Mahalanobis distance=7636.3, p=0.14393 Permutation (2000 replicates, all avialans, on only first 63 PC axes): Mahalanobis distance=1445.6, p=0.30035 Permutation (2000 replicates, Anchiornis, Aurornis, Xiaotingia as avialans, on only first 63 PC axes): Mahalanobis distance=354.79, p=0.6017 Dromaeosaurids vs. Avialans Permutation (2000 replicates, Mesozoic avialans only, on only 41 PC axes): Mahalanobis distance=4154.1, p=0.16092 Permutation (2000 replicates, all avialans, on only first 47 PC axes): Mahalanobis distance=2231.2, p=0.21689 Permutation (2000 replicates, Anchiornis, Aurornis, Xiaotingia as avialans, on only first 50 PC axes): Mahalanobis distance=829.46, p=0.38181 Troodontids vs. Avialans Permutation (2000 replicates, Mesozoic avialans only, on only 36 PC axes): Mahalanobis distance=32207, p=0.05997 Permutation (2000 replicates, all avialans, on only first 42 PC axes): Mahalanobis distance=831780, p=0.014493 Permutation (2000 replicates, Anchiornis, Aurornis, Xiaotingia as avialans, on only first 42 PC axes): Mahalanobis distance=91317, p=0.034983 Additional Comparisons for Context Compsognathids vs. ornithomimosaurs: 17 axes, Mahalanobis distance=3900.2, p=0.10345 Therizinosauroids vs. alvarezsauroids: 23 axes, Mahalanobis distance=1666.2, p=0.17791 Troodontids vs. dromaeosaurids: 35 axes, Mahalanobis distance=381.96, p=0.41679 Oviraptorosaurs vs. deinonychosaurs: 45axes, Mahalanobis distance=135.71, p=0.037981 Ornithomimosaurs vs. alvarezsauroids: 24 axes, Mahalanobis distance=146.34, p=0.11094 Compsognathids vs. tyrannosauroids: 21 axes, Mahalanobis distance=132.31, p=0.21239 Ornithomimosaurs vs. tyrannosauroids: 29 axes, Mahalanobis distance=783720, p=0.00049975 Oviraptorosaurs vs. therizinosauroids: 20 axes, Mahalanobis distance=29042, p=0.032984

Table S3, Related to Disparity and Morphospace Occupation: Comparative Disparity Values Group SoR PoR SoV PoV Mesozoic avialans 15158 117 114969 829 alvarezsauroids 12428 94 104782 689 compsognathids 8926 60 115644 509 dromaeosaurids 15260 118 114125 836 ornithomimosaurs 12941 97 114011 754 oviraptorosaurs 11805 90 115127 754 therizinosauroids 12168 91 105167 667 troodontids 14160 109 111963 791 tyrannosauroids 15069 114 111335 754 (SoR=sum of ranges; PoR=product of ranges; SoV=sum of variances; PoV=product of variances)

Supplemental Experimental Procedures Note: Datasets, appendices and code relevant to this section are posted on Dryad: doi:10.5061/dryad.84t75 1) Phylogenetic Analysis Taxon Sampling: The cladistic analysis includes 152 taxa scored for 853 characters. This analysis is an expanded version of the American Museum of Natural History s Theropod Working group (TWiG) dataset. This dataset has grown iteratively over the past decade with the addition of new taxa and characters, and previous versions have been presented by [S1-S10]. The most recent versions include a large amount of data relevant to avialan phylogeny that was originally presented by [S11]. These studies are considered precursors to the current analysis and many of the character data employed here were first established in these earlier works. Several other authors have also used published TWiG phylogenies as a backbone for additional phylogenetic work, especially analyses targeting the interrelationships of certain coelurosaurian subgroups [eg. S12-S21]. The focus of most previous work from the Theropod Working Group, and the focal point of all published TWiG phylogenies, is maniraptoran theropods (therizinosauroids, oviraptorosauroids, paravians, most likely alvarezsauroids). More specifically, the overwhelming focus has been on the paravian theropods, which include dromaeosaurids, troodontids, and avialans (birds). This focus reflects longstanding interest in the origin of birds and the relationships of birds and their closest dinosaurian relatives. In this paper we add a wealth of new data relevant to non-maniraptoran basal coelurosaurs (tyrannosauroids, ornithomimosaurs, compsognathids, and many singleton taxa), as well as non-paravian maniraptorans (therizinosauroids, alvarezsauroids). As a result, the cladistic analysis presented here includes a nearly complete sample of Mesozoic coelurosaurs, but the majority of new data (new characters and taxa, revised character scores) are relevant to basal coelurosaurs. Compared to the hitherto most recent TWiG dataset [S9], this analysis includes 41 new taxa, all of which are basal coelurosaurs except for two derived paravians closely related to birds that have been described very recently (Eosinopteryx, Aurornis). This section includes a list of basal coelurosaur taxa included in the analysis, sources of coding data, and notes relevant to individual taxa. General Comments: The starting point for this analysis was the latest published version of the TWiG dataset [S9]. As previous TWiG work has largely focused on the paravian theropods, character scores for these taxa were mostly accepted without revision. In some cases, however, paravian taxa had to be rescored when characters were modified (e.g., by the addition of one or more new states to encapsulate wider variation among coelurosaurs). Character scores for non-paravian maniraptorans were also largely accepted without critical revision, although scores relevant to therizinosauroids and alvarezsauroids were carefully checked. Character scores for non-maniraptoran basal coelurosaurs, however, were carefully checked and in some cases modified. Several new basal coelurosaurs, alvarezsauroids, and therizinosauroids were added to the dataset of [S9], along with the paravians Eosinopteryx and Aurornis, but no new oviraptorosauroids were added. The analysis presented here includes several new characters and these were scored for both basal coelurosaurs and maniraptorans. The following is a brief description of taxon data sources; a full explanation can be found in [S22]. Outgroup Taxa: The outgroups employed here are the non-coelurosaurian tetanurans Allosaurus and Sinraptor. These taxa were scored based on the literature and personal observation of specimens. The Utah Museum of Natural History, American Museum of Natural History, and Carnegie Museum of Natural History collections of Allosaurus were studied firsthand, as was the holotype of Sinraptor

(IVPP 10600). Monographs of both taxa were also used to score characters (Allosaurus: [S23]; Sinraptor: [S24]). Paravians, Oviraptorosaurs, and Therizinosauroids: Maniraptorans were scored for new characters based on the literature and personal observation of specimens. Several maniraptorans were studied firsthand as part of this project. The complete Utah Museum of Natural History collection of the basal therizinosauroid Falcarius was studied, as was the American Museum of Natural History temporary collection of IGM Gobi oviraptorosauroid material. Characters were also scored directly for some Mongolian troodontids from the AMNH and IGM collections (Byronosaurus: IGM 100/983; Saurornithoides: AMNH FARB 6516), although most new scores for troodontids were based on the literature (including those for Eosinopteyx and Aurornis). Several dromaeosaurids were studied firsthand, including Austroraptor (MML 195), Balaur (EME PV.313; LVP [FGGUB] R.1580-1585), Bambiraptor (AMNH FR 30556), Buitreraptor (MPCA 245, 238), Deinonychus (YPM 5025 and hypodigm series), Dromaeosaurus (AMNH FARB 5356), Tsaagan (IGM 100/1015), Unenlagia/Neuquenraptor (MCF PVPH 77, 78), and Velociraptor (AMNH temporary collection of IGM specimens: see [S25-S26]). Finally, the basal avialan Archaeopteryx was also observed firsthand (Berlin and Eichstatt specimens), as was the enigmatic Epidexipteryx (IVPP V15471). Note that for all new characters, the five extant bird taxa included in the dataset (Crypturellus, Chauna, Anas, Crax, and Gallus) were scored in a very conservative manner, due to the great morphological differences between extant birds and basal coelurosaurs (which all new characters relate to). This was a pragmatic decision because it is often very difficult to confidently score living taxa for characters relevant to taxa such as tyrannosauroids and therizinosauroids, and therefore the possibility of making incorrect primary homology hypotheses is high. The extant birds have essentially been scored for only those characters that relate to skeletal ratios or measurements, or straightforward anatomical features that require no ambiguity to score in the living species. Alvarezsauroids: The alvarezsauroids Mononykus (AMNH IGM collection, including casts), Patagonykus (MCF PVPH 37), and Shuvuuia (IGM 100/975, 100/99, 100/10001) were studied firsthand. The basal alvarezsauroid Haplocheirus was scored based on extensive photographs provided by Jonah Choiniere, as well as the initial description of the taxon [S18]. Other alvarezsauroids were scored based on the literature and on notes and advice provided by Choiniere, whose dissertation and postdoctoral work focused largely on alvarezsauroids. Character scores for TWiG characters and some new characters were taken from [S18-20]. These scores were carefully checked and in rare cases modified. Tyrannosauroids: The character dataset of [S27], which focused on the ingroup phylogeny of tyrannosauroids, was incorporated into the dataset used here. The tyrannosauroid dataset was constructed based on extensive first-hand observation of tyrannosauroid specimens, as detailed by [S22, S27]. Ornithomimosaurs: Several ornithomimosaurian taxa were studied firsthand whereas others were scored based on the literature and photographs. Studied specimens include the holotype of Pelecanimimus polydon (LH 7777), the holotype of Shenzhousaurus orientalis (NGMC 97-4-002), the full lectotype and paratype series of Archaeornithomimus asiaticus (American Museum of Natural History specimens), casts of Sinornithomimus dongi in the University of Chicago research collection, the vast Polish Academy of Sciences collection of Gallimimus bullatus and the well-preserved Gallimimus skull IGM 100/1133, and the collection of Struthiomimus altus and Ornithomimus edmonticus material in the AMNH and Royal Ontario Museum collections.

There is considerable uncertainty about the alpha level taxonomy of Late Cretaceous ornithomimosaurs from North America, particularly the number of different species among specimens that are commonly referred to as Struthiomimus, Ornithomimus, and Dromiceiomimus (see [S28]). The likely synonymy of Ornithomimus and Dromiceiomimus is accepted here, but considerable specimenlevel work on North American Late Cretaceous orntihomimosaurs is needed before the systematics of these taxa are resolved. We consider those specimens labeled as Struthiomimus in the AMNH collection to belong to this taxon, and consider keystone specimens of Struthiomimus and Ornithomimus described in publications such as [S28-S29] to belong to the taxon they are assigned to. We are cognizant, however, that future work may show that some of these assignments are incorrect. Compsognathids and Additional Basal Coelurosaurs: Many compsognathids and other basal coelurosaurs were studied firsthand whereas others were scored based on the literature and photographs. Studied specimens include the holotype and syntype of Coelurus fragilis (YPM 2012, 1991-1993), the holotype (BSP AS I 563) and the referred French specimen (MNHN CNJ 79) of Compsognathus longipes, the holotype of Juravenator starki (JME Sch 200), the holotype of Mirischia asymmetrica (SMNK 2349 PAL), the holotype of Ornitholestes hermanni (AMNH FARB 619), the holotype of Sinosauropteryx prima (NGMC 2123), the holotype of Tanycolagreus topwilsoni (TPII 2000-09-29), and the holotype of Tugulusaurus faciles (IVPP V4025). Excluded Taxa: Some basal coelurosaur taxa were excluded from the analysis for various reasons. Some taxa were excluded because they are represented only by highly immature specimens, and therefore the sub-adult or adult morphologies of these taxa are unknown. It is likely that such immature specimens would not be placed accurately in a phylogenetic analysis, and thus these taxa were excluded. Scipionyx was not included because the holotype and only known specimen is a remarkably young individual, which perhaps died soon after hatchling [S30-S31]. Similarly, the tyrannosauroid Raptorex was excluded because its holotype is also a young individual which probably died within the first five years of life [S32]. Note, however, that a few taxa are included in the analysis even though they are based on young specimens (e.g., Juravenator and potentially other compsognathids, Epidendrosaurus). All compsognathid taxa are retained because detailed histological data on the ages of the relevant specimens is not yet available. Furthermore, Juravenator is retained because it is known from a nearly complete skeleton that can be scored for more characters than nearly any other basal coelurosaur, whereas Epidendrosaurus is retained because it is one of the few examples of a newly discovered and aberrant coelurosaurian subgroup, Scansoriopterygidae, whose phylogenetic placement demands testing in a large-scale analysis. However, when both Juravenator and Epidendrosaurus are removed in certain iterations of this analysis to gauge the effect of their inclusion on the results, the topology of the remainder of the tree does not change. Other taxa were excluded because they are known only from highly incomplete remains and/or because they are not described in detail in the literature. These taxa were carefully considered during the start of this project and were excluded when it became clear that they could not be scored for the vast majority of characters in the analysis. Some of these taxa could potentially be included, but were stricken from the analysis because they were not examined firsthand and are the subject of only brief reports in the literature. Xinjiangovenator was excluded because it is represented only by fragmentary hindlimb material (tibia and fibula: [S33]), whereas Santanaraptor [S34] and Yixianosaurus [S35-36] were excluded because they are known from fragmentary specimens that were not able to be observed firsthand. Finally, the recently described Yutyrannus was excluded even though it is known from a reasonably complete specimen [S37]. This decision was made because it has yet to be examined firsthand and the published figures are not adequate for carefully checking the character scores used by the authors in their phylogenetic analysis, which is a variation of the Brusatte et al. [S27] analysis that is incorporated into this dataset.