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Figure S1. Phylogenetic trees used for analysis.

Figure S2. Simulations validate the performance of the trait MEDUSA (tm2 algorithm) method.

Table S1. Trait MEDUSA (tm2 algorithm) for femur length (body size) across all phylogenies.

Table S2. Trait MEDUSA (tm2 algorithm) for rates of forelimb length evolution across all phylogenies.

Table S3. Trait MEDUSA (tm2 algorithm) for rates of body size (femur length) and forelimb length evolution (measured simultaneously) across all phylogenies.

Table S4. Trait MEDUSA (tm2 algorithm) for rates of body size, forelimb length, and simultaneous body size and forelimb length evolution using alternative data (Dececchi and Larrson 2013).

Table S5. Trait MEDUSA (tm2 algorithm) for rates of body size, forelimb length, and simultaneous body size and forelimb length evolution using a phylogeny with alternative branch lengths to the main phylogeny.

Table S6. Results from trait MEDUSA of simultaneous femur and forelimb evolution using different branch-scaling methods from the R packages paleotree.

Table S7. Results from the trait MEDUSA measure of body size evolution using different branch-scaling methods from the R packages paleotree.

Table S8. Results from the trait Medusa measure of forelimb evolution using different branch-scaling methods from the R packages paleotree.

Table S9. Tests of directional evolution performed on pruned phylogenies representing Paraves and Aves extracted from different phylogenies.

Table S10. Results from the OUwie models (BM1, BMS, OU1, OUM, OUMV, OUMA, OUMVA) across phylogenies indicating changes in the optimum between the “theropods” on the tree, and either the Aves or the Paraves.

Table S11. A model of a split in the Aves, Paraves, and other for various OUwie models (BMS, OU1, OUM, OUMV, OUMA, OUMVA) for body size (femur length) and forelimb length).

Table S12. PGLS models to clarify that differences between the main phylogeny and Godefroit et al. (2013) phylogeny are not due to sample size (a), and a lot of the differences can be explained by reclassification of just two taxa (Anchiornis and Xiaotingia) when phylogenies are reduced to the same size (b).

Table S13. Use of alternative data sources for body size and forelimb length (Dececchi and Larrson 2013).

Table S14. A PGLS model of 3 regimes (Aves, other Paraves, and other taxa) with interactions between femur and forelimb length is the best-fitting model.

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