Supplementary Figures. Supplementary Figure S1. Cladogram showing distribution of sternal features in Archosauria.

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1 Supplementary Information Insight into the Early Evolution of the Avian Sternum from Juvenile Enantiornithines Xiaoting Zheng, Xiaoli Wang, Jingmai O Connor, Zhonghe Zhou. Supplementary Figures Supplementary Figure S1. Cladogram showing distribution of sternal features in Archosauria.

2 Supplementary Figure S2. Counter-slab of juvenile enantiornithine, STM 34-1.

3 Supplementary Figure S3. Close up of the sternal region of STM Abbreviations: co, caudal ossification; lo, lateral ossification, po, proximal ossification. Scale bar 5 mm.

4 Supplementary Figure S4. Juvenile enantiornithine STM 34-9, which preserves the caudal, proximal and right lateral sternal ossifications (see Figure 2 for close up of sternal region). Supplementary Figure S5. Close up of the sternal region of IVPP V15664A. Abbreviations: co, caudal ossification; lo, lateral ossification. Scale bar 5 mm.

5 Supplementary Figure S6. Close up of the sternal region of IVPP V Abbreviation: lo, lateral ossification. Scale bar 5 mm.

6 Supplementary Figure S7. Close up of the sternal region STM showing the possible cranio-lateral ossification preserved in association with the sternum. Abbreviations: clo, craniolateral ossification. Scale bar 5 mm. Table S1. List of the free sternal ossifications preserved in individual specimens of juvenile enantiornithines.

7 Supplementary Table Caudal Proximal Lateral (paired) Craniolateral (paired) STM 34-1 Present Present Present STM 34-2 Present Present STM 34-7 Present Present Present STM 34-9 Present Present Present STM (fused) (fused) (fused) Present GMV 2156 Present Present GMV 2158 Present Present GMV 2159 Present Present Present IVPP V15036? Present IVPP V15664 Present Present IVPP V12552 (fused) (fused) (fused) DNHM D2522 (fused) (fused) (fused) Present LH 2814 (fused) (fused) (fused) Present Supplementary Table S1. Preservation of sternal ossifications in early juvenile and subadult enantiornithines. Supplementary Methods Definitions of Homology For terminology regarding homology we follow Hall (2007) and thus consider the features to fit the requirements of homology, but falling within the parallelism category 51. Parallelism is defined as the presence (or formation) of a feature in related lineages but not in their most recent common ancestor and/or sister group [indicating] the presence of similar genetic and developmental mechanisms in different lineages and the response of those lineages to internal or external (mutational or environmental) influences to produce similar phenotypes (Hall 2007, 438). Given the close phylogenetic placement of enantiornithines and ornithuromorphs but divergent developmental pathways (autapomorphic in Enantiornithes) the similarity (homology) of the sternum is best explained through parallelism (given the absence of a sternum in Archaeopteryx and at least one clade of Cretaceous bird, parallelism among Mesozoic birds is not unexpected). However, in the strictest sense, these features are not completely homologous. Using the Unified Biological Homology Concept, for a feature to be homologous, they must share a common development, although this may later be subject to apomorphic change 52. Strict statements of homology must co-exist with qualifying statements; since all life shares a common ancestor, all living organisms share homologous features in the broadest sense. 51 Ornithothoracine sternal features are homologous at some levels (similarity) but not at others (developmental). There is vast literature covering the various proposed definitions for homology, and currently the most widely utilized are the taxic homology concept and the developmental homology concept; the Unified Biological Homology Concept is a modified version of the latter

8 Argument against the use of the taxic homology concept: the taxic homology concept states that if a monophyletic group possesses a feature it is homologous. 53 However, a phylogeny is based on interpretation of morphological features; in this case, sternal features were assumed, based on a test of homology (topographic similarity) to be the same. However, ontogenetic similarity is another test of homology, and our results suggest that previous conclusions regarding the primary homology of these features were incorrect. To infer that, because a feature (assumed to be homologous by a given researcher) is shared by a group in a phylogenetic hypothesis, that therefore it is homologous is circular reasoning. We do not follow the strict taxic (phylogenetic or cladistic) definition of homology for this reason (contra de Queiroz 1985, de Pinna 1991) 53,55. Argument in support of the Unified Biological Concept of Homology: although there is concern over the polarization of ontogenetic characters, recent theory suggests that this is no longer the case, and the ontogenetic method remains a powerful tool for understanding homology 2,4,6. In this study we have used this method to suggest the sterna of enantiornithines is only functionally homologous to that of ornithuromorphs and that specific sternal features were evolved independently and thus are not in fact true biological homologues that share the same developmental pathway. a crucial test of a putative homologue is whether its ontogenetic model and its phylogenetic hypothesis are congruent. If they are consistent, we not only have an explanation of the homologue but also have further confirmation that the character in question is a homologue. If the ontogenetic model and phylogenetic hypothesis are inconsistent, then something is wrong with either our explanation of the homologue or the hypothesis that we are investigating a homologue. 52 We suggest this is the case with the ornithothoracine sternum and that sternal characters shared by both ornithothoracine clades do not represent true biological transformations. Craniolateral processes in non-avian dinosaurs, enantiornithines, and ornithuromorphs are homologous in the sense they are parallelisms but are not developmentally homologous and thus do not fulfill the requirements of the Unified Biological Homology Concept. 52,54 Supplementary References 51 Hall, B.K., Homology and Homoplasy in Philosophy of Biology, edited by M. Matthen (North-Holland, Netherlands, 2007), pp Ereshefsky, M., Homology: integrating phylogeny and development. Biol Theory 4 (3), (2209). 53 de Pinna, M.C.C., Concepts and tests of homology in the cladistic paradigm. Cladistics 7, (1991). 54 Wagner, G.P., The biological homology concept. Annu Rev Ecol Syst 20, (1989). 55 de Queiroz, K., The ontogenetic method for determing character polarity and its relevance to phylogenetic systematics. Syst Zool 34 (3), (1985).