Bayesian tip dating reveals heterogeneous morphological clocks in Mesozoic birds Chi Zhang1,2,* and Min Wang1,2 1Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China 2Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China ∗Corresponding author: E-mail: [email protected] Supplementary Information Figures Dromaeosauridae Archaeopteryx Jeholornis Chongmingia Sapeornis Confuciusornis_sanctus Changchengornis Confuciusornis_dui Yangavis Eoconfuciusornis Pengornis Eopengornis Protopteryx 15.5 Boluochia Longipteryx Longirostravis Rapaxavis Shanweiniao Concornis Elsornis Gobipteryx Neuquenornis Eoalulavis Cathayornis Eocathayornis Eoenantiornis Linyiornis mean relative rate Fortunguavis Sulcavis Bohaiornis 0.3 Parabohaiornis Longusunguis Zhouornis Shenqiornis Vescornis Dunhuangia 1.0 Piscivorenantiornis Pterygornis Qiliania Cruralispennia Monoenantiornis Archaeorhynchus Jianchangornis Schizooura Bellulornis Vorona Patagopteryx Songlingornis Iteravis Yanornis clade probability Yixianornis Piscivoravis Longicrusavis 0.5 Hongshanornis Parahongshanornis Archaeornithura Tianyuornis Apsaravis Gansus Ichthyornis Vegavis Anas Hesperornis Gallus Parahesperornis Baptornis_varneri Baptornis_advenus Enaliornis -175 -150 -125 -100 - 7 5 - 5 0 - 2 5 0 Figure S1. Dated phylogeny (time tree) of the Mesozoic birds under the partitioned analysis. The color of the branch represents the mean relative clock rate of the skull at that branch. The node ages are the posterior medians and the error bars denote the 95% HPD intervals. The shade of the dot at an internal node represents the posterior probability of the corresponding clade. Dromaeosauridae Archaeopteryx Jeholornis Chongmingia Sapeornis Confuciusornis_sanctus Changchengornis Confuciusornis_dui Yangavis Eoconfuciusornis Pengornis Eopengornis Protopteryx 15.5 Boluochia Longipteryx Longirostravis Rapaxavis Shanweiniao Concornis Elsornis Gobipteryx Neuquenornis Eoalulavis Cathayornis Eocathayornis Eoenantiornis Linyiornis mean relative rate Fortunguavis Sulcavis Bohaiornis 0.3 Parabohaiornis Longusunguis Zhouornis Shenqiornis Vescornis Dunhuangia 1.0 Piscivorenantiornis Pterygornis Qiliania Cruralispennia Monoenantiornis Archaeorhynchus Jianchangornis Schizooura Bellulornis Vorona Patagopteryx Songlingornis Iteravis Yanornis clade probability Yixianornis Piscivoravis Longicrusavis 0.5 Hongshanornis Parahongshanornis Archaeornithura Tianyuornis Apsaravis Gansus Ichthyornis Vegavis Anas Hesperornis Gallus Parahesperornis Baptornis_varneri Baptornis_advenus Enaliornis -175 -150 -125 -100 - 7 5 - 5 0 - 2 5 0 Figure S2. Dated phylogeny (time tree) of the Mesozoic birds under the partitioned analysis. The color of the branch represents the mean relative clock rate of the axial skeleton at that branch. See legend to Figure S1. Dromaeosauridae Archaeopteryx Jeholornis Chongmingia Sapeornis Confuciusornis_sanctus Changchengornis Confuciusornis_dui Yangavis Eoconfuciusornis Pengornis Eopengornis Protopteryx 15.5 Boluochia Longipteryx Longirostravis Rapaxavis Shanweiniao Concornis Elsornis Gobipteryx Neuquenornis Eoalulavis Cathayornis Eocathayornis Eoenantiornis Linyiornis mean relative rate Fortunguavis Sulcavis Bohaiornis 0.3 Parabohaiornis Longusunguis Zhouornis Shenqiornis Vescornis Dunhuangia 1.0 Piscivorenantiornis Pterygornis Qiliania Cruralispennia Monoenantiornis Archaeorhynchus Jianchangornis Schizooura Bellulornis Vorona Patagopteryx Songlingornis Iteravis Yanornis clade probability Yixianornis Piscivoravis Longicrusavis 0.5 Hongshanornis Parahongshanornis Archaeornithura Tianyuornis Apsaravis Gansus Ichthyornis Vegavis Anas Hesperornis Gallus Parahesperornis Baptornis_varneri Baptornis_advenus Enaliornis -175 -150 -125 -100 - 7 5 - 5 0 - 2 5 0 Figure S3. Dated phylogeny (time tree) of the Mesozoic birds under the partitioned analysis. The color of the branch represents the mean relative clock rate of the pectoral girdle and sternum at that branch. See legend to Figure S1. Dromaeosauridae Archaeopteryx Jeholornis Chongmingia Sapeornis Confuciusornis_sanctus Changchengornis Confuciusornis_dui Yangavis Eoconfuciusornis Pengornis Eopengornis Protopteryx 15.5 Boluochia Longipteryx Longirostravis Rapaxavis Shanweiniao Concornis Elsornis Gobipteryx Neuquenornis Eoalulavis Cathayornis Eocathayornis Eoenantiornis Linyiornis mean relative rate Fortunguavis Sulcavis Bohaiornis 0.3 Parabohaiornis Longusunguis Zhouornis Shenqiornis Vescornis Dunhuangia 1.0 Piscivorenantiornis Pterygornis Qiliania Cruralispennia Monoenantiornis Archaeorhynchus Jianchangornis Schizooura Bellulornis Vorona Patagopteryx Songlingornis Iteravis Yanornis clade probability Yixianornis Piscivoravis Longicrusavis 0.5 Hongshanornis Parahongshanornis Archaeornithura Tianyuornis Apsaravis Gansus Ichthyornis Vegavis Anas Hesperornis Gallus Parahesperornis Baptornis_varneri Baptornis_advenus Enaliornis -175 -150 -125 -100 - 7 5 - 5 0 - 2 5 0 Figure S4. Dated phylogeny (time tree) of the Mesozoic birds under the partitioned analysis. The color of the branch represents the mean relative clock rate of the forelimb at that branch. See legend to Figure S1. Dromaeosauridae Archaeopteryx Jeholornis Chongmingia Sapeornis Confuciusornis_sanctus Changchengornis Confuciusornis_dui Yangavis Eoconfuciusornis Pengornis Eopengornis Protopteryx 15.5 Boluochia Longipteryx Longirostravis Rapaxavis Shanweiniao Concornis Elsornis Gobipteryx Neuquenornis Eoalulavis Cathayornis Eocathayornis Eoenantiornis Linyiornis mean relative rate Fortunguavis Sulcavis Bohaiornis 0.3 Parabohaiornis Longusunguis Zhouornis Shenqiornis Vescornis Dunhuangia 1.0 Piscivorenantiornis Pterygornis Qiliania Cruralispennia Monoenantiornis Archaeorhynchus Jianchangornis Schizooura Bellulornis Vorona Patagopteryx Songlingornis Iteravis Yanornis clade probability Yixianornis Piscivoravis Longicrusavis 0.5 Hongshanornis Parahongshanornis Archaeornithura Tianyuornis Apsaravis Gansus Ichthyornis Vegavis Anas Hesperornis Gallus Parahesperornis Baptornis_varneri Baptornis_advenus Enaliornis -175 -150 -125 -100 - 7 5 - 5 0 - 2 5 0 Figure S5. Dated phylogeny (time tree) of the Mesozoic birds under the partitioned analysis. The color of the branch represents the mean relative clock rate of the pelvic girdle at that branch. See legend to Figure S1. Dromaeosauridae Archaeopteryx Jeholornis Chongmingia Sapeornis Confuciusornis_sanctus Changchengornis Confuciusornis_dui Yangavis Eoconfuciusornis Pengornis Eopengornis Protopteryx 15.5 Boluochia Longipteryx Longirostravis Rapaxavis Shanweiniao Concornis Elsornis Gobipteryx Neuquenornis Eoalulavis Cathayornis Eocathayornis Eoenantiornis Linyiornis mean relative rate Fortunguavis Sulcavis Bohaiornis 0.3 Parabohaiornis Longusunguis Zhouornis Shenqiornis Vescornis Dunhuangia 1.0 Piscivorenantiornis Pterygornis Qiliania Cruralispennia Monoenantiornis Archaeorhynchus Jianchangornis Schizooura Bellulornis Vorona Patagopteryx Songlingornis Iteravis Yanornis clade probability Yixianornis Piscivoravis Longicrusavis 0.5 Hongshanornis Parahongshanornis Archaeornithura Tianyuornis Apsaravis Gansus Ichthyornis Vegavis Anas Hesperornis Gallus Parahesperornis Baptornis_varneri Baptornis_advenus Enaliornis -175 -150 -125 -100 - 7 5 - 5 0 - 2 5 0 Figure S6. Dated phylogeny (time tree) of the Mesozoic birds under the partitioned analysis. The color of the branch represents the mean relative clock rate of the hindlimb at that branch. See legend to Figure S1. Character description The dataset used in present study is based on a comprehensive morphological matrix recently available for Mesozoic birds (Wang et al., 2018). The dataset contains 68 taxa and 280 morphological characters. Character descriptions: 1. Premaxillae in adults: unfused (0); fused only rostrally (1); completely fused (2). (ORDERED) 2. Maxillary process of the premaxilla: restricted to its rostral portion (0); subequal or longer than the facial contribution of the maxilla (1). 3. Frontal process of the premaxilla: short (0); relatively long, approaching the rostral border of the antorbital fenestra (1); very long, extending caudally near the level of lacrimals (2). (ORDERED) 4. Premaxillary teeth: present throughout (0); present but rostral tip edentulous (1); present but restricted to rostral portion (2); absent (3). 5. Caudal margin of naris: far rostral than the rostral border of the antorbital fossa (0); nearly reaching or overlapping the rostral border of the antorbital fossa (1). 6. Naris longitudinal axis: considerably shorter than the long axis of the antorbital fossa (0); subequal or longer (1). 7. Maxillary teeth: present (0); absent (1). 8. Dorsal (ascending) ramus of the maxilla: present with two fenestra (the promaxilllary and maxillary fenestra) (0); present with one fenestra (1); unfenestrated (2); ramus absent (3). (ORDERED) 9. Caudal margin of choana: located rostrally, not overlapping the region of the orbit (0); displaced caudally, at the same level or overlapping the rostral margin of the orbit (1). 10. Rostral margin of the jugal: away from the caudal margin of the naris (0); or very close to (leveled with) the caudal margin of the naris (1). 11. Contact between palatine and maxilla/premaxilla: palatine contact maxilla only (0); contacts premaxilla and maxilla (1). 12. Vomer and pterygoid articulation: present, well developed (0); reduced, narrow process of pterygoid passes dorsally over palatine to contact vomer (1);