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Supplement to Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction
<p>This repository contains the supplementary files for:</p> <p>Allen BJ, Volkova Oliveria MV, Stadler T, Vaughan TG, Warnock RCM. 2024. Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction. Cambridge Prisms: Extinction.</p> <p><strong>Description of files</strong></p> <p>This repository contains the cleaned tree files, tables of age constraints, XML files for running the analyses in BEAST2, and R code to process the datasets.</p> <p>Benson1clean.tree, Benson2clean.tree, Lloyd1clean.tree, Lloyd2clean.tree - the cleaned tree files containing the phylogenies inputted into BEAST2, with tip names matched to age data from the Paleobiology Database</p> <p>Tree modifications log.xlsx - a description of the modifications made to each input phylogeny compared to their state in the data supplement of their original papers</p> <p>dinosaur_ages.csv - the raw dinosaur age data downloaded from the Paleobiology Database</p> <p>tip_constraints.csv - the dinosaur age data converted into a format to input into BEAST2, to provide age constraints for tips</p> <p>change_times.txt - a text file describing the change times for the piecewise constant trajectories in the two phylodynamic analyses</p> <p>BDSKY.xml, PiecewiseCoalescent.xml - XML files describing the BEAST2 configuration for each of the two phylodynamic models</p> <p>BDSKY_logs.zip, BDSKY_trees.zip, Coalescent_logs.zip, Coalescent_trees.zip - compressed folders containing the output log files and inferred phylogenies for each of the 16 analysed phylogenies</p> <p>Supplementary_tables.zip - Tables containing summary statistics for each of the parameters inferred in each of the models</p> <p><strong>Description of R code</strong></p> <p>The R code is subdivided into the following files:</p> <p>Wrangle_trees.R - code for checking, cleaning, and splitting the phylogenies used in the analyses</p> <p>PBDB_tip_constraints.R - code for converting the raw age data from the Paleobiology Database into a format ready for input into BEAST2 as tip constraints</p> <p>BDSKY_post_processing.R, Coalescent_post_processing.R - code for cleaning and plotting data from the BEAST2 log files, for each of the two phylodynamic models</p>
Data from: Macroevolutionary trends in theropod dinosaur feeding mechanics
<p>Figure S1. Comparison of von Mises stress plots of non-avialan theropod mandibles under a posterior-bite scenario. Left: original mandible; Right: simulated deformed mandible, showing the deformation (displacement) of the original mandible under loading and the biomechanical performance of this simulated form (see methods). Silhouettes modified from PhyloPic.</p> <p>Figure S2. Ancestral state reconstruction of (A) average mandibular stress and (B) bite efficiency of the non-avialan theropods studied under an anterior-bite scenario using linear parsimony.</p> <p>Figure S3. Ancestral state reconstruction of (A) average mandibular stress and (B) bite efficiency of theropods under posterior-bite scenario using linear parsimony.</p> <p>Figure S4. Workflow of the analyses conducted in this study, using the oviraptorosaurian <em>Gigantoraptor erlianensis</em> as an example.</p> <p>Figure S5. Biomechanical performance of the original and simulated deformed mandibles of non-avialan theropods under an anterior-bite scenario. Average mandibular stress of (A) major clades; (B) dietary groups; (C) theropod taxa. Bite efficiency of (D) major clades; (E) dietary groups; (F) theropod taxa. See Figure S5B for legend. Silhouettes modified from PhyloPic.</p> <p>Figure S6. Biomechanical performance of the original and simulated deformed mandibles of non-avialan theropods under a posterior-bite scenario. Average mandibular stress of (A) major clades; (B) dietary groups; (C) theropod taxa. Bite efficiency of (D) major clades; (E) dietary groups; (F) theropod taxa. See Figure S6B for legend. Silhouettes modified from PhyloPic.</p> <p>Figure S7. Ancestral state reconstruction of average mandibular stress of theropods under anterior-bite scenario using maximum likelihood.</p> <p>Figure S8. Ancestral state reconstruction of average mandibular stress of theropods under posterior-bite scenario using maximum likelihood.</p> <p>Figure S9. Ancestral state reconstruction of bite efficiency of theropods under anterior-bite scenario using maximum likelihood.</p> <p>Figure S10. Ancestral state reconstruction of bite efficiency of theropods under posterior-bite scenario using maximum likelihood.</p> <p>Figure S11. Comparison of maximum principal strain plots of non-avialan theropod mandibles under an anterior-bite scenario. Left: original mandible; Right: simulated deformed mandible, showing the deformation (displacement) of the original mandible under loading and the biomechanical performance of this simulated form (see methods). Silhouettes modified from PhyloPic.</p> <p>Figure S12. Comparison of maximum principal strain plots of non-avialan theropod mandibles under a posterior-bite scenario. Left: original mandible; Right: simulated deformed mandible, showing the deformation (displacement) of the original mandible under loading and the biomechanical performance of this simulated form (see methods). Silhouettes modified from PhyloPic.</p> <p>Figure S13. Comparison of maximum principal strain plot of the tyrannosauroids <em>Tyrannosaurus</em> and <em>Tarbosaurus</em> through ontogeny.</p> <p>Figure S14. Ancestral state reconstruction of the phylogenetic generalized least square regression residuals of (A) relative average mandibular stress and (B) relative bite efficiency of the non-avialan theropods studied under an anterior-bite scenario using linear parsimony.</p> <p>Figure S15. Ancestral state reconstruction of the phylogenetic generalized least square regression residuals of (A) relative average mandibular stress and (B) relative bite efficiency of the non-avialan theropods studied under a posterior-bite scenario using linear parsimony.</p> <p>Figure S16. Ancestral state reconstruction of the phylogenetic generalized least square regression residuals of average mandibular stress of theropods under anterior-bite scenario using maximum likelihood.</p> <p>Figure S17. Ancestral state reconstruction of the phylogenetic generalized least square regression residuals of average mandibular stress of theropods under posterior-bite scenario using maximum likelihood.</p> <p>Figure S18. Ancestral state reconstruction of the phylogenetic generalized least square regression residuals of bite efficiency of theropods under anterior-bite scenario using maximum likelihood.</p> <p>Figure S19. Ancestral state reconstruction of the phylogenetic generalized least square regression residuals of bite efficiency of theropods under posterior-bite scenario using maximum likelihood.</p> <p>Figure S20. Time-scaled composite phylogeny used in this study. Outgroup taxa relationships follow Novas, et al. <sup>1</sup>. Coelurosaurian phylogenetic relationships follow Pei, et al. <sup>2</sup>. The placement of <em>Raptorex</em> in Tyrannosauroidea follows Brusatte and Carr <sup>3</sup>. The placement of <em>Deinocheirus</em> in Ornithomimosauria follows Lee, et al. <sup>4</sup>. The placement of <em>Jianchangosaurus</em> in Therizinosauria follows Yao, et al. <sup>5</sup>. The detailed phylogeny of Oviraptorosauria follows Qiu, et al. <sup>6</sup> (for early-diverging taxa) and Funston <sup>7</sup> (for Caenagnathidae and Oviraptoridae).</p> <p>Figure S21. Phylogeny used in this study with node numbers labelled. See Data S1F-G for reconstructed ancestral states of biomechanical characters using maximum likelihood.</p> <p>Supplemental references</p>
Figure 24 in A new hadrosauriform dinosaur from the Wessex Formation, Wealden Group (Early Cretaceous), of the Isle of Wight, southern England
Figure 24. Brighstoneus simmondsi. gen. et sp. nov. Life restoration by John Sibbick.
Data from: The megaherbivore gap after the non-avian dinosaur extinctions modified trait evolution and diversification of tropical palms
<p><span>The Cretaceous–Paleogene (K-Pg) extinction of the non-avian dinosaurs (66 Ma) led to a 25 million year gap of megaherbivores (>1000 kg) before the evolution of megaherbivorous mammals in the Late Eocene (40 Ma). The botanical consequences of this 'Paleocene megaherbivore gap' (PMHG) remain poorly explored. We hypothesize that the absence of megaherbivores should result in changes in the diversification and trait evolution of associated plant lineages. We used phylogenetic time- and trait-dependent diversification models with palms (Arecaceae) and show that the PMHG was characterized by speciation slowdowns, decreased evolution of armature, and increased evolution of megafaunal (</span>≥<span>4cm) fruits. This suggests that the absence of browsing by megaherbivores during the PMHG may have led to a loss of defence traits, but absence of megaherbivorous seed dispersers did not lead to a loss of megafaunal fruits. Instead, increases in PMHG fruit sizes may be explained by Late Paleocene rising temperatures, rainforest expansion, and the subsequent radiation of seed dispersing birds and mammals. We show that the profound impact of the PMHG on plant diversification can be detected even with the overwriting of adaptations by the subsequent Late Eocene opening-up of megaherbivore-associated ecological opportunities. Our study provides a quantitative, comparative framework to assess </span>diversification and adaptation during one of the most enigmatic periods in angiosperm history.</p>
Data for Han et al., 2022, PNAS, "Low dinosaur biodiversity in central China 2 million years prior to the end-Cretaceous mass extinction"
<p>This zip file contains data presented in the PNAS paper “Low dinosaur biodiversity in central China 2 million years prior to the end-Cretaceous mass extinction” by Han et al., 2022. </p> <p>Folder “Thermal Demag RawData” contains four subfolders that contain all the thermal demagnetization data used in this paper. Magnetic remanence measurements of the natural remanent magnetization (NRM) and the remanences after thermal demagnetization were performed by a three-axis cryogenic magnetometer (2G 760) in a magnetically shielded room (residual field < 300 nT). </p>
Figure 3 in First dinosaur record from the Marília Formation (Maastrichtian) in the Gurinhatã municipality, Minas Gerais state, Brazil
Figure 3. An indeterminate lithostrotian sauropod partial right ulna, Paleo-UFG/V-0039, in (A) Anterior View; (B) Medial View; (C) Posterior View; (D) Lateral View; (E) Proximal View; (F) Distal view.
Figure 2 in First dinosaur record from the Marília Formation (Maastrichtian) in the Gurinhatã municipality, Minas Gerais state, Brazil
Figure 2. Geological map of the Gurinhatã, Detached formations that outcrops in the municipality.Geographic coordinate system: SIRGAS 2000. Source:IBGE/April 2019.
Figure 1 in First dinosaur record from the Marília Formation (Maastrichtian) in the Gurinhatã municipality, Minas Gerais state, Brazil
Figure 1. Location map of the municipality of Gurinhatã, Minas Gerais state. Geographic coordinate system: SIRGAS 2000. Source: IBGE/April 2019.
Figure 4 in First dinosaur record from the Marília Formation (Maastrichtian) in the Gurinhatã municipality, Minas Gerais state, Brazil
Figure 4. Proximal view of different titanosauriforms for comparison. (A) Sonorosaurus (from D'Emic et al., 2016); (B) Wintonotitan (from Poropat et al., 2014); (C) Haestasaurus (from Upchurch et al., 2015); (D) Yongjinglong (from Li et al., 2014); (E) Angolatitan (from Mateus et al., 2011); (F) Atsinganosaurus (from Díez Díaz et al., 2018); (G) Dreadnoughtus (from Ullmann & Lacovara, 2014); (H) Rapetosaurus (from Curry Rogers, 2009); (I) Neuquensaurus (from Otero, 2010); (J) Elaltitan (from Mannion & Otero, 2012); (K) Diamantinasaurus (from Poropat et al., 2015); (L) Malawisaurus (from Gomani, 2005); (M) Lohuecotitan (from Díez Díaz et al., 2016); (N) Mendozasaurus (from González-Riga et al., 2018); (O) Lirainosaurus (from Díez Díaz et al., 2013); and (P) Paleo-UFG/V-0039. Not in scale.
Figure 5 in First dinosaur record from the Marília Formation (Maastrichtian) in the Gurinhatã municipality, Minas Gerais state, Brazil
Figure 5. An indeterminate lithostrotian sauropod partial right ulna, paleo-ufg/v-0039, in (A) anterior view; (B) proximal view; (C) explanatory drawning of the right ulna in anterior view.
Softening the steps to gigantism in sauropod dinosaurs through the evolution of a pedal pad
<p class="01Indent"><span>How sauropod dinosaurs were able to withstand the forces associated with their immense size represents one of the most challenging biomechanical scenarios in the evolution of terrestrial tetrapods, but also one lacking robust biomechanical testing. Here, we use finite element analyses to quantify the biomechanical effects of foot skeletal postures with and without the presence of a soft tissue pad in sauropodomorphs. We find that none of the models can maintain bone stresses that fall within optimal bone safety factors in the absence of a soft tissue pad. Our findings suggest that a soft tissue pad in sauropods would have reduced bone stresses by combining the mechanical advantages of a functionally plantigrade foot and the plesiomorphic digitigrade saurischians conditions. The acquisition of a developed soft tissue pad by the Late-Triassic–Early-Jurassic may represent one of the key adaptations for the evolution of gigantism that has become emblematic of these dinosaurs. </span></p>
Sauropod dinosaur tooth
**Ejemplar: ** diente saurópodo grupo Turiasauria (en revisión) **Edad:** Titoniense-Berriasiense 152-140 Ma. (Jurásico Sup--Cretácico Inf.) **Localidad:** comarca los Serranos (Aras de los Olmos, Valencia, España) **Descripción:** ejemplar con corona casi completa de unos 2´7 cm. de altura y con evidencias de alteración en el esmalte. Raiz ausente. **Dimensión ejemplar:** 27 x 15 x 7 mm. **Sigla museo, colección y entidad: ** MGUV 29094 / CPAO 0130, colección paleontológica Aras de los Olmos (Valencia), depósito MUVHN **Técnica digitalización / parámetros:** fotogrametría cámara Pentax K-1 Mark II, 96 fotografías con plataforma giratoria **Software empleado: ** Metashape 1.6, calidad alta **Archivo 3D: Obj 22´4 Mb , textura Jpg 7´5 , ** **Autor digitalización: **José Antonio Villena Gómez. **Cita ejemplar: ** colección paleontológica Aras de los Olmos (MUVHN)  Source: Objaverse 1.0 / Sketchfab
PARASOUROLOPHUS - DINOSAUR
PARASOUROLOPHUS is a genus of herbivorous hadrosaurid ornithopod dinosaur that lived around North America and possibly Asia during the Late Cretaceous Period, about 76.5–73 million years ago.[2] It was a herbivore that walked both as a biped and as a quadruped. The genus was first described in 1922 by William Parks from a skull and partial skeleton found in Alberta. Part of a diverse family of Cretaceous dinosaurs, they are known for their bizarre head adornments. Visual recognition and sex, acoustic resonance, and thermoregulation have been proposed as functional explanations for the crest. Source: Objaverse 1.0 / Sketchfab
Teropod dinosaur tooth
**Ejemplar: ** diente terópodo allosaurideo (en revisión) **Edad:** Titoniense-Berriasiense 152-140 Ma. (Jurásico Sup--Cretácico Inf.) **Localidad:** comarca los Serranos (Aras de los Olmos-la Yesa, Valencia, España) **Descripción:** ejemplar con corona completa de unos 3 cm. de altura y raiz ausente. Presencia de dentículos en carena mesial y distal **Dimensión ejemplar:** 30 x 14 x 9 mm. **Sigla museo, colección y entidad: ** MGUV 7059, colección paleontológica Aras de los Olmos (Valencia), depósito MUVHN **Donación:** Juan Abella Pérez **Técnica digitalización / parámetros:** fotogrametría cámara Pentax K-1 Mark II, 73 fotografías con plataforma giratoria **Software empleado: ** Metashape 1.6, calidad alta **Archivo 3D: Obj 79 Mb , textura Jpg 9 Mb ** **Autor digitalización: **José Antonio Villena Gómez. **Cita ejemplar: ** colección paleontológica Museo Universidad de Valencia de Historia Natural ![]() Source: Objaverse 1.0 / Sketchfab
Vèrtebra de titanosaure, C.I. Dinosaures Fumanya
**CAT** Vèrtebra de titanosaure procedent del jaciment de Peguera-1, a Fígols, situat dins el complex paleontològic de Fumanya. Es va trobar en la campanya d'excavació del 2005 i s'ha datat del període Maastrichtià, fa 65.000 anys. Les seves dimensions són 45 × 80 × 40 cm. **ES** Vértebra de titanosaurio procedente del yacimiento de Peguera-1, en Fígols, situado dentro del complejo paleontológico de Fumanya. Fue encontrado en la campaña de excavación de 2005 y ha sido datado del periodo Maastrichtiense, hace 65.000 años. Sus dimensiones son 45 x 80 x 40 cm. **EN** Titanosaur vertebra from the site at Peguera-1, in Fígols, part of the Fumanya paleontological complex. It was found during the dig of 2005, and is dated from the Maastrichtian stage, some 65,000 years ago. The size is 45 x 80 x 40 cm. Model: Jaime Salguero. Source: Objaverse 1.0 / Sketchfab
FIGURE 4 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality
FIGURE 4. Iguanodontian phylogeny presented by Norman (2015). Consensus of three MPTs.
FIGURE 2 in The use of aerial and close-range photogrammetry in the study of dinosaur tracksites: Lower Cretaceous (upper Aptian/lower Albian) Molfetta ichnosite (Apulia, southern Italy)
FIGURE 2. Molfetta tracksite - Map of the trampled surface.
World Dinosaur Dataset.
<p>CSV file with 18 + 15 attributes of 318 dinosaurs from around the world from the Triassic to the Cretaceous.</p> <p>The dataset attributes represent different characteristics of the dinosaurs. Among the most important attributes are the dinosaur's name, length and weight, mobility, type of diet, the period in which the animal lived, the locations where its fossils were found, its discoverer, taxonomy, and comments about the dinosaur. There is also an attribute with a web link pointing to the dinosaur's image.</p>
FIG. 1 in Crocodylomorph and dinosaur tracks from the lowermost Jurassic of Le Veillon (western France): ichnotaxonomic revision of the type material (Lapparent collection)
FIG. 1. — Simplified geological map of the study area and location of the tracksite of Le Veillon.
Fig. 11 in New hadrosaurid dinosaurs from the uppermost Cretaceous of northeastern China
Fig. 11. Pubis shape in various hadrosaurids. A, original data; B–F, after Brett−Surman (1989).
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OpenNeuro
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