Materials and taxonomy

The body outline in Fig. 1 and the other figures in the manuscript show the details of nine basal paravian specimens (STM-0-7, 114, 118, 125, 127, 132, 133, 144 and 147) that can all be referred to Anchiornis. These specimens are deposited in the Shandong Tianyu Museum of Nature in Pingyi, China. Anchiornis has been referred to a basal bird2, a basal troodontid3,a basal deinonychosaur8 or an averaptoran28 so in the absence of taxonomic consensus it is referred more simply to a basal paravian in this study. Two diagnostic features of Anchiornis huxleyi were included in the original description2 (IVPP V14378, housed at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, China): extreme shortness of the ischium and a sculpturing pattern of numerous small pits on the ventral surface of the coracoid. The ventral position of the latter makes it a difficult feature to observe so it is no surprise that it has yet to be confirmed in other Anchiornis specimens and in the nine aforementioned specimens. An extremely short ischium is observed in STM-0-7, 118, 127 and 132, but this character is not exposed in the other five specimens figured in the manuscript. Unlike Xiaotingia, metacarpal III is thinner than metacarpal II in all of the body outline specimens. Unlike Eosinopteryx, STM-0-114, 125 and 132 have more than 23 caudal vertebrae, but this is uncertain in the six other figured specimens. Unlike Aurornis, no evidence of an elongate metatarsal I is observed in the body outline specimens, although in STM-0-133 the metatarsals are not well exposed. The overall similarities in the exposed portions of all of the body outline specimens indicate that these individuals can be referred to Anchiornis (for example, a short deltopectoral crest, a straight ulna, and so on.); these characters were also used to refer LPM-B00169 to this genus3 (housed at the Liaoning Paleontological Museum in Shenyang, China).

LSF imaging protocol and theory

LSF images were collected using the protocol of Kaye et al.1. Anchiornis specimens were imaged with 405 and 532 nm, 500 mw lasers. An appropriate long pass blocking filter was used in front of the camera lens to prevent image saturation by the laser. The laser was projected into a vertical line by a Laserline Optics Canada lens, which was mechanically swept repeatedly over the specimen during the photo’s time exposure in a dark room. The images were post processed in Photoshop for sharpness, colour balance and saturation.

Fluorescence emanates from luminescent centres in the mineral lattice31. The mineral lattice is not pure but incorporates organic and inorganic molecules into the lattice at the time of formation32. The luminescent centre contains the contaminating molecule in close association with the electron clouds of the mineral31. Photons entering the lattice statistically transfer their energy to the electron clouds and cause changes in electron excitation levels. The excited vibrational energy states of the electrons then decay through multiple random paths some of which emit photons while others do not. The excitation and decay process is defined by ligand field theory which applies group theory and quantum mechanics to electrostatic theory31. A full description of ligand field theory is beyond the scope of this paper. Pertinent to fossil analysis, the contaminants of the mineral structure are typically on a parts-per-million basis, which makes fluorescence a sensitive analytical tool33. A colour change represents a different electron decay process from a different atomic arrangement31. Due to the complexity of the decay path, specific colours cannot be attributed to a particular molecular arrangement just from an image31. However, differences in colours do represent changes in the luminescent centre’s makeup. Additional complex laboratory analysis can determine the nature of the luminescent centre which is the target of further study.

Skeletal reconstruction

The skeletal reconstruction was illustrated in Adobe Photoshop CC 2015. Individual bones were scaled from high-resolution photographs exhibiting minimal parallax using the Photoshop Ruler Tool. The virtual scaling was set according to scale bars photographed in the same plane as the specimens, using Photoshop’s Custom Scaling tool (Image -> Analysis -> Set Measurement Scale). Bones were illustrated so that individual measurements end at the edge of the white portion of the bone, as opposed to the middle or outside of the black bounding line. The skeletal diagram is based primarily on STM-0-118. Missing caudal elements were cross-scaled from STM-0-114. Major elements were illustrated on separate layers to facilitate rotation and transformation into plausible life positions. Presacral vertebrae provided the lengths and representative heights of vertebral elements, but were not preserved with the lateral aspect visible in sufficient quantities to determine the exact curvature of articulation in the neck and back. Articulated and well-exposed presacral series of basal paravians (for example, Jinfengopteryx) were used as supplementary guides for reconstructing vertebral curvature in Anchiornis. Forelimb elements were articulated following the left forelimb of STM-0-144, which is preserved with joint angles consistent with contemporary biomechanics work. Hind limb elements of STM-0-118 and STM-0–114 were preserved in articulation, and in good accordance with published interpretations of theropod limb kinematics17,18, and were the basis for the pose in Fig. 1.

Soft tissue reconstruction

Examples of soft-tissue preservation were inspected for a lack of continuity and evidence of taphonomic distortion. To reduce discrepancies between specimens of differing size, tissue depth was measured as a percentage of bone width or length. Soft-tissue remains represented by multiple specimens exhibiting similar depth and no signs of distortion were taken at face value and reproduced directly in Fig. 1, including most distal limb elements. The propatagium depth at the elbow varied in specimens based on the angle of the elbow, a condition also seen in extant birds24,25, so the depth reconstructed in Fig. 1 was matched to specimens of similar degrees of elbow flexion. Soft-tissue elements that showed some degree of distortion were used as a qualitative guide for reconstructing the remaining soft-tissue silhouette (represented in black in Fig. 1), and other portions were based on dissections of birds and published theropod myology13,20. We assigned anatomical terms of soft tissues based on the morphology we observed, in accordance with traditional morphological interpretations of vertebrate fossils (for example, bones, scales, feathers, propatagium).

Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request. The data reported in this paper are detailed in the main text and in the Supplementary Information.