Chemical analysis has rarely been applied to vertebrate fossils; such as the exceptionally preserved 120 Mya Chinese bird Confuciusornis. Ideally such analysis would measure and map the chemistry of bone, soft tissue structures, and the embedding rock matrix. Mapping such a fossil in situ would place constraints on the mass transfer between embedding matrix and the preserved specimen, and therefore aid in distinguishing taphonomic processes from original chemical zonation remnant from the fossil itself. Conventional nondestructive analytical methods face serious problems in this case and most recent technological advances have been targeted at developing nanometer-scale rather than decimeter-scale capabilities. However, the recent development of Synchrotron Rapid Scanning X-ray Fluorescence (SRS-XRF) at the Stanford Synchrotron Radiation Lightsource now allows large specimens to be non-destructively analyzed and imaged using major, minor, and trace element concentrations, permitting the identification of endogenous and exogenous phases.

High-resolution SRS-XRF maps show how an entire Confuciusornis specimen, along with large sections of the mudstone matrix, can be chemically mapped (for Si, P, S, Cl, Ca, Ba, Mn, Fe, Zn, Cu, Br, and Pb). The results from this work unequivocally show that the feathers in this Confuciusornis are not simply impressions. This technique has shown that some trace metals (e.g., copper) correlate with discrete biological structures in a range of extinct and extant organisms, most notably in feathers of Confuciusornis. Additionally, x-ray absorption spectroscopy shows that the chemical inventory of fossils commonly consists of organo-metallic and organo-sulfur compounds coordinated in a manner similar to extant organisms. The application of SRS-XRF imaging can help identify and map the crucial elements associated with original soft tissues. In the case of Confuciusornis this evidence suggests that copper can be used as a biomarker for the distribution of the darker eumelanin pigment, providing the first accurate reconstruction of dark pigment patterns across an entire extinct organism.