The Geiseltal Konservat-Lagerstätte (Eocene, Germany) is represented by ca. 50,000 fossil specimens, which are about 45 million years old. Early studies of the vertebrates reported remarkable (sub)cellular details of muscle, cartilage, blood vessels, feathers, hair, reptile scales and bacteria. The mode of preservation was reported as three-dimensional silica replacements, which is unknown from other vertebrate Konservat-Lagerstätten. These claims of cellular fidelity, however, have not been verified using modern techniques. Here, we tested these claims by analysing soft tissues from five anurans from Geiseltal using Scanning Electron Microscopy, Energy-dispersive X-ray spectroscopy, Fourier-transform infrared spectroscopy, Synchrotron rapid scanning-x-ray fluorescence (SRS-XRF) and Raman spectroscopy. Our results show that soft tissues occur as layers of carbonaceous melanosomes and phosphatized residues; there is no evidence for silica in association with the preserved soft tissues. The preserved melanosomes exhibit tissue-specific geometries. The Eberth-Katschenko layer of the dermis is preserved in calcium phosphate and nervous tissue is defined by euhedral aragonite. Our analysis reveals phosphatisation rather than silicification as the preferred mode of soft tissue replacement for Geiseltal vertebrates. These features – carbonaceous melanosome films and phosphatized soft tissues – recur in other Konservat-Lagerstätten through space and time. This recognition sheds new light on the taphonomic pathways available for preservation of vertebrate soft tissues in the fossil record.

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