Fossil feathers, hairs and eyes are regularly preserved as carbonized traces comprised of masses of micrometre-sized bodies that are spherical, oblate or elongate in shape. For a long time, these minute structures were regarded as the remains of biofilms of keratinophilic bacteria, but recently they have been reinterpreted as melanosomes; that is, colour-bearing organelles. Resolving this fundamental difference in interpretation is crucial: if endogenous then the fossil microbodies would represent a significant advancement in the fields of palaeontology and evolutionary biology given, for example, the possibility to reconstruct integumentary colours and plumage colour patterns. It has previously been shown that certain trace elements occur in fossils as organometallic compounds, and hence may be used as biomarkers for melanin pigments. Here we expand this knowledge by demonstrating the presence of molecularly preserved melanin in intimate association with melanosome-like microbodies isolated from an argentinoid fish eye from the early Eocene of Denmark.

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An approach for including the intermolecular part of the zero-point vibrational energy in the calculations of intermolecular interactions is presented. The approach is applied to the water complexes of water, ammonia, dimethyl ether, formaldehyde, formamide, acetone and formic acid adopting a model potential. Effects on structure, interaction energy and intermolecular vibration frequencies are discussed. The model is successful in predicting the experimental far infrared spectra, and provides further insights in the assignment of these spectra.

The water–hydroxyl radical complex was prepared by irradiating peroxy radicals in hydrogen-doped argon matrices. The low water content of the matrices made it possible to observe the fundamental bands of the complexed water molecule. The experimental results are compared with the results from ab initio calculations. The complex rotates around the O–O axis in the matrix.

The infrared spectrum of the water–formamide complex in argon matrices has been recorded from 10 to 4000 cm−1. The interaction energy of the complex forming molecules has been calculated from a theoretical potential. One global and three different local minima have been found for this potential. Intermolecular vibration frequencies have been calculated for each minimum. The results are compared with the experimentally observed far infrared spectrum. In agreement with microwave measurements and ab initio calculations, the global minimum of the complex is found, both from calculations and experiment, to have a cyclic structure with water forming a hydrogen bond to the amide oxygen and receiving a hydrogen bond from an amide hydrogen. In addition to the cyclic complex, we observe one of the local minimum structures of the complex, where water accepts a hydrogen bond from the amide NH on the CH side of the amide.

Feathers are amongst the most complex epidermal structures known, and they have a well-documented evolutionary trajectory across non-avian dinosaurs and basal birds. Moreover, melanosome-like microbodies preserved in association with fossil plumage have been used to reconstruct original colour, behaviour and physiology. However, these putative ancient melanosomes might alternatively represent microorganismal residues, a conflicting interpretation compounded by a lack of unambiguous chemical data. We therefore used sensitive molecular imaging, supported by multiple independent analytical tests, to demonstrate that the filamentous epidermal appendages in a new specimen of the Jurassic paravian Anchiornis comprise remnant eumelanosomes and fibril-like microstructures, preserved as endogenous eumelanin and authigenic calcium phosphate. These results provide novel insights into the early evolution of feathers at the sub-cellular level, and unequivocally determine that melanosomes can be preserved in fossil feathers.

Colour, derived primarily from melanin and/or carotenoid pigments, is integral to many aspects of behaviour in living vertebrates, including social signalling, sexual display and crypsis. Thus, identifying biochromes in extinct animals can shed light on the acquisition and evolution of these biological traits. Both eumelanin and melanin-containing cellular organelles (melanosomes) are preserved in fossils, but recognizing traces of ancient melanin-based coloration is fraught with interpretative ambiguity, especially when observations are based on morphological evidence alone. Assigning microbodies (or, more often reported, their ‘mouldic impressions’) as melanosome traces without adequately excluding a bacterial origin is also problematic because microbes are pervasive and intimately involved in organismal degradation. Additionally, some forms synthesize melanin. In this review, we survey both vertebrate and microbial melanization, and explore the conflicts influencing assessment of microbodies preserved in association with ancient animal soft tissues. We discuss the types of data used to interpret fossil melanosomes and evaluate whether these are sufficient for definitive diagnosis. Finally, we outline an integrated morphological and geochemical approach for detecting endogenous pigment remains and associated microstructures in multimillion-year-old fossils.