Proteome degradation in ancient bone: Diagenesis and phylogenetic potential

The species composition of vertebrate remains found on archaeological and palaeontological sites has proved to be a valuable source of information for reconstructions of past animal husbandry practices as well as for recovering palaeobiological and palaeoecological information. Molecular analyses provide an objective alternative method of species identification to traditional morphological approaches, particularly useful with fragmentary material; the most well-known being the analysis of DNA. However, more recent proteomics techniques are proving to offer powerful new approaches for obtaining molecular species identification and molecular phylogenies from much deeper within the archaeological record. Collagen is the most abundant and stable protein that can survive for millions of years in biomineralised tissues, but it has been well established for several decades that many other, potentially more informative, non-collagenous proteins (NCPs) also survive long into the archaeological and even geological records. This study investigates the potential mechanisms for biomolecule survival in ancient bone, as well as the extent to which the NCPs that do survive over hundreds of thousands of years yield useful phylogenetic information. Some of these NCPs are shown to yield species-specific information making them ideal for palaeoenvironmental inferences. •At least 23 non-collagenous proteins (NCPs) survive in bone beyond ancient DNA.•At least five other surviving NCPs are more variable than albumin.•Several NCPs show species-specificity useful for palaeoenvironmental inferences.•Short-term biomolecule survival may be related to bone mineral association.•Long-term biomolecule survival may be related to entrapment within remodelled bone.