From Fragments to Fingerprints: Assessing the Relationship Between Taphonomic Features, Deamidation and ZooMS Taxonomic Identification Success in the late Middle Pleistocene layer I2 at the Site of Bau de l’Aubesier

Zooarchaeology by Mass Spectrometry (ZooMS) has revolutionized the taxonomic identification of highly fragmented faunal and hominin remains, especially in highly fragmented Pleistocene assemblages. However, its success ultimately depends on the survival and quality of collagen. While glutamine deamidation has been proposed as a molecular indicator of collagen preservation, its reliability and relationship to other taphonomic variables remain insufficiently understood. This study addresses this issue through an integrated methodological analysis of faunal remains from the late Middle Pleistocene site of Bau de l’Aubesier (southeastern France). Combining traditional zooarchaeological and taphonomic observations with deamidation, it evaluates how taphonomy, bone biology, and post-depositional processes influence collagen degradation and the likelihood of successful ZooMS identification. A total of 257 bone fragments were analysed using both randomized and targeted sampling strategies,...Show moreZooarchaeology by Mass Spectrometry (ZooMS) has revolutionized the taxonomic identification of highly fragmented faunal and hominin remains, especially in highly fragmented Pleistocene assemblages. However, its success ultimately depends on the survival and quality of collagen. While glutamine deamidation has been proposed as a molecular indicator of collagen preservation, its reliability and relationship to other taphonomic variables remain insufficiently understood. This study addresses this issue through an integrated methodological analysis of faunal remains from the late Middle Pleistocene site of Bau de l’Aubesier (southeastern France). Combining traditional zooarchaeological and taphonomic observations with deamidation, it evaluates how taphonomy, bone biology, and post-depositional processes influence collagen degradation and the likelihood of successful ZooMS identification. A total of 257 bone fragments were analysed using both randomized and targeted sampling strategies, documenting macroscopic features such as weathering, bone color, bone tissue type, and fracture mode. These were statistically compared with ZooMS identification success and glutamine deamidation values. Most tested variables, including species, bone tissue, sample mass, and fracture mode, showed no significant association with either ZooMS success or deamidation values. However, one variable emerged as a meaningful predictor. Light-brown bones produced substantially more successful spectra than most other macroscopic categories. These findings indicate that ZooMS outcomes are only weakly constrained by most routinely recorded taphonomic variables, while suggesting that certain visible surface features, particularly bone color, may be informative under specific preservation contexts. Although based on a limited sample size, the observed associations imply that integrating simple macroscopic observations with molecular metrics such as deamidation can contribute to a minimally destructive framework for assessing collagen preservation in Middle Pleistocene assemblages. Rather than serving as deterministic predictors, such visual indicators should be regarded as predictive indicators that, when combined with molecular data, may help refine and optimize future biomolecular selection strategies.Show less

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From Fragments to Fingerprints: Assessing the Relationship Between Taphonomic Features, Deamidation and ZooMS Taxonomic Identification Success in the late Middle Pleistocene layer I2 at the Site of Bau de l’Aubesier