The influence of fragmentation on a combined ZooMS and zooarchaeological study at Geißenklösterle Cave in the Swabian Jura, Southwestern Germany

• ZooMS study of 988 bones from the Palaeolithic site, Geißenklösterle Cave. • Carnivore damage three times more prevalent on indeterminate fossils than those with diagnostic features. • Fragment size influences species identifications in ZooMS studies. • Earliest anthropogenic modification on Rhinocerotidae remains in the Swabian Jura. Geißenklösterle Cave, a Palaeolithic site located in the Swabian Jura of southern Germany, has yielded multiple Middle Palaeolithic strata and some of the earliest evidence for the Aurignacian and Gravettian in Europe. Rich assemblages of three-dimensional figurines, personal ornaments, and musical instruments position Geißenklösterle Cave, and the complex of caves in the region, as significant in our understanding of the Palaeolithic in Europe. Extensive osseous assemblages preserved through the Palaeolithic layers of the site have allowed for thorough zooarchaeological research, aimed at reconstructing site use and human behavior. Drawing from this established research, we applied ZooMS (Zooarchaeology by Mass Spectrometry) to 988 morphologically non-identifiable bone fragments from Geißenklösterle Cave to develop strategies for the integration of non-diagnostic material into the previously established datasets. Our results indicate excellent preservation conditions for collagen, with a 98.4% success rate for ZooMS. The inclusion of taphonomic analyses in our study suggests predators played a significantly bigger role in bone fragmentation at the site than previously assumed, with 31% of bones included in this study exhibiting some kind of carnivore damage. Rare instances of anthropogenic modifications on bones were also identified, including the earliest instance of a cut-mark on a woolly rhinoceros ( Coelodonta antiquitatis ) bone in the Swabian Jura. Finally, we demonstrate the potential biases introduced through sampling strategies regarding the size of bone fragments analyzed in our study. Our results provide valuable insights for the discourse on both Palaeolithic archaeology as well as the best-practice integration of ZooMS into the zooarchaeological workflow.