Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave

Abstract

Denisova Cave, a Pleistocene site in the Altai Mountains of Russian Siberia, has yielded significant fossil and lithic evidence for the Pleistocene in Northern Asia. Abundant animal and human bones have been discovered at the site, however, these tend to be highly fragmented, necessitating new approaches to identifying important hominin and faunal fossils. Here we report the results for 8253 bone fragments using ZooMS. Through the integration of this new ZooMS-based data with the previously published macroscopically-identified fauna we aim to create a holistic picture of the zooarchaeological record of the site. We identify trends associated with climate variability throughout the Middle and Upper Pleistocene as well as patterns explaining the process of bone fragmentation. Where morphological analysis of bones from the site have identified a high proportion of carnivore bones (30.2%), we find that these account for only 7.6% of the ZooMS assemblage, with large mammals between 3 and 5 more abundant overall. Our analysis suggests a cyclical pattern in fragmentation of bones which sees initial fragmentation by hominins using percussive tools and secondary carnivore action, such as gnawing and digestion, likely furthering the initial human-induced fragmentation.

A primer for ZooMS applications in archaeology

“…Improvements in scalability, automation, and high-throughput processing mean ZooMS can be used as a screening tool in order to identify species of interest among otherwise unidentifiable fragmentary remains. This approach has been highly successful in identifying a handful of hominin remains from nearly 10,000 bone fragments at Denisova cave ( 13 – 15 ), human remains at other Late Pleistocene and Early Holocene sites ( 16 , 17 ), and extinct megafauna ( 18 ).…”

“…Currently, most ZooMS work focuses on developing markers, screening for specific species, or answering questions that involve a limited number of species. As ZooMS expands, there will need to be an expanded focus on situating ZooMS identifications within broader zooarchaeological frameworks and incorporating ZooMS data into standard zooarchaeological metrics, such as number of identified specimens, minimum number of individuals, and minimum number of elements ( 14 , 22 ). Because ZooMS can be conducted on fragmentary remains that would otherwise not be counted in these metrics, creating standards for how to report ZooMS results that allow comparison and integration with morphologically identified zooarchaeological datasets will be essential.…”

Leveraging palaeoproteomics to address conservation and restoration agendas

“…The spectra are compared to a reference database of spectra from known taxa to taxonomically identify collagen-bearing materials. This approach is increasingly used in the field of archaeology to taxonomically identify highly fragmented and/or morphologically unidentifiable faunal remains ( Buckley et al., 2017b ; Sinet-Mathiot et al., 2019 ; Brown et al., 2021b ). ZooMS is a relatively cheap and fast method ( Buckley et al., 2009 ; Welker et al., 2015b ; Richter et al., 2020 ), making it applicable to larger-scale assemblages than many other biomolecular methods.…”

“…However, the trade-off for this information is increased cost and time input per sample. Although studies using peptide mass fingerprinting can easily analyze hundreds or even thousands of samples ( Richter et al., 2011 ; Brown et al., 2016 , 2021b ), most shotgun palaeoproteomic studies analyze only a fraction of this amount.…”

Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters

“…[34,35]) and to identify human remains (e.g. [36][37][38]). There is a growing number of publications applying ZooMS to fish remains (e.g.…”