Benchmarking Biomolecular Preservation and Ancient DNA Recovery from Bronze Age Italian Livestock Remains: Preliminary Results from the HERDS Project

Ancient DNA (aDNA) preservation in archaeological remains is strongly influenced by environmental and taphonomic factors, with warm and humid climates posing a major challenge for biomolecular analyses. While these issues are well documented for human remains, systematic assessments of aDNA preservation in domestic animals across heterogeneous climatic contexts remain limited. Here, we present a methodological evaluation of aDNA preservation in Bronze Age livestock remains (sheep, goat, cattle, and pig) from multiple archaeological sites distributed across the Italian peninsula, within the framework of the HERDS project. Leveraging a geographically broad dataset, we explore patterns of DNA degradation along latitudinal and environmental gradients. We assess DNA preservation according to skeletal element, comparing different bone districts to identify those yielding higher endogenous DNA content, from a nuclear and a mitochondrial perspective. Preservation is further evaluated at the site level, and compared to ZooMS (zooarchaeology by mass spectrometry) results, providing an overview of Bronze Age Italian archaeological contexts that are more favorable to the survival of biomolecules. We also report sequencing coverage, success rates of molecular sex determination at the site level, and mitochondrial DNA haplogroup assignments. The preliminary results reveal substantial variability in DNA preservation across skeletal elements and sites. However, no clear latitudinal trend was revealed by neither DNA nor ZooMS results, highlighting the importance of context-specific sampling and laboratory strategies. The petrous portion yields a higher recovery of endogenous DNA compared to teeth; however, this difference is statistically significant only for nuclear DNA, whereas mitochondrial DNA shows a non-significant increase. This study provides a practical methodological framework and reference dataset for future aDNA investigations of domestic animals in environmentally challenging regions, such as the Italian peninsula. In particular, targeted mitochondrial DNA capture and deep sequencing of samples with higher endogenous DNA content will enable high-resolution genetic analyses, offering deeper insight into the diversity and evolutionary history of ancient Italian livestock. As a foundational phase of the HERDS project, the results outlined here pave the way for future palaeogenetic reconstructions of Bronze Age animal husbandry in the Italian peninsula.