L'Hote, L. | bioRxiv Science

bioRxiv2026

PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data

Ancient genomics has enabled discovery of diverse pathogens across various time periods, host species, and material types. However, existing palaeogenomic pipelines predominantly focus on screening data from human hosts, or do not incorporate microbial screening methodologies. We present PIGSTI (Pathogen anImal Genome Sequence ToolkIt), a bioinformatic pipeline specifically designed for both the initial screening and subsequent detection of pathogens in shotgun sequencing data from ancient animal remains. PIGSTI's integrated Snakemake workflow performs both host detection, genome mapping and pathogen identification, generating outputs suitable for population genetics and phylogenetic analyses. Testing on 952 newly sequenced and publicly available animal palaeogenomic datasets, we identified ~15 ancient zoonotic and animal pathogens with high confidence, including the first documented case of Rickettsia felis and Leptospira borgpetersenii in an ancient animal. Our results demonstrate PIGSTI's utility for screening pathogen diversity in ancient animal hosts and reconstructing historical host-pathogen relationships.

genomics↗

bioRxiv2025

Genetic analysis of 7,000 year old preserved goat leather from Cueva de los Murcielagos (Albunol, Spain).

Advances in ancient DNA research have expanded the range of materials from which genetic information can be recovered, enabling the analysis of atypical materials. These often preserve both host and exogenous DNA, for example due to handling or native microbes, offering a window into past diversity. Here we report one such exceptional material: a well-preserved goat leather specimen from Cueva de los Murcielagos (Albunol, Spain), associated with an Early Neolithic context. Archaeozoological analyses show clear evidence of tanning and anthropogenic modification of the skin, while radiocarbon dating confirms it to be [~]7,250-7,000 years old. We generated genome-wide data from the leather (Murcielagos1) and demonstrated that it derives from a domestic goat of European ancestry. Comparisons with modern goats show highest affinity to the Bermeya breed from northern Spain, demonstrating genetic connectivity in goat herds from the Neolithic to present day Iberia. We additionally recover fragmented DNA from the leather deriving from human and canid sources, the former likely reflecting handling/wearing of the leather and the latter indicating post-depositional disturbance. Murcielagos1 represents one of the oldest nuclear genome data from organic remains outside of high altitude, high latitude regions, and demonstrates the value of ancient DNA analysis in exceptional cases of organic preservation.

genomics↗