The genomic consequences of domestication for ruminant pathogen evolution and herd diversity across ten millennia

Palaeogenomics has transformed our understanding of the genetic consequences of domestication, particularly for livestock species, first brought into the anthropological sphere ~10,000 years ago in Southwest Asia. However, we know little of how domestication shaped the evolution and frequency of pathogens affecting livestock. Moreover, the evolution and occurrence of zoonoses - pathogens infecting both animals and humans - in Neolithic and later societies has been debated, but studies have focused on human remains to obtain ancient pathogen genomes, neglecting animal sources.HERDPATH will address this deficit through large-scale palaeogenomic screening of faunal remains from Eurasia across 10,000 years. Focusing on sheep and goats, two of our oldest domesticates and which share a high number of common diseases with humans, HERDPATH will analyse both pathogen and ruminant genomes to reveal the dynamic between ancestry, husbandry-induced inbreeding, immune gene variation, and pathogen occurrence through time. Bioinformatic screening will produce a temporal, multi-species archive of pathogen-positive livestock, providing the first molecular baseline of infectious disease presence in domestic herds. Time-stamped pathogen genomes will permit the timing of key evolutionary events such as host adaptation and the origin of lineages circulating today. Using data derived from multiple livestock species, HERDPATH will explore the co-evolutionary trajectory of pathogens and immune genes since domestication.Exploiting temporal genomes from underexplored sources will reveal how domestication shaped pathogen evolution towards increasing host adaptation, helping us to model the evolutionary dynamics of future livestock disease, zoonosis outbreaks, and food security. HERDPATH will be a step-change in our understanding of the consequences of domestication; how it drove pathogen evolution and the genetic makeup of our herds, shaped animal health, and our own health in return.