Whole genomes of ancient sheep from Iberia from the Neolithic to the Roman Era

As one of the first domestic livestock species, sheep have played a fundamental role in human societies since the Neolithic. However, their demographic history remains poorly understood. To shed light on the demographic dynamics of sheep at the western edge of the Mediterranean, we sequenced $22$ ancient sheep genomes from Iberia (dating from $\sim7,147$ to $\sim1,700$ calBP, sequenced up to $8.74\times$ coverage) along with one modern European mouflon from Corsica. We provide evidence for an initial maritime introduction into Iberia, and show that European mouflons are descendants of feralized Neolithic sheep. Furthermore, we identify a secondary influx of "Eastern" genetic ancestry coinciding with the arrival of human Steppe ancestry in Iberia -- an event that likely aligns with the spread of woolly sheep across Europe. A third population expansion is observed during the Roman period, a time when historical sources reference the trade of fine-wool sheep. This Roman-era expansion appears to have significantly influenced the genetic makeup of modern European sheep, contributing to the development of popular modern-day breeds such as Merino. In addition to these major events, we see indications of additional, minor episodes of prehistoric gene flow into the Iberian population, suggesting that western European sheep experienced more dynamic demographic changes than other domestic animals, humans, or sheep populations elsewhere. Together, these results highlight the dynamic history of Iberian sheep populations and demonstrate how human cultural and demographic shifts have left their hoofprints in the sheep gene pool, marking them as a valuable proxy for understanding the human past.