Genomic Diversity of Aurochs From a Mediterranean Ice‐Age Refugium

The aurochs, the wild ancestor of domestic cattle, was a keystone herbivore in Late Pleistocene Eurasian ecosystems and a major prey species for Palaeolithic hunter-gatherers. Despite its significance, the genetic structure of aurochs populations that survived the Last Glacial Maximum (LGM) remains poorly understood, especially in southeastern Europe. Here, we present the first directly dated ancient genomes of aurochs from the eastern Adriatic region, recovered from the Upper Palaeolithic site of Šandalja (Istria, Croatia). Two female individuals, dated to approximately 14,800-14,200 and 11,800-11,400 calibrated years before present, were sequenced for low-coverage whole genomes and near-complete mitochondrial genomes. Bayesian phylogenetic analyses and median-joining network reconstruction place both specimens within mitochondrial haplogroup P, the dominant European aurochs lineage. However, they do not cluster within the main P sub-haplogroup observed in most ancient aurochs samples and in modern cattle carrying P-type mitochondrial lineages. Instead, one specimen is placed within an 'alternative' P sub-haplogroup, whereas the position of the other appears more isolated and should be interpreted cautiously, as it may be influenced by limited sequence coverage and the resulting uncertainty in phylogenetic placement. At the nuclear genomic level, the two Šandalja aurochs show affinity to Late Pleistocene and Early Holocene aurochs from Italy. Although based on a limited number of specimens, this pattern is consistent with possible genetic connectivity across the Adriatic region, potentially associated with the now-submerged Great Adriatic Plain (GAP). Overall, our results suggest regional structure among Late Pleistocene aurochs, potentially associated with the exposed Adriatic Plain as a refugium and dispersal corridor between the Apennine and Balkan Peninsulas. By filling a major geographic and temporal gap in the aurochs genomic record, this study highlights the Adriatic Basin as a potentially overlooked centre of Pleistocene megafaunal diversity and refines models of postglacial recolonization and cattle evolutionary history.