Ancient DNA and dating evidence for the dispersal of hippos into central Europe during the last glacial

Late Pleistocene hippo fossils (Hippopotamus amphibius) from Europe have generally been associated with the last interglacial period (Eemian, 129-115 thousand years ago [kya]).¹^,²^,³^,⁴ As a widely accepted indicator species for temperate climate conditions, it was assumed they went extinct with the onset of the last glacial (Weichselian) around 115 kya.²^,⁵ Their origin and relationships to extant African common hippos and the exact age of their extinction in central Europe, however, remain unclear. Here, we address these questions using an integrated approach applied to hippos from the Upper Rhine Graben in central Europe. By sequencing the paleogenome of a European hippo, we reveal its close genetic links to modern hippos from Africa. Six additional partial mitochondrial genomes confirm that European representatives were part of the same, once widespread species that is today restricted to sub-Saharan Africa. Surprisingly, radiocarbon dating shows that hippos were present in central Europe during the middle Weichselian (a period spanning from earlier than 47 kya until ∼31 kya), i.e., well into the last glacial. Similar radiocarbon dates for woolly mammoth and woolly rhino fossils from the same sites imply the presence of both faunas during this period. Despite the paleogenome's low coverage, we are able to confidently estimate its genome-wide diversity by recalibrating the sequencing quality scores and assessing post-mortem damage. The low genome-wide diversity recovered suggests that it belonged to a small, isolated population. Overall, our combined data imply that hippos inhabited the Upper Rhine Graben refugium during temperate phases of the middle Weichselian.