The time scales of pathogen evolution are of major concern in the context of public and veterinary health, epidemiology and evolutionary biology. Dating the emergence of a pathogen often relies on estimates of evolutionary rates derived from nucleotide sequence data. For many viruses, this has yielded estimates of evolutionary origins only a few hundred years in the past. Here we demonstrate through the incorporation of geographic information from virus sampling that evolutionary age estimates of two European hantaviruses are severely underestimated because of pervasive mutational saturation of nucleotide sequences. We detected very strong relationships between spatial distance and genetic divergence for both Puumala and Tula hantavirus – irrespective whether nucleotide or derived amino acid sequences were analyzed. Extrapolations from these relationships dated the emergence of these viruses most conservatively to at least 3,700 and 2,500 years ago, respectively. Our minimum estimates for the age of these hantaviruses are ten to a hundred times older than results from current non-spatial methods and in much better accordance with the biogeography of these viruses and their respective hosts. Spatial information can thus provide valuable insights on the deeper time scales of pathogen evolution and improve our understanding of disease emergence.

PUUV_SPartial Puumala virus S-segment sequence alignment. Sequence names contain GenBank accession number, individual sample name, year of sample collection, latitude and longitude coordinates in this order. Coordinates of eponymous settlements were used when not stated in the original articles.TULV_SPartial Tula virus S-segment sequence alignment. Sequence names contain GenBank accession number, individual sample name, year of sample collection, latitude and longitude coordinates in this order. Coordinates of eponymous settlements were used when not stated in the original articles.PUUVConcatenated Puumala virus full coding sequence alignment. Sequence names contain GenBank accession numbers for all three segments, individual sample name, latitude and longitude coordinates in this order. Coordinates of eponymous settlements were used when not stated in the original articles.