GBS data of a Microtus arvalis Central Lineage

Viral speciation and phylogenetic divergence is most commonly driven by co-divergence with their hosts or by host-shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent mere byproducts of high evolutionary rates or rather distinct cryptic or incipient virus species. Here, we test these alternatives with genomic data from the contact area between two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from 42 sampling locations for the presence of TULV RNA. Sequencing yielded 23 TULV Central North and 21 TULV Central South genomes which differed by 14.9-18.5% at the nucleotide and 2.2-3.7% at the amino acid level without evidence of recombination or reassortment. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis and genomic SNPs showed gradual mixing of host populations across it consistent with isolation by distance. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in M. arvalis. We suggest that these parapatric TULV clades represent functionally distinct species which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating of the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.